X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAAConsClient.java;h=58d0fa948f8eac370cf0af35f82f976a6c308f30;hb=05539806560b8f623b152362251ca5b651907ade;hp=054c9ab0b25f170b25e9d2aa301ccec92b53fcb4;hpb=b2c4d6c467255b5e30caf4cac1be372b89db0eea;p=jalview.git

diff --git a/src/jalview/ws/jws2/AAConsClient.java b/src/jalview/ws/jws2/AAConsClient.java
index 054c9ab..58d0fa9 100644
--- a/src/jalview/ws/jws2/AAConsClient.java
+++ b/src/jalview/ws/jws2/AAConsClient.java
@@ -1,18 +1,9 @@
 package jalview.ws.jws2;
 
-
-import jalview.analysis.AlignSeq;
-import jalview.analysis.SeqsetUtils;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.workers.AlignCalcWorker;
-import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
@@ -22,335 +13,33 @@ import java.util.List;
 import java.util.Map;
 import java.util.TreeSet;
 
-import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Score;
-import compbio.data.sequence.ScoreManager;
 import compbio.metadata.Argument;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.WrongParameterException;
 
-public class AAConsClient extends AlignCalcWorker
+public class AAConsClient extends JabawsAlignCalcWorker
 {
 
-  public AAConsClient(AlignViewportI alignViewport,
-          AlignmentViewPanel alignPanel)
-  {
-    super(alignViewport, alignPanel);
-  }
-
-  @SuppressWarnings("unchecked")
-  SequenceAnnotation aaservice;
-
-  private ScoreManager scoremanager;
-
-  private WsParamSetI preset;
-
-  private List<Argument> arguments;
-  
-  public WsParamSetI getPreset()
-  {
-    return preset;
-  }
-  public List<Argument> getArguments()
-  {
-    return arguments;
-  }
-  /**
-   * reconfigure and restart the AAConsClient. This method will spawn a new thread that will wait until any current jobs are finished, modify the parameters and restart the conservation calculation with the new values.
-   * @param newpreset
-   * @param newarguments
-   */
-  public void updateParameters(final WsParamSetI newpreset, final List<Argument> newarguments)
-  {
-    if (calcMan.isWorking(this))
-    {
-      new Thread(new Runnable() {
-        @Override
-        public void run()
-        {
-         
-          try {Thread.sleep(200);
-          } catch (InterruptedException x) {};
-            updateParameters(newpreset, newarguments);
-          }
-        }
-      ).start();
-    } else {
-      preset=newpreset;
-      arguments=newarguments;
-      calcMan.startWorker(this);
-    }
-  }
- 
-
   public AAConsClient(Jws2Instance service, AlignFrame alignFrame,
           WsParamSetI preset, List<Argument> paramset)
   {
-    this(alignFrame.getCurrentView(), alignFrame.alignPanel);
-    this.preset = preset;
-    this.arguments = paramset;
-    aaservice = (SequenceAnnotation) service.service;
-
+    super(service, alignFrame, preset, paramset);
+    submitGaps = true;
+    alignedSeqs = true;
+    nucleotidesAllowed = false;
+    proteinAllowed = true;
+    gapMap=new boolean[0];
   }
 
-  public List<Option> getJabaArguments()
+  public String getServiceActionText()
   {
-    List<Option> newargs = new ArrayList<Option>();
-    if (preset != null && preset instanceof JabaWsParamSet)
-    {
-      newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
-    }
-    if (arguments != null && arguments.size() > 0)
-    {
-      for (Argument rg : arguments)
-      {
-        if (Option.class.isAssignableFrom(rg.getClass()))
-        {
-          newargs.add((Option) rg);
-        }
-      }
-    }
-    return newargs;
-  }
-
-  @Override
-  public void run()
-  {
-    if (aaservice == null)
-    {
-      return;
-    }
-
-    try
-    {
-      if (checkDone())
-      {
-        return; 
-      }
-      AlignmentI alignment = alignViewport.getAlignment();
-
-      int aWidth = -1;
-
-      if (alignment == null || (aWidth = alignment.getWidth()) < 0 || alignment.isNucleotide())
-      {
-        calcMan.workerComplete(this);
-        return;
-      }
-
-      /*
-       * AlignmentAnnotation
-       * strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
-       * Hashtable[]
-       * hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
-       * strucConsensus.annotations = null; strucConsensus.annotations = new
-       * Annotation[aWidth];
-       * 
-       * hStrucConsensus = new Hashtable[aWidth];
-       */
-      AlignmentAnnotation[] aa = alignViewport.getAlignment()
-              .getAlignmentAnnotation();
-      /*
-       * AlignmentAnnotation rnaStruc = null; // select rna struct to use for
-       * calculation for (int i = 0; i < aa.length; i++) { if
-       * (aa[i].getRNAStruc() != null && aa[i].isValidStruc()) { rnaStruc =
-       * aa[i]; break; } } // check to see if its valid
-       * 
-       * if (rnaStruc==null || !rnaStruc.isValidStruc()) {
-       * calcMan.workerComplete(this); return; }
-       */
-      List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
-
-      boolean submitGaps = true;
-      int minlen = 10;
-      for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
-      {
-
-        if (sq.getEnd() - sq.getStart() > minlen - 1)
-        {
-          String newname = SeqsetUtils.unique_name(seqs.size() + 1);
-          // make new input sequence with or without gaps
-          seqs.add(new compbio.data.sequence.FastaSequence(newname,
-                  (submitGaps) ? sq.getSequenceAsString() : AlignSeq
-                          .extractGaps(jalview.util.Comparison.GapChars,
-                                  sq.getSequenceAsString())));
-        }
-      }
-
-      String rslt;
-      if (preset == null)
-      {
-        rslt=aaservice.analize(seqs);
-      }
-      else
-      {
-        try {
-        rslt=aaservice.customAnalize(seqs,  getJabaArguments());
-        } catch (WrongParameterException x)
-        {
-          throw new JobSubmissionException("Invalid paremeter set. Check Jalview implementation.",x);
-          
-        }
-      }
-      boolean finished = false;
-      long rpos = 0;
-      do
-      {
-        JobStatus status = aaservice.getJobStatus(rslt);
-        if (status.equals(JobStatus.FINISHED))
-        {
-          finished = true;
-        }
-        long cpos;
-        do
-        {
-          cpos = rpos;
-          ChunkHolder stats = aaservice.pullExecStatistics(rslt, rpos);
-          if (stats != null)
-          {
-            System.out.print(stats.getChunk());
-            rpos = stats.getNextPosition();
-          }
-        } while (rpos > cpos);
-
-        if (!finished && status.equals(JobStatus.FAILED))
-        {
-          try
-          {
-            Thread.sleep(200);
-          } catch (InterruptedException x)
-          {
-          }
-          ;
-        }
-
-      } while (!finished);
-      try
-      {
-        Thread.sleep(200);
-      } catch (InterruptedException x)
-      {
-      }
-      ;
-      scoremanager = aaservice.getAnnotation(rslt);
-      if (scoremanager != null)
-      {
-        updateResultAnnotation(true);
-      }
-    } catch (JobSubmissionException x)
-    {
-
-      System.err.println("submission error:");
-      x.printStackTrace();
-      calcMan.workerCannotRun(this);
-    } catch (ResultNotAvailableException x)
-    {
-      System.err.println("collection error:");
-      x.printStackTrace();
-      calcMan.workerCannotRun(this);
-
-    } catch (OutOfMemoryError error)
-    {
-      calcMan.workerCannotRun(this);
-
-      // consensus = null;
-      // hconsensus = null;
-      ap.raiseOOMWarning("calculating Amino acid consensus using AACons service", error);
-    }
-    catch (Exception x)
-    {
-      calcMan.workerCannotRun(this);
-
-      // consensus = null;
-      // hconsensus = null;
-      System.err.println("Blacklisting worker due to unexpected exception:");
-      x.printStackTrace();
-    }
-    finally {
-
-    calcMan.workerComplete(this);
-    if (ap != null)
-    {
-      ap.paintAlignment(true);
-    }
-    }
-
-  }
-
-  /**
-   * notify manager that we have started, and wait for a free calculation slot
-   * @return true if slot is obtained and work still valid, false if another thread has done our work for us.
-   */
-  private boolean checkDone()
-  {
-    calcMan.notifyStart(this);
-    // ap.paintAlignment(false);
-    while (!calcMan.notifyWorking(this))
-    {
-      if (calcMan.isWorking(this))
-      {
-        return true;
-      }
-      try
-      {
-        if (ap != null)
-        {
-          ap.paintAlignment(false);
-        }
-
-        Thread.sleep(200);
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-    }
-    if (alignViewport.isClosed())
-    {
-      abortAndDestroy();
-      return true;
-    }
-    return false;
+    return "calculating Amino acid consensus using AACons service";
   }
 
   /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
-  public void updateAnnotation()
-  {
-    updateResultAnnotation(false);
-  }
-
-  private AlignmentAnnotation findOrCreate(String name, boolean autoCalc,
-          SequenceI seqRef, SequenceGroup groupRef)
-  {
-    for (AlignmentAnnotation annot : alignViewport.getAlignment()
-            .getAlignmentAnnotation())
-    {
-      if (annot.autoCalculated == autoCalc
-              && annot.getCalcId().equals(name)
-              && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
-      {
-        return annot;
-      }
-    }
-    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
-            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
-    annot.hasText=false;
-    annot.setCalcId(new String(name));
-    annot.autoCalculated = autoCalc;
-    if (seqRef != null)
-    {
-      annot.setSequenceRef(seqRef);
-    }
-    annot.groupRef = groupRef;
-    alignViewport.getAlignment().addAnnotation(annot);
 
-    return annot;
-  }
   public void updateResultAnnotation(boolean immediate)
   {
 
@@ -361,8 +50,9 @@ public class AAConsClient extends AlignCalcWorker
       Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
       int alWidth = alignViewport.getAlignment().getWidth();
       AlignmentI alignment;
-      int ann = (alignment=alignViewport.getAlignment()).getAlignmentAnnotation().length;
-      ArrayList<AlignmentAnnotation> ourAnnot=new ArrayList<AlignmentAnnotation>();
+      int ann = (alignment = alignViewport.getAlignment())
+              .getAlignmentAnnotation().length;
+      ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
       for (String score : scoremap.keySet())
       {
         TreeSet<Score> scores = scoremap.get(score);
@@ -383,42 +73,67 @@ public class AAConsClient extends AlignCalcWorker
           else
           {
             // simple annotation row
-            annotation = findOrCreate(scr.getMethod(), true, null, null);
+            annotation = alignViewport.getAlignment().findOrCreateAnnotation(scr.getMethod(), true, null, null);
             Annotation[] elm = new Annotation[alWidth];
-            if (alWidth==scr.getScores().size())
-            {
-            Iterator<Float> vals = scr.getScores().iterator();
-            float m=0f,x=0f;
-            for (int i = 0; vals.hasNext(); i++)
+            if (alWidth == gapMap.length) // scr.getScores().size())
             {
-              float val = vals.next().floatValue();
-              if (i==0) { m=val;x=val;} else { if (m>val) { m=val; }; if (x<val) { x=val;}}
-              elm[i] = new Annotation("",""+val,' ',val);
-            }
-            
-            annotation.annotations = elm;
-            annotation.belowAlignment = true;
-            if (x<0)
-            {
-              x=0;
-            }
-            x+=(x-m)*0.1;
-            annotation.graphMax=x;
-            annotation.graphMin=m;
-            annotation.validateRangeAndDisplay();
-            ourAnnot.add(annotation);
+              Iterator<Float> vals = scr.getScores().iterator();
+              float m = 0f, x = 0f;
+              for (int i = 0; vals.hasNext(); i++)
+              {
+                float val = vals.next().floatValue();
+                if (i == 0)
+                {
+                  m = val;
+                  x = val;
+                }
+                else
+                {
+                  if (m > val)
+                  {
+                    m = val;
+                  }
+                  ;
+                  if (x < val)
+                  {
+                    x = val;
+                  }
+                }
+                // if we're at a gapped column then skip to next ungapped position
+                if (gapMap != null && gapMap.length > 0)
+                {
+                  while (!gapMap[i])
+                  {
+                    elm[i++]=new Annotation("", "" , ' ', Float.NaN);
+                  }
+                }
+                elm[i] = new Annotation("", "" + val, ' ', val);
+              }
+
+              annotation.annotations = elm;
+              annotation.belowAlignment = true;
+              if (x < 0)
+              {
+                x = 0;
+              }
+              x += (x - m) * 0.1;
+              annotation.graphMax = x;
+              annotation.graphMin = m;
+              annotation.validateRangeAndDisplay();
+              ourAnnot.add(annotation);
             }
           }
         }
       }
-      if (ourAnnot.size()>0)
+      if (ourAnnot.size() > 0)
       {
-        List<AlignmentAnnotation> our=ourAnnots;
+        List<AlignmentAnnotation> our = ourAnnots;
         ourAnnots = ourAnnot;
-        if (our!=null) {
-          if (our.size()>0)
+        if (our != null)
+        {
+          if (our.size() > 0)
           {
-            for (AlignmentAnnotation an:our)
+            for (AlignmentAnnotation an : our)
             {
               if (!ourAnnots.contains(an))
               {
@@ -430,15 +145,22 @@ public class AAConsClient extends AlignCalcWorker
           our.clear();
         }
       }
-      //if (ann != alignViewport.getAlignment().getAlignmentAnnotation().length)
+      // if (ann !=
+      // alignViewport.getAlignment().getAlignmentAnnotation().length)
       {
         ap.adjustAnnotationHeight();
       }
-     /* else
-      {
-        ap.paintAlignment(true);
-      }*/
+      /*
+       * else { ap.paintAlignment(true); }
+       */
     }
   }
 
+  public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
+  {
+    // List<AlignmentAnnotation>
+    // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
+    // TODO Auto-generated method stub
+
+  }
 }