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[Jmol-commits] SF.net SVN: jmol: [5447] branches/v10_9/Jmol/src/org/jmol/adapter/smarter
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From: <ni...@us...> - 2006-08-30 18:20:39
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Revision: 5447
http://svn.sourceforge.net/jmol/?rev=5447&view=rev
Author: nicove
Date: 2006-08-30 11:20:20 -0700 (Wed, 30 Aug 2006)
Log Message:
-----------
More logger features (Exceptions)
Bob (?):
I left a few TODO in some files, because the exception handling is very strange in some files:
A NullPointerException was created but not thrown, so it was useless.
I commented out the creation of the NullPointerException
Modified Paths:
--------------
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/CubeReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GamessReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/JaguarReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/NWChemReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyXMLReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/QchemReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanSmolReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java
branches/v10_9/Jmol/src/org/jmol/adapter/smarter/XmlReader.java
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/CubeReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/CubeReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -26,6 +26,8 @@
import java.io.BufferedReader;
+import org.jmol.util.Logger;
+
/**
* Gaussian cube file format
*
@@ -87,7 +89,7 @@
*/
} catch (Exception ex) {
atomSetCollection.errorMessage = "Could not read Cube file:" + ex + "\n line:\n" + line;
- ex.printStackTrace();
+ Logger.error("Could not read Cube file line " + line, ex);
}
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GamessReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GamessReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GamessReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -28,6 +28,8 @@
import java.util.Hashtable;
import java.util.Vector;
+import org.jmol.util.Logger;
+
class GamessReader extends AtomSetCollectionReader {
final static float angstromsPerBohr = 0.529177f;
@@ -72,8 +74,9 @@
}
} catch (Exception e) {
logger.log(e + " at line: " + line);
- e.printStackTrace();
- new NullPointerException();
+ Logger.error(null, e);
+ //TODO: Why this ?
+ //new NullPointerException();
}
logger.log(orbitals.size() + " molecular orbitals read");
moData.put("calculationType", calculationType);
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -29,6 +29,8 @@
import java.util.Hashtable;
import java.util.Vector;
+import org.jmol.util.Logger;
+
/**
* Reader for Gaussian 94/98/03 output files.
*
@@ -186,7 +188,7 @@
lineNum++;
}
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/JaguarReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/JaguarReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/JaguarReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -27,6 +27,8 @@
import java.io.BufferedReader;
import java.util.StringTokenizer;
+import org.jmol.util.Logger;
+
/**
* Jaguar reader tested for the two samples files in CVS. Both
* these files were created with Jaguar version 4.0, release 20.
@@ -48,7 +50,7 @@
}
}
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/Mol2Reader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -27,6 +27,7 @@
import java.io.BufferedReader;
import org.jmol.api.JmolAdapter;
+import org.jmol.util.Logger;
/**
* A minimal multi-file reader for TRIPOS SYBYL mol2 files.
@@ -52,9 +53,9 @@
try {
processMolecule(reader);
} catch (Exception e) {
- logger.log(e + " at line: " + line);
- e.printStackTrace();
- new NullPointerException();
+ Logger.error("Could not read file at line: " + line, e);
+ //TODO: Why this?
+ //new NullPointerException();
}
if (desiredModelNumber > 0)
break;
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/NWChemReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/NWChemReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/NWChemReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -26,6 +26,8 @@
import java.io.BufferedReader;
+import org.jmol.util.Logger;
+
/**
* A reader for NWChem 4.6
* NWChem is a quantum chemistry program developed at
@@ -114,7 +116,7 @@
}
}
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -27,6 +27,8 @@
import java.io.BufferedReader;
import java.util.Hashtable;
+import org.jmol.util.Logger;
+
/*
* Wavefunction Odyssey reader -- old style
*
@@ -53,7 +55,7 @@
if (discardLinesUntilContains(reader, "HESSIAN") != null)
readBonds(reader);
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyXMLReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyXMLReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/OdysseyXMLReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -27,6 +27,8 @@
import java.io.BufferedReader;
import java.util.Hashtable;
+import org.jmol.util.Logger;
+
/*
* Wavefunction Odyssey reader -- old style
*
@@ -51,7 +53,7 @@
if (discardLinesUntilContains(reader, "<bonds") != null)
readBonds(reader);
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/QchemReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/QchemReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/QchemReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -25,6 +25,8 @@
package org.jmol.adapter.smarter;
import java.io.BufferedReader;
+
+import org.jmol.util.Logger;
/**
* A reader for Q-Chem 2.1
* Q-Chem is a quantum chemistry program developed
@@ -66,7 +68,7 @@
++lineNum;
}
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -25,6 +25,7 @@
package org.jmol.adapter.smarter;
import org.jmol.api.JmolAdapter;
+import org.jmol.util.Logger;
import java.io.BufferedReader;
import java.util.Properties;
@@ -66,7 +67,7 @@
}
return "unknown reader error";
} catch (Exception e) {
- e.printStackTrace();
+ org.jmol.util.Logger.error(null, e);
return "" + e;
}
}
@@ -88,7 +89,7 @@
}
return "unknown reader error";
} catch (Exception e) {
- e.printStackTrace();
+ org.jmol.util.Logger.error(null, e);
return "" + e;
}
}
@@ -112,7 +113,7 @@
return "unknown reader error";
}
} catch (Exception e) {
- e.printStackTrace();
+ org.jmol.util.Logger.error(null, e);
return "" + e;
}
}
@@ -138,7 +139,7 @@
}
return "unknown DOM reader error";
} catch (Exception e) {
- e.printStackTrace();
+ org.jmol.util.Logger.error(null, e);
return "" + e;
}
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanArchive.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -30,6 +30,7 @@
import javax.vecmath.Vector3f;
import org.jmol.api.JmolAdapter;
+import org.jmol.util.Logger;
class SpartanArchive {
@@ -92,9 +93,9 @@
line = reader.readLine();
}
} catch (Exception e) {
- logger.log("Spartan archive reader error on line: " + line);
- e.printStackTrace();
- new Exception(e);
+ Logger.error("Spartan archive reader error on line: " + line, e);
+ //TODO: Why this?
+ //new Exception(e);
}
return atomCount;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -27,6 +27,8 @@
import java.io.BufferedReader;
import java.util.Hashtable;
+import org.jmol.util.Logger;
+
/*
* perhaps unnecessary ? I think this was for when all you had was
* a piece of the archive file that started with:
@@ -63,7 +65,7 @@
readFrequencies(reader);
}
} catch (Exception ex) {
- ex.printStackTrace();
+ Logger.error("Could not read file", ex);
atomSetCollection.errorMessage = "Could not read file:" + ex;
return atomSetCollection;
}
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanSmolReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanSmolReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/SpartanSmolReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -27,6 +27,8 @@
import java.io.BufferedReader;
import java.util.Hashtable;
+import org.jmol.util.Logger;
+
/*
* Spartan SMOL and .spartan compound document reader
*
@@ -84,9 +86,9 @@
line = reader.readLine();
}
} catch (Exception e) {
- logger.log(e + " at line: " + line);
- e.printStackTrace();
- new NullPointerException();
+ Logger.error("Could not read file at line: " + line, e);
+ //TODO: Why this?
+ //new NullPointerException();
}
// info out of order -- still a chance, at least for first model
if (atomCount > 0 && spartanArchive != null && bondData != null)
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/WebMOReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -28,6 +28,8 @@
import java.util.Hashtable;
import java.util.Vector;
+import org.jmol.util.Logger;
+
/**
* A molecular orbital reader for WebMO files.
*<p>
@@ -82,9 +84,9 @@
line = reader.readLine();
}
} catch (Exception e) {
- logger.log(e + " at line: " + line);
- e.printStackTrace();
- new NullPointerException();
+ Logger.error("Could not read file at line: " + line, e);
+ //TODO: Why this?
+ //new NullPointerException();
}
logger.log(orbitals.size() + " molecular orbitals read");
moData.put("mos", orbitals);
Modified: branches/v10_9/Jmol/src/org/jmol/adapter/smarter/XmlReader.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/adapter/smarter/XmlReader.java 2006-08-30 18:14:11 UTC (rev 5446)
+++ branches/v10_9/Jmol/src/org/jmol/adapter/smarter/XmlReader.java 2006-08-30 18:20:20 UTC (rev 5447)
@@ -212,8 +212,7 @@
try {
xmlReader.parse(is);
} catch (Exception e) {
- e.printStackTrace();
- Logger.error("ERROR IN XmlReader.parseReaderXML" + e);
+ Logger.error("ERROR IN XmlReader.parseReaderXML", e);
}
}
@@ -299,8 +298,7 @@
xmlReader.setContentHandler(handler);
xmlReader.setErrorHandler(handler);
} catch (Exception e) {
- e.printStackTrace();
- Logger.error("ERROR IN XmlReader.JmolXmlHandler.setHandler\n" + e);
+ Logger.error("ERROR IN XmlReader.JmolXmlHandler.setHandler", e);
}
}
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