JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

[jalview.git] / src / jalview / ws / jws1 / MsaWSThread.java

diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index be21de7..9ad936b 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.java
@@ -23,9 +23,10 @@ package jalview.ws.jws1;
 import jalview.analysis.AlignSeq;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -95,9 +96,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       int nseqs = 0;
       if (minlen < 0)
       {
-        throw new Error(
-                MessageManager
-                        .getString("error.implementation_error_minlen_must_be_greater_zero"));
+        throw new Error(MessageManager.getString(
+                "error.implementation_error_minlen_must_be_greater_zero"));
       }
       for (int i = 0; i < seqs.length; i++)
       {
@@ -107,7 +107,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         }
       }
       boolean valid = nseqs > 1; // need at least two seqs
-      vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]
+      vamsas.objects.simple.Sequence[] seqarray = (valid)
+              ? new vamsas.objects.simple.Sequence[nseqs]
               : null;
       for (int i = 0, n = 0; i < seqs.length; i++)
       {
@@ -131,8 +132,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           String empty = null;
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
-            empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
-                    .extractGaps(jalview.util.Comparison.GapChars,
+            empty = (submitGaps) ? seqs[i].getSequenceAsString()
+                    : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
           emptySeqs.add(new String[] { newname, empty });
@@ -147,6 +148,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
      * 
      * @return true if getAlignment will return a valid alignment result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete && result != null && result.isFinished()
@@ -273,6 +275,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
      * 
      * @return boolean true if job can be submitted.
      */
+    @Override
     public boolean hasValidInput()
     {
       if (seqs.getSeqs() != null)
@@ -285,7 +288,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
   String alTitle; // name which will be used to form new alignment window.
 
-  Alignment dataset; // dataset to which the new alignment will be
+  AlignmentI dataset; // dataset to which the new alignment will be
 
   // associated.
 
@@ -327,7 +330,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
           WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
           String wsname, String title, AlignmentView _msa, boolean subgaps,
-          boolean presorder, Alignment seqset)
+          boolean presorder, AlignmentI seqset)
   {
     this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
     OutputHeader = wsInfo.getProgressText();
@@ -359,11 +362,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean isCancellable()
   {
     return true;
   }
 
+  @Override
   public void cancelJob()
   {
     if (!jobComplete && jobs != null)
@@ -405,12 +410,12 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           {
             cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
                     + exc + "\n");
-            Cache.log.warn(
+            Cache.warn(
                     "Exception whilst cancelling " + jobs[job].getJobId(),
                     exc);
           }
-          wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
-                  + cancelledMessage + "\n");
+          wsInfo.setProgressText(jobs[job].getJobnum(),
+                  OutputHeader + cancelledMessage + "\n");
         }
       }
       if (cancelled)
@@ -430,26 +435,28 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public void pollJob(AWsJob job) throws Exception
   {
     ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId());
   }
 
+  @Override
   public void StartJob(AWsJob job)
   {
     if (!(job instanceof MsaWSJob))
     {
       throw new Error(MessageManager.formatMessage(
-              "error.implementation_error_msawbjob_called",
-              new String[] { job.getClass().toString() }));
+              "error.implementation_error_msawbjob_called", new String[]
+              { job.getClass().toString() }));
     }
     MsaWSJob j = (MsaWSJob) job;
     if (j.isSubmitted())
     {
-      if (Cache.log.isDebugEnabled())
+      if (Cache.isDebugEnabled())
       {
-        Cache.log.debug("Tried to submit an already submitted job "
-                + j.getJobId());
+        Cache.debug(
+                "Tried to submit an already submitted job " + j.getJobId());
       }
       return;
     }
@@ -459,8 +466,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       j.setSubmitted(true);
       j.result = new MsaResult();
       j.result.setFinished(true);
-      j.result.setStatus(MessageManager
-              .getString("label.empty_alignment_job"));
+      j.result.setStatus(
+              MessageManager.getString("label.empty_alignment_job"));
       ((MsaResult) j.result).setMsa(null);
     }
     try
@@ -480,7 +487,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         {
           throw new Exception(MessageManager.formatMessage(
                   "exception.web_service_returned_null_try_later",
-                  new String[] { WsUrl }));
+                  new String[]
+                  { WsUrl }));
         }
 
         throw new Exception(jobsubmit.getJobId());
@@ -489,11 +497,10 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     {
       // TODO: JBPNote catch timeout or other fault types explicitly
       // For unexpected errors
-      System.err
-              .println(WebServiceName
-                      + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
-                      + "When contacting Server:" + WsUrl + "\n"
-                      + e.toString() + "\n");
+      System.err.println(WebServiceName
+              + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+              + "When contacting Server:" + WsUrl + "\n" + e.toString()
+              + "\n");
       j.setAllowedServerExceptions(0);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.getJobnum(),
@@ -521,6 +528,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     return msa;
   }
 
+  @Override
   public void parseResult()
   {
     int results = 0; // number of result sets received
@@ -534,9 +542,10 @@ class MsaWSThread extends JWS1Thread implements WSClientI
                 && jobs[j].hasResults())
         {
           results++;
-          // if (Cache.log.isDebugEnabled())
+          // if (Cache.isDebugEnabled())
           // {
-          // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
+          // System.out.println("Job lob for job
+          // "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
           // System.out.println(jobs[j].getStatus());
           // }
 
@@ -549,8 +558,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
             String[] lines = valign.getMethod();
             for (int line = 0; line < lines.length; line++)
             {
-              wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line]
-                      + "\n");
+              wsInfo.appendProgressText(jobs[j].getJobnum(),
+                      lines[line] + "\n");
             }
             // JBPNote The returned files from a webservice could be
             // hidden behind icons in the monitor window that,
@@ -562,8 +571,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     } catch (Exception ex)
     {
 
-      Cache.log.error("Unexpected exception when processing results for "
-              + alTitle, ex);
+      Cache.error(
+              "Unexpected exception when processing results for " + alTitle,
+              ex);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
     }
     if (results > 0)
@@ -571,6 +581,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       wsInfo.showResultsNewFrame
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(true);
@@ -579,6 +590,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       wsInfo.mergeResults
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(false);
@@ -622,7 +634,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       orders[j] = null;
     }
     SequenceI[] alignment = (SequenceI[]) newview[0];
-    ColumnSelection columnselection = (ColumnSelection) newview[1];
+    HiddenColumns hidden = (HiddenColumns) newview[1];
     Alignment al = new Alignment(alignment);
     // TODO: add 'provenance' property to alignment from the method notes
     // accompanying each subjob
@@ -636,8 +648,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI
 
     if (newFrame)
     {
-      AlignFrame af = new AlignFrame(al, columnselection,
-              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+              AlignFrame.DEFAULT_HEIGHT);
 
       // initialise with same renderer settings as in parent alignframe.
       af.getFeatureRenderer().transferSettings(this.featureSettings);
@@ -661,7 +673,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
             while (j < l)
             {
               if (((AlignmentOrder) alorders.get(i))
-                      .equals(((AlignmentOrder) alorders.get(j))))
+                      .equals((alorders.get(j))))
               {
                 alorders.remove(j);
                 l--;
@@ -704,6 +716,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;