From: <ha...@us...> - 2010-06-22 14:40:03
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Revision: 13453 http://jmol.svn.sourceforge.net/jmol/?rev=13453&view=rev Author: hansonr Date: 2010-06-22 14:39:56 +0000 (Tue, 22 Jun 2010) Log Message: ----------- version=12.0.RC21_dev # bug fix: acceptance of curly " from Microsoft Word text clipping in scripts Modified Paths: -------------- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java trunk/Jmol/src/org/jmol/script/ScriptCompiler.java trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java trunk/Jmol/src/org/jmol/util/CifDataReader.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java =================================================================== --- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java 2010-06-22 11:45:25 UTC (rev 13452) +++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java 2010-06-22 14:39:56 UTC (rev 13453) @@ -163,6 +163,14 @@ continuing = false; } + protected void finalizeReader() throws Exception { + super.finalizeReader(); + String header = tokenizer.getFileHeader(); + if (header.length() > 0) + atomSetCollection.setAtomSetCollectionAuxiliaryInfo("fileHeader", + header); + } + public void applySymmetryAndSetTrajectory() throws Exception { // This speeds up calculation, because no crosschecking // No special-position atoms in mmCIF files, because there will Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2010-06-22 11:45:25 UTC (rev 13452) +++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2010-06-22 14:39:56 UTC (rev 13453) @@ -252,6 +252,7 @@ private boolean compile0(boolean isFull) { + script = script.replace('\u201C', '"').replace('\u201D', '"'); script = cleanScriptComments(script); cchScript = this.script.length(); Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java =================================================================== --- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-22 11:45:25 UTC (rev 13452) +++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-06-22 14:39:56 UTC (rev 13453) @@ -13794,7 +13794,8 @@ private Object getCapSlabObject(StringBuffer sb, int i) throws ScriptException { Object propertyValue = null; - sb.append(" ").append(getToken(i).value).append(" "); + if (sb != null) + sb.append(" ").append(getToken(i).value).append(" "); int tok = tokAt(i + 1); Point4f plane = null; switch (tok) { Modified: trunk/Jmol/src/org/jmol/util/CifDataReader.java =================================================================== --- trunk/Jmol/src/org/jmol/util/CifDataReader.java 2010-06-22 11:45:25 UTC (rev 13452) +++ trunk/Jmol/src/org/jmol/util/CifDataReader.java 2010-06-22 14:39:56 UTC (rev 13453) @@ -71,7 +71,9 @@ public int ichPeeked; public int fieldCount; public String[] loopData; - + public StringBuffer fileHeader = new StringBuffer(); + private boolean isHeader = true; + //////////////////////////////////////////////////////////////// // special tokenizer class //////////////////////////////////////////////////////////////// @@ -85,6 +87,10 @@ this.br = br; } + public String getFileHeader() { + return fileHeader.toString(); + } + public static Hashtable readCifData(BufferedReader br) { CifDataReader cdr = new CifDataReader(br); return cdr.getAllCifData(); @@ -138,7 +144,16 @@ public String readLine() { try { - return (line = (reader != null ? reader.readLine() : br.readLine())); + line = (reader != null ? reader.readLine() : br.readLine()); + if (line == null) + return null; + if (isHeader) { + if (line.startsWith("#")) + fileHeader.append(line).append('\n'); + else + isHeader = false; + } + return line; } catch (Exception e) { return null; } Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-06-22 11:45:25 UTC (rev 13452) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-06-22 14:39:56 UTC (rev 13453) @@ -3,6 +3,8 @@ version=12.0.RC21_dev +# bug fix: acceptance of curly " from Microsoft Word text clipping in scripts +# bug fix: lcaocartoon cap broken # bug fix: isosurface boundbox not read from state # bug fix: translucent isosurface colorscheme saved but not read from state # new feature: modelkit mode invert ring stereochemistry This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |