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65b9471
)
tidied up system.out messages and moved many to stderr.
author
jprocter
<Jim Procter>
Wed, 25 May 2005 13:35:22 +0000
(13:35 +0000)
committer
jprocter
<Jim Procter>
Wed, 25 May 2005 13:35:22 +0000
(13:35 +0000)
34 files changed:
src/MCview/PDBChain.java
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src/MCview/PDBfile.java
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src/MCview/rotCanvas.java
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src/jalview/analysis/Conservation.java
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src/jalview/analysis/NJTree.java
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src/jalview/analysis/PCA.java
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src/jalview/appletgui/AlignFrame.java
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src/jalview/appletgui/AlignViewport.java
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src/jalview/appletgui/AlignmentPanel.java
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src/jalview/appletgui/OverviewPanel.java
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src/jalview/appletgui/RotatableCanvas.java
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src/jalview/bin/Jalview.java
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src/jalview/datamodel/Alignment.java
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src/jalview/datamodel/BinarySequence.java
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/AlignViewport.java
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src/jalview/gui/AlignmentPanel.java
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src/jalview/gui/Jalview2XML.java
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src/jalview/gui/OverviewPanel.java
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src/jalview/gui/RotatableCanvas.java
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src/jalview/io/BLCFile.java
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src/jalview/io/ClustalFile.java
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src/jalview/io/EBIFetchClient.java
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src/jalview/io/JPredFile.java
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src/jalview/io/JalviewFileChooser.java
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src/jalview/io/JalviewFileView.java
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src/jalview/io/MSFfile.java
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src/jalview/io/NewickFile.java
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src/jalview/io/PfamFile.java
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src/jalview/io/WSWUBlastClient.java
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src/jalview/math/Matrix.java
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src/jalview/schemes/NucleotideColourScheme.java
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src/jalview/ws/JPredClient.java
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src/jalview/ws/MsaWSClient.java
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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
\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
} 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(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
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
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
}
\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
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
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
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
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
}
\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
}
\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
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
}
\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
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
}
\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
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
}
\r
distance[i][j] = (float)score;
\r
if (score > maxscore) {
\r
@@
-522,6
+522,11
@@
public class NJTree {
return found;
\r
}
\r
\r
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
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
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
}
\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
}
\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
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
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
}
\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
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
{
\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
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
}
\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
\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
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
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
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
}
\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
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
}
\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
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
}
\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
}
\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 {
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)
}
}
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
}
\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
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
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
}
\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
\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
\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
}
\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
\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
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
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
\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
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
}
\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
}
\r
\r
if (flag) {
\r
@@
-111,7
+112,7
@@
public class ClustalFile extends AlignFile {
seqs.addElement(newSeq);
\r
\r
} else {
\r
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
}
\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
\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
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
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
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
return receivedfileName;
\r
}
\r
else
\r
- System.out.println(receivedfileName);
\r
+ System.err.println(receivedfileName);
\r
}catch(Exception ex)
\r
}catch(Exception ex)
\r
- {}
\r
+ {
\r
+ ex.printStackTrace();
\r
+ }
\r
\r
return "ERROR";
\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
{
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;
String line;
QuerySeqPosition = -1;
noSeqs = 0;
@@
-136,7
+136,7
@@
System.out.println("all read in ");
}
else if (id.equals("jnetconf"))
{
}
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++)
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)
{
}
catch (java.io.IOException e)
{
- System.out.println("Exception " + e);
+ System.err.println("Exception " + e);
e.printStackTrace();
}
}
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
*************************************************************************/
\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
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
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
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
}
\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
}
\r
\r
this.noSeqs = headers.size();
\r
@@
-111,7
+112,7
@@
public class MSFfile extends AlignFile {
seqs.addElement(newSeq);
\r
\r
} else {
\r
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
}
\r
}
\r
\r
@@
-133,7
+134,8
@@
public class MSFfile extends AlignFile {
}
\r
}
\r
} catch (Exception e) {
\r
}
\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
}
\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)
{
}
catch (java.io.IOException e)
{
- System.out.println("Exception\n" + e);
+ System.err.println("Exception\n" + e);
e.printStackTrace();
}
}
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
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
\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
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
}
\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
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
\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
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
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
} 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
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
} 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
\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
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
}
\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
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)
{
}
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();
}
e.toString() + "\n");
e.printStackTrace();
}