Index: src/org/jmol/adapter/smarter/CifReader.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/CifReader.java,v retrieving revision 1.16 diff -u -r1.16 CifReader.java --- src/org/jmol/adapter/smarter/CifReader.java 15 Jul 2004 09:10:40 -0000 1.16 +++ src/org/jmol/adapter/smarter/CifReader.java 18 Sep 2004 08:25:23 -0000 @@ -655,7 +655,7 @@ *

*/ - class RidiculousFileFormatTokenizer { + static class RidiculousFileFormatTokenizer { String str; int ich; int cch; Index: src/org/jmol/adapter/smarter/CmlReader.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/CmlReader.java,v retrieving revision 1.18 diff -u -r1.18 CmlReader.java --- src/org/jmol/adapter/smarter/CmlReader.java 31 May 2004 23:47:25 -0000 1.18 +++ src/org/jmol/adapter/smarter/CmlReader.java 18 Sep 2004 08:25:25 -0000 @@ -38,8 +38,6 @@ * A CML2 Reader, it does not support the old CML1 architecture. */ class CmlReader extends ModelReader { - - SAXParser saxp; Model readModel(BufferedReader reader) throws Exception { SAXParserFactory spf = SAXParserFactory.newInstance(); Index: src/org/jmol/adapter/smarter/Model.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/Model.java,v retrieving revision 1.15 diff -u -r1.15 Model.java --- src/org/jmol/adapter/smarter/Model.java 3 Aug 2004 08:36:24 -0000 1.15 +++ src/org/jmol/adapter/smarter/Model.java 18 Sep 2004 08:25:26 -0000 @@ -51,7 +51,6 @@ float[] pdbScaleMatrix; float[] pdbScaleTranslate; - int pdbStructureRecordCount; String[] pdbStructureRecords; Model(String modelTypeName) { @@ -60,6 +59,7 @@ protected void finalize() { // System.out.println("Model.finalize() called"); + try{super.finalize();}catch(Throwable t){} } void finish() { @@ -147,7 +147,7 @@ void setModelName(String modelName) { if (modelName != null) { - modelName.trim(); + modelName = modelName.trim(); if (modelName.length() > 0) this.modelName = modelName; } Index: src/org/jmol/adapter/smarter/ShelxReader.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/ShelxReader.java,v retrieving revision 1.11 diff -u -r1.11 ShelxReader.java --- src/org/jmol/adapter/smarter/ShelxReader.java 26 Aug 2004 17:38:12 -0000 1.11 +++ src/org/jmol/adapter/smarter/ShelxReader.java 18 Sep 2004 08:25:27 -0000 @@ -50,7 +50,6 @@ boolean endReached; Model readModel(BufferedReader reader) throws Exception { - this.logger = logger; model = new Model("shelx"); model.coordinatesAreFractional = true; Index: src/org/jmol/g3d/Cylinder3D.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/jmol/g3d/Cylinder3D.java,v retrieving revision 1.5 diff -u -r1.5 Cylinder3D.java --- src/org/jmol/g3d/Cylinder3D.java 4 Aug 2004 17:44:15 -0000 1.5 +++ src/org/jmol/g3d/Cylinder3D.java 18 Sep 2004 08:25:30 -0000 @@ -283,8 +283,8 @@ xMax = x; zXMax = zRaster[i]; } - if (y == 0) { - } + //if (y == 0) { + //} } if (yRaster[i] == -y) { // 0 will run through here too int x = -xRaster[i]; Index: src/org/openscience/jmol/viewer/JmolViewer.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolViewer.java,v retrieving revision 1.200 diff -u -r1.200 JmolViewer.java --- src/org/openscience/jmol/viewer/JmolViewer.java 13 Sep 2004 02:39:59 -0000 1.200 +++ src/org/openscience/jmol/viewer/JmolViewer.java 18 Sep 2004 08:25:55 -0000 @@ -1883,7 +1883,7 @@ final AtomIterator nullAtomIterator = new NullAtomIterator(); - class NullAtomIterator implements AtomIterator { + static class NullAtomIterator implements AtomIterator { public boolean hasNext() { return false; } public Atom next() { return null; } public void release() {} @@ -1892,7 +1892,7 @@ final BondIterator nullBondIterator = new NullBondIterator(); - class NullBondIterator implements BondIterator { + static class NullBondIterator implements BondIterator { public boolean hasNext() { return false; } public Bond next() { return null; } } Index: src/org/openscience/jmol/viewer/datamodel/Bspt.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Bspt.java,v retrieving revision 1.7 diff -u -r1.7 Bspt.java --- src/org/openscience/jmol/viewer/datamodel/Bspt.java 28 May 2004 14:44:18 -0000 1.7 +++ src/org/openscience/jmol/viewer/datamodel/Bspt.java 18 Sep 2004 08:25:55 -0000 @@ -347,7 +347,7 @@ boolean isLeafWithSpace(); } - class Node implements Element { + static class Node implements Element { Element eleLE; int dim; int dimMax; @@ -410,7 +410,7 @@ } } - class Leaf implements Element { + static class Leaf implements Element { int count; Tuple[] tuples; Index: src/org/openscience/jmol/viewer/datamodel/FrameBuilder.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/FrameBuilder.java,v retrieving revision 1.52 diff -u -r1.52 FrameBuilder.java --- src/org/openscience/jmol/viewer/datamodel/FrameBuilder.java 30 Aug 2004 18:12:49 -0000 1.52 +++ src/org/openscience/jmol/viewer/datamodel/FrameBuilder.java 18 Sep 2004 08:25:55 -0000 @@ -39,9 +39,6 @@ this.adapter = adapter; } - protected void finalize() { - } - boolean fileHasHbonds; public Frame buildFrame(Object clientFile) { Index: src/org/openscience/jmol/viewer/datamodel/Mmset.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Mmset.java,v retrieving revision 1.7 diff -u -r1.7 Mmset.java --- src/org/openscience/jmol/viewer/datamodel/Mmset.java 15 Jun 2004 20:49:29 -0000 1.7 +++ src/org/openscience/jmol/viewer/datamodel/Mmset.java 18 Sep 2004 08:25:55 -0000 @@ -144,7 +144,7 @@ models[i].calcHydrogenBonds(); } - class Structure { + static class Structure { String typeName; byte type; char startChainID; Index: src/org/openscience/jmol/viewer/managers/MouseManager.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers/MouseManager.java,v retrieving revision 1.35 diff -u -r1.35 MouseManager.java --- src/org/openscience/jmol/viewer/managers/MouseManager.java 17 Jun 2004 14:42:38 -0000 1.35 +++ src/org/openscience/jmol/viewer/managers/MouseManager.java 18 Sep 2004 08:25:57 -0000 @@ -473,7 +473,7 @@ // exitMeasurementMode(); return; } - if (measurementCount == 3 & !dblClick) + if (measurementCount == 3 && !dblClick) return; measurementCountPlusIndices[++measurementCount] = atomIndex; measurementCountPlusIndices[0] = measurementCount; Index: src/org/openscience/jmol/viewer/script/Compiler.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Compiler.java,v retrieving revision 1.46 diff -u -r1.46 Compiler.java --- src/org/openscience/jmol/viewer/script/Compiler.java 13 Sep 2004 02:40:00 -0000 1.46 +++ src/org/openscience/jmol/viewer/script/Compiler.java 18 Sep 2004 08:26:02 -0000 @@ -43,7 +43,7 @@ String errorMessage; String errorLine; - final boolean logMessages = false; + static final boolean logMessages = false; private void log(String message) { if (logMessages) @@ -92,7 +92,6 @@ int ichToken; int cchToken; - String strToken; Token[] atokenCommand; int ichCurrentCommand; Index: src/org/openscience/jmol/viewer/script/Eval.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Eval.java,v retrieving revision 1.185 diff -u -r1.185 Eval.java --- src/org/openscience/jmol/viewer/script/Eval.java 13 Sep 2004 15:10:37 -0000 1.185 +++ src/org/openscience/jmol/viewer/script/Eval.java 18 Sep 2004 08:26:35 -0000 @@ -167,18 +167,21 @@ return LoadError((String) t); BufferedReader reader = new BufferedReader(new InputStreamReader((InputStream) t)); - String script = ""; + StringBuffer script = new StringBuffer(); try { while (true) { String command = reader.readLine(); if (command == null) break; - script += command + "\n"; + script.append(command); + script.append("\n"); } } catch (IOException e) { + try{reader.close();}catch(IOException ioe){} return IOError(filename); } - return loadScript(filename, script); + try{reader.close();}catch(IOException ioe){} + return loadScript(filename, script.toString()); } boolean LoadError(String msg) { @@ -196,20 +199,21 @@ } public String toString() { - String str; - str = "Eval\n"; - str += " pc:" + pc + "\n"; - str += aatoken.length + " statements\n"; + StringBuffer str=new StringBuffer(); + str.append("Eval\n pc:"); + str.append(pc); str.append("\n"); + str.append(aatoken.length); str.append(" statements\n"); for (int i = 0; i < aatoken.length; ++i) { - str += " |"; + str.append(" |"); Token[] atoken = aatoken[i]; for (int j = 0; j < atoken.length; ++j) { - str += " " + atoken[j]; + str.append(' '); + str.append(atoken[j]); } - str += "\n"; + str.append("\n"); } - str += "END\n"; - return str; + str.append("END\n"); + return str.toString(); } public void clearDefinitionsAndLoadPredefined() {