JAL-1620 version bump and release notes

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index eda64b5..6449a2b 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,8 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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;
@@ -10,18 +27,34 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
 
-public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker implements
+        AlignCalcWorkerI
 {
   public StrucConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
     super(alignViewport, alignPanel);
   }
+
+  AlignmentAnnotation strucConsensus;
+
+  Hashtable[] hStrucConsensus;
+
+  private long nseq = -1;
+
+  @Override
   public void run()
   {
     try
     {
+      if (calcMan.isPending(this))
+      {
+        return;
+      }
       calcMan.notifyStart(this);
       while (!calcMan.notifyWorking(this))
       {
@@ -29,7 +62,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         {
           if (ap != null)
           {
-            ap.paintAlignment(false);
+            // ap.paintAlignment(false);
           }
 
           Thread.sleep(200);
@@ -41,6 +74,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -51,8 +85,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
         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];
 
@@ -61,21 +95,38 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
       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)
+        if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
         {
           rnaStruc = aa[i];
           break;
         }
       }
+      // check to see if its valid
 
-      jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
-              alignment.getWidth(), hStrucConsensus, true, rnaStruc);
+      if (rnaStruc == null || !rnaStruc.isValidStruc())
+      {
+        calcMan.workerComplete(this);
+        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;
+      }
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
-      if (alignViewport.getGlobalColourScheme()!= null)
+      if (alignViewport.getGlobalColourScheme() != null)
       {
         alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
       }
@@ -87,19 +138,22 @@ public class StrucConsensusThread extends AlignCalcWorker implements AlignCalcWo
       // consensus = null;
       // hconsensus = null;
       ap.raiseOOMWarning("calculating RNA structure consensus", error);
-    }
-
-    calcMan.workerComplete(this);
-    if (ap != null)
+    } finally
     {
-      ap.paintAlignment(true);
+      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);
@@ -107,16 +161,14 @@ 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,
+      StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
+              0, hStrucConsensus.length,
               alignViewport.getIgnoreGapsConsensus(),
-            alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 
-}
\ No newline at end of file
+}