JAL-2335 filterNonStandardResidues configurable for jabaws clients

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

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 8299e3c..b0210d8 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -21,17 +21,24 @@
 package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.WebserviceInfo;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.PileUpfile;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
@@ -71,6 +78,7 @@ class JPredThread extends JWS1Thread implements WSClientI
      * @return true if getResultSet will return a valid alignment and prediction
      *         result.
      */
+    @Override
     public boolean hasResults()
     {
       if (subjobComplete && result != null && result.isFinished()
@@ -82,6 +90,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       return false;
     }
 
+    @Override
     public boolean hasValidInput()
     {
       if (sequence != null)
@@ -105,49 +114,49 @@ class JPredThread extends JWS1Thread implements WSClientI
         return null;
       }
       AlignmentI al = null;
-      ColumnSelection alcsel = null;
+      HiddenColumns alhidden = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
       JpredResult result = (JpredResult) this.result;
 
-      jalview.bin.Cache.log.debug("Parsing output from JNet job.");
+      Cache.log.debug("Parsing output from JNet job.");
       // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
       // "File");
-      jalview.io.JPredFile prediction = new jalview.io.JPredFile(
-              result.getPredfile(), "Paste");
+      JPredFile prediction = new JPredFile(
+              result.getPredfile(), DataSourceType.PASTE);
       SequenceI[] preds = prediction.getSeqsAsArray();
-      jalview.bin.Cache.log.debug("Got prediction profile.");
+      Cache.log.debug("Got prediction profile.");
 
       if ((this.msa != null) && (result.getAligfile() != null))
       {
-        jalview.bin.Cache.log.debug("Getting associated alignment.");
+        Cache.log.debug("Getting associated alignment.");
         // we ignore the returned alignment if we only predicted on a single
         // sequence
-        String format = new jalview.io.IdentifyFile().identify(
-                result.getAligfile(), "Paste");
+        FileFormatI format = new IdentifyFile().identify(
+                result.getAligfile(), DataSourceType.PASTE);
 
-        if (jalview.io.FormatAdapter.isValidFormat(format))
+        if (format != null)
         {
           SequenceI sqs[];
           if (predMap != null)
           {
             Object[] alandcolsel = input
-                    .getAlignmentAndColumnSelection(getGapChar());
+                    .getAlignmentAndHiddenColumns(getGapChar());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
-            alcsel = (ColumnSelection) alandcolsel[1];
+            alhidden = (HiddenColumns) alandcolsel[1];
           }
           else
           {
             al = new FormatAdapter().readFile(result.getAligfile(),
-                    "Paste", format);
+                    DataSourceType.PASTE, format);
             sqs = new SequenceI[al.getHeight()];
 
             for (int i = 0, j = al.getHeight(); i < j; i++)
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs))
+            if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
             {
               throw (new Exception(
                       MessageManager
@@ -164,15 +173,15 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             al.setDataset(null);
           }
-          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+          JnetAnnotationMaker.add_annotation(prediction, al,
                   FirstSeq, false, predMap);
 
         }
         else
         {
           throw (new Exception(MessageManager.formatMessage(
-                  "exception.unknown_format_for_file", new String[] {
-                      format, result.getAligfile() })));
+                  "exception.unknown_format_for_file", new String[] { "",
+                      result.getAligfile() })));
         }
       }
       else
@@ -183,7 +192,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           char gc = getGapChar();
           SequenceI[] sqs = (SequenceI[]) input
-                  .getAlignmentAndColumnSelection(gc)[0];
+                  .getAlignmentAndHiddenColumns(gc)[0];
           if (this.msaIndex >= sqs.length)
           {
             throw new Error(
@@ -228,7 +237,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+            alhidden = HiddenColumns.propagateInsertions(profileseq, al,
                     input);
           }
         }
@@ -243,7 +252,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                   alant.sequenceRef);
         }
       }
-      return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
+      return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
     }
 
     /**
@@ -355,8 +364,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (msf.length > 1)
         {
           msa = new vamsas.objects.simple.Msfalignment();
-          jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
-          msa.setMsf(pileup.print(msf));
+          PileUpfile pileup = new PileUpfile();
+          msa.setMsf(pileup.print(msf, true));
         }
       }
     }
@@ -420,6 +429,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public void StartJob(AWsJob j)
   {
     if (!(j instanceof JPredJob))
@@ -502,6 +512,7 @@ class JPredThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public void parseResult()
   {
     int results = 0; // number of result sets received
@@ -529,6 +540,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       wsInfo.showResultsNewFrame
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(true);
@@ -537,6 +549,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       wsInfo.mergeResults
               .addActionListener(new java.awt.event.ActionListener()
               {
+                @Override
                 public void actionPerformed(java.awt.event.ActionEvent evt)
                 {
                   displayResults(false);
@@ -612,7 +625,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             if (res[1] != null)
             {
               af = new AlignFrame((Alignment) res[0],
-                      (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+                      (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
                       AlignFrame.DEFAULT_HEIGHT);
             }
             else
@@ -638,7 +651,8 @@ class JPredThread extends JWS1Thread implements WSClientI
              */
 
             af = new AlignFrame((Alignment) res[0],
-                    (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ (HiddenColumns) res[1],
+                    AlignFrame.DEFAULT_WIDTH,
                     AlignFrame.DEFAULT_HEIGHT);
           }
           Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
@@ -652,21 +666,25 @@ class JPredThread extends JWS1Thread implements WSClientI
     }
   }
 
+  @Override
   public void pollJob(AWsJob job) throws Exception
   {
     ((JPredJob) job).result = server.getresult(job.getJobId());
   }
 
+  @Override
   public boolean isCancellable()
   {
     return false;
   }
 
+  @Override
   public void cancelJob()
   {
     throw new Error(MessageManager.getString("error.implementation_error"));
   }
 
+  @Override
   public boolean canMergeResults()
   {
     return false;