Revision: 18300
http://sourceforge.net/p/jmol/code/18300
Author: hansonr
Date: 2013-06-06 20:56:00 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
___version=13.0.16
bug fix: COMPARE move of group saved in state may not be correct when restored
bug fix: restore command broken
Modified Paths:
--------------
branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlMolproReader.java
branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java
branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
branches/v13_0/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java
branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
branches/v13_0/Jmol/src/org/jmol/shapespecial/DotsRenderer.java
branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -1484,8 +1484,9 @@
}
}
} catch (Exception e) {
- Logger.error(line + "\nError in TLS parser: ");
- e.printStackTrace();
+ Logger.error(line + "\nError in TLS parser: " + e);
+ if (!viewer.isApplet())
+ e.printStackTrace();
tlsGroups = null;
break;
}
Modified:
branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlMolproReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlMolproReader.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlMolproReader.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -54,8 +54,9 @@
try {
atomSetCollection.cloneLastAtomSet();
} catch (Exception e) {
- e.printStackTrace();
- atomSetCollection.errorMessage = "Error processing normalCoordinate: "
+ e.getMessage();
+ if (!viewer.isApplet())
+ e.printStackTrace();
+ atomSetCollection.errorMessage = "Error processing normalCoordinate: "
+ e;
vibrationNumber = 0;
return;
}
Modified: branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -185,6 +185,7 @@
AtomSetCollection atomSetCollection,
BufferedReader reader, Object xmlReader,
JmolXmlHandler handler) {
this.parent = parent;
+ this.viewer = parent.viewer;
this.atomSetCollection = atomSetCollection;
this.reader = reader;
if (xmlReader instanceof XMLReader) {
@@ -202,8 +203,9 @@
try {
xmlReader.parse(is);
} catch (Exception e) {
- e.printStackTrace();
- atomSetCollection.errorMessage = "XML parsing error: " + e.getMessage();
+ if (!viewer.isApplet())
+ e.printStackTrace();
+ atomSetCollection.errorMessage = "XML parsing error: " + e;
}
}
@@ -280,7 +282,8 @@
else
parent.applySymmetryAndSetTrajectory();
} catch (Exception e) {
- e.printStackTrace();
+ if (!viewer.isApplet())
+ e.printStackTrace();
Logger.error("applySymmetry failed: " + e);
}
}
@@ -480,11 +483,11 @@
private Object jsObjectCall(Object jsObject, String method,
Object[] args) {
- return parent.viewer.getJsObjectInfo(jsObject, method, args);
+ return viewer.getJsObjectInfo(jsObject, method, args);
}
private Object jsObjectGetMember(Object jsObject, String name) {
- return parent.viewer.getJsObjectInfo(jsObject, name, null);
+ return viewer.getJsObjectInfo(jsObject, name, null);
}
}
}
Modified:
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
---
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-06-06 13:48:46 UTC (rev 18299)
+++
branches/v13_0/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -380,7 +380,8 @@
}
private void setError(Throwable e) {
- e.printStackTrace();
+ if (!viewer.isApplet())
+ e.printStackTrace();
if (line == null)
atomSetCollection.errorMessage = "Unexpected end of file after line "
+ --ptLine + ":\n" + prevline;
Modified: branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/adapter/smarter/Resolver.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -275,9 +275,8 @@
}
return atomSetCollectionReader;
} catch (Exception e) {
- err = "uncaught error in file loading for " + className;
+ err = "uncaught error in file loading for " + className + " " + e;
Logger.error(err);
- e.printStackTrace();
return err;
}
}
Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -541,9 +541,8 @@
try {
readSurfaceData(false);
} catch (Exception e) {
- e.printStackTrace();
- Logger.error("Exception in SurfaceReader::readSurfaceData: "
- + e.getMessage());
+ //e.printStackTrace();
+ Logger.error("Exception in SurfaceReader::readSurfaceData: " + e);
}
return;
}
Modified: branches/v13_0/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/jvxl/readers/VolumeDataReader.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -88,7 +88,7 @@
try {
readSurfaceData(isMapData);
} catch (Exception e) {
- e.printStackTrace();
+ Logger.info("VolumeDataReader error " + e);
return false;
}
return true;
Modified: branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -550,8 +550,9 @@
} catch (Exception ex) {
viewer.setStringProperty("_errormessage", "" + ex);
if (e.thisContext == null) {
- Logger.error("Error evaluating context");
- ex.printStackTrace();
+ Logger.error("Error evaluating context" + ex);
+ if (!viewer.isApplet())
+ ex.printStackTrace();
}
return false;
}
Modified: branches/v13_0/Jmol/src/org/jmol/shapespecial/DotsRenderer.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/shapespecial/DotsRenderer.java
2013-06-06 13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/shapespecial/DotsRenderer.java
2013-06-06 20:56:00 UTC (rev 18300)
@@ -92,8 +92,9 @@
renderConvex(Graphics3D.getColixInherited(dots.colixes[i],
atom.getColix()), map, nPoints);
} catch (Exception e) {
- System.out.println("Dots rendering error");
- e.printStackTrace();
+ System.out.println("Dots rendering error " + e);
+ if (!viewer.isApplet())
+ e.printStackTrace();
// ignore -- some sort of fluke
}
}
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06
13:48:46 UTC (rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-06
20:56:00 UTC (rev 18300)
@@ -15,6 +15,7 @@
___version=13.0.16
+bug fix: COMPARE move of group saved in state may not be correct when restored
bug fix: restore command broken
bug fix: antialiasing or resizing stray lines problem solved (introduced in
11.0, 08/2006!)
bug fix: "display add" by itself should not do anything
Modified: branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-06 13:48:46 UTC
(rev 18299)
+++ branches/v13_0/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-06 20:56:00 UTC
(rev 18300)
@@ -3247,6 +3247,8 @@
// atom coordinates may be moved here
// but this is not included as an atomMovedCallback
modelSet.setAtomData(type, name, coordinateData, isDefault);
+ if (type == AtomCollection.TAINT_COORD)
+ checkCoordinatesChanged();
refreshMeasures(true);
}
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