JAL-3878 Add getCalcName to AlignCalcWorkerI.

[jalview.git] / src / jalview / workers / StrucConsensusThread.java

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 9143ad7..a53f344 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,46 +1,62 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
-import java.util.Hashtable;
-
-import jalview.analysis.AAFrequency;
 import jalview.analysis.StructureFrequency;
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 
-public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+import java.util.Hashtable;
+
+public class StrucConsensusThread extends AlignCalcWorker
 {
   public StrucConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     super(alignViewport, alignPanel);
   }
-  public void run()
+
+  AlignmentAnnotation strucConsensus;
+
+  Hashtable[] hStrucConsensus;
+
+  private long nseq = -1;
+
+  @Override
+  public String getCalcName()
   {
-    try
-    {
-      calcMan.notifyStart(this);
-      while (!calcMan.notifyWorking(this))
-      {
-        try
-        {
-          if (ap != null)
-          {
-            ap.paintAlignment(false);
-          }
+    return "Struc Consensus";
+  }
 
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
+  @Override
+  public void run()
+  {
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -48,11 +64,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
 
       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
       {
-        calcMan.workerComplete(this);
         return;
       }
-      AlignmentAnnotation strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
-      Hashtable[] hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+      strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
+      hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
       strucConsensus.annotations = null;
       strucConsensus.annotations = new Annotation[aWidth];
 
@@ -62,52 +77,45 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
               .getAlignmentAnnotation();
       AlignmentAnnotation rnaStruc = null;
       // select rna struct to use for calculation
-      for (int i = 0; i < aa.length; i++)
+      if (aa != null)
       {
-        if (aa[i].getRNAStruc() != null)
+        for (int i = 0; i < aa.length; i++)
         {
-          rnaStruc = aa[i];
-          break;
+          if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+          {
+            rnaStruc = aa[i];
+            break;
+          }
         }
       }
       // check to see if its valid
-      
-      if (rnaStruc==null || !rnaStruc.isValidStruc())
+
+      if (rnaStruc == null || !rnaStruc.isValidStruc())
+      {
+        return;
+      }
+
+      try
+      {
+        final SequenceI[] arr = alignment.getSequencesArray();
+        nseq = arr.length;
+        jalview.analysis.StructureFrequency.calculate(arr, 0,
+                alignment.getWidth(), hStrucConsensus, true, rnaStruc);
+      } catch (ArrayIndexOutOfBoundsException x)
       {
-        calcMan.workerComplete(this);
         return;
       }
-      
-      jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
-              alignment.getWidth(), hStrucConsensus, true, rnaStruc);
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
-      if (alignViewport.getGlobalColourScheme()!= null)
-      {
-        alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
-      }
-
-    } catch (OutOfMemoryError error)
-    {
-      calcMan.workerCannotRun(this);
-
-      // consensus = null;
-      // hconsensus = null;
-      ap.raiseOOMWarning("calculating RNA structure consensus", error);
-    }
-
-    calcMan.workerComplete(this);
-    if (ap != null)
-    {
-      ap.paintAlignment(true);
-    }
 
   }
+
   /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
+  @Override
   public void updateAnnotation()
   {
     updateResultAnnotation(false);
@@ -115,16 +123,14 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
 
   public void updateResultAnnotation(boolean immediate)
   {
-    AlignmentAnnotation strucConsensus = alignViewport
-            .getAlignmentStrucConsensusAnnotation();
-    Hashtable[] hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
-    if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
+    if (immediate || !calcMan.isWorking(this) && strucConsensus != null
+            && hStrucConsensus != null)
     {
-      StructureFrequency.completeConsensus(strucConsensus,
-              hStrucConsensus, 0, hStrucConsensus.length,
-              alignViewport.getIgnoreGapsConsensus(),
-            alignViewport.isShowSequenceLogo());
+      StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
+              0, hStrucConsensus.length,
+              alignViewport.isIgnoreGapsConsensus(),
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 
-}
\ No newline at end of file
+}