$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/25479.java 191 202 /home/jeff/BigCloneBench/sample/default/111615.java 181 189 ---------------------------------------- public String visitClassType(ClassType type, Void p) { StringBuilder sb = new StringBuilder(); sb.append("C{"); if (type.outerType != null) { sb.append(print(type.outerType)); sb.append("."); } sb.append(type.name); if (type.typeArgs != null) sb.append(print("<", type.typeArgs, ">")); sb.append("}"); return sb.toString(); } ---------------------------------------- public String visitClassSigType(ClassSigType type, Void p) { StringBuilder sb = new StringBuilder(); sb.append("CS{"); if (type.typeParamTypes != null) sb.append(print("<", type.typeParamTypes, ">")); sb.append(print(type.superclassType)); if (type.superinterfaceTypes != null) sb.append(print("i(", type.superinterfaceTypes, ")")); sb.append("}"); return sb.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1725393.java 1122 1133 /home/jeff/BigCloneBench/sample/selected/1778922.java 1122 1133 ---------------------------------------- protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) { if (ssid1.length == ssid2.length) { for (int i = 0; i < ssid1.length; i++) { if (ssid1[i] != ssid2[i]) { return false; } } return true; } else { return false; } } ---------------------------------------- protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) { if (ssid1.length == ssid2.length) { for (int i = 0; i < ssid1.length; i++) { if (ssid1[i] != ssid2[i]) { return false; } } return true; } else { return false; } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/1297.java 56 63 /home/jeff/BigCloneBench/sample/default/54578.java 56 63 ---------------------------------------- private static void add(Configuration cfg, String s) { int pos = s.indexOf('='); if (pos == -1) { cfg.put(s, ""); } else { cfg.put(s.substring(0, pos), s.substring(pos + 1)); } } ---------------------------------------- private static void add(Configuration cfg, String s) { int pos = s.indexOf('='); if (pos == -1) { cfg.put(s, ""); } else { cfg.put(s.substring(0, pos), s.substring(pos + 1)); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2638229.java 91 96 /home/jeff/BigCloneBench/sample/selected/2001558.java 27 32 ---------------------------------------- public static TsHandler getInstance() { if (instance == null) { instance = new TsHandler(); } return instance; } ---------------------------------------- public static synchronized UserService getInstance() { if (instance == null) { instance = new UserService(); } return instance; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/6320.java 297 306 /home/jeff/BigCloneBench/sample/default/19573.java 297 306 ---------------------------------------- public void query() throws IOException, TransformerConfigurationException { SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance(); Templates xslt = loadDcmDirXSL(tf); DirReader reader = fact.newDirReader(dirFile); try { query("", 1, 0, reader.getFirstRecordBy(null, keys, ignoreCase), tf, xslt); } finally { reader.close(); } } ---------------------------------------- public void query() throws IOException, TransformerConfigurationException { SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance(); Templates xslt = loadDcmDirXSL(tf); DirReader reader = fact.newDirReader(dirFile); try { query("", 1, 0, reader.getFirstRecordBy(null, keys, ignoreCase), tf, xslt); } finally { reader.close(); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/114239.java 1532 1546 /home/jeff/BigCloneBench/sample/default/59932.java 1006 1019 ---------------------------------------- public void test124() throws Exception { byte[] buffer; ByteArrayOutputStream stream = new ByteArrayOutputStream(); CsvWriter writer = new CsvWriter(stream, ',', Charset.forName("ISO-8859-1")); writer.setRecordDelimiter(';'); writer.setUseTextQualifier(false); writer.setEscapeMode(CsvWriter.ESCAPE_MODE_BACKSLASH); writer.write("1;2"); writer.endRecord(); writer.close(); buffer = stream.toByteArray(); stream.close(); String data = Charset.forName("ISO-8859-1").decode(ByteBuffer.wrap(buffer)).toString(); Assert.assertEquals("1\\;2;", data); } ---------------------------------------- public void test56() throws Exception { byte[] buffer; ByteArrayOutputStream stream = new ByteArrayOutputStream(); CsvWriter writer = new CsvWriter(stream, '\t', Charset.forName("ISO-8859-1")); writer.write("1,2"); writer.write("3"); writer.write("blah \"some stuff in quotes\""); writer.endRecord(); writer.close(); buffer = stream.toByteArray(); stream.close(); String data = Charset.forName("ISO-8859-1").decode(ByteBuffer.wrap(buffer)).toString(); Assert.assertEquals("1,2\t3\t\"blah \"\"some stuff in quotes\"\"\"\r\n", data); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/67669.java 168 184 /home/jeff/BigCloneBench/sample/default/106112.java 187 203 ---------------------------------------- public void test5() throws Exception { String data = "1\n2"; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("1", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("1", reader.getRawRecord()); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("2", reader.get(0)); Assert.assertEquals(1L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("2", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); Assert.assertEquals("", reader.getRawRecord()); reader.close(); } ---------------------------------------- public void test6() throws Exception { String data = "1\r\n2"; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("1", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("1", reader.getRawRecord()); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("2", reader.get(0)); Assert.assertEquals(1L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("2", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); Assert.assertEquals("", reader.getRawRecord()); reader.close(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2202740.java 153 183 /home/jeff/BigCloneBench/sample/selected/225359.java 151 181 ---------------------------------------- private boolean _jspx_meth_html_005flink_005f0(PageContext _jspx_page_context) throws Throwable { PageContext pageContext = _jspx_page_context; JspWriter out = _jspx_page_context.getOut(); org.apache.struts.taglib.html.LinkTag _jspx_th_html_005flink_005f0 = (org.apache.struts.taglib.html.LinkTag) _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.get(org.apache.struts.taglib.html.LinkTag.class); _jspx_th_html_005flink_005f0.setPageContext(_jspx_page_context); _jspx_th_html_005flink_005f0.setParent(null); _jspx_th_html_005flink_005f0.setStyleId("incluir"); _jspx_th_html_005flink_005f0.setHref("login.do"); int _jspx_eval_html_005flink_005f0 = _jspx_th_html_005flink_005f0.doStartTag(); if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.SKIP_BODY) { if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) { out = _jspx_page_context.pushBody(); _jspx_th_html_005flink_005f0.setBodyContent((javax.servlet.jsp.tagext.BodyContent) out); _jspx_th_html_005flink_005f0.doInitBody(); } do { out.write("Início"); int evalDoAfterBody = _jspx_th_html_005flink_005f0.doAfterBody(); if (evalDoAfterBody != javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_AGAIN) break; } while (true); if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) { out = _jspx_page_context.popBody(); } } if (_jspx_th_html_005flink_005f0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) { _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0); return true; } _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0); return false; } ---------------------------------------- private boolean _jspx_meth_html_005flink_005f0(PageContext _jspx_page_context) throws Throwable { PageContext pageContext = _jspx_page_context; JspWriter out = _jspx_page_context.getOut(); org.apache.struts.taglib.html.LinkTag _jspx_th_html_005flink_005f0 = (org.apache.struts.taglib.html.LinkTag) _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.get(org.apache.struts.taglib.html.LinkTag.class); _jspx_th_html_005flink_005f0.setPageContext(_jspx_page_context); _jspx_th_html_005flink_005f0.setParent(null); _jspx_th_html_005flink_005f0.setStyleId("incluir"); _jspx_th_html_005flink_005f0.setHref("login.do"); int _jspx_eval_html_005flink_005f0 = _jspx_th_html_005flink_005f0.doStartTag(); if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.SKIP_BODY) { if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) { out = _jspx_page_context.pushBody(); _jspx_th_html_005flink_005f0.setBodyContent((javax.servlet.jsp.tagext.BodyContent) out); _jspx_th_html_005flink_005f0.doInitBody(); } do { out.write("Início"); int evalDoAfterBody = _jspx_th_html_005flink_005f0.doAfterBody(); if (evalDoAfterBody != javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_AGAIN) break; } while (true); if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) { out = _jspx_page_context.popBody(); } } if (_jspx_th_html_005flink_005f0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) { _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0); return true; } _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0); return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/939512.java 85 90 /home/jeff/BigCloneBench/sample/selected/1656760.java 328 333 ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_MyChannel(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { EventChannel _ob_r = MyChannel(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); EventChannelHelper.write(out, _ob_r); return out; } ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_op_remove_all_filters(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { org.omg.CORBA.portable.OutputStream out = null; remove_all_filters(); out = handler.createReply(); return out; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/70505.java 524 546 /home/jeff/BigCloneBench/sample/default/103146.java 629 646 ---------------------------------------- private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveSeries(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeSeries(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/497716.java 267 277 /home/jeff/BigCloneBench/sample/selected/522719.java 320 330 ---------------------------------------- public static int nullSafeHashCode(Object[] array) { if (array == null) { return 0; } int hash = INITIAL_HASH; int arraySize = array.length; for (int i = 0; i < arraySize; i++) { hash = MULTIPLIER * hash + nullSafeHashCode(array[i]); } return hash; } ---------------------------------------- public static int nullSafeHashCode(float[] array) { if (array == null) { return 0; } int hash = INITIAL_HASH; int arraySize = array.length; for (int i = 0; i < arraySize; i++) { hash = MULTIPLIER * hash + hashCode(array[i]); } return hash; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1169293.java 339 364 /home/jeff/BigCloneBench/sample/selected/69355.java 228 253 ---------------------------------------- public boolean Great(Float x) { long e1 = m_E; long e2 = x.m_E; long v1 = m_Val; long v2 = x.m_Val; while (e1 != e2) { if (e1 > e2) { if (Math.abs(v1) < maxLimit) { v1 *= 10; e1--; } else { v2 /= 10; e2++; } } else if (e1 < e2) { if (Math.abs(v2) < maxLimit) { v2 *= 10; e2--; } else { v1 /= 10; e1++; } } } return v1 > v2; } ---------------------------------------- public boolean Great(Float x) { long e1 = m_E; long e2 = x.m_E; long v1 = m_Val; long v2 = x.m_Val; while (e1 != e2) { if (e1 > e2) { if (Math.abs(v1) < Long.MAX_VALUE / 100) { v1 *= 10; e1--; } else { v2 /= 10; e2++; } } else if (e1 < e2) { if (Math.abs(v2) < Long.MAX_VALUE / 100) { v2 *= 10; e2--; } else { v1 /= 10; e1++; } } } return v1 > v2; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2576682.java 8 39 /home/jeff/BigCloneBench/sample/selected/871670.java 12 42 ---------------------------------------- public boolean download(String address, String localFileName) { OutputStream out = null; URLConnection conn = null; InputStream in = null; try { URL url = new URL(address); out = new BufferedOutputStream(new FileOutputStream(localFileName)); conn = url.openConnection(); in = conn.getInputStream(); byte[] buffer = new byte[1024]; int numRead; long numWritten = 0; while ((numRead = in.read(buffer)) != -1) { out.write(buffer, 0, numRead); numWritten += numRead; } return true; } catch (Exception exception) { exception.printStackTrace(); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException ioe) { } } return false; } ---------------------------------------- public static void download(String address, String localFileName) { OutputStream out = null; URLConnection conn = null; InputStream in = null; try { URL url = new URL(address); out = new BufferedOutputStream(new FileOutputStream(localFileName)); conn = url.openConnection(); in = conn.getInputStream(); byte[] buffer = new byte[1024]; int numRead; long numWritten = 0; while ((numRead = in.read(buffer)) != -1) { out.write(buffer, 0, numRead); numWritten += numRead; } System.out.println(localFileName + "\t" + numWritten); } catch (Exception exception) { exception.printStackTrace(); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException ioe) { } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/124923.java 1041 1055 /home/jeff/BigCloneBench/sample/default/102869.java 1138 1153 ---------------------------------------- public void test58() throws Exception { byte[] buffer; ByteArrayOutputStream stream = new ByteArrayOutputStream(); CsvWriter writer = new CsvWriter(stream, '\t', Charset.forName("ISO-8859-1")); writer.write("data\r\nmore data"); writer.write(" 3\t", false); writer.write(" 3\t"); writer.write(" 3\t", true); writer.endRecord(); writer.close(); buffer = stream.toByteArray(); stream.close(); String data = Charset.forName("ISO-8859-1").decode(ByteBuffer.wrap(buffer)).toString(); Assert.assertEquals("\"data\r\nmore data\"\t3\t3\t\" 3\t\"\r\n", data); } ---------------------------------------- public void test74() throws Exception { byte[] buffer; ByteArrayOutputStream stream = new ByteArrayOutputStream(); CsvWriter writer = new CsvWriter(stream, ',', Charset.forName("ISO-8859-1")); writer.setEscapeMode(CsvWriter.ESCAPE_MODE_BACKSLASH); writer.setUseTextQualifier(false); writer.write("1,2"); writer.write("3"); writer.write("blah \"some stuff in quotes\""); writer.endRecord(); writer.close(); buffer = stream.toByteArray(); stream.close(); String data = Charset.forName("ISO-8859-1").decode(ByteBuffer.wrap(buffer)).toString(); Assert.assertEquals("1\\,2,3,blah \"some stuff in quotes\"\r\n", data); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/73115.java 121 131 /home/jeff/BigCloneBench/sample/default/73188.java 121 131 ---------------------------------------- Converter(SkinProperty[] allProps, Hashtable romizedProps) { this.allProps = new Hashtable(); for (int i = 0; i < allProps.length; ++i) { SkinProperty p = allProps[i]; this.allProps.put(p.name, p); } this.allPropsArray = allProps; this.romizedProps = romizedProps; this.missingProps = new Vector(); this.unknownProps = new Vector(); } ---------------------------------------- Converter(SkinProperty[] allProps, Hashtable romizedProps) { this.allProps = new Hashtable(); for (int i = 0; i < allProps.length; ++i) { SkinProperty p = allProps[i]; this.allProps.put(p.name, p); } this.allPropsArray = allProps; this.romizedProps = romizedProps; this.missingProps = new Vector(); this.unknownProps = new Vector(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/57136.java 215 226 /home/jeff/BigCloneBench/sample/default/73101.java 200 214 ---------------------------------------- public void execute(String[] args, int offset) throws InterruptedException, IOException, GeneralSecurityException { switch(mode) { case ECHO: echo(); break; case SEND: send(args, offset); break; default: throw new RuntimeException("Illegal mode: " + mode); } } ---------------------------------------- public void execute(String[] args, int offset) throws InterruptedException, IOException, GeneralSecurityException { switch(mode) { case ECHO: echo(); break; case SEND: send(args, offset); break; case POLL: poll(); break; default: throw new RuntimeException("Illegal mode: " + mode); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/6937.java 509 520 /home/jeff/BigCloneBench/sample/default/132787.java 509 520 ---------------------------------------- private void doRemove(DirWriter w, int[] counter, boolean delFiles) throws IOException { for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) { if (patientIDs.contains(rec.getDataset().getString(Tags.PatientID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } counter[1] += w.remove(rec); } else if (doRemoveStudy(w, rec, counter, delFiles)) { counter[1] += w.remove(rec); } } } ---------------------------------------- private void doRemove(DirWriter w, int[] counter, boolean delFiles) throws IOException { for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) { if (patientIDs.contains(rec.getDataset().getString(Tags.PatientID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } counter[1] += w.remove(rec); } else if (doRemoveStudy(w, rec, counter, delFiles)) { counter[1] += w.remove(rec); } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/51387.java 43 52 /home/jeff/BigCloneBench/sample/default/122700.java 43 52 ---------------------------------------- public void testCommas() { String sequence = "1,2,3,4,5"; assertEquals(sequence, sequenceUsingDo(1, 5)); assertEquals(sequence, sequenceUsingFor(1, 5)); assertEquals(sequence, sequenceUsingWhile(1, 5)); sequence = "8"; assertEquals(sequence, sequenceUsingDo(8, 8)); assertEquals(sequence, sequenceUsingFor(8, 8)); assertEquals(sequence, sequenceUsingWhile(8, 8)); } ---------------------------------------- public void testCommas() { String sequence = "1,2,3,4,5"; assertEquals(sequence, sequenceUsingDo(1, 5)); assertEquals(sequence, sequenceUsingFor(1, 5)); assertEquals(sequence, sequenceUsingWhile(1, 5)); sequence = "8"; assertEquals(sequence, sequenceUsingDo(8, 8)); assertEquals(sequence, sequenceUsingFor(8, 8)); assertEquals(sequence, sequenceUsingWhile(8, 8)); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/18466.java 401 406 /home/jeff/BigCloneBench/sample/default/33571.java 379 384 ---------------------------------------- private void doOverwrite(Dataset ds) { for (Iterator it = overwrite.iterator(); it.hasNext(); ) { DcmElement el = (DcmElement) it.next(); ds.putXX(el.tag(), el.vr(), el.getByteBuffer()); } } ---------------------------------------- private void doOverwrite(Dataset ds) { for (Iterator it = overwrite.iterator(); it.hasNext(); ) { DcmElement el = (DcmElement) it.next(); ds.putXX(el.tag(), el.vr(), el.getByteBuffer()); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/10101.java 640 645 /home/jeff/BigCloneBench/sample/default/41669.java 519 524 ---------------------------------------- public String _getFileNameRoot() { if (0 < writer__iFileNameRoots.length) { return writer__iFileNameRoots[writer__iCurrentFileIndex]; } return ""; } ---------------------------------------- public String _getFileNameRoot() { if (0 < writer__iFileNameRoots.length) { return writer__iFileNameRoots[writer__iCurrentFileIndex]; } return ""; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2213635.java 61 66 /home/jeff/BigCloneBench/sample/selected/1138251.java 45 50 ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_MyAdmin(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { SupplierAdmin _ob_r = MyAdmin(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); SupplierAdminHelper.write(out, _ob_r); return out; } ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_supports_dynamic_properties(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { boolean _ob_r = supports_dynamic_properties(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); out.write_boolean(_ob_r); return out; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/124021.java 8 31 /home/jeff/BigCloneBench/sample/default/50984.java 14 37 ---------------------------------------- public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } ---------------------------------------- public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/238734.java 462 477 /home/jeff/BigCloneBench/sample/selected/967656.java 308 324 ---------------------------------------- private boolean _jspx_meth_html_005fhidden_005f3(javax.servlet.jsp.tagext.JspTag _jspx_th_html_005fform_005f0, PageContext _jspx_page_context) throws Throwable { PageContext pageContext = _jspx_page_context; JspWriter out = _jspx_page_context.getOut(); org.apache.struts.taglib.html.HiddenTag _jspx_th_html_005fhidden_005f3 = (org.apache.struts.taglib.html.HiddenTag) _005fjspx_005ftagPool_005fhtml_005fhidden_005fstyleId_005fproperty_005fnobody.get(org.apache.struts.taglib.html.HiddenTag.class); _jspx_th_html_005fhidden_005f3.setPageContext(_jspx_page_context); _jspx_th_html_005fhidden_005f3.setParent((javax.servlet.jsp.tagext.Tag) _jspx_th_html_005fform_005f0); _jspx_th_html_005fhidden_005f3.setProperty("idProcedimento"); _jspx_th_html_005fhidden_005f3.setStyleId("idProcedimento"); int _jspx_eval_html_005fhidden_005f3 = _jspx_th_html_005fhidden_005f3.doStartTag(); if (_jspx_th_html_005fhidden_005f3.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) { _005fjspx_005ftagPool_005fhtml_005fhidden_005fstyleId_005fproperty_005fnobody.reuse(_jspx_th_html_005fhidden_005f3); return true; } _005fjspx_005ftagPool_005fhtml_005fhidden_005fstyleId_005fproperty_005fnobody.reuse(_jspx_th_html_005fhidden_005f3); return false; } ---------------------------------------- private boolean _jspx_meth_html_005ftext_005f2(javax.servlet.jsp.tagext.JspTag _jspx_th_html_005fform_005f0, PageContext _jspx_page_context) throws Throwable { PageContext pageContext = _jspx_page_context; JspWriter out = _jspx_page_context.getOut(); org.apache.struts.taglib.html.TextTag _jspx_th_html_005ftext_005f2 = (org.apache.struts.taglib.html.TextTag) _005fjspx_005ftagPool_005fhtml_005ftext_005fstyleId_005fsize_005fproperty_005fnobody.get(org.apache.struts.taglib.html.TextTag.class); _jspx_th_html_005ftext_005f2.setPageContext(_jspx_page_context); _jspx_th_html_005ftext_005f2.setParent((javax.servlet.jsp.tagext.Tag) _jspx_th_html_005fform_005f0); _jspx_th_html_005ftext_005f2.setProperty("paciente"); _jspx_th_html_005ftext_005f2.setStyleId("paciente"); _jspx_th_html_005ftext_005f2.setSize("50"); int _jspx_eval_html_005ftext_005f2 = _jspx_th_html_005ftext_005f2.doStartTag(); if (_jspx_th_html_005ftext_005f2.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) { _005fjspx_005ftagPool_005fhtml_005ftext_005fstyleId_005fsize_005fproperty_005fnobody.reuse(_jspx_th_html_005ftext_005f2); return true; } _005fjspx_005ftagPool_005fhtml_005ftext_005fstyleId_005fsize_005fproperty_005fnobody.reuse(_jspx_th_html_005ftext_005f2); return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/682167.java 160 192 /home/jeff/BigCloneBench/sample/selected/682167.java 194 226 ---------------------------------------- public static String stripTags(String in, boolean stripBRTag) { if (in == null) return null; char ch; int i = 0; int last = 0; char[] input = in.toCharArray(); int len = input.length; StringBuilder out = new StringBuilder((int) (len * 1.3)); for (; i < len; i++) { ch = input[i]; if (ch > '>') { } else if (ch == '<') { if (!stripBRTag && i + 3 < len && input[i + 1] == 'b' && input[i + 2] == 'r' && input[i + 3] == '>') { i += 3; continue; } if (i > last) { if (last > 0) out.append(" "); out.append(input, last, i - last); } last = i + 1; } else if (ch == '>') { last = i + 1; } } if (last == 0) { return in; } if (i > last) { out.append(input, last, i - last); } return out.toString(); } ---------------------------------------- public static String escapeHTMLTags(String in) { if (in == null) return null; char ch; int i = 0; int last = 0; char[] input = in.toCharArray(); int len = input.length; StringBuilder out = new StringBuilder((int) (len * 1.3)); for (; i < len; i++) { ch = input[i]; if (ch > '>') { } else if (ch == '<') { if (i > last) out.append(input, last, i - last); last = i + 1; out.append(LT_ENCODE); } else if (ch == '>') { if (i > last) out.append(input, last, i - last); last = i + 1; out.append(GT_ENCODE); } else if (ch == '"') { if (i > last) out.append(input, last, i - last); last = i + 1; out.append(QUOTE_ENCODE); } } if (last == 0) { return in; } if (i > last) { out.append(input, last, i - last); } return out.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/24546.java 667 685 /home/jeff/BigCloneBench/sample/default/94821.java 662 680 ---------------------------------------- private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { File file = w.getRefFile(rec.getRefFileIDs()); if (!file.exists()) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { File file = w.getRefFile(rec.getRefFileIDs()); if (!file.exists()) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/31509.java 253 269 /home/jeff/BigCloneBench/sample/default/111936.java 231 247 ---------------------------------------- public void echo() throws InterruptedException, IOException, GeneralSecurityException { long t1 = System.currentTimeMillis(); int count = 0; for (int i = 0; i < repeatWhole; ++i) { ActiveAssociation active = openAssoc(); if (active != null) { if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) { log.error(messages.getString("noPCEcho")); } else for (int j = 0; j < repeatSingle; ++j, ++count) { active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null); } active.release(true); } } long dt = System.currentTimeMillis() - t1; log.info(MessageFormat.format(messages.getString("echoDone"), new Object[] { new Integer(count), new Long(dt) })); } ---------------------------------------- public void echo() throws InterruptedException, IOException, GeneralSecurityException { long t1 = System.currentTimeMillis(); int count = 0; for (int i = 0; i < repeatWhole; ++i) { ActiveAssociation active = openAssoc(); if (active != null) { if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) { log.error(messages.getString("noPCEcho")); } else for (int j = 0; j < repeatSingle; ++j, ++count) { active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null); } active.release(true); } } long dt = System.currentTimeMillis() - t1; log.info(MessageFormat.format(messages.getString("echoDone"), new Object[] { new Integer(count), new Long(dt) })); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2252238.java 13 21 /home/jeff/BigCloneBench/sample/selected/2507460.java 331 342 ---------------------------------------- public static void pump(InputStream in, OutputStream out) throws IOException { byte[] buffer = new byte[1]; int bytes_read = 0; while (bytes_read != -1) { bytes_read = in.read(buffer); if (bytes_read == -1) break; out.write(buffer, 0, bytes_read); } } ---------------------------------------- public static void copy(InputStream in, OutputStream out) throws IOException { synchronized (in) { synchronized (out) { byte[] buffer = new byte[256]; while (true) { int bytesRead = in.read(buffer); if (bytesRead == -1) break; out.write(buffer, 0, bytesRead); } } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/293134.java 72 80 /home/jeff/BigCloneBench/sample/selected/2727194.java 76 84 ---------------------------------------- public static String getExtension(File f) { String ext = null; String s = f.getName(); int i = s.lastIndexOf('.'); if (i > 0 && i < s.length() - 1) { ext = s.substring(i + 1).toLowerCase(); } return ext; } ---------------------------------------- public static String getExtension(File f) { String ext = null; String s = f.getName(); int i = s.lastIndexOf('.'); if (i > 0 && i < s.length() - 1) { ext = s.substring(i + 1).toLowerCase(); } return ext; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/97360.java 548 570 /home/jeff/BigCloneBench/sample/default/35432.java 648 665 ---------------------------------------- private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveInstances(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeInstances(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/129715.java 548 570 /home/jeff/BigCloneBench/sample/default/106446.java 522 544 ---------------------------------------- private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveInstances(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveSeries(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/12172.java 64 71 /home/jeff/BigCloneBench/sample/default/91574.java 54 62 ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/45886.java 73 82 /home/jeff/BigCloneBench/sample/default/120094.java 64 71 ---------------------------------------- String sequenceUsingWhile(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; while (i <= stop) { if (i > start) builder.append(','); builder.append(i); i++; } return builder.toString(); } ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1059992.java 1101 1112 /home/jeff/BigCloneBench/sample/selected/1521582.java 1122 1133 ---------------------------------------- protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) { if (ssid1.length == ssid2.length) { for (int i = 0; i < ssid1.length; i++) { if (ssid1[i] != ssid2[i]) { return false; } } return true; } else { return false; } } ---------------------------------------- protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) { if (ssid1.length == ssid2.length) { for (int i = 0; i < ssid1.length; i++) { if (ssid1[i] != ssid2[i]) { return false; } } return true; } else { return false; } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/34946.java 185 192 /home/jeff/BigCloneBench/sample/selected/2634974.java 247 258 ---------------------------------------- public int indexOf(Object elem) { if (elem == null) { for (int i = 0; i < size; i++) if (elementData[i] == null) return i; } else { for (int i = 0; i < size; i++) if (elem.equals(elementData[i])) return i; } return -1; } ---------------------------------------- public int lastIndexOf(Object o) { if (o == null) { for (int i = size - 1; i >= 0; i--) { if (array[i] == null) return (i); } } else { for (int i = size - 1; i >= 0; i--) { if (o.equals(array[i])) return (i); } } return (-1); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/10254.java 64 71 /home/jeff/BigCloneBench/sample/default/121888.java 64 71 ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/113632.java 27 46 /home/jeff/BigCloneBench/sample/default/44695.java 27 46 ---------------------------------------- private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } ---------------------------------------- private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/28532.java 369 379 /home/jeff/BigCloneBench/sample/default/119807.java 546 557 ---------------------------------------- public void test18() throws Exception { String data = "1\r"; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("1", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("1", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- public void test29() throws Exception { String data = "\"double\\\"\\\"double quotes\""; CsvReader reader = CsvReader.parse(data); reader.setEscapeMode(CsvReader.ESCAPE_MODE_BACKSLASH); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("double\"\"double quotes", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("\"double\\\"\\\"double quotes\"", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/16641.java 308 322 /home/jeff/BigCloneBench/sample/default/98990.java 308 322 ---------------------------------------- private int query(String prefix, int no, int level, DirRecord dr, SAXTransformerFactory tf, Templates xslt) throws IOException, TransformerConfigurationException { int count = 1; for (; dr != null; dr = dr.getNextSiblingBy(null, keys, ignoreCase)) { if (level >= qrLevel) { Dataset ds = dr.getDataset(); String prompt = POS_FORMAT.format(ds.getItemOffset()) + prefix + count + " [" + dr.getType() + "] #" + no; ds.writeDataset(getTransformerHandler(tf, xslt, prompt), dict); ++no; } else { no = query(prefix + count + '.', no, level + 1, dr.getFirstChildBy(null, keys, ignoreCase), tf, xslt); } ++count; } return no; } ---------------------------------------- private int query(String prefix, int no, int level, DirRecord dr, SAXTransformerFactory tf, Templates xslt) throws IOException, TransformerConfigurationException { int count = 1; for (; dr != null; dr = dr.getNextSiblingBy(null, keys, ignoreCase)) { if (level >= qrLevel) { Dataset ds = dr.getDataset(); String prompt = POS_FORMAT.format(ds.getItemOffset()) + prefix + count + " [" + dr.getType() + "] #" + no; ds.writeDataset(getTransformerHandler(tf, xslt, prompt), dict); ++no; } else { no = query(prefix + count + '.', no, level + 1, dr.getFirstChildBy(null, keys, ignoreCase), tf, xslt); } ++count; } return no; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/97360.java 650 667 /home/jeff/BigCloneBench/sample/default/35432.java 648 665 ---------------------------------------- private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeInstances(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeInstances(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/243138.java 383 414 /home/jeff/BigCloneBench/sample/selected/342350.java 314 335 ---------------------------------------- private void drawAnchorBox(Graphics2D g2) { Rectangle r = getAnchorRect(); int x = r.x; int y = r.y; int width = r.x + r.width - 6; int height = r.y + r.height - 6; int centerx = (x + width) / 2; int centery = (y + height) / 2; Vector selPts = new Vector(); selPts.add(new Point(centerx, centery)); VGArrow vgArrow = (VGArrow) refBase; int quart = vgArrow.getArrowHeadQuarter(); if (quart == 0 | quart == 4) { selPts.add(new Point(x, y)); selPts.add(new Point(width, height)); } else if (quart == 2 | quart == 6) { selPts.add(new Point(x, height)); selPts.add(new Point(width, y)); } if (quart == 1 | quart == 5) { selPts.add(new Point(x, height / 2)); selPts.add(new Point(width, height / 2)); } if (quart == 3 | quart == 7) { selPts.add(new Point(width / 2, 0)); selPts.add(new Point(width / 2, height)); } g2.setColor(Color.green); for (Point kPkt : selPts) { g2.fillRect(kPkt.x, kPkt.y, 6, 6); } } ---------------------------------------- private void drawAnchorBox(Graphics2D g2) { Rectangle r = getAnchorRect(); int x = r.x; int y = r.y; int width = r.x + r.width - 6; int height = r.y + r.height - 6; int centerx = (x + width) / 2; int centery = (y + height) / 2; Vector selPts = new Vector(); selPts.add(new Point(x, y)); selPts.add(new Point(x, height)); selPts.add(new Point(width, y)); selPts.add(new Point(width, height)); selPts.add(new Point(centerx, y)); selPts.add(new Point(centerx, height)); selPts.add(new Point(x, centery)); selPts.add(new Point(width, centery)); g2.setColor(Color.green); for (Point kPkt : selPts) { g2.fillRect(kPkt.x, kPkt.y, 6, 6); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/113166.java 126 138 /home/jeff/BigCloneBench/sample/default/76337.java 126 138 ---------------------------------------- public void testCasting() { List students = new ArrayList(); students.add(new Student("a")); students.add(new Student("b")); List names = new ArrayList(); Iterator it = students.iterator(); while (it.hasNext()) { Student student = (Student) it.next(); names.add(student.getLastName()); } assertEquals("a", names.get(0)); assertEquals("b", names.get(1)); } ---------------------------------------- public void testCasting() { List students = new ArrayList(); students.add(new Student("a")); students.add(new Student("b")); List names = new ArrayList(); Iterator it = students.iterator(); while (it.hasNext()) { Student student = (Student) it.next(); names.add(student.getLastName()); } assertEquals("a", names.get(0)); assertEquals("b", names.get(1)); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/26122.java 620 625 /home/jeff/BigCloneBench/sample/default/118575.java 579 584 ---------------------------------------- public void _setFileNameSuffix(String rSuffix) { if (null == rSuffix) { return; } writer__iFileNameSuffix = rSuffix; } ---------------------------------------- public void _setFileNameSuffix(String rSuffix) { if (null == rSuffix) { return; } writer__iFileNameSuffix = rSuffix; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/47314.java 148 158 /home/jeff/BigCloneBench/sample/selected/1366120.java 119 129 ---------------------------------------- public int compare(int row1, int row2) { compares++; for (int level = 0; level < sortingColumns.size(); level++) { int column = sortingColumns.elementAt(level); int result = compareRowsByColumn(row1, row2, column); if (result != 0) { return ascending ? result : -result; } } return 0; } ---------------------------------------- public int compare(int row1, int row2) { compares++; for (int level = 0; level < sortingColumns.size(); level++) { Integer column = (Integer) sortingColumns.elementAt(level); int result = compareRowsByColumn(row1, row2, column.intValue()); if (result != 0) { return ascending ? result : -result; } } return 0; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/76273.java 159 173 /home/jeff/BigCloneBench/sample/default/11030.java 159 173 ---------------------------------------- public void testPartialDimensions() { final int rows = 3; int[][] matrix = new int[rows][]; matrix[0] = new int[] { 0 }; matrix[1] = new int[] { 1, 2 }; matrix[2] = new int[] { 3, 4, 5 }; assertEquals(1, matrix[1][0]); assertEquals(5, matrix[2][2]); int[][] matrix2 = { { 0 }, { 1, 2 }, { 3, 4, 5 } }; assertEquals(1, matrix2[1][0]); assertEquals(5, matrix2[2][2]); int[] z1 = { 3, 4, 5 }; int[] z2 = { 3, 4, 5 }; assertTrue(Arrays.equals(z1, z2)); } ---------------------------------------- public void testPartialDimensions() { final int rows = 3; int[][] matrix = new int[rows][]; matrix[0] = new int[] { 0 }; matrix[1] = new int[] { 1, 2 }; matrix[2] = new int[] { 3, 4, 5 }; assertEquals(1, matrix[1][0]); assertEquals(5, matrix[2][2]); int[][] matrix2 = { { 0 }, { 1, 2 }, { 3, 4, 5 } }; assertEquals(1, matrix2[1][0]); assertEquals(5, matrix2[2][2]); int[] z1 = { 3, 4, 5 }; int[] z2 = { 3, 4, 5 }; assertTrue(Arrays.equals(z1, z2)); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/497716.java 752 771 /home/jeff/BigCloneBench/sample/selected/1782576.java 705 724 ---------------------------------------- public static String nullSafeToString(long[] array) { if (array == null) { return NULL_STRING; } int length = array.length; if (length == 0) { return EMPTY_ARRAY; } StringBuilder sb = new StringBuilder(); for (int i = 0; i < length; i++) { if (i == 0) { sb.append(ARRAY_START); } else { sb.append(ARRAY_ELEMENT_SEPARATOR); } sb.append(array[i]); } sb.append(ARRAY_END); return sb.toString(); } ---------------------------------------- public static String nullSafeToString(int[] array) { if (array == null) { return NULL_STRING; } int length = array.length; if (length == 0) { return EMPTY_ARRAY; } StringBuffer buffer = new StringBuffer(); for (int i = 0; i < length; i++) { if (i == 0) { buffer.append(ARRAY_START); } else { buffer.append(ARRAY_ELEMENT_SEPARATOR); } buffer.append(array[i]); } buffer.append(ARRAY_END); return buffer.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/8509.java 231 247 /home/jeff/BigCloneBench/sample/default/128156.java 231 247 ---------------------------------------- public void echo() throws InterruptedException, IOException, GeneralSecurityException { long t1 = System.currentTimeMillis(); int count = 0; for (int i = 0; i < repeatWhole; ++i) { ActiveAssociation active = openAssoc(); if (active != null) { if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) { log.error(messages.getString("noPCEcho")); } else for (int j = 0; j < repeatSingle; ++j, ++count) { active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null); } active.release(true); } } long dt = System.currentTimeMillis() - t1; log.info(MessageFormat.format(messages.getString("echoDone"), new Object[] { new Integer(count), new Long(dt) })); } ---------------------------------------- public void echo() throws InterruptedException, IOException, GeneralSecurityException { long t1 = System.currentTimeMillis(); int count = 0; for (int i = 0; i < repeatWhole; ++i) { ActiveAssociation active = openAssoc(); if (active != null) { if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) { log.error(messages.getString("noPCEcho")); } else for (int j = 0; j < repeatSingle; ++j, ++count) { active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null); } active.release(true); } } long dt = System.currentTimeMillis() - t1; log.info(MessageFormat.format(messages.getString("echoDone"), new Object[] { new Integer(count), new Long(dt) })); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/114239.java 334 353 /home/jeff/BigCloneBench/sample/default/73729.java 1684 1702 ---------------------------------------- public void test16() throws Exception { String data = "\r\r\n1\r"; CsvReader reader = CsvReader.parse(data); reader.setDelimiter('\r'); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("", reader.get(0)); Assert.assertEquals("", reader.get(1)); Assert.assertEquals("", reader.get(2)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(3, reader.getColumnCount()); Assert.assertEquals("\r\r", reader.getRawRecord()); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("1", reader.get(0)); Assert.assertEquals("", reader.get(1)); Assert.assertEquals(1L, reader.getCurrentRecord()); Assert.assertEquals(2, reader.getColumnCount()); Assert.assertEquals("1\r", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- public void test138() throws Exception { CsvReader reader = CsvReader.parse("1;; ;1"); reader.setRecordDelimiter(';'); Assert.assertTrue(reader.getSkipEmptyRecords()); Assert.assertTrue(reader.readRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("1", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertTrue(reader.readRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("", reader.get(0)); Assert.assertEquals(1L, reader.getCurrentRecord()); Assert.assertTrue(reader.readRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("1", reader.get(0)); Assert.assertEquals(2L, reader.getCurrentRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/453804.java 146 151 /home/jeff/BigCloneBench/sample/selected/615198.java 132 137 ---------------------------------------- protected IDocumentProvider getDocumentProvider(IEditorInput input) { if (input instanceof IFileEditorInput || input instanceof URIEditorInput) { return edu.toronto.cs.openome_model.diagram.part.Openome_modelDiagramEditorPlugin.getInstance().getDocumentProvider(); } return super.getDocumentProvider(input); } ---------------------------------------- protected IDocumentProvider getDocumentProvider(IEditorInput input) { if (input instanceof IFileEditorInput || input instanceof URIEditorInput) { return FilesystemDiagramEditorPlugin.getInstance().getDocumentProvider(); } return super.getDocumentProvider(input); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1030949.java 677 687 /home/jeff/BigCloneBench/sample/selected/900584.java 673 682 ---------------------------------------- public Matrix arrayTimes(Matrix B) { checkMatrixDimensions(B); Matrix X = new Matrix(m, n); double[][] C = X.getArray(); for (int i = 0; i < m; i++) { for (int j = 0; j < n; j++) { C[i][j] = A[i][j] * B.A[i][j]; } } return X; } ---------------------------------------- public Matrix times(double s) { Matrix X = new Matrix(m, n); double[][] C = X.getArray(); for (int i = 0; i < m; i++) { for (int j = 0; j < n; j++) { C[i][j] = s * A[i][j]; } } return X; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2242014.java 269 292 /home/jeff/BigCloneBench/sample/selected/2095100.java 334 357 ---------------------------------------- private String decodePercent(String str) throws InterruptedException { try { StringBuffer sb = new StringBuffer(); for (int i = 0; i < str.length(); i++) { char c = str.charAt(i); switch(c) { case '+': sb.append(' '); break; case '%': sb.append((char) Integer.parseInt(str.substring(i + 1, i + 3), 16)); i += 2; break; default: sb.append(c); break; } } return new String(sb.toString().getBytes()); } catch (Exception e) { sendError(HTTP_BADREQUEST, "BAD REQUEST: Bad percent-encoding."); return null; } } ---------------------------------------- private String decodePercent(String str) throws InterruptedException { try { StringBuffer sb = new StringBuffer(); for (int i = 0; i < str.length(); i++) { char c = str.charAt(i); switch(c) { case '+': sb.append(' '); break; case '%': sb.append((char) Integer.parseInt(str.substring(i + 1, i + 3), 16)); i += 2; break; default: sb.append(c); break; } } return new String(sb.toString().getBytes()); } catch (Exception e) { sendError(HTTP_BADREQUEST, "BAD REQUEST: Bad percent-encoding."); return null; } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2666453.java 788 820 /home/jeff/BigCloneBench/sample/selected/2666453.java 1017 1050 ---------------------------------------- public void cosRegisterPeer(java.lang.String peerName, tcg.syscontrol.cos.ICosProcessManager p_peerManager) throws tcg.syscontrol.cos.CosFailedToRegisterException { while (true) { if (!this._is_local()) { org.omg.CORBA.portable.InputStream _is = null; try { org.omg.CORBA.portable.OutputStream _os = _request("cosRegisterPeer", true); _os.write_string(peerName); tcg.syscontrol.cos.ICosProcessManagerHelper.write(_os, p_peerManager); _is = _invoke(_os); return; } catch (org.omg.CORBA.portable.RemarshalException _rx) { } catch (org.omg.CORBA.portable.ApplicationException _ax) { String _id = _ax.getId(); if (_id.equals("IDL:tcg/syscontrol/cos/CosFailedToRegisterException:1.0")) { throw tcg.syscontrol.cos.CosFailedToRegisterExceptionHelper.read(_ax.getInputStream()); } throw new RuntimeException("Unexpected exception " + _id); } finally { this._releaseReply(_is); } } else { org.omg.CORBA.portable.ServantObject _so = _servant_preinvoke("cosRegisterPeer", _opsClass); if (_so == null) throw new org.omg.CORBA.UNKNOWN("local invocations not supported!"); ICosProcessManagerOperations _localServant = (ICosProcessManagerOperations) _so.servant; try { _localServant.cosRegisterPeer(peerName, p_peerManager); } finally { _servant_postinvoke(_so); } return; } } } ---------------------------------------- public tcg.syscontrol.cos.ICosManagedProcess cosGetActiveManagedProcess(short index) throws tcg.syscontrol.cos.CosIndexOutOfBoundException { while (true) { if (!this._is_local()) { org.omg.CORBA.portable.InputStream _is = null; try { org.omg.CORBA.portable.OutputStream _os = _request("cosGetActiveManagedProcess", true); _os.write_ushort(index); _is = _invoke(_os); tcg.syscontrol.cos.ICosManagedProcess _result = tcg.syscontrol.cos.ICosManagedProcessHelper.read(_is); return _result; } catch (org.omg.CORBA.portable.RemarshalException _rx) { } catch (org.omg.CORBA.portable.ApplicationException _ax) { String _id = _ax.getId(); if (_id.equals("IDL:tcg/syscontrol/cos/CosIndexOutOfBoundException:1.0")) { throw tcg.syscontrol.cos.CosIndexOutOfBoundExceptionHelper.read(_ax.getInputStream()); } throw new RuntimeException("Unexpected exception " + _id); } finally { this._releaseReply(_is); } } else { org.omg.CORBA.portable.ServantObject _so = _servant_preinvoke("cosGetActiveManagedProcess", _opsClass); if (_so == null) throw new org.omg.CORBA.UNKNOWN("local invocations not supported!"); ICosProcessManagerOperations _localServant = (ICosProcessManagerOperations) _so.servant; tcg.syscontrol.cos.ICosManagedProcess _result; try { _result = _localServant.cosGetActiveManagedProcess(index); } finally { _servant_postinvoke(_so); } return _result; } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/120462.java 150 156 /home/jeff/BigCloneBench/sample/default/118160.java 150 156 ---------------------------------------- private static int toTag(String tagStr) { try { return (int) Long.parseLong(tagStr, 16); } catch (NumberFormatException e) { return Tags.forName(tagStr); } } ---------------------------------------- private static int toTag(String tagStr) { try { return (int) Long.parseLong(tagStr, 16); } catch (NumberFormatException e) { return Tags.forName(tagStr); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/50297.java 30 44 /home/jeff/BigCloneBench/sample/default/83276.java 30 44 ---------------------------------------- public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } ---------------------------------------- public Configuration(URL url) { InputStream in = null; try { load(in = url.openStream()); } catch (Exception e) { throw new RuntimeException("Could not load configuration from " + url, e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/45048.java 253 269 /home/jeff/BigCloneBench/sample/default/57136.java 243 259 ---------------------------------------- public void echo() throws InterruptedException, IOException, GeneralSecurityException { long t1 = System.currentTimeMillis(); int count = 0; for (int i = 0; i < repeatWhole; ++i) { ActiveAssociation active = openAssoc(); if (active != null) { if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) { log.error(messages.getString("noPCEcho")); } else for (int j = 0; j < repeatSingle; ++j, ++count) { active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null); } active.release(true); } } long dt = System.currentTimeMillis() - t1; log.info(MessageFormat.format(messages.getString("echoDone"), new Object[] { new Integer(count), new Long(dt) })); } ---------------------------------------- public void echo() throws InterruptedException, IOException, GeneralSecurityException { long t1 = System.currentTimeMillis(); int count = 0; for (int i = 0; i < repeatWhole; ++i) { ActiveAssociation active = openAssoc(); if (active != null) { if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) { log.error(messages.getString("noPCEcho")); } else for (int j = 0; j < repeatSingle; ++j, ++count) { active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null); } active.release(true); } } long dt = System.currentTimeMillis() - t1; log.info(MessageFormat.format(messages.getString("echoDone"), new Object[] { new Integer(count), new Long(dt) })); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/44659.java 54 62 /home/jeff/BigCloneBench/sample/default/112296.java 54 62 ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/41662.java 113 124 /home/jeff/BigCloneBench/sample/default/56904.java 113 124 ---------------------------------------- private boolean found(List> table, String target) { boolean found = false; search: for (List row : table) { for (String value : row) { if (value.equals(target)) { found = true; break search; } } } return found; } ---------------------------------------- private boolean found(List> table, String target) { boolean found = false; search: for (List row : table) { for (String value : row) { if (value.equals(target)) { found = true; break search; } } } return found; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/79086.java 705 713 /home/jeff/BigCloneBench/sample/default/81123.java 707 715 ---------------------------------------- private static void exit(String prompt, boolean error) { if (prompt != null) { System.err.println(prompt); } if (error) { System.err.println(messages.getString("try")); } System.exit(1); } ---------------------------------------- private static void exit(String prompt, boolean error) { if (prompt != null) { System.err.println(prompt); } if (error) { System.err.println(messages.getString("try")); } System.exit(1); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/82401.java 83 91 /home/jeff/BigCloneBench/sample/default/8578.java 83 91 ---------------------------------------- public static boolean url(String url, String pkglisturl, DocErrorReporter reporter) { String errMsg = composeExternPackageList(url, pkglisturl); if (errMsg != null) { reporter.printError(errMsg); return false; } else { return true; } } ---------------------------------------- public static boolean url(String url, String pkglisturl, DocErrorReporter reporter) { String errMsg = composeExternPackageList(url, pkglisturl); if (errMsg != null) { reporter.printError(errMsg); return false; } else { return true; } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/44026.java 667 685 /home/jeff/BigCloneBench/sample/default/134647.java 667 685 ---------------------------------------- private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { File file = w.getRefFile(rec.getRefFileIDs()); if (!file.exists()) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { File file = w.getRefFile(rec.getRefFileIDs()); if (!file.exists()) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/80510.java 264 274 /home/jeff/BigCloneBench/sample/default/106112.java 264 274 ---------------------------------------- public void test11() throws Exception { String data = "\"July 4th, 2005\""; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("July 4th, 2005", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("\"July 4th, 2005\"", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- public void test11() throws Exception { String data = "\"July 4th, 2005\""; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("July 4th, 2005", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("\"July 4th, 2005\"", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/79290.java 300 338 /home/jeff/BigCloneBench/sample/default/112571.java 309 347 ---------------------------------------- private boolean sendFile(ActiveAssociation active, File file) throws InterruptedException, IOException { InputStream in = null; DcmParser parser = null; Dataset ds = null; try { try { in = new BufferedInputStream(new FileInputStream(file)); parser = pFact.newDcmParser(in); FileFormat format = parser.detectFileFormat(); if (format != null) { ds = oFact.newDataset(); parser.setDcmHandler(ds.getDcmHandler()); parser.parseDcmFile(format, Tags.PixelData); if (parser.getReadTag() == Tags.PixelData) { if (parser.getStreamPosition() + parser.getReadLength() > file.length()) { throw new EOFException("Pixel Data Length: " + parser.getReadLength() + " exceeds file length: " + file.length()); } } log.info(MessageFormat.format(messages.getString("readDone"), new Object[] { file })); } else { log.error(MessageFormat.format(messages.getString("failformat"), new Object[] { file })); return false; } } catch (IOException e) { log.error(MessageFormat.format(messages.getString("failread"), new Object[] { file, e })); return false; } sendDataset(active, file, parser, ds); return true; } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } ; } } } ---------------------------------------- private boolean sendFile(ActiveAssociation active, File file, Dataset mergeDataset) throws InterruptedException, IOException { InputStream in = null; DcmParser parser = null; Dataset ds = null; try { try { in = new BufferedInputStream(new FileInputStream(file)); parser = pFact.newDcmParser(in); try { FileFormat format = parser.detectFileFormat(); ds = oFact.newDataset(); parser.setDcmHandler(ds.getDcmHandler()); parser.parseDcmFile(format, Tags.PixelData); if (parser.getReadTag() == Tags.PixelData) { if (parser.getStreamPosition() + parser.getReadLength() > file.length()) { throw new EOFException("Pixel Data Length: " + parser.getReadLength() + " exceeds file length: " + file.length()); } } log.info(MessageFormat.format(messages.getString("readDone"), new Object[] { file })); } catch (DcmParseException e) { log.error(MessageFormat.format(messages.getString("failformat"), new Object[] { file })); return false; } } catch (IOException e) { log.error(MessageFormat.format(messages.getString("failread"), new Object[] { file, e })); return false; } sendDataset(active, file, parser, merge(ds, mergeDataset)); return true; } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } ; } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/76273.java 64 71 /home/jeff/BigCloneBench/sample/default/115412.java 54 62 ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/103762.java 546 568 /home/jeff/BigCloneBench/sample/default/67675.java 548 570 ---------------------------------------- private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveInstances(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveInstances(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/330378.java 1030 1046 /home/jeff/BigCloneBench/sample/selected/2198965.java 1131 1147 ---------------------------------------- public void test_18_119_writeObject() { Object objToSave = null; Object objLoaded; try { objToSave = Locale.CHINESE; if (DEBUG) System.out.println("Obj = " + objToSave); objLoaded = dumpAndReload(objToSave); assertTrue(MSG_TEST_FAILED + objToSave, Locale.CHINESE.equals(objLoaded)); } catch (IOException e) { fail("IOException serializing " + objToSave + " : " + e.getMessage()); } catch (ClassNotFoundException e) { fail("ClassNotFoundException reading Object type : " + e.getMessage()); } catch (Error err) { System.out.println("Error when obj = " + objToSave); throw err; } } ---------------------------------------- public void test_18_38_writeObject() { Object objToSave = null; try { java.io.IOException ex = new java.io.NotActiveException(FOO); objToSave = ex; if (DEBUG) System.out.println("Obj = " + objToSave); dumpAndReload(objToSave); assertTrue(MSG_TEST_FAILED + objToSave, true); } catch (IOException e) { fail("IOException serializing " + objToSave + " : " + e.getMessage()); } catch (ClassNotFoundException e) { fail("ClassNotFoundException reading Object type : " + e.getMessage()); } catch (Error err) { System.out.println("Error when obj = " + objToSave); throw err; } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/74326.java 73 85 /home/jeff/BigCloneBench/sample/default/99553.java 73 85 ---------------------------------------- private static void encapsulate(Configuration cfg, File pdfFile, File dcmFile) throws IOException { final DcmObjectFactory df = DcmObjectFactory.getInstance(); Dataset ds = df.newDataset(); for (Iterator it = cfg.entrySet().iterator(); it.hasNext(); ) { Map.Entry e = (Map.Entry) it.next(); put(ds, toTags(StringUtils.split((String) e.getKey(), '/')), (String) e.getValue()); } addUIDs(ds); addContentDateTime(ds); ds.setFileMetaInfo(df.newFileMetaInfo(ds, UIDs.ExplicitVRLittleEndian)); write(pdfFile, dcmFile, ds); System.out.println("Encapsulate " + pdfFile + " into " + dcmFile); } ---------------------------------------- private static void encapsulate(Configuration cfg, File pdfFile, File dcmFile) throws IOException { final DcmObjectFactory df = DcmObjectFactory.getInstance(); Dataset ds = df.newDataset(); for (Iterator it = cfg.entrySet().iterator(); it.hasNext(); ) { Map.Entry e = (Map.Entry) it.next(); put(ds, toTags(StringUtils.split((String) e.getKey(), '/')), (String) e.getValue()); } addUIDs(ds); addContentDateTime(ds); ds.setFileMetaInfo(df.newFileMetaInfo(ds, UIDs.ExplicitVRLittleEndian)); write(pdfFile, dcmFile, ds); System.out.println("Encapsulate " + pdfFile + " into " + dcmFile); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/45206.java 54 62 /home/jeff/BigCloneBench/sample/default/113986.java 54 62 ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/139001.java 29 43 /home/jeff/BigCloneBench/sample/selected/2515946.java 30 44 ---------------------------------------- static void setChannel(Channel ch, int val) { try { if (!ch.isConnected()) { ch.requestConnection(); } ch.putVal(val); Thread.sleep(CaMonitorScalar.caputExtraTimeOut); } catch (ConnectionException e) { e.printStackTrace(); } catch (PutException e) { e.printStackTrace(); } catch (InterruptedException e) { e.printStackTrace(); } } ---------------------------------------- static void setChannel(Channel ch, double val) { try { if (!ch.isConnected()) { ch.requestConnection(); } ch.putVal(val); Thread.sleep(CaMonitorIntArray.caputExtraTimeOut); } catch (ConnectionException e) { e.printStackTrace(); } catch (PutException e) { e.printStackTrace(); } catch (InterruptedException e) { e.printStackTrace(); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/47340.java 19 34 /home/jeff/BigCloneBench/sample/default/78023.java 19 34 ---------------------------------------- public void testPalindrome() { assertFalse(isPalindrome("abcdef")); assertFalse(isPalindrome("abccda")); assertTrue(isPalindrome("abccba")); assertFalse(isPalindrome("abcxba")); assertTrue(isPalindrome("a")); assertTrue(isPalindrome("aa")); assertFalse(isPalindrome("ab")); assertTrue(isPalindrome("")); assertTrue(isPalindrome("aaa")); assertTrue(isPalindrome("aba")); assertTrue(isPalindrome("abbba")); assertTrue(isPalindrome("abba")); assertFalse(isPalindrome("abbaa")); assertFalse(isPalindrome("abcda")); } ---------------------------------------- public void testPalindrome() { assertFalse(isPalindrome("abcdef")); assertFalse(isPalindrome("abccda")); assertTrue(isPalindrome("abccba")); assertFalse(isPalindrome("abcxba")); assertTrue(isPalindrome("a")); assertTrue(isPalindrome("aa")); assertFalse(isPalindrome("ab")); assertTrue(isPalindrome("")); assertTrue(isPalindrome("aaa")); assertTrue(isPalindrome("aba")); assertTrue(isPalindrome("abbba")); assertTrue(isPalindrome("abba")); assertFalse(isPalindrome("abbaa")); assertFalse(isPalindrome("abcda")); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/107391.java 125 141 /home/jeff/BigCloneBench/sample/default/121997.java 125 141 ---------------------------------------- public void run() { int exitCode = -99; boolean exited = false; do { try { exitCode = tac.exitValue(); exited = true; } catch (IllegalThreadStateException e) { System.out.println("still alive!"); try { Thread.sleep(1000); } catch (Exception ee) { } } } while (!exited); System.out.println("exitValue(): Process exited with code " + exitCode); } ---------------------------------------- public void run() { int exitCode = -99; boolean exited = false; do { try { exitCode = tac.exitValue(); exited = true; } catch (IllegalThreadStateException e) { System.out.println("still alive!"); try { Thread.sleep(1000); } catch (Exception ee) { } } } while (!exited); System.out.println("exitValue(): Process exited with code " + exitCode); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/106446.java 546 568 /home/jeff/BigCloneBench/sample/default/53104.java 570 590 ---------------------------------------- private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveInstances(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doRemoveInstances(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (sopInstUIDs.contains(rec.getRefSOPInstanceUID()) || matchFileIDs(rec.getRefFileIDs())) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/100859.java 19 34 /home/jeff/BigCloneBench/sample/default/16496.java 19 34 ---------------------------------------- public void testPalindrome() { assertFalse(isPalindrome("abcdef")); assertFalse(isPalindrome("abccda")); assertTrue(isPalindrome("abccba")); assertFalse(isPalindrome("abcxba")); assertTrue(isPalindrome("a")); assertTrue(isPalindrome("aa")); assertFalse(isPalindrome("ab")); assertTrue(isPalindrome("")); assertTrue(isPalindrome("aaa")); assertTrue(isPalindrome("aba")); assertTrue(isPalindrome("abbba")); assertTrue(isPalindrome("abba")); assertFalse(isPalindrome("abbaa")); assertFalse(isPalindrome("abcda")); } ---------------------------------------- public void testPalindrome() { assertFalse(isPalindrome("abcdef")); assertFalse(isPalindrome("abccda")); assertTrue(isPalindrome("abccba")); assertFalse(isPalindrome("abcxba")); assertTrue(isPalindrome("a")); assertTrue(isPalindrome("aa")); assertFalse(isPalindrome("ab")); assertTrue(isPalindrome("")); assertTrue(isPalindrome("aaa")); assertTrue(isPalindrome("aba")); assertTrue(isPalindrome("abbba")); assertTrue(isPalindrome("abba")); assertFalse(isPalindrome("abbaa")); assertFalse(isPalindrome("abcda")); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/112239.java 414 423 /home/jeff/BigCloneBench/sample/default/54915.java 506 515 ---------------------------------------- public void addTCP(final short port) { Thread t; t = new Thread(new Runnable() { public void run() { serveTCP(port); } }); t.start(); } ---------------------------------------- public void addTCP(final InetAddress addr, final short port) { Thread t; t = new Thread(new Runnable() { public void run() { serveTCP(addr, port); } }); t.start(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/14709.java 517 539 /home/jeff/BigCloneBench/sample/default/115118.java 546 568 ---------------------------------------- private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveSeries(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveInstances(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/15109.java 90 172 /home/jeff/BigCloneBench/sample/default/33993.java 90 172 ---------------------------------------- public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } ---------------------------------------- public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/401339.java 136 142 /home/jeff/BigCloneBench/sample/selected/615198.java 132 137 ---------------------------------------- protected void setDocumentProvider(IEditorInput input) { if (input instanceof IFileEditorInput || input instanceof URIEditorInput) { setDocumentProvider(FilesystemDiagramEditorPlugin.getInstance().getDocumentProvider()); } else { super.setDocumentProvider(input); } } ---------------------------------------- protected IDocumentProvider getDocumentProvider(IEditorInput input) { if (input instanceof IFileEditorInput || input instanceof URIEditorInput) { return FilesystemDiagramEditorPlugin.getInstance().getDocumentProvider(); } return super.getDocumentProvider(input); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/23336.java 194 203 /home/jeff/BigCloneBench/sample/default/123780.java 194 203 ---------------------------------------- public void testRetroCollections() { { List names = new Vector(); Map dictionary = new Hashtable(); } { List names = new Vector(); Map dictionary = new Hashtable(); } } ---------------------------------------- public void testRetroCollections() { { List names = new Vector(); Map dictionary = new Hashtable(); } { List names = new Vector(); Map dictionary = new Hashtable(); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/93534.java 210 223 /home/jeff/BigCloneBench/sample/default/10394.java 216 229 ---------------------------------------- private ActiveAssociation openAssoc() throws IOException, GeneralSecurityException { Association assoc = aFact.newRequestor(newSocket(url.getHost(), url.getPort())); assoc.setAcTimeout(acTimeout); assoc.setDimseTimeout(dimseTimeout); assoc.setSoCloseDelay(soCloseDelay); assoc.setPackPDVs(packPDVs); PDU assocAC = assoc.connect(assocRQ); if (!(assocAC instanceof AAssociateAC)) { return null; } ActiveAssociation retval = aFact.newActiveAssociation(assoc, null); retval.start(); return retval; } ---------------------------------------- private ActiveAssociation openAssoc() throws IOException, GeneralSecurityException { Association assoc = aFact.newRequestor(newSocket(url.getHost(), url.getPort())); assoc.setAcTimeout(acTimeout); assoc.setDimseTimeout(dimseTimeout); assoc.setSoCloseDelay(soCloseDelay); assoc.setPackPDVs(packPDVs); PDU assocAC = assoc.connect(assocRQ); if (!(assocAC instanceof AAssociateAC)) { return null; } ActiveAssociation retval = aFact.newActiveAssociation(assoc, null); retval.start(); return retval; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2696114.java 459 471 /home/jeff/BigCloneBench/sample/selected/825557.java 664 676 ---------------------------------------- public static int[] split(String s, String delimiter, int x) { String[] array = split(s, delimiter); int[] newArray = new int[array.length]; for (int i = 0; i < array.length; i++) { int value = x; try { value = Integer.parseInt(array[i]); } catch (Exception e) { } newArray[i] = value; } return newArray; } ---------------------------------------- public static long[] split(String s, String delimiter, long x) { String[] array = split(s, delimiter); long[] newArray = new long[array.length]; for (int i = 0; i < array.length; i++) { long value = x; try { value = Long.parseLong(array[i]); } catch (Exception e) { } newArray[i] = value; } return newArray; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/939512.java 127 132 /home/jeff/BigCloneBench/sample/selected/459626.java 80 85 ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_push_suppliers(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { int[] _ob_r = push_suppliers(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); ProxyIDSeqHelper.write(out, _ob_r); return out; } ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_default_consumer_admin(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { TypedConsumerAdmin _ob_r = default_consumer_admin(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); TypedConsumerAdminHelper.write(out, _ob_r); return out; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/62853.java 970 989 /home/jeff/BigCloneBench/sample/default/11754.java 970 989 ---------------------------------------- public void test54() throws Exception { byte[] buffer; ByteArrayOutputStream stream = new ByteArrayOutputStream(); CsvWriter writer = new CsvWriter(stream, ',', Charset.forName("ISO-8859-1")); writer.write("1,2"); writer.write("3"); writer.write("blah \"some stuff in quotes\""); writer.endRecord(); Assert.assertFalse(writer.getForceQualifier()); writer.setForceQualifier(true); Assert.assertTrue(writer.getForceQualifier()); writer.write("1,2"); writer.write("3"); writer.write("blah \"some stuff in quotes\""); writer.close(); buffer = stream.toByteArray(); stream.close(); String data = Charset.forName("ISO-8859-1").decode(ByteBuffer.wrap(buffer)).toString(); Assert.assertEquals("\"1,2\",3,\"blah \"\"some stuff in quotes\"\"\"\r\n\"1,2\",\"3\",\"blah \"\"some stuff in quotes\"\"\"", data); } ---------------------------------------- public void test54() throws Exception { byte[] buffer; ByteArrayOutputStream stream = new ByteArrayOutputStream(); CsvWriter writer = new CsvWriter(stream, ',', Charset.forName("ISO-8859-1")); writer.write("1,2"); writer.write("3"); writer.write("blah \"some stuff in quotes\""); writer.endRecord(); Assert.assertFalse(writer.getForceQualifier()); writer.setForceQualifier(true); Assert.assertTrue(writer.getForceQualifier()); writer.write("1,2"); writer.write("3"); writer.write("blah \"some stuff in quotes\""); writer.close(); buffer = stream.toByteArray(); stream.close(); String data = Charset.forName("ISO-8859-1").decode(ByteBuffer.wrap(buffer)).toString(); Assert.assertEquals("\"1,2\",3,\"blah \"\"some stuff in quotes\"\"\"\r\n\"1,2\",\"3\",\"blah \"\"some stuff in quotes\"\"\"", data); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/93572.java 64 71 /home/jeff/BigCloneBench/sample/default/66539.java 64 71 ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1017245.java 479 487 /home/jeff/BigCloneBench/sample/selected/211182.java 440 450 ---------------------------------------- public double normF() { double f = 0; for (int i = 0; i < m; i++) { for (int j = 0; j < n; j++) { f = Maths.hypot(f, A[i][j]); } } return f; } ---------------------------------------- public double norm1() { double f = 0; for (int j = 0; j < n; j++) { double s = 0; for (int i = 0; i < m; i++) { s += Math.abs(A[i][j]); } f = Math.max(f, s); } return f; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/478993.java 259 273 /home/jeff/BigCloneBench/sample/selected/1726071.java 257 271 ---------------------------------------- public static View findView(DiagramEditPart diagramEditPart, EObject targetElement, LazyElement2ViewMap lazyElement2ViewMap) { boolean hasStructuralURI = false; if (targetElement.eResource() instanceof XMLResource) { hasStructuralURI = ((XMLResource) targetElement.eResource()).getID(targetElement) == null; } View view = null; if (hasStructuralURI && !lazyElement2ViewMap.getElement2ViewMap().isEmpty()) { view = (View) lazyElement2ViewMap.getElement2ViewMap().get(targetElement); } else if (findElementsInDiagramByID(diagramEditPart, targetElement, lazyElement2ViewMap.editPartTmpHolder) > 0) { EditPart editPart = (EditPart) lazyElement2ViewMap.editPartTmpHolder.get(0); lazyElement2ViewMap.editPartTmpHolder.clear(); view = editPart.getModel() instanceof View ? (View) editPart.getModel() : null; } return (view == null) ? diagramEditPart.getDiagramView() : view; } ---------------------------------------- public static View findView(org.eclipse.gmf.runtime.diagram.ui.editparts.DiagramEditPart diagramEditPart, EObject targetElement, LazyElement2ViewMap lazyElement2ViewMap) { boolean hasStructuralURI = false; if (targetElement.eResource() instanceof XMLResource) { hasStructuralURI = ((XMLResource) targetElement.eResource()).getID(targetElement) == null; } View view = null; if (hasStructuralURI && !lazyElement2ViewMap.getElement2ViewMap().isEmpty()) { view = (View) lazyElement2ViewMap.getElement2ViewMap().get(targetElement); } else if (findElementsInDiagramByID(diagramEditPart, targetElement, lazyElement2ViewMap.editPartTmpHolder) > 0) { EditPart editPart = (EditPart) lazyElement2ViewMap.editPartTmpHolder.get(0); lazyElement2ViewMap.editPartTmpHolder.clear(); view = editPart.getModel() instanceof View ? (View) editPart.getModel() : null; } return (view == null) ? diagramEditPart.getDiagramView() : view; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/21403.java 175 180 /home/jeff/BigCloneBench/sample/default/130398.java 175 180 ---------------------------------------- public void testArrayEquality() { int[] a = { 1, 2, 3 }; int[] b = { 1, 2, 3 }; assertFalse(a.equals(b)); assertFalse(a == b); } ---------------------------------------- public void testArrayEquality() { int[] a = { 1, 2, 3 }; int[] b = { 1, 2, 3 }; assertFalse(a.equals(b)); assertFalse(a == b); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/22303.java 955 967 /home/jeff/BigCloneBench/sample/default/73729.java 762 773 ---------------------------------------- public void test52() throws Exception { String data = "\\xfa\\u0afa\\xFA\\u0AFA"; CsvReader reader = CsvReader.parse(data); reader.setUseTextQualifier(false); reader.setEscapeMode(CsvReader.ESCAPE_MODE_BACKSLASH); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("úૺúૺ", reader.get(0)); Assert.assertEquals("\\xfa\\u0afa\\xFA\\u0AFA", reader.getRawRecord()); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- public void test41() throws Exception { String data = "double\\\\\\\\double backslash"; CsvReader reader = CsvReader.parse(data); reader.setUseTextQualifier(false); reader.setEscapeMode(CsvReader.ESCAPE_MODE_BACKSLASH); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("double\\\\double backslash", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/14709.java 517 539 /home/jeff/BigCloneBench/sample/default/129715.java 650 667 ---------------------------------------- private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveSeries(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeInstances(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/849450.java 189 197 /home/jeff/BigCloneBench/sample/selected/361180.java 604 613 ---------------------------------------- public double[][] getArrayCopy() { double[][] C = new double[m][n]; for (int i = 0; i < m; i++) { for (int j = 0; j < n; j++) { C[i][j] = A[i][j]; } } return C; } ---------------------------------------- public Matrix uminus() { Matrix X = new Matrix(m, n); double[][] C = X.getArray(); for (int i = 0; i < m; i++) { for (int j = 0; j < n; j++) { C[i][j] = -A[i][j]; } } return X; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/682654.java 133 139 /home/jeff/BigCloneBench/sample/selected/69006.java 142 147 ---------------------------------------- public void cancel() { try { transport.close(); } catch (Exception e) { return; } } ---------------------------------------- public void finalize() { try { close(); } catch (Exception e) { } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/98684.java 522 544 /home/jeff/BigCloneBench/sample/default/63015.java 631 648 ---------------------------------------- private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveSeries(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeSeries(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/45886.java 73 82 /home/jeff/BigCloneBench/sample/default/56146.java 54 62 ---------------------------------------- String sequenceUsingWhile(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; while (i <= stop) { if (i > start) builder.append(','); builder.append(i); i++; } return builder.toString(); } ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2290446.java 189 194 /home/jeff/BigCloneBench/sample/selected/2356990.java 59 64 ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_max_link_follow_policy(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { FollowOption _ob_r = max_link_follow_policy(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); FollowOptionHelper.write(out, _ob_r); return out; } ---------------------------------------- private org.omg.CORBA.portable.OutputStream _OB_att_get_def_follow_policy(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) { FollowOption _ob_r = def_follow_policy(); org.omg.CORBA.portable.OutputStream out = handler.createReply(); FollowOptionHelper.write(out, _ob_r); return out; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/72479.java 179 257 /home/jeff/BigCloneBench/sample/default/22797.java 179 257 ---------------------------------------- void calculateDiscoveryRates(int nBioReps, CombinationPair nullhyp) { if (proteinList == null) return; this.overallFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()]; this.nullhypothesisFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()]; this.nullhypothesisFilterPassProteins = new Vector>>(); for (int gi = 0; gi < this.GStatisticCutoffs.size(); gi++) { this.nullhypothesisFilterPassProteins.add(new Vector>()); for (int pi = 0; pi < this.PValueCutoffs.size(); pi++) { this.nullhypothesisFilterPassProteins.elementAt(gi).add(new Vector()); this.overallFilterPassCount[gi][pi] = 0; this.nullhypothesisFilterPassCount[gi][pi] = 0; } } CombinationGenerator combos = new CombinationGenerator(nBioReps); int[] groupsCount = new int[nBioReps]; BitSet[] selections = new BitSet[nBioReps]; double selectionRate = (double) this.nMaxPermutations / combos.getTotal().doubleValue(); if (selectionRate < 1.0) { System.out.println("Randomly sampling " + Math.round(combos.getTotal().doubleValue() * selectionRate) + " (" + (int) Math.ceil(selectionRate * 100.0) + "%) of " + combos.getTotal().intValue() + " data permutations..."); } else { System.out.println("Processing " + combos.getTotal().intValue() + " data permutations..."); } for (int order = 0; order < nBioReps; order++) { int orderSize = combos.getOrderSize(order); selections[order] = new BitSet(orderSize); if (selectionRate < 1.0) { Random r = new Random(orderSize); int nSelect = 1 + (int) ((double) orderSize * selectionRate); nSelect = Math.min(nSelect, orderSize); for (int i = nSelect; i > 0; ) { int slot = r.nextInt(orderSize); if (!selections[order].get(slot)) { selections[order].set(slot); i--; } } } else { selections[order].set(0, orderSize); } } double progress = 0; int last_pct = 0; while (combos.hasMore()) { CombinationPair pair = combos.getNext(); int order = pair.getOrder(); int pctdone = (int) (100.0 * ++progress / combos.getTotal().doubleValue()); if (pctdone != last_pct) { last_pct = pctdone; System.out.print(((last_pct % 5) == 0) ? (last_pct + "%") : "."); } if (selections[order].get(groupsCount[order]++)) { this.nPermutationsTried++; boolean bNullHyp = pair.equals(nullhyp); for (Protein prot : this.proteinList) { ProteinPermutation perm = prot.doPermutation(pair); if (bNullHyp) { prot.nullHypothesis = perm; } for (int gi = 0; gi < GStatisticCutoffs.size(); gi++) { if (perm.getGStatistic() >= GStatisticCutoffs.get(gi)) { for (int pi = PValueCutoffs.size(); pi-- > 0; ) { if (perm.getPValue() <= PValueCutoffs.get(pi)) { this.overallFilterPassCount[gi][pi]++; if (bNullHyp) { this.nullhypothesisFilterPassCount[gi][pi]++; this.nullhypothesisFilterPassProteins.elementAt(gi).elementAt(pi).add(prot); } } else { break; } } } else { break; } } } } } } ---------------------------------------- void calculateDiscoveryRates(int nBioReps, CombinationPair nullhyp) { if (proteinList == null) return; this.overallFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()]; this.nullhypothesisFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()]; this.nullhypothesisFilterPassProteins = new Vector>>(); for (int gi = 0; gi < this.GStatisticCutoffs.size(); gi++) { this.nullhypothesisFilterPassProteins.add(new Vector>()); for (int pi = 0; pi < this.PValueCutoffs.size(); pi++) { this.nullhypothesisFilterPassProteins.elementAt(gi).add(new Vector()); this.overallFilterPassCount[gi][pi] = 0; this.nullhypothesisFilterPassCount[gi][pi] = 0; } } CombinationGenerator combos = new CombinationGenerator(nBioReps); int[] groupsCount = new int[nBioReps]; BitSet[] selections = new BitSet[nBioReps]; double selectionRate = (double) this.nMaxPermutations / combos.getTotal().doubleValue(); if (selectionRate < 1.0) { System.out.println("Randomly sampling " + Math.round(combos.getTotal().doubleValue() * selectionRate) + " (" + (int) Math.ceil(selectionRate * 100.0) + "%) of " + combos.getTotal().intValue() + " data permutations..."); } else { System.out.println("Processing " + combos.getTotal().intValue() + " data permutations..."); } for (int order = 0; order < nBioReps; order++) { int orderSize = combos.getOrderSize(order); selections[order] = new BitSet(orderSize); if (selectionRate < 1.0) { Random r = new Random(orderSize); int nSelect = 1 + (int) ((double) orderSize * selectionRate); nSelect = Math.min(nSelect, orderSize); for (int i = nSelect; i > 0; ) { int slot = r.nextInt(orderSize); if (!selections[order].get(slot)) { selections[order].set(slot); i--; } } } else { selections[order].set(0, orderSize); } } double progress = 0; int last_pct = 0; while (combos.hasMore()) { CombinationPair pair = combos.getNext(); int order = pair.getOrder(); int pctdone = (int) (100.0 * ++progress / combos.getTotal().doubleValue()); if (pctdone != last_pct) { last_pct = pctdone; System.out.print(((last_pct % 5) == 0) ? (last_pct + "%") : "."); } if (selections[order].get(groupsCount[order]++)) { this.nPermutationsTried++; boolean bNullHyp = pair.equals(nullhyp); for (Protein prot : this.proteinList) { ProteinPermutation perm = prot.doPermutation(pair); if (bNullHyp) { prot.nullHypothesis = perm; } for (int gi = 0; gi < GStatisticCutoffs.size(); gi++) { if (perm.getGStatistic() >= GStatisticCutoffs.get(gi)) { for (int pi = PValueCutoffs.size(); pi-- > 0; ) { if (perm.getPValue() <= PValueCutoffs.get(pi)) { this.overallFilterPassCount[gi][pi]++; if (bNullHyp) { this.nullhypothesisFilterPassCount[gi][pi]++; this.nullhypothesisFilterPassProteins.elementAt(gi).elementAt(pi).add(prot); } } else { break; } } } else { break; } } } } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/35053.java 629 646 /home/jeff/BigCloneBench/sample/default/103146.java 667 685 ---------------------------------------- private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeSeries(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { File file = w.getRefFile(rec.getRefFileIDs()); if (!file.exists()) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/98981.java 522 544 /home/jeff/BigCloneBench/sample/default/98684.java 570 590 ---------------------------------------- private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else if (doRemoveSeries(w, rec, counter, delFiles)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doRemoveInstances(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (sopInstUIDs.contains(rec.getRefSOPInstanceUID()) || matchFileIDs(rec.getRefFileIDs())) { if (delFiles) { deleteRefFiles(w, rec, counter); } toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[1] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1913823.java 76 92 /home/jeff/BigCloneBench/sample/selected/2503307.java 133 148 ---------------------------------------- protected byte[] padBuffer() { int n = (int) (count % BLOCK_SIZE); int padding = (n < 112) ? (112 - n) : (240 - n); byte[] result = new byte[padding + 16]; result[0] = (byte) 0x80; long bits = count << 3; padding += 8; result[padding++] = (byte) (bits >>> 56); result[padding++] = (byte) (bits >>> 48); result[padding++] = (byte) (bits >>> 40); result[padding++] = (byte) (bits >>> 32); result[padding++] = (byte) (bits >>> 24); result[padding++] = (byte) (bits >>> 16); result[padding++] = (byte) (bits >>> 8); result[padding] = (byte) bits; return result; } ---------------------------------------- protected byte[] padBuffer() { int n = (int) (count % BLOCK_SIZE); int padding = (n < 56) ? (56 - n) : (120 - n); byte[] result = new byte[padding + 8]; result[0] = (byte) 0x80; long bits = count << 3; result[padding++] = (byte) bits; result[padding++] = (byte) (bits >>> 8); result[padding++] = (byte) (bits >>> 16); result[padding++] = (byte) (bits >>> 24); result[padding++] = (byte) (bits >>> 32); result[padding++] = (byte) (bits >>> 40); result[padding++] = (byte) (bits >>> 48); result[padding] = (byte) (bits >>> 56); return result; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2372569.java 604 623 /home/jeff/BigCloneBench/sample/selected/2701118.java 665 684 ---------------------------------------- public static String nullSafeToString(char[] array) { if (array == null) { return NULL_STRING; } int length = array.length; if (length == 0) { return EMPTY_ARRAY; } StringBuffer buffer = new StringBuffer(); for (int i = 0; i < length; i++) { if (i == 0) { buffer.append(ARRAY_START); } else { buffer.append(ARRAY_ELEMENT_SEPARATOR); } buffer.append("'").append(array[i]).append("'"); } buffer.append(ARRAY_END); return buffer.toString(); } ---------------------------------------- public static String nullSafeToString(float[] array) { if (array == null) { return NULL_STRING; } int length = array.length; if (length == 0) { return EMPTY_ARRAY; } StringBuffer buffer = new StringBuffer(); for (int i = 0; i < length; i++) { if (i == 0) { buffer.append(ARRAY_START); } else { buffer.append(ARRAY_ELEMENT_SEPARATOR); } buffer.append(array[i]); } buffer.append(ARRAY_END); return buffer.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/44157.java 113 124 /home/jeff/BigCloneBench/sample/default/86457.java 113 124 ---------------------------------------- private boolean found(List> table, String target) { boolean found = false; search: for (List row : table) { for (String value : row) { if (value.equals(target)) { found = true; break search; } } } return found; } ---------------------------------------- private boolean found(List> table, String target) { boolean found = false; search: for (List row : table) { for (String value : row) { if (value.equals(target)) { found = true; break search; } } } return found; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1700428.java 102 110 /home/jeff/BigCloneBench/sample/selected/74985.java 238 246 ---------------------------------------- public static Properties getUrlAsProperties(String urlString) throws IOException { Properties props = new Properties(); InputStream in = null; String propfile = urlString; in = getUrlAsStream(propfile); props.load(in); in.close(); return props; } ---------------------------------------- public static Properties getUrlAsProperties(String urlString) throws IOException { Properties props = new Properties(); InputStream in = null; String propfile = urlString; in = getUrlAsStream(propfile); props.load(in); in.close(); return props; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1827694.java 50 58 /home/jeff/BigCloneBench/sample/selected/1827694.java 74 82 ---------------------------------------- public static final String toString(short[] array) { if (array == null) return "null"; StringBuffer sb = new StringBuffer(128).append('['); for (int j = 0; j < array.length; ++j) { sb.append(array[j]); if (j != array.length - 1) sb.append(", "); } return sb.append(']').toString(); } ---------------------------------------- public static final String toString(char[] array) { if (array == null) return "null"; StringBuffer sb = new StringBuffer(128).append('['); for (int j = 0; j < array.length; ++j) { sb.append(array[j]); if (j != array.length - 1) sb.append(", "); } return sb.append(']').toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/132039.java 573 587 /home/jeff/BigCloneBench/sample/default/68839.java 573 587 ---------------------------------------- private void initTLS(Configuration cfg) { try { cipherSuites = url.getCipherSuites(); if (cipherSuites == null) { return; } tls = SSLContextAdapter.getInstance(); char[] keypasswd = cfg.getProperty("tls-key-passwd", "passwd").toCharArray(); tls.setKey(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty("tls-key", "identity.p12")), keypasswd), keypasswd); tls.setTrust(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty("tls-cacerts", "cacerts.jks")), cfg.getProperty("tls-cacerts-passwd", "passwd").toCharArray())); tls.init(); } catch (Exception ex) { throw new RuntimeException("Could not initalize TLS configuration: ", ex); } } ---------------------------------------- private void initTLS(Configuration cfg) { try { cipherSuites = url.getCipherSuites(); if (cipherSuites == null) { return; } tls = SSLContextAdapter.getInstance(); char[] keypasswd = cfg.getProperty("tls-key-passwd", "passwd").toCharArray(); tls.setKey(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty("tls-key", "identity.p12")), keypasswd), keypasswd); tls.setTrust(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty("tls-cacerts", "cacerts.jks")), cfg.getProperty("tls-cacerts-passwd", "passwd").toCharArray())); tls.init(); } catch (Exception ex) { throw new RuntimeException("Could not initalize TLS configuration: ", ex); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/467737.java 139 148 /home/jeff/BigCloneBench/sample/selected/467737.java 206 216 ---------------------------------------- public String getTextValue(String parentTag, String elementName) { Document rootDom = this.getDom(); NodeList nl = rootDom.getElementsByTagName(parentTag); Element ele = null; if (nl != null && nl.getLength() > 0) { ele = (Element) nl.item(0); return getTextValue(ele, elementName); } return null; } ---------------------------------------- public ArrayList getElementsUnderSpecifiedElement(String elementName) { ArrayList resultList = new ArrayList(); Document rootDom = this.getDom(); NodeList nl = rootDom.getElementsByTagName(elementName); Element ele = null; if (nl != null && nl.getLength() > 0) { ele = (Element) nl.item(0); return getElementsUnderSpecifiedElement(ele); } return resultList; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/70505.java 631 648 /home/jeff/BigCloneBench/sample/default/90537.java 631 648 ---------------------------------------- private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeSeries(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeSeries(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/73729.java 133 146 /home/jeff/BigCloneBench/sample/default/73729.java 356 366 ---------------------------------------- public void test3() throws Exception { String data = ","; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("", reader.get(0)); Assert.assertEquals("", reader.get(1)); Assert.assertEquals(',', reader.getDelimiter()); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(2, reader.getColumnCount()); Assert.assertEquals(",", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); Assert.assertEquals("", reader.getRawRecord()); reader.close(); } ---------------------------------------- public void test17() throws Exception { String data = "\"double\"\"\"\"double quotes\""; CsvReader reader = CsvReader.parse(data); Assert.assertTrue(reader.readRecord()); Assert.assertEquals("double\"\"double quotes", reader.get(0)); Assert.assertEquals(0L, reader.getCurrentRecord()); Assert.assertEquals(1, reader.getColumnCount()); Assert.assertEquals("\"double\"\"\"\"double quotes\"", reader.getRawRecord()); Assert.assertFalse(reader.readRecord()); reader.close(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/104630.java 43 52 /home/jeff/BigCloneBench/sample/default/103574.java 43 52 ---------------------------------------- public void testCommas() { String sequence = "1,2,3,4,5"; assertEquals(sequence, sequenceUsingDo(1, 5)); assertEquals(sequence, sequenceUsingFor(1, 5)); assertEquals(sequence, sequenceUsingWhile(1, 5)); sequence = "8"; assertEquals(sequence, sequenceUsingDo(8, 8)); assertEquals(sequence, sequenceUsingFor(8, 8)); assertEquals(sequence, sequenceUsingWhile(8, 8)); } ---------------------------------------- public void testCommas() { String sequence = "1,2,3,4,5"; assertEquals(sequence, sequenceUsingDo(1, 5)); assertEquals(sequence, sequenceUsingFor(1, 5)); assertEquals(sequence, sequenceUsingWhile(1, 5)); sequence = "8"; assertEquals(sequence, sequenceUsingDo(8, 8)); assertEquals(sequence, sequenceUsingFor(8, 8)); assertEquals(sequence, sequenceUsingWhile(8, 8)); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1017245.java 357 367 /home/jeff/BigCloneBench/sample/selected/1017245.java 375 385 ---------------------------------------- public void setMatrix(int i0, int i1, int j0, int j1, Matrix X) { try { for (int i = i0; i <= i1; i++) { for (int j = j0; j <= j1; j++) { A[i][j] = X.get(i - i0, j - j0); } } } catch (ArrayIndexOutOfBoundsException e) { throw new ArrayIndexOutOfBoundsException("Submatrix indices"); } } ---------------------------------------- public void setMatrix(int[] r, int[] c, Matrix X) { try { for (int i = 0; i < r.length; i++) { for (int j = 0; j < c.length; j++) { A[r[i]][c[j]] = X.get(i, j); } } } catch (ArrayIndexOutOfBoundsException e) { throw new ArrayIndexOutOfBoundsException("Submatrix indices"); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/40097.java 64 71 /home/jeff/BigCloneBench/sample/default/57783.java 54 62 ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- String sequenceUsingDo(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; do { if (i > start) builder.append(','); builder.append(i); } while (++i <= stop); return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/76192.java 687 703 /home/jeff/BigCloneBench/sample/default/95647.java 687 703 ---------------------------------------- private static Properties loadConfig() { InputStream in = DcmDir.class.getResourceAsStream("dcmdir.cfg"); try { Properties retval = new Properties(); retval.load(in); return retval; } catch (Exception e) { throw new RuntimeException("Could not read dcmdir.cfg", e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } ---------------------------------------- private static Properties loadConfig() { InputStream in = DcmDir.class.getResourceAsStream("dcmdir.cfg"); try { Properties retval = new Properties(); retval.load(in); return retval; } catch (Exception e) { throw new RuntimeException("Could not read dcmdir.cfg", e); } finally { if (in != null) { try { in.close(); } catch (IOException ignore) { } } } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/115118.java 260 270 /home/jeff/BigCloneBench/sample/default/3389.java 260 270 ---------------------------------------- public void list() throws IOException, TransformerConfigurationException { SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance(); Templates xslt = loadDcmDirXSL(tf); DirReader reader = fact.newDirReader(dirFile); reader.getFileSetInfo().writeFile2(getTransformerHandler(tf, xslt, FILE_SET_INFO), dict, null, 128, null); try { list("", reader.getFirstRecord(onlyInUse), tf, xslt); } finally { reader.close(); } } ---------------------------------------- public void list() throws IOException, TransformerConfigurationException { SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance(); Templates xslt = loadDcmDirXSL(tf); DirReader reader = fact.newDirReader(dirFile); reader.getFileSetInfo().writeFile2(getTransformerHandler(tf, xslt, FILE_SET_INFO), dict, null, 128, null); try { list("", reader.getFirstRecord(onlyInUse), tf, xslt); } finally { reader.close(); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/70505.java 631 648 /home/jeff/BigCloneBench/sample/default/6937.java 648 665 ---------------------------------------- private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeSeries(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException { boolean matchAll = true; LinkedList toRemove = new LinkedList(); for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeInstances(w, rec, counter)) { toRemove.add(rec); } else { matchAll = false; } } if (matchAll) { return true; } for (Iterator it = toRemove.iterator(); it.hasNext(); ) { counter[0] += w.remove((DirRecord) it.next()); } return false; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/10720.java 325 337 /home/jeff/BigCloneBench/sample/default/6871.java 325 337 ---------------------------------------- int getTemplateCommand(String line) { int startMatch = line.indexOf(templateMarker) + templateMarker.length() + 1; if (DEBUG) System.out.println("getting template command :" + line.substring(startMatch)); for (int i = 0; i < commands.length; ++i) { String current = commands[i]; if (line.regionMatches(startMatch, current, 0, current.length())) { params = line.substring(startMatch + current.length()); if (DEBUG) System.out.println("command is " + commands[i] + ". params =" + params); return i; } } return INVALID_COMMAND; } ---------------------------------------- int getTemplateCommand(String line) { int startMatch = line.indexOf(templateMarker) + templateMarker.length() + 1; if (DEBUG) System.out.println("getting template command :" + line.substring(startMatch)); for (int i = 0; i < commands.length; ++i) { String current = commands[i]; if (line.regionMatches(startMatch, current, 0, current.length())) { params = line.substring(startMatch + current.length()); if (DEBUG) System.out.println("command is " + commands[i] + ". params =" + params); return i; } } return INVALID_COMMAND; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2465371.java 1418 1456 /home/jeff/BigCloneBench/sample/selected/2465371.java 1504 1542 ---------------------------------------- private static void sort1(byte x[], int off, int len) { if (len < 7) { for (int i = off; i < len + off; i++) for (int j = i; j > off && x[j - 1] > x[j]; j--) swap(x, j, j - 1); return; } int m = off + len / 2; if (len > 7) { int l = off; int n = off + len - 1; if (len > 40) { int s = len / 8; l = med3(x, l, l + s, l + 2 * s); m = med3(x, m - s, m, m + s); n = med3(x, n - 2 * s, n - s, n); } m = med3(x, l, m, n); } byte v = x[m]; int a = off, b = a, c = off + len - 1, d = c; while (true) { while (b <= c && x[b] <= v) { if (x[b] == v) swap(x, a++, b); b++; } while (c >= b && x[c] >= v) { if (x[c] == v) swap(x, c, d--); c--; } if (b > c) break; swap(x, b++, c--); } int s, n = off + len; s = Math.min(a - off, b - a); vecswap(x, off, b - s, s); s = Math.min(d - c, n - d - 1); vecswap(x, b, n - s, s); if ((s = b - a) > 1) sort1(x, off, s); if ((s = d - c) > 1) sort1(x, n - s, s); } ---------------------------------------- private static void sort1(double x[], int off, int len) { if (len < 7) { for (int i = off; i < len + off; i++) for (int j = i; j > off && x[j - 1] > x[j]; j--) swap(x, j, j - 1); return; } int m = off + len / 2; if (len > 7) { int l = off; int n = off + len - 1; if (len > 40) { int s = len / 8; l = med3(x, l, l + s, l + 2 * s); m = med3(x, m - s, m, m + s); n = med3(x, n - 2 * s, n - s, n); } m = med3(x, l, m, n); } double v = x[m]; int a = off, b = a, c = off + len - 1, d = c; while (true) { while (b <= c && x[b] <= v) { if (x[b] == v) swap(x, a++, b); b++; } while (c >= b && x[c] >= v) { if (x[c] == v) swap(x, c, d--); c--; } if (b > c) break; swap(x, b++, c--); } int s, n = off + len; s = Math.min(a - off, b - a); vecswap(x, off, b - s, s); s = Math.min(d - c, n - d - 1); vecswap(x, b, n - s, s); if ((s = b - a) > 1) sort1(x, off, s); if ((s = d - c) > 1) sort1(x, n - s, s); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/676014.java 55 67 /home/jeff/BigCloneBench/sample/selected/2242458.java 241 253 ---------------------------------------- public IStructuredSelection findSelection(IEditorInput anInput) { IDiagramDocument document = SiseorDiagramEditorPlugin.getInstance().getDocumentProvider().getDiagramDocument(anInput); if (document == null) { return StructuredSelection.EMPTY; } Diagram diagram = document.getDiagram(); IFile file = WorkspaceSynchronizer.getFile(diagram.eResource()); if (file != null) { SiseorNavigatorItem item = new SiseorNavigatorItem(diagram, file, false); return new StructuredSelection(item); } return StructuredSelection.EMPTY; } ---------------------------------------- private ISelection getNavigatorSelection() { IDiagramDocument document = getDiagramDocument(); if (document == null) { return StructuredSelection.EMPTY; } Diagram diagram = document.getDiagram(); IFile file = WorkspaceSynchronizer.getFile(diagram.eResource()); if (file != null) { PlwebNavigatorItem item = new PlwebNavigatorItem(diagram, file, false); return new StructuredSelection(item); } return StructuredSelection.EMPTY; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/41265.java 243 252 /home/jeff/BigCloneBench/sample/default/21681.java 243 252 ---------------------------------------- private TransformerHandler getTransformerHandler(SAXTransformerFactory tf, Templates tpl, String dsprompt) throws TransformerConfigurationException, IOException { TransformerHandler th = tf.newTransformerHandler(tpl); th.setResult(new StreamResult(System.out)); Transformer t = th.getTransformer(); t.setParameter("maxlen", maxlen); t.setParameter("vallen", vallen); t.setParameter("vallen", vallen); t.setParameter("dsprompt", dsprompt); return th; } ---------------------------------------- private TransformerHandler getTransformerHandler(SAXTransformerFactory tf, Templates tpl, String dsprompt) throws TransformerConfigurationException, IOException { TransformerHandler th = tf.newTransformerHandler(tpl); th.setResult(new StreamResult(System.out)); Transformer t = th.getTransformer(); t.setParameter("maxlen", maxlen); t.setParameter("vallen", vallen); t.setParameter("vallen", vallen); t.setParameter("dsprompt", dsprompt); return th; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2096828.java 349 359 /home/jeff/BigCloneBench/sample/selected/2069719.java 366 376 ---------------------------------------- public static int nullSafeHashCode(byte[] array) { if (array == null) { return 0; } int hash = INITIAL_HASH; int arraySize = array.length; for (int i = 0; i < arraySize; i++) { hash = MULTIPLIER * hash + array[i]; } return hash; } ---------------------------------------- public static int nullSafeHashCode(long[] array) { if (array == null) { return 0; } int hash = INITIAL_HASH; int arraySize = array.length; for (int i = 0; i < arraySize; i++) { hash = MULTIPLIER * hash + hashCode(array[i]); } return hash; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/3389.java 621 629 /home/jeff/BigCloneBench/sample/default/87896.java 619 627 ---------------------------------------- private int doPurge(DirWriter w) throws IOException { int[] counter = { 0 }; for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeStudy(w, rec, counter)) { counter[0] += w.remove(rec); } } return counter[0]; } ---------------------------------------- private int doPurge(DirWriter w) throws IOException { int[] counter = { 0 }; for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) { if (doPurgeStudy(w, rec, counter)) { counter[0] += w.remove(rec); } } return counter[0]; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/345560.java 608 619 /home/jeff/BigCloneBench/sample/selected/345560.java 627 638 ---------------------------------------- private void sampleJComboBoxActionPerformed(java.awt.event.ActionEvent evt) { if (sampleJComboBox.getSelectedIndex() == 0) { editSampleJButton.setEnabled(false); } else if (sampleJComboBox.getSelectedIndex() == sampleJComboBox.getItemCount() - 1) { editSampleJButton.setEnabled(false); sampleJComboBox.setSelectedIndex(0); new NewSampleDialog(this, true); } else { editSampleJButton.setEnabled(true); } validateInput(); } ---------------------------------------- private void protocolJComboBoxActionPerformed(java.awt.event.ActionEvent evt) { if (protocolJComboBox.getSelectedIndex() == 0) { editProtocolJButton.setEnabled(false); } else if (protocolJComboBox.getSelectedIndex() == protocolJComboBox.getItemCount() - 1) { editProtocolJButton.setEnabled(false); protocolJComboBox.setSelectedIndex(0); new NewProtocolDialog(this, true); } else { editProtocolJButton.setEnabled(true); } validateInput(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2181514.java 120 131 /home/jeff/BigCloneBench/sample/selected/699527.java 23 34 ---------------------------------------- public static void copyFile(File in, File out, boolean append) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out, append).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } ---------------------------------------- public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/85301.java 73 82 /home/jeff/BigCloneBench/sample/default/72306.java 64 71 ---------------------------------------- String sequenceUsingWhile(int start, int stop) { StringBuilder builder = new StringBuilder(); int i = start; while (i <= stop) { if (i > start) builder.append(','); builder.append(i); i++; } return builder.toString(); } ---------------------------------------- String sequenceUsingFor(int start, int stop) { StringBuilder builder = new StringBuilder(); for (int i = start; i <= stop; i++) { if (i > start) builder.append(','); builder.append(i); } return builder.toString(); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/default/110979.java 50 61 /home/jeff/BigCloneBench/sample/default/87351.java 50 61 ---------------------------------------- public List tokenize(String s, List result) { StringTokenizer stk = new StringTokenizer(s, ", "); while (stk.hasMoreTokens()) { String tk = stk.nextToken(); if (tk.startsWith("$")) { tokenize(getProperty(tk.substring(1), ""), result); } else { result.add(tk); } } return result; } ---------------------------------------- public List tokenize(String s, List result) { StringTokenizer stk = new StringTokenizer(s, ", "); while (stk.hasMoreTokens()) { String tk = stk.nextToken(); if (tk.startsWith("$")) { tokenize(getProperty(tk.substring(1), ""), result); } else { result.add(tk); } } return result; } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/1882693.java 962 973 /home/jeff/BigCloneBench/sample/selected/2215261.java 963 974 ---------------------------------------- public InputStream(java.io.InputStream in, int options) { super(in); this.breakLines = (options & DONT_BREAK_LINES) != DONT_BREAK_LINES; this.encode = (options & ENCODE) == ENCODE; this.bufferLength = encode ? 4 : 3; this.buffer = new byte[bufferLength]; this.position = -1; this.lineLength = 0; this.options = options; this.alphabet = getAlphabet(options); this.decodabet = getDecodabet(options); } ---------------------------------------- public InputStream(java.io.InputStream in, int options) { super(in); this.breakLines = (options & DONT_BREAK_LINES) != DONT_BREAK_LINES; this.encode = (options & ENCODE) == ENCODE; this.bufferLength = encode ? 4 : 3; this.buffer = new byte[bufferLength]; this.position = -1; this.lineLength = 0; this.options = options; this.alphabet = getAlphabet(options); this.decodabet = getDecodabet(options); } ---------------------------------------- $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ /home/jeff/BigCloneBench/sample/selected/2530759.java 352 367 /home/jeff/BigCloneBench/sample/selected/472295.java 343 357 ---------------------------------------- public void newProperties(PropertySheet ps) throws PropertyException { logger = ps.getLogger(); propsFile = ps.getString(PROP_PROPERTIES_FILE, PROP_PROPERTIES_FILE_DEFAULT); logMath = (LogMath) ps.getComponent(PROP_LOG_MATH, LogMath.class); unitManager = (UnitManager) ps.getComponent(PROP_UNIT_MANAGER, UnitManager.class); binary = ps.getBoolean(PROP_IS_BINARY, getIsBinaryDefault()); sparseForm = ps.getBoolean(PROP_SPARSE_FORM, getSparseFormDefault()); vectorLength = ps.getInt(PROP_VECTOR_LENGTH, getVectorLengthDefault()); model = ps.getString(PROP_MODEL, getModelDefault()); dataDir = ps.getString(PROP_DATA_LOCATION, getDataLocationDefault()) + "/"; distFloor = ps.getFloat(PROP_MC_FLOOR, PROP_MC_FLOOR_DEFAULT); mixtureWeightFloor = ps.getFloat(PROP_MW_FLOOR, PROP_MW_FLOOR_DEFAULT); varianceFloor = ps.getFloat(PROP_VARIANCE_FLOOR, PROP_VARIANCE_FLOOR_DEFAULT); useCDUnits = ps.getBoolean(PROP_USE_CD_UNITS, PROP_USE_CD_UNITS_DEFAULT); fileNameClasseMllr = ps.getString("classeMllr", ""); } ---------------------------------------- public void newProperties(PropertySheet ps) throws PropertyException { logger = ps.getLogger(); propsFile = ps.getString(PROP_PROPERTIES_FILE, PROP_PROPERTIES_FILE_DEFAULT); logMath = (LogMath) ps.getComponent(PROP_LOG_MATH, LogMath.class); unitManager = (UnitManager) ps.getComponent(PROP_UNIT_MANAGER, UnitManager.class); binary = ps.getBoolean(PROP_IS_BINARY, getIsBinaryDefault()); sparseForm = ps.getBoolean(PROP_SPARSE_FORM, getSparseFormDefault()); vectorLength = ps.getInt(PROP_VECTOR_LENGTH, getVectorLengthDefault()); model = ps.getString(PROP_MODEL, getModelDefault()); dataDir = ps.getString(PROP_DATA_LOCATION, getDataLocationDefault()) + "/"; distFloor = ps.getFloat(PROP_MC_FLOOR, PROP_MC_FLOOR_DEFAULT); mixtureWeightFloor = ps.getFloat(PROP_MW_FLOOR, PROP_MW_FLOOR_DEFAULT); varianceFloor = ps.getFloat(PROP_VARIANCE_FLOOR, PROP_VARIANCE_FLOOR_DEFAULT); useCDUnits = ps.getBoolean(PROP_USE_CD_UNITS, PROP_USE_CD_UNITS_DEFAULT); } ----------------------------------------