JAL - 3690 AlignCalc rebuilt - FutureTask-based manager

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a9334ff..77210ee 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -24,6 +24,9 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignCalcManagerI2;
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeaturesDisplayedI;
@@ -31,6 +34,7 @@ import jalview.api.ViewStyleI;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
@@ -55,6 +59,7 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
+import jalview.workers.AlignCalcManager2;
 import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.InformationThread;
@@ -731,13 +736,13 @@ public abstract class AlignmentViewport
   /**
    * results of cDNA complement consensus visible portion of view
    */
-  protected Hashtable[] hcomplementConsensus = null;
+  protected Hashtable<String, Object>[] hcomplementConsensus = null;
 
   /**
    * results of secondary structure base pair consensus for visible portion of
    * view
    */
-  protected Hashtable[] hStrucConsensus = null;
+  protected Hashtable<String, Object>[] hStrucConsensus = null;
 
   protected Conservation hconservation = null;
   
@@ -766,7 +771,8 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public void setComplementConsensusHash(Hashtable[] hconsensus)
+  public void setComplementConsensusHash(
+          Hashtable<String, Object>[] hconsensus)
   {
     this.hcomplementConsensus = hconsensus;
   }
@@ -790,19 +796,20 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public Hashtable[] getComplementConsensusHash()
+  public Hashtable<String, Object>[] getComplementConsensusHash()
   {
     return hcomplementConsensus;
   }
 
   @Override
-  public Hashtable[] getRnaStructureConsensusHash()
+  public Hashtable<String, Object>[] getRnaStructureConsensusHash()
   {
     return hStrucConsensus;
   }
 
   @Override
-  public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+  public void setRnaStructureConsensusHash(
+          Hashtable<String, Object>[] hStrucConsensus)
   {
     this.hStrucConsensus = hStrucConsensus;
 
@@ -844,7 +851,7 @@ public abstract class AlignmentViewport
     return strucConsensus;
   }
 
-  protected AlignCalcManagerI calculator = new AlignCalcManager();
+  protected AlignCalcManagerI2 calculator = new AlignCalcManager2();
 
   /**
    * trigger update of conservation annotation
@@ -858,8 +865,8 @@ public abstract class AlignmentViewport
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(
-            jalview.workers.ConservationThread.class) == null)
+    if (calculator.getWorkersOfClass(
+            jalview.workers.ConservationThread.class).isEmpty())
     {
       calculator.registerWorker(
               new jalview.workers.ConservationThread(this, ap));
@@ -876,8 +883,7 @@ public abstract class AlignmentViewport
     {
       return;
     }
-    if (calculator
-            .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+    if (calculator.getWorkersOfClass(ConsensusThread.class).isEmpty())
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -908,11 +914,9 @@ public abstract class AlignmentViewport
       }
       if (doConsensus)
       {
-        if (calculator.getRegisteredWorkersOfClass(
-                ComplementConsensusThread.class) == null)
+        if (calculator.getWorkersOfClass(ComplementConsensusThread.class).isEmpty())
         {
-          calculator
-                  .registerWorker(new ComplementConsensusThread(this, ap));
+          calculator.registerWorker(new ComplementConsensusThread(this, ap));
         }
       }
     }
@@ -921,8 +925,7 @@ public abstract class AlignmentViewport
   @Override
   public void initInformationWorker(final AlignmentViewPanel ap)
   {
-    if (calculator
-            .getRegisteredWorkersOfClass(InformationThread.class) == null)
+    if (calculator.getWorkersOfClass(InformationThread.class).isEmpty())
     {
       calculator.registerWorker(new InformationThread(this, ap));
     }
@@ -943,8 +946,7 @@ public abstract class AlignmentViewport
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(
-            StrucConsensusThread.class) == null)
+    if (calculator.getWorkersOfClass(StrucConsensusThread.class).isEmpty())
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -963,7 +965,7 @@ public abstract class AlignmentViewport
     {
       return false;
     }
-    if (calculator.workingInvolvedWith(alignmentAnnotation))
+    if (calculator.isWorkingWithAnnotation(alignmentAnnotation))
     {
       // System.err.println("grey out ("+alignmentAnnotation.label+")");
       return true;
@@ -1016,7 +1018,7 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignCalcManagerI getCalcManager()
+  public AlignCalcManagerI2 getCalcManager()
   {
     return calculator;
   }
@@ -1090,9 +1092,15 @@ public abstract class AlignmentViewport
       // TODO: decouple settings setting from calculation when refactoring
       // annotation update method from alignframe to viewport
       this.showSequenceLogo = showSequenceLogo;
-      calculator.updateAnnotationFor(ConsensusThread.class);
-      calculator.updateAnnotationFor(ComplementConsensusThread.class);
-      calculator.updateAnnotationFor(StrucConsensusThread.class);
+      for (AlignCalcWorkerI worker : calculator.getWorkers())
+      {
+        if (worker.getClass().equals(ConsensusThread.class) ||
+                worker.getClass().equals(ComplementConsensusThread.class) ||
+                worker.getClass().equals(StrucConsensusThread.class))
+        {
+          worker.updateAnnotation();
+        }
+      }
     }
     this.showSequenceLogo = showSequenceLogo;
   }
@@ -1919,7 +1927,7 @@ public abstract class AlignmentViewport
       }
     } while (end < max);
 
-    int[][] startEnd = new int[regions.size()][2];
+    // int[][] startEnd = new int[regions.size()][2];
 
     return regions;
   }
@@ -2277,7 +2285,7 @@ public abstract class AlignmentViewport
      * TODO reorder the annotation rows according to group/sequence ordering on
      * alignment
      */
-    boolean sortg = true;
+    // boolean sortg = true;
 
     // remove old automatic annotation
     // add any new annotation
@@ -2390,7 +2398,7 @@ public abstract class AlignmentViewport
   public void clearSequenceColours()
   {
     sequenceColours.clear();
-  };
+  }
 
   @Override
   public AlignViewportI getCodingComplement()
@@ -3122,6 +3130,36 @@ public abstract class AlignmentViewport
   }
 
   @Override
+  public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+  {
+    AlignmentI alignmentToExport = null;
+    String[] omitHidden = null;
+    alignmentToExport = null;
+
+    if (hasHiddenColumns() && !options.isExportHiddenColumns())
+    {
+      omitHidden = getViewAsString(false,
+              options.isExportHiddenSequences());
+    }
+
+    int[] alignmentStartEnd = new int[2];
+    if (hasHiddenRows() && options.isExportHiddenSequences())
+    {
+      alignmentToExport = getAlignment().getHiddenSequences()
+              .getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = getAlignment();
+    }
+    alignmentStartEnd = getAlignment().getHiddenColumns()
+            .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+            omitHidden, alignmentStartEnd);
+    return ed;
+  }
+  
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -3142,7 +3180,6 @@ public abstract class AlignmentViewport
   {
     hmmNormaliseSequenceLogo = state;
   }
-
   /**
    * flag set to indicate if structure views might be out of sync with sequences
    * in the alignment