From e5127e5f27f02c8f328539eaac68eabfbee1d135 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 25 May 2005 13:35:22 +0000 Subject: [PATCH] tidied up system.out messages and moved many to stderr. --- src/MCview/PDBChain.java | 4 ++-- src/MCview/PDBfile.java | 5 +++-- src/MCview/rotCanvas.java | 2 +- src/jalview/analysis/Conservation.java | 6 ++++-- src/jalview/analysis/NJTree.java | 7 ++++++- src/jalview/analysis/PCA.java | 4 ++-- src/jalview/appletgui/AlignFrame.java | 2 +- src/jalview/appletgui/AlignViewport.java | 2 +- src/jalview/appletgui/AlignmentPanel.java | 2 +- src/jalview/appletgui/OverviewPanel.java | 2 +- src/jalview/appletgui/RotatableCanvas.java | 2 +- src/jalview/bin/Jalview.java | 3 ++- src/jalview/datamodel/Alignment.java | 4 ++-- src/jalview/datamodel/BinarySequence.java | 2 +- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/gui/AlignViewport.java | 2 +- src/jalview/gui/AlignmentPanel.java | 2 +- src/jalview/gui/Jalview2XML.java | 3 ++- src/jalview/gui/OverviewPanel.java | 2 +- src/jalview/gui/RotatableCanvas.java | 2 +- src/jalview/io/BLCFile.java | 3 ++- src/jalview/io/ClustalFile.java | 5 +++-- src/jalview/io/EBIFetchClient.java | 12 +++++++----- src/jalview/io/JPredFile.java | 6 +++--- src/jalview/io/JalviewFileChooser.java | 2 +- src/jalview/io/JalviewFileView.java | 2 +- src/jalview/io/MSFfile.java | 8 +++++--- src/jalview/io/NewickFile.java | 2 +- src/jalview/io/PfamFile.java | 2 +- src/jalview/io/WSWUBlastClient.java | 6 +++--- src/jalview/math/Matrix.java | 8 ++++---- src/jalview/schemes/NucleotideColourScheme.java | 2 +- src/jalview/ws/JPredClient.java | 2 +- src/jalview/ws/MsaWSClient.java | 2 +- 34 files changed, 69 insertions(+), 53 deletions(-) diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 92627d5..2e0ce30 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -122,7 +122,7 @@ public class PDBChain { // Keep totting up the sequence if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) { - System.out.println("Null aa3Hash for " + tmpat.resName); + System.err.println("PDBReader:Null aa3Hash for " + tmpat.resName); } else { String tmpres2 = ResidueProperties.aa[((Integer)ResidueProperties.getAA3Hash().get(tmpat.resName)).intValue()]; @@ -131,7 +131,7 @@ public class PDBChain { // System.out.println(tmpat.resName + " " + tmpres2); } sequence = new Sequence("PDB_seq",seq,1,seq.length()); - System.out.println("Sequence = " + seq); + System.out.println("PDB Sequence is :\nSequence = " + seq); System.out.println("No of residues = " +residues.size()); } diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index b06e98f..44bf1bc 100755 --- 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); } } catch(NumberFormatException e) { - System.out.println("Caught" + e); - System.out.println("Atom not added"); + System.err.println("Caught" + e); + System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString()); } } } @@ -135,6 +135,7 @@ public class PDBfile extends jalview.io.FileParse { PDBfile pdb = new PDBfile("enkp1.pdb","File"); } catch(IOException e) { System.out.println(e); + e.printStackTrace(); System.exit(0); } } diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java index 9b822f3..eb5fd64 100755 --- a/src/MCview/rotCanvas.java +++ b/src/MCview/rotCanvas.java @@ -1,5 +1,5 @@ package MCview; - +// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug import java.awt.*; import java.awt.event.*; import java.util.*; diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 74381fd..deeb2e9 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -62,7 +62,7 @@ public class Conservation { } } else { // JBPNote INFO level debug - System.out.println("calcSeqNum called with out of range sequence index for Alignment\n"); + System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n"); } } Vector total = new Vector(); @@ -351,7 +351,8 @@ public void findQuality(int start, int end) { x[ii] += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4; } } catch (Exception e) { - System.out.println("Exception : " + e); + System.err.println("Exception during quality calculation."); + e.printStackTrace(); } //System.out.println("X " + ii + " " + x[ii]); x[ii] /= (size); @@ -373,6 +374,7 @@ public void findQuality(int start, int end) { sr = (double)BLOSUM62[i][seqNum]+4; } catch (Exception e) { System.out.println("Exception in sr: " + e); + e.printStackTrace(); } //Calculate X with another loop over residues diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java index f44f990..d56464c 100755 --- a/src/jalview/analysis/NJTree.java +++ b/src/jalview/analysis/NJTree.java @@ -430,7 +430,7 @@ public class NJTree { k + 1), sequence[j].getSequence(k, k + 1)); - }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");} + }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();} } distance[i][j] = (float)score; if (score > maxscore) { @@ -522,6 +522,11 @@ public class NJTree { return found; } + /** + * printNode is mainly for debugging purposes. + * + * @param node SequenceNode + */ public void printNode(SequenceNode node) { if (node == null) { return; diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java index 0f397d8..0d998b5 100755 --- a/src/jalview/analysis/PCA.java +++ b/src/jalview/analysis/PCA.java @@ -1,4 +1,4 @@ -// PCA.java +// PCA.java package jalview.analysis; import jalview.math.*; @@ -68,7 +68,7 @@ public class PCA implements Runnable { } public static void printMemory(Runtime rt) { - System.out.println("Free memory = " + rt.freeMemory()); + System.out.println("PCA:Free memory = " + rt.freeMemory()); } public Matrix getM() { diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 0003d14..78c956b 100755 --- 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); if(restore.getLength()==0) { - System.out.println(hi.getHidden().elementAt(i)); + // log.System.out.println(hi.getHidden().elementAt(i)); restore.setSequence(hi.getHidden().elementAt(i).toString()); viewport.alignment.getSequences().insertElementAt( restore, diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java index 0b6ec1a..cef87f7 100755 --- a/src/jalview/appletgui/AlignViewport.java +++ b/src/jalview/appletgui/AlignViewport.java @@ -302,7 +302,7 @@ public class AlignViewport } public void setEndRes(int res) { if (res > alignment.getWidth()-1) { - System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); + // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); res = alignment.getWidth()-1; } if (res < 0) { diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 68746e3..0075862 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -76,7 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene { public void keyPressed(KeyEvent evt) { - System.out.println(evt.getKeyCode()); + // System.out.println(evt.getKeyCode()); log. switch(evt.getKeyCode()) { case 27: // escape key diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 3ba88b4..94bff0e 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -215,7 +215,7 @@ public class OverviewPanel extends Panel implements Runnable } }catch(OutOfMemoryError error) - { System.out.println("out of memory"); } + { System.err.println("Out of memory when trying to calculate the overview window image!"); } av.setRenderGaps(oldRenderGaps); diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java index 51b436f..ac42ad2 100755 --- 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); scale = findScale(); } else if (evt.getKeyChar() == 's') { - System.out.println("Rectangle selection"); + System.err.println("DEBUG: Rectangle selection"); // log.debug if (rectx2 != -1 && recty2 != -1) { rectSelect(rectx1,recty1,rectx2,recty2); diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 23c7547..ffa844a 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -81,7 +81,8 @@ public class Jalview extends JApplet try { initLogger(); } catch (Exception e) { - System.out.println("Problems initializing the log4j system\n"+e); + System.err.println("Problems initializing the log4j system\n"); + e.printStackTrace(); } try{ UIManager.setLookAndFeel( diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 15a1455..d953598 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -291,10 +291,10 @@ public class Alignment implements AlignmentI len = getHeight()/2; } else { len = (getHeight()+1)/2; - System.out.println("Sort len is odd = " + len); + System.out.println("DEBUG:Sort len is odd = " + len); // log. } for (int i = 0; i < len; i++) { - System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); + System.out.println("DEBUG:Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName()); // log. SequenceI tmp = seqs[i]; sequences.setElementAt(seqs[getHeight()-i-1],i); sequences.setElementAt(tmp,getHeight()-i-1); diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java index b029641..dffa1a6 100755 --- a/src/jalview/datamodel/BinarySequence.java +++ b/src/jalview/datamodel/BinarySequence.java @@ -104,6 +104,6 @@ public class BinarySequence extends Sequence { } public static void printMemory(Runtime rt) { - System.out.println("Free memory = " + rt.freeMemory()); + System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log. } } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 0c0e3d7..de2d8ef 100755 --- 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 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -308,7 +308,7 @@ public class AlignViewport } public void setEndRes(int res) { if (res > alignment.getWidth()-1) { - System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); + // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1)); res = alignment.getWidth()-1; } if (res < 0) { diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 71b326e..9895753 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -684,7 +684,7 @@ class PreviewPanel extends JPanel if(image!=null) g.drawImage(image,0,0,this); else - System.out.println("image is null"); + System.out.println("DEBUG:image is null"); } } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 12f2cb2..6b6bd86 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -294,7 +294,8 @@ public class Jalview2XML } catch(Exception ex) - { System.out.println("HERE"+ex); return; } + { System.err.println("Exception whilst loading jalview XML file : "+ex+"\n"); + ex.printStackTrace(); return; } } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 3257ce5..a0d8151 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -215,7 +215,7 @@ public class OverviewPanel extends JPanel implements Runnable } }catch(OutOfMemoryError error) - { System.out.println("out of memory"); } + { System.err.println("Out of memory when trying to calculate the overview window image!"); } av.setRenderGaps(oldRenderGaps); diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java index b4af354..9dc5754 100755 --- 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); scale = findScale(); } else if (evt.getKeyChar() == 's') { - System.out.println("Rectangle selection"); + System.err.println("DEBUG: Rectangle selection"); // log.debug if (rectx2 != -1 && recty2 != -1) { rectSelect(rectx1,recty1,rectx2,recty2); diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java index 78c1c24..84d8a9d 100755 --- a/src/jalview/io/BLCFile.java +++ b/src/jalview/io/BLCFile.java @@ -94,7 +94,8 @@ public class BLCFile extends AlignFile { }catch(Exception ex) { - System.out.println("err"); + System.err.println("Error during blockfile read."); + ex.printStackTrace(); starts.addElement("0"); ends.addElement("0"); } diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java index 98c500a..1d2590b 100755 --- a/src/jalview/io/ClustalFile.java +++ b/src/jalview/io/ClustalFile.java @@ -67,7 +67,8 @@ public class ClustalFile extends AlignFile { } } } catch (IOException e) { - System.out.println("Exception parsing clustal file " + e); + System.err.println("Exception parsing clustal file " + e); + e.stacktrace(); } if (flag) { @@ -111,7 +112,7 @@ public class ClustalFile extends AlignFile { seqs.addElement(newSeq); } else { - System.out.println("Can't find sequence for " + headers.elementAt(i)); + System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i)); } } } diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java index be2f01e..db34357 100755 --- a/src/jalview/io/EBIFetchClient.java +++ b/src/jalview/io/EBIFetchClient.java @@ -112,18 +112,18 @@ public class EBIFetchClient if (null == ret) { - System.out.println("Received null "); + System.err.println("Received null "); throw new AxisFault("", "Received null", null, null); } if (ret instanceof String) { - System.out.println("Received problem response from server: " + ret); + System.err.println("Received problem response from server: " + ret); throw new AxisFault("", (String) ret, null, null); } if (! (ret instanceof DataHandler)) { //The wrong type of object that what was expected. - System.out.println("Received problem response from server:" + + System.err.println("Received problem response from server:" + ret.getClass().getName()); throw new AxisFault("", "Received problem response from server:" + ret.getClass().getName(), null, null); @@ -149,9 +149,11 @@ public class EBIFetchClient return receivedfileName; } else - System.out.println(receivedfileName); + System.err.println(receivedfileName); }catch(Exception ex) - {} + { + ex.printStackTrace(); + } return "ERROR"; } diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java index 08f7d17..b2226db 100755 --- 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 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -243,7 +243,7 @@ public class JalviewFileChooser extends JFileChooser *************************************************************************/ protected final boolean lt(File a, File b) { - System.out.println("LT called?"); + System.out.println("DEBUG:LT called?"); boolean less = false; switch (col) { diff --git a/src/jalview/io/JalviewFileView.java b/src/jalview/io/JalviewFileView.java index cdf873a..3c96a28 100755 --- a/src/jalview/io/JalviewFileView.java +++ b/src/jalview/io/JalviewFileView.java @@ -69,7 +69,7 @@ public class JalviewFileView extends FileView if (imgURL != null) { return new ImageIcon(imgURL); } else { - System.err.println("Couldn't find file: " + path); + System.err.println("JalviewFileView.createImageIcon: Couldn't find file: " + path); return null; } } diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java index b9cad0a..9495f82 100755 --- a/src/jalview/io/MSFfile.java +++ b/src/jalview/io/MSFfile.java @@ -71,7 +71,8 @@ public class MSFfile extends AlignFile { } } } catch (IOException e) { - System.out.println("Exception parsing MSFFile " + e); + System.err.println("Exception parsing MSFFile " + e); + e.printStackTrace(); } this.noSeqs = headers.size(); @@ -111,7 +112,7 @@ public class MSFfile extends AlignFile { seqs.addElement(newSeq); } else { - System.out.println("Can't find sequence for " + headers.elementAt(i)); + System.err.println("MSFFile Parser: Can't find sequence for " + headers.elementAt(i)); } } @@ -133,7 +134,8 @@ public class MSFfile extends AlignFile { } } } catch (Exception e) { - System.err.println("Exception " + e); + System.err.println("Exception during MSF Checksum calculation"); + e.printStackTrace(); } } return check % 10000; diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index c3fd9374..85ab084 100755 --- 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 --- 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)"); } else - System.out.println("Can't find sequence for " + headers.elementAt(i)); + System.err.println("PFAM File reader: Can't find sequence for " + headers.elementAt(i)); } diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index 1622187..ace3e0d 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -111,7 +111,7 @@ public class WSWUBlastClient jobsRunning --; } Thread.sleep(5000); - System.out.println("I'm alive "+seqid+" "+jobid); + // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug } catch (Exception ex) {} @@ -140,12 +140,12 @@ public class WSWUBlastClient String result = (String) call.invoke(new Object[] {params, seqbytes}); jobid = result; - System.out.println(jobid); + System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'"); } catch (Exception exp) { - System.err.println("ERROR:\n" + exp.toString()); + System.err.println("WSWUBlastClient error:\n" + exp.toString()); exp.printStackTrace(); } } diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index d08fe22..0f45978 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -224,8 +224,8 @@ public class Matrix { if (m != l) { iter++; if (iter == 30) { - System.out.print("Too many iterations in tqli"); - System.exit(0); + System.err.print("Too many iterations in tqli"); + System.exit(0); // JBPNote - should this really be here ??? } else { // System.out.println("Iteration " + iter); } @@ -395,8 +395,8 @@ public class Matrix { if (m != l) { iter++; if (iter == 30) { - System.out.print("Too many iterations in tqli"); - System.exit(0); + System.err.print("Too many iterations in tqli"); + System.exit(0); // JBPNote - same as above - not a graceful exit! } else { // System.out.println("Iteration " + iter); } diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java index dc06175..5c65894 100755 --- a/src/jalview/schemes/NucleotideColourScheme.java +++ b/src/jalview/schemes/NucleotideColourScheme.java @@ -11,7 +11,7 @@ public class NucleotideColourScheme extends ResidueColourScheme public Color findColour(String n) { - System.out.println("called"); + // System.out.println("called"); log.debug return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()]; } diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 0d7145c..0940be6 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -170,7 +170,7 @@ public class JPredClient extends WSClient } catch (Exception e) { - System.out.println("JPredWS Client: Failed to submit the prediction\n" + + System.err.println("JPredWS Client: Failed to submit the prediction\n" + e.toString() + "\n"); e.printStackTrace(); } diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java index 876c0c1..4e358a0 100755 --- 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(); } -- 1.7.10.2