tidied up system.out messages and moved many to stderr.

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 92627d5..2e0ce30 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -122,7 +122,7 @@ public class PDBChain {
 \r
       // Keep totting up the sequence\r
       if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {\r
-        System.out.println("Null aa3Hash for " + tmpat.resName);\r
+        System.err.println("PDBReader:Null aa3Hash for " + tmpat.resName);\r
       } else {\r
         String tmpres2 =\r
           ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()];\r
@@ -131,7 +131,7 @@ public class PDBChain {
       //      System.out.println(tmpat.resName + " " + tmpres2);\r
     }\r
     sequence = new Sequence("PDB_seq",seq,1,seq.length());\r
-    System.out.println("Sequence = " + seq);\r
+    System.out.println("PDB Sequence is :\nSequence = " + seq);\r
     System.out.println("No of residues = " +residues.size());\r
   }\r
 \r

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index b06e98f..44bf1bc 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -69,8 +69,8 @@ public class PDBfile extends jalview.io.FileParse {
               tmpchain.atoms.addElement(tmpatom);\r
             }\r
           } catch(NumberFormatException e) {\r
-            System.out.println("Caught" +  e);\r
-            System.out.println("Atom not added");\r
+            System.err.println("Caught" +  e);\r
+            System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());\r
           }\r
         }\r
       }\r
@@ -135,6 +135,7 @@ public class PDBfile extends jalview.io.FileParse {
       PDBfile pdb = new PDBfile("enkp1.pdb","File");\r
     } catch(IOException e) {\r
       System.out.println(e);\r
+      e.printStackTrace();\r
       System.exit(0);\r
     }\r
   }\r

diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java
index 9b822f3..eb5fd64 100755 (executable)
--- a/src/MCview/rotCanvas.java
+++ b/src/MCview/rotCanvas.java
@@ -1,5 +1,5 @@
 package MCview;\r
-\r
+// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug\r
 import java.awt.*;\r
 import java.awt.event.*;\r
 import java.util.*;\r

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 74381fd..deeb2e9 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -62,7 +62,7 @@ public class Conservation {
        }\r
      } else {\r
        // JBPNote INFO level debug\r
-       System.out.println("calcSeqNum called with out of range sequence index for Alignment\n");\r
+       System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");\r
      }\r
    }\r
    Vector total = new Vector();\r
@@ -351,7 +351,8 @@ public void findQuality(int start, int end) {
            x[ii]  += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;\r
          }\r
        } catch (Exception e) {\r
-         System.out.println("Exception : "  + e);\r
+         System.err.println("Exception during quality calculation.");\r
+          e.printStackTrace();\r
        }\r
        //System.out.println("X " + ii + " " + x[ii]);\r
        x[ii] /= (size);\r
@@ -373,6 +374,7 @@ public void findQuality(int start, int end) {
             sr = (double)BLOSUM62[i][seqNum]+4;\r
           } catch (Exception e) {\r
             System.out.println("Exception in sr: " + e);\r
+            e.printStackTrace();\r
           }\r
           //Calculate X with another loop over residues\r
 \r

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index f44f990..d56464c 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -430,7 +430,7 @@ public class NJTree {
                   k + 1),\r
                                                 sequence[j].getSequence(k,\r
                   k + 1));\r
-            }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}\r
+            }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}\r
           }\r
           distance[i][j] = (float)score;\r
           if (score > maxscore) {\r
@@ -522,6 +522,11 @@ public class NJTree {
     return found;\r
   }\r
 \r
+  /**\r
+   * printNode is mainly for debugging purposes.\r
+   *\r
+   * @param node SequenceNode\r
+   */\r
   public void printNode(SequenceNode node) {\r
     if (node == null) {\r
       return;\r

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 0f397d8..0d998b5 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,4 +1,4 @@
-// PCA.java \r
+// PCA.java\r
 package jalview.analysis;\r
 \r
 import jalview.math.*;\r
@@ -68,7 +68,7 @@ public class PCA implements Runnable {
   }\r
 \r
   public static void printMemory(Runtime rt) {\r
-    System.out.println("Free memory = " + rt.freeMemory());\r
+    System.out.println("PCA:Free memory = " + rt.freeMemory());\r
   }\r
 \r
   public Matrix getM() {\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0003d14..78c956b 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -166,7 +166,7 @@ public class AlignFrame extends GAlignFrame
           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
           if(restore.getLength()==0)\r
           {\r
-            System.out.println(hi.getHidden().elementAt(i));\r
+            // log.System.out.println(hi.getHidden().elementAt(i));\r
             restore.setSequence(hi.getHidden().elementAt(i).toString());\r
             viewport.alignment.getSequences().insertElementAt(\r
                restore,\r

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 0b6ec1a..cef87f7 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -302,7 +302,7 @@ public class AlignViewport
   }\r
   public void setEndRes(int res) {\r
     if (res > alignment.getWidth()-1) {\r
-      System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
+      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
        res = alignment.getWidth()-1;\r
     }\r
     if (res < 0) {\r

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 68746e3..0075862 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -76,7 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   {\r
      public void keyPressed(KeyEvent evt)\r
      {\r
-       System.out.println(evt.getKeyCode());\r
+       // System.out.println(evt.getKeyCode()); log.\r
        switch(evt.getKeyCode())\r
        {\r
          case  27: // escape key\r

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 3ba88b4..94bff0e 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -215,7 +215,7 @@ public class OverviewPanel extends Panel implements Runnable
       }\r
 \r
     }catch(OutOfMemoryError error)\r
-    {     System.out.println("out of memory");   }\r
+    {     System.err.println("Out of memory when trying to calculate the overview window image!");   }\r
 \r
 \r
     av.setRenderGaps(oldRenderGaps);\r

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 51b436f..ac42ad2 100755 (executable)
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -332,7 +332,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
       scalefactor = (float)(scalefactor * 0.9);\r
       scale = findScale();\r
     } else if (evt.getKeyChar() == 's') {\r
-      System.out.println("Rectangle selection");\r
+      System.err.println("DEBUG: Rectangle selection"); // log.debug\r
       if (rectx2 != -1 && recty2 != -1) {\r
         rectSelect(rectx1,recty1,rectx2,recty2);\r
 \r

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 23c7547..ffa844a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -81,7 +81,8 @@ public class Jalview extends JApplet
     try {\r
       initLogger();\r
     } catch (Exception e) {\r
-      System.out.println("Problems initializing the log4j system\n"+e);\r
+      System.err.println("Problems initializing the log4j system\n");\r
+      e.printStackTrace();\r
     }\r
     try{\r
        UIManager.setLookAndFeel(\r

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 15a1455..d953598 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -291,10 +291,10 @@ public class Alignment implements AlignmentI
       len = getHeight()/2;\r
     } else {\r
       len = (getHeight()+1)/2;\r
-      System.out.println("Sort len is odd = " + len);\r
+      System.out.println("DEBUG:Sort len is odd = " + len); // log.\r
     }\r
     for (int i = 0; i < len; i++) {\r
-      System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());\r
+      System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); // log.\r
       SequenceI tmp = seqs[i];\r
       sequences.setElementAt(seqs[getHeight()-i-1],i);\r
       sequences.setElementAt(tmp,getHeight()-i-1);\r

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index b029641..dffa1a6 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -104,6 +104,6 @@ public class BinarySequence extends Sequence {
   }\r
 \r
   public static void printMemory(Runtime rt) {\r
-    System.out.println("Free memory = " + rt.freeMemory());\r
+    System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
   }\r
 }\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0c0e3d7..de2d8ef 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1239,7 +1239,7 @@ public class AlignFrame extends GAlignFrame
     if (seq!=null) {
       JPredClient ct = new JPredClient(title, seq);
     } else {
-      System.out.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
+      System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
     }
   }
   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 610426f..82d2e3e 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -308,7 +308,7 @@ public class AlignViewport
   }\r
   public void setEndRes(int res) {\r
     if (res > alignment.getWidth()-1) {\r
-      System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
+      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
        res = alignment.getWidth()-1;\r
     }\r
     if (res < 0) {\r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 71b326e..9895753 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -684,7 +684,7 @@ class PreviewPanel extends JPanel
     if(image!=null)\r
       g.drawImage(image,0,0,this);\r
     else\r
-      System.out.println("image is null");\r
+      System.out.println("DEBUG:image is null");\r
   }\r
 }\r
 \r

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 12f2cb2..6b6bd86 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -294,7 +294,8 @@ public class Jalview2XML
 \r
     }\r
     catch(Exception ex)\r
-    {   System.out.println("HERE"+ex); return; }\r
+    {   System.err.println("Exception whilst loading jalview XML file : "+ex+"\n");\r
+     ex.printStackTrace(); return; }\r
 \r
   }\r
 \r

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 3257ce5..a0d8151 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -215,7 +215,7 @@ public class OverviewPanel extends JPanel implements Runnable
       }\r
 \r
     }catch(OutOfMemoryError error)\r
-    {     System.out.println("out of memory");   }\r
+    {     System.err.println("Out of memory when trying to calculate the overview window image!");   }\r
 \r
 \r
     av.setRenderGaps(oldRenderGaps);\r

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index b4af354..9dc5754 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -334,7 +334,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       scalefactor = (float)(scalefactor * 0.9);\r
       scale = findScale();\r
     } else if (evt.getKeyChar() == 's') {\r
-      System.out.println("Rectangle selection");\r
+      System.err.println("DEBUG: Rectangle selection"); // log.debug\r
       if (rectx2 != -1 && recty2 != -1) {\r
         rectSelect(rectx1,recty1,rectx2,recty2);\r
 \r

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 78c1c24..84d8a9d 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -94,7 +94,8 @@ public class BLCFile extends AlignFile {
 \r
           }catch(Exception ex)\r
           {\r
-            System.out.println("err");\r
+            System.err.println("Error during blockfile read.");\r
+            ex.printStackTrace();\r
             starts.addElement("0");\r
             ends.addElement("0");\r
           }\r

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 98c500a..1d2590b 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -67,7 +67,8 @@ public class ClustalFile extends AlignFile {
        }\r
       }\r
     } catch (IOException e) {\r
-      System.out.println("Exception parsing clustal file " + e);\r
+      System.err.println("Exception parsing clustal file " + e);\r
+      e.stacktrace();\r
     }\r
 \r
     if (flag) {\r
@@ -111,7 +112,7 @@ public class ClustalFile extends AlignFile {
           seqs.addElement(newSeq);\r
 \r
         } else {\r
-          System.out.println("Can't find sequence for " + headers.elementAt(i));\r
+          System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));\r
         }\r
       }\r
     }\r

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index be2f01e..db34357 100755 (executable)
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -112,18 +112,18 @@ public class EBIFetchClient
 \r
         if (null == ret)\r
         {\r
-          System.out.println("Received null ");\r
+          System.err.println("Received null ");\r
           throw new AxisFault("", "Received null", null, null);\r
         }\r
         if (ret instanceof String)\r
         {\r
-          System.out.println("Received problem response from server: " + ret);\r
+          System.err.println("Received problem response from server: " + ret);\r
           throw new AxisFault("", (String) ret, null, null);\r
         }\r
         if (! (ret instanceof DataHandler))\r
         {\r
           //The wrong type of object that what was expected.\r
-          System.out.println("Received problem response from server:" +\r
+          System.err.println("Received problem response from server:" +\r
                              ret.getClass().getName());\r
           throw new AxisFault("", "Received problem response from server:" +\r
                               ret.getClass().getName(), null, null);\r
@@ -149,9 +149,11 @@ public class EBIFetchClient
           return receivedfileName;\r
         }\r
         else\r
-          System.out.println(receivedfileName);\r
+          System.err.println(receivedfileName);\r
       }catch(Exception ex)\r
-      {}\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
 \r
       return "ERROR";\r
     }\r

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 08f7d17..b2226db 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -62,7 +62,7 @@ public class JPredFile
   public void parse()
       throws IOException
   {
-System.out.println("all read in ");
+    // JBPNote log.System.out.println("all read in ");
     String line;
     QuerySeqPosition = -1;
     noSeqs = 0;
@@ -136,7 +136,7 @@ System.out.println("all read in ");
       }
       else if (id.equals("jnetconf"))
       {
-        System.out.println("here");
+        // log.debug System.out.println("here");
         id = "Prediction Confidence";
         this.conf = new Vector(numSymbols);
         for (int i = 0; i < numSymbols; i++)
@@ -241,7 +241,7 @@ System.out.println("all read in ");
       }
       catch (java.io.IOException e)
       {
-        System.out.println("Exception " + e);
+        System.err.println("Exception " + e);
         e.printStackTrace();
       }
     }

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 03daa17..eca6e43 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -243,7 +243,7 @@ public class JalviewFileChooser extends JFileChooser
       *************************************************************************/\r
      protected final boolean lt(File a, File b)\r
      {\r
-       System.out.println("LT called?");\r
+       System.out.println("DEBUG:LT called?");\r
        boolean less = false;\r
        switch (col)\r
        {\r

diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java
index cdf873a..3c96a28 100755 (executable)
--- a/src/jalview/io/JalviewFileView.java
+++ b/src/jalview/io/JalviewFileView.java
@@ -69,7 +69,7 @@ public class JalviewFileView extends FileView
       if (imgURL != null) {\r
           return new ImageIcon(imgURL);\r
       } else {\r
-          System.err.println("Couldn't find file: " + path);\r
+          System.err.println("JalviewFileView.createImageIcon: Couldn't find file: " + path);\r
           return null;\r
       }\r
   }\r

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index b9cad0a..9495f82 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -71,7 +71,8 @@ public class MSFfile extends AlignFile {
       }\r
     }\r
     } catch (IOException e) {\r
-      System.out.println("Exception parsing MSFFile " + e);\r
+      System.err.println("Exception parsing MSFFile " + e);\r
+      e.printStackTrace();\r
     }\r
 \r
     this.noSeqs = headers.size();\r
@@ -111,7 +112,7 @@ public class MSFfile extends AlignFile {
         seqs.addElement(newSeq);\r
 \r
       } else {\r
-        System.out.println("Can't find sequence for " + headers.elementAt(i));\r
+        System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i));\r
       }\r
     }\r
 \r
@@ -133,7 +134,8 @@ public class MSFfile extends AlignFile {
           }\r
         }\r
       } catch (Exception e) {\r
-        System.err.println("Exception " + e);\r
+        System.err.println("Exception during MSF Checksum calculation");\r
+        e.printStackTrace();\r
       }\r
     }\r
     return check % 10000;\r

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index c3fd937..85ab084 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -508,7 +508,7 @@ public class NewickFile extends FileParse
   }
   catch (java.io.IOException e)
   {
-    System.out.println("Exception\n" + e);
+    System.err.println("Exception\n" + e);
     e.printStackTrace();
   }
 }

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index e17f831..3a02041 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -125,7 +125,7 @@ public class PfamFile extends AlignFile {
           throw new IOException("Not a valid protein sequence - (PFAM input)");\r
       }\r
       else\r
-        System.out.println("Can't find sequence for " + headers.elementAt(i));\r
+        System.err.println("PFAM File reader: Can't find sequence for " + headers.elementAt(i));\r
 \r
     }\r
 \r

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 1622187..ace3e0d 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -111,7 +111,7 @@ public class WSWUBlastClient
                 jobsRunning --;\r
           }\r
           Thread.sleep(5000);\r
-          System.out.println("I'm alive "+seqid+" "+jobid);\r
+          // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
         }\r
         catch (Exception ex)\r
         {}\r
@@ -140,12 +140,12 @@ public class WSWUBlastClient
         String result = (String) call.invoke(new Object[]\r
                                              {params, seqbytes});\r
         jobid = result;\r
-        System.out.println(jobid);\r
+        System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'");\r
 \r
       }\r
       catch (Exception exp)\r
       {\r
-        System.err.println("ERROR:\n" + exp.toString());\r
+        System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
         exp.printStackTrace();\r
       }\r
     }\r

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index d08fe22..0f45978 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -224,8 +224,8 @@ public class Matrix {
         if (m != l) {\r
           iter++;\r
           if (iter == 30) {\r
-            System.out.print("Too many iterations in tqli");\r
-            System.exit(0);\r
+            System.err.print("Too many iterations in tqli");\r
+            System.exit(0); // JBPNote - should this really be here ???\r
           } else {\r
             //     System.out.println("Iteration " + iter);\r
           }\r
@@ -395,8 +395,8 @@ public class Matrix {
         if (m != l) {\r
           iter++;\r
           if (iter == 30) {\r
-            System.out.print("Too many iterations in tqli");\r
-            System.exit(0);\r
+            System.err.print("Too many iterations in tqli");\r
+            System.exit(0); // JBPNote - same as above - not a graceful exit!\r
           } else {\r
             //     System.out.println("Iteration " + iter);\r
           }\r

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index dc06175..5c65894 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -11,7 +11,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
 \r
   public Color findColour(String n)\r
   {\r
-    System.out.println("called");\r
+    // System.out.println("called"); log.debug\r
     return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];\r
   }\r
 \r

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 0d7145c..0940be6 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -170,7 +170,7 @@ public class JPredClient extends WSClient
       }\r
       catch (Exception e)\r
       {\r
-        System.out.println("JPredWS Client: Failed to submit the prediction\n" +\r
+        System.err.println("JPredWS Client: Failed to submit the prediction\n" +\r
                            e.toString() + "\n");\r
         e.printStackTrace();\r
       }\r

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 876c0c1..4e358a0 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -210,7 +210,7 @@ public class MsaWSClient
       }
       catch (Exception e)
       {
-        System.out.println(ServiceName + " Client: Failed to submit the prediction\n" +
+        System.err.println(ServiceName + " Client: Failed to submit the prediction\n" +
                            e.toString() + "\n");
         e.printStackTrace();
       }