JAL-3285 add unmerged features into AlignmentViewport

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 39a1c18..1a9684f 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -98,13 +98,15 @@ public abstract class AlignmentViewport
 
   protected Deque<CommandI> redoList = new ArrayDeque<>();
 
-  protected String sequenceSetID;
-
+  /**
+   * alignment displayed in the viewport. Please use get/setter
+   */
+  protected AlignmentI alignment;
+  
   /*
    * probably unused indicator that view is of a dataset rather than an
    * alignment
    */
-  protected boolean isDataset = false;
 
   private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
 
@@ -133,12 +135,7 @@ public abstract class AlignmentViewport
   protected AlignmentAnnotation conservation;
 
   protected AlignmentAnnotation quality;
-
-  /**
-   * alignment displayed in the viewport
-   */
-  private AlignmentI alignment;
-
+  
   /**
    * results of alignment consensus analysis for visible portion of view
    */
@@ -641,6 +638,14 @@ public abstract class AlignmentViewport
     return alignment.getGapCharacter();
   }
 
+  protected String sequenceSetID;
+
+  /**
+   * probably unused indicator that view is of a dataset rather than an
+   * alignment
+   */
+  protected boolean isDataset = false;
+  
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -651,6 +656,18 @@ public abstract class AlignmentViewport
     return isDataset;
   }
 
+  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+  protected ColumnSelection colSel = new ColumnSelection();
+
+  public boolean autoCalculateConsensus = true;
+
+  protected boolean autoCalculateStrucConsensus = true;
+
+  protected boolean ignoreGapsInConsensusCalculation = false;
+
+  protected ResidueShaderI residueShading = new ResidueShader();
+  
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
@@ -724,6 +741,41 @@ public abstract class AlignmentViewport
   {
     return residueShading;
   }
+  
+  protected AlignmentAnnotation consensus;
+
+  protected AlignmentAnnotation complementConsensus;
+
+  protected AlignmentAnnotation gapcounts;
+
+  protected AlignmentAnnotation strucConsensus;
+
+  protected AlignmentAnnotation conservation;
+
+  protected AlignmentAnnotation quality;
+
+  protected AlignmentAnnotation[] groupConsensus;
+
+  protected AlignmentAnnotation[] groupConservation;
+
+  /**
+   * results of alignment consensus analysis for visible portion of view
+   */
+  protected ProfilesI hconsensus = null;
+
+  /**
+   * results of cDNA complement consensus visible portion of view
+   */
+  protected Hashtable[] hcomplementConsensus = null;
+
+  /**
+   * results of secondary structure base pair consensus for visible portion of
+   * view
+   */
+  protected Hashtable[] hStrucConsensus = null;
+
+  protected Conservation hconservation = null;
+  
   @Override
   public void setConservation(Conservation cons)
   {
@@ -743,9 +795,9 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public void setConsensusProfiles(ProfilesI hconsensus)
+  public void setSequenceConsensusHash(ProfilesI hconsensus)
   {
-    this.consensusProfiles = hconsensus;
+    this.hconsensus = hconsensus;
   }
 
   @Override
@@ -755,9 +807,9 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public ProfilesI getConsensusProfiles()
+  public ProfilesI getSequenceConsensusHash()
   {
-    return consensusProfiles;
+    return hconsensus;
   }
 
   @Override
@@ -810,9 +862,9 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignmentAnnotation getOccupancyAnnotation()
+  public AlignmentAnnotation getAlignmentGapAnnotation()
   {
-    return occupancy;
+    return gapcounts;
   }
 
   @Override
@@ -975,9 +1027,12 @@ public abstract class AlignmentViewport
     conservation = null;
     quality = null;
     consensusProfiles = null;
+    groupConsensus = null;
+    groupConservation = null;
+    hconsensus = null;
     hconservation = null;
     hcomplementConsensus = null;
-    occupancy = null;
+    gapcounts = null;
     calculator = null;
     residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
@@ -1311,6 +1366,7 @@ public abstract class AlignmentViewport
     ignoreGapsInConsensusCalculation = b;
     if (ap != null)
     {
+      updateConsensus(ap);
       if (residueShading != null)
       {
         residueShading.setThreshold(residueShading.getThreshold(),
@@ -1761,8 +1817,7 @@ public abstract class AlignmentViewport
     }
     else
     {
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment,
-              true);
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
     }
 
     return sequences;
@@ -1956,6 +2011,18 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
+    if (autoCalculateConsensus)
+    {
+      updateConsensus(ap);
+    }
+    if (hconsensus != null && autoCalculateConsensus)
+    {
+      updateConservation(ap);
+    }
+    if (autoCalculateStrucConsensus)
+    {
+      updateStrucConsensus(ap);
+    }
 
     // Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
@@ -1990,7 +2057,7 @@ public abstract class AlignmentViewport
     {
       rs.alignmentChanged(alignment, hiddenRepSequences);
 
-      rs.setConsensus(consensusProfiles);
+      rs.setConsensus(hconsensus);
       if (rs.conservationApplied())
       {
         rs.setConservation(Conservation.calculateConservation("All",
@@ -2015,7 +2082,7 @@ public abstract class AlignmentViewport
     // depending on if the user wants to see the annotation or not in a
     // specific alignment
 
-    if (consensusProfiles == null && !isDataset)
+    if (hconsensus == null && !isDataset)
     {
       if (!alignment.isNucleotide())
       {
@@ -2031,7 +2098,7 @@ public abstract class AlignmentViewport
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
 
-      initOccupancy();
+      initGapCounts();
 
       initComplementConsensus();
     }
@@ -2090,20 +2157,20 @@ public abstract class AlignmentViewport
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initOccupancy()
+  private void initGapCounts()
   {
     if (showOccupancy)
     {
-      occupancy = new AlignmentAnnotation("Occupancy",
+      gapcounts = new AlignmentAnnotation("Occupancy",
               MessageManager.getString("label.occupancy_descr"),
               new Annotation[1], 0f, alignment.getHeight(),
               AlignmentAnnotation.BAR_GRAPH);
-      occupancy.hasText = true;
-      occupancy.autoCalculated = true;
-      occupancy.scaleColLabel = true;
-      occupancy.graph = AlignmentAnnotation.BAR_GRAPH;
+      gapcounts.hasText = true;
+      gapcounts.autoCalculated = true;
+      gapcounts.scaleColLabel = true;
+      gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
 
-      alignment.addAnnotation(occupancy);
+      alignment.addAnnotation(gapcounts);
     }
   }