X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=6f3a2af49b835a7f5e8c4380e50d69e97504a1d0;hb=6235128370382f0fecdf3ba1cc683052c5aa11e7;hp=029280b2cb83657d8ec02f73598787d9d4652a19;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 029280b..6f3a2af 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -40,7 +40,9 @@ import jalview.workers.AlignCalcManager;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -402,7 +404,8 @@ public abstract class AlignmentViewport implements AlignViewportI
     if (autoCalculateStrucConsensus && strucConsensus == null
             && alignment.isNucleotide() && alignment.hasRNAStructure())
     {
-
+      // secondary structure has been added - so init the consensus line
+      initRNAStructure();
     }
 
     // see note in mantis : issue number 8585
@@ -593,6 +596,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return null or the currently selected sequence region
    */
+  @Override
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -605,6 +609,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          - group holding references to sequences in this alignment view
    * 
    */
+  @Override
   public void setSelectionGroup(SequenceGroup sg)
   {
     selectionGroup = sg;
@@ -780,6 +785,8 @@ public abstract class AlignmentViewport implements AlignViewportI
 
   protected boolean showConsensus = true;
 
+  Hashtable sequenceColours;
+
   /**
    * Property change listener for changes in alignment
    * 
@@ -1053,6 +1060,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return array of references to sequence objects
    */
+  @Override
   public SequenceI[] getSequenceSelection()
   {
     SequenceI[] sequences = null;
@@ -1075,6 +1083,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
@@ -1091,6 +1100,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          boolean true to just return the selected view
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {
@@ -1109,6 +1119,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    *          is true)
    * @return AlignmentView
    */
+  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly, boolean markGroups)
   {
@@ -1124,6 +1135,7 @@ public abstract class AlignmentViewport implements AlignViewportI
    * 
    * @return String[]
    */
+  @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
     String[] selection = null;
@@ -1318,62 +1330,80 @@ public abstract class AlignmentViewport implements AlignViewportI
     {
       if (!alignment.isNucleotide())
       {
-        if (showConservation)
-        {
-          if (conservation == null)
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                    "Conservation of total alignment less than "
-                            + getConsPercGaps() + "% gaps",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated = true;
-            alignment.addAnnotation(conservation);
-          }
-        }
-        if (showQuality)
-        {
-          if (quality == null)
-          {
-            quality = new AlignmentAnnotation("Quality",
-                    "Alignment Quality based on Blosum62 scores",
-                    new Annotation[1], 0f, 11f,
-                    AlignmentAnnotation.BAR_GRAPH);
-            quality.hasText = true;
-            quality.autoCalculated = true;
-            alignment.addAnnotation(quality);
-          }
-        }
+        initConservation();
+        initQuality();
       }
       else
       {
-        if (alignment.hasRNAStructure())
-        {
-          strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-                  new Annotation[1], 0f, 100f,
-                  AlignmentAnnotation.BAR_GRAPH);
-          strucConsensus.hasText = true;
-          strucConsensus.autoCalculated = true;
-        }
+        initRNAStructure();
       }
+      initConsensus();
+    }
+  }
 
-      consensus = new AlignmentAnnotation("Consensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
+  private void initConsensus()
+  {
 
-      if (showConsensus)
+    consensus = new AlignmentAnnotation("Consensus", "PID",
+            new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+    consensus.hasText = true;
+    consensus.autoCalculated = true;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(consensus);
+    }
+  }
+
+  private void initConservation()
+  {
+    if (showConservation)
+    {
+      if (conservation == null)
       {
-        alignment.addAnnotation(consensus);
-        if (strucConsensus != null)
-        {
-          alignment.addAnnotation(strucConsensus);
-        }
+        conservation = new AlignmentAnnotation("Conservation",
+                "Conservation of total alignment less than "
+                        + getConsPercGaps() + "% gaps",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
+        alignment.addAnnotation(conservation);
+      }
+    }
+  }
+  private void initQuality()
+  {
+    if (showQuality)
+    {
+      if (quality == null)
+      {
+        quality = new AlignmentAnnotation("Quality",
+                "Alignment Quality based on Blosum62 scores",
+                new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
+        quality.hasText = true;
+        quality.autoCalculated = true;
+        alignment.addAnnotation(quality);
       }
     }
   }
+  private void initRNAStructure()
+  {
+    if (alignment.hasRNAStructure() && strucConsensus==null)
+    {
+      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+              new Annotation[1], 0f, 100f,
+              AlignmentAnnotation.BAR_GRAPH);
+      strucConsensus.hasText = true;
+      strucConsensus.autoCalculated = true;
 
+      if (showConsensus)
+      {
+        alignment.addAnnotation(strucConsensus);
+      }
+    }
+  }
   /*
    * (non-Javadoc)
    * 
@@ -1387,7 +1417,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     int charHeight = getCharHeight();
     if (aa != null)
     {
-      boolean graphgrp[] = null;
+      BitSet graphgrp = new BitSet();
       for (int i = 0; i < aa.length; i++)
       {
         if (aa[i] == null)
@@ -1401,17 +1431,13 @@ public abstract class AlignmentViewport implements AlignViewportI
         }
         if (aa[i].graphGroup > -1)
         {
-          if (graphgrp == null)
-          {
-            graphgrp = new boolean[aa.length];
-          }
-          if (graphgrp[aa[i].graphGroup])
+          if (graphgrp.get(aa[i].graphGroup))
           {
             continue;
           }
           else
           {
-            graphgrp[aa[i].graphGroup] = true;
+            graphgrp.set(aa[i].graphGroup);
           }
         }
         aa[i].height = 0;
@@ -1516,4 +1542,60 @@ public abstract class AlignmentViewport implements AlignViewportI
     oldrfs.clear();
   }
 
+  @Override
+  public Color getSequenceColour(SequenceI seq)
+  {
+    Color sqc=Color.white;
+    if (sequenceColours != null)
+    {
+      sqc = (Color) sequenceColours.get(seq);
+      if (sqc == null) {
+        sqc = Color.white;
+      }
+    }
+    return sqc;
+  }
+
+  @Override
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+  @Override
+  public void updateSequenceIdColours()
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+    for (SequenceGroup sg : alignment.getGroups())
+    {
+      if (sg.idColour != null)
+      {
+        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+        {
+          sequenceColours.put(s, sg.idColour);
+        }
+      }
+    }
+  }
+
+  @Override
+  public void clearSequenceColours()
+  {
+    sequenceColours = null;
+  };
 }