[Jmol-commits] CVS: Jmol/src/org/jmol/adapter/smarter QchemReader.java,1.4,1.5 HinReader.java,1.8,1.9 GaussianReader.java,1.26,1.27 CmlReader.java,1.24,1.25 MopacReader.java,1.7,1.8 SpartanReader.java,1.4,1.5 GamessReader.java,1.7,1.8 CifReader.java,1.24,1.25 JaguarReader.java,1.6,1.7 Resolver.java,1.2,1.3

[Nico <ni...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15196/src/org/jmol/adapter/smarter

Modified Files:
	QchemReader.java HinReader.java GaussianReader.java 
	CmlReader.java MopacReader.java SpartanReader.java 
	GamessReader.java CifReader.java JaguarReader.java 
	Resolver.java 
Log Message:
Removed some warnings (Eclipse)

Index: QchemReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/QchemReader.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- QchemReader.java	22 Oct 2004 05:17:31 -0000	1.4
+++ QchemReader.java	7 Nov 2004 10:43:38 -0000	1.5
@@ -99,7 +99,7 @@
     String line;
     while ((line = reader.readLine()) != null &&
            !line.startsWith(" --")) {
-    String centerNumber = parseToken(line, 0, 5);
+    /*String centerNumber = */parseToken(line, 0, 5);
     String aname = parseToken(line, 6, 12);
     if (aname.indexOf("X") == 1) {
       // skip dummy atoms
@@ -123,7 +123,8 @@
     int modelNumber = 1;
     String line;
     while ((line = reader.readLine()) != null &&
-           ! line.startsWith(" Frequency:"));
+           ! line.startsWith(" Frequency:")) {
+    }
     if (line == null)
       return;
     do {

Index: HinReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/HinReader.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- HinReader.java	22 Oct 2004 05:17:31 -0000	1.8
+++ HinReader.java	7 Nov 2004 10:43:38 -0000	1.9
@@ -86,7 +86,7 @@
   void processMol(String line) {
     atomSetCollection.newAtomSet();
     String molName = getMolName(line);
-    atomSetCollection.setAtomSetName(getMolName(line));
+    atomSetCollection.setAtomSetName(molName);
     atomIndex = 0;
     baseAtomIndex = atomSetCollection.atomCount;
   }

Index: GaussianReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/GaussianReader.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- GaussianReader.java	6 Nov 2004 23:20:21 -0000	1.26
+++ GaussianReader.java	7 Nov 2004 10:43:38 -0000	1.27
@@ -303,8 +303,8 @@
     String[] red_masses; String[] frc_consts; String[] intensities;
  
     while ((line = reader.readLine()) != null &&
-            line.indexOf(":")<0)
-      ;
+            line.indexOf(":")<0) {
+    }
     if (line == null)
       throw (new Exception("No frequencies encountered"));
     

Index: CmlReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/CmlReader.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- CmlReader.java	5 Nov 2004 18:46:54 -0000	1.24
+++ CmlReader.java	7 Nov 2004 10:43:39 -0000	1.25
@@ -363,16 +363,16 @@
           System.out.println("CRYSTAL atts.title: " + title);
           if (title != null) {
               int i = 6;
-              while (--i >= 0 && ! title.equals(AtomSetCollection.notionalUnitcellTags[i]))
-                  ;
+              while (--i >= 0 && ! title.equals(AtomSetCollection.notionalUnitcellTags[i])) {
+              }
               if (i >= 0)
                   notionalUnitcell[i] = parseFloat(chars);
           }
           System.out.println("CRYSTAL atts.dictRef: " + dictRef);
           if (dictRef != null) {
               int i = 6;
-              while (--i >= 0 && ! dictRef.equals("cml:" + AtomSetCollection.notionalUnitcellTags[i]))
-                  ;
+              while (--i >= 0 && ! dictRef.equals("cml:" + AtomSetCollection.notionalUnitcellTags[i])) {
+              }
               if (i >= 0)
                   notionalUnitcell[i] = parseFloat(chars);
           }

Index: MopacReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/MopacReader.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- MopacReader.java	5 Nov 2004 18:46:54 -0000	1.7
+++ MopacReader.java	7 Nov 2004 10:43:39 -0000	1.8
@@ -44,8 +44,9 @@
 
     String line;
     while ((line = input.readLine()) != null && ! line.startsWith(" ---")) {
-      if (line.indexOf("MOLECULAR POINT GROUP") >= 0)
-        hasSymmetry = true;
+      if (line.indexOf("MOLECULAR POINT GROUP") >= 0) {
+        //hasSymmetry = true;
+      }
     }
 
     while ((line = input.readLine()) != null) {
@@ -79,8 +80,11 @@
    * </pre>
    * They are expected to be found in the file <i>before</i> the 
    * cartesian coordinate section.
+   * 
+   * @param input
+   * @throws Exception
    */
-  void processAtomicCharges(BufferedReader input) throws Exception {
+void processAtomicCharges(BufferedReader input) throws Exception {
     discardLines(input, 2);
     //    System.out.println("Reading atomic charges");
     baseAtomIndex = atomSetCollection.atomCount;
@@ -111,6 +115,9 @@
    *      2         C        1.3952    0.0000    0.0000
    *      3         C        2.0927    1.2078    0.0000
    * </pre>
+   * 
+   * @param input
+   * @throws Exception
    */
   void processCoordinates(BufferedReader input) throws Exception {
     //    System.out.println("Reading coordinates");
@@ -239,6 +246,6 @@
   /**
    * Whether the input file has symmetry elements reported.
    */
-  private boolean hasSymmetry = false;
+  //private boolean hasSymmetry = false;
   
 }

Index: SpartanReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/SpartanReader.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- SpartanReader.java	22 Oct 2004 19:07:41 -0000	1.4
+++ SpartanReader.java	7 Nov 2004 10:43:39 -0000	1.5
@@ -34,7 +34,6 @@
     atomSetCollection = new AtomSetCollection("spartan");
 
     try {
-      String line;
       if (discardLinesUntilContains(reader, "Cartesian Coordinates (Ang") !=
           null)
         readAtoms(reader);
@@ -55,9 +54,8 @@
   void readAtoms(BufferedReader reader) throws Exception {
     discardLinesUntilBlank(reader);
     String line;
-    int atomNum;
     while ((line = reader.readLine()) != null &&
-           (atomNum = parseInt(line, 0, 3)) > 0) {
+           (/*atomNum = */parseInt(line, 0, 3)) > 0) {
       String elementSymbol = parseToken(line, 4, 6);
       String atomName = parseToken(line, 7, 13);
       float x = parseFloat(line, 17, 30);
@@ -74,10 +72,6 @@
 
   void readFrequencies(BufferedReader reader) throws Exception {
     int totalFrequencyCount = 0;
-    float[] frequencies = new float[5];
-    float[] xComponents = new float[5];
-    float[] yComponents = new float[5];
-    float[] zComponents = new float[5];
 
     while (true) {
       String line = discardLinesUntilNonBlank(reader);

Index: GamessReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/GamessReader.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- GamessReader.java	22 Oct 2004 05:17:31 -0000	1.7
+++ GamessReader.java	7 Nov 2004 10:43:39 -0000	1.8
@@ -36,7 +36,6 @@
     atomSetCollection = new AtomSetCollection("gamess");
 
     try {
-      String line;
       discardLinesUntilContains(reader, "COORDINATES (BOHR)");
       readAtomsInBohrCoordinates(reader);
       discardLinesUntilContains(reader, "FREQUENCIES IN CM");
@@ -75,7 +74,6 @@
   void readFrequencies(BufferedReader reader) throws Exception {
     int totalFrequencyCount = 0;
     int atomCountInFirstModel = atomSetCollection.atomCount;
-    float[] frequencies = new float[5];
     float[] xComponents = new float[5];
     float[] yComponents = new float[5];
     float[] zComponents = new float[5];

Index: CifReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/CifReader.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- CifReader.java	5 Nov 2004 18:46:54 -0000	1.24
+++ CifReader.java	7 Nov 2004 10:43:39 -0000	1.25
@@ -270,8 +270,8 @@
         break;
       if (chFirst == ' ') {
         int i;
-        for (i = lineLength; --i >= 0 && line.charAt(i) == ' '; )
-          ;
+        for (i = lineLength; --i >= 0 && line.charAt(i) == ' '; ) {
+        }
         if (i < 0)
           break;
       }

Index: JaguarReader.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/JaguarReader.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- JaguarReader.java	22 Oct 2004 05:17:31 -0000	1.6
+++ JaguarReader.java	7 Nov 2004 10:43:39 -0000	1.7
@@ -40,7 +40,6 @@
 
     try {
       String line;
-      int lineNum = 0;
       while ((line = reader.readLine()) != null) {
         if (line.startsWith("  final geometry:")) {
           readAtoms(reader);
@@ -119,8 +118,8 @@
     int modelNumber = 1;
     String line;
     while ((line = reader.readLine()) != null &&
-           ! line.startsWith("  frequencies "))
-      ;
+           ! line.startsWith("  frequencies ")) {
+    }
     if (line == null)
       return;
     // determine number of freqs on this line (starting with "frequencies")
@@ -129,8 +128,8 @@
       int freqCount = new StringTokenizer(line).countTokens() - 1;
       System.out.println("  #freqs= " + freqCount);
       while ((line = reader.readLine()) != null &&
-           ! line.startsWith("  intensities "))
-      ;
+           ! line.startsWith("  intensities ")) {
+      }
       for (int atomCenterNumber = 0; atomCenterNumber < atomCount; atomCenterNumber++) {
         // this assumes that the atoms are given in the same order as their
         // atomic coordinates, and disregards the label which is should use

Index: Resolver.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/adapter/smarter/Resolver.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- Resolver.java	26 Oct 2004 11:11:12 -0000	1.2
+++ Resolver.java	7 Nov 2004 10:43:39 -0000	1.3
@@ -82,7 +82,7 @@
       }
     }
     try {
-      int atomCount = Integer.parseInt(lines[0].trim());
+      /*int atomCount = */Integer.parseInt(lines[0].trim());
       return "Xyz";
     } catch (NumberFormatException e) {
     }
@@ -218,8 +218,8 @@
       int ichBeginningOfLine = ichCurrent;
       char ch = 0;
       while (ichCurrent < cchBuf &&
-             (ch = buf[ichCurrent++]) != '\r' && ch != '\n')
-        ;
+             (ch = buf[ichCurrent++]) != '\r' && ch != '\n') {
+      }
       if (ch == '\r' && ichCurrent < cchBuf && buf[ichCurrent] == '\n')
         ++ichCurrent;
       int cchLine = ichCurrent - ichBeginningOfLine;