JAL-4158 first attempt at stashing colours for contact matrix groups and allowing...

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index f2e207c..1b1889e 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,7 +1,10 @@
 package jalview.datamodel;
 
+import java.awt.Color;
 import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Spliterator;
 import java.util.StringTokenizer;
@@ -171,7 +174,53 @@ public abstract class ContactMatrix implements ContactMatrixI
   {
     return "Contact Matrix";
   }
-
+  List<BitSet> groups=null;
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    groups = colGroups;
+    colorMap=new HashMap<>();
+  }
+  @Override
+  public boolean hasGroups()
+  {
+    return groups!=null && groups.size()>0;
+  }
+  @Override
+  public List<BitSet> getGroups()
+  {
+    return groups;
+  }
+  @Override
+  public BitSet getGroupsFor(int column)
+  {
+    for (BitSet gp:groups) {
+      if (gp.get(column))
+      {
+        return gp;
+      }
+    }
+    return ContactMatrixI.super.getGroupsFor(column);
+  }
+  HashMap<BitSet,Color> colorMap = new HashMap<>();
+  @Override 
+  public Color getColourForGroup(BitSet bs)
+  {
+    if (bs==null) {
+      return Color.white;
+    }
+    Color groupCol=colorMap.get(bs);
+    if (groupCol==null)
+    {
+      return Color.white;
+    }
+    return groupCol;
+  }
+  @Override 
+  public void setColorForGroup(BitSet bs,Color color)
+  {
+    colorMap.put(bs,color);
+  }
   public static String contactToFloatString(ContactMatrixI cm)
   {
     StringBuilder sb = new StringBuilder();

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 9eabb10..1c169ef 100644 (file)
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -1,5 +1,6 @@
 package jalview.datamodel;
 
+import java.awt.Color;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.List;
@@ -66,4 +67,10 @@ public interface ContactMatrixI
   default double getCutHeight() {
     return 0;
   }
+
+  void updateGroups(List<BitSet> colGroups);
+
+  void setColorForGroup(BitSet bs, Color color);
+
+  default Color getColourForGroup(BitSet bs) { return Color.white;};
 }

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 731948b..c3f3670 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,5 +1,10 @@
 package jalview.datamodel;
 
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
 /**
  * Dummy contact matrix based on sequence distance
  * 
@@ -118,4 +123,40 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   {
     return width;
   }
+  private List<BitSet> groups=null;
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    groups = colGroups;
+  }
+  @Override
+  public boolean hasGroups()
+  {
+    return groups!=null;
+  }
+  @Override
+  public List<BitSet> getGroups()
+  {
+    return groups;
+  }  
+
+  HashMap<BitSet,Color> colorMap = new HashMap<>();
+  @Override 
+  public Color getColourForGroup(BitSet bs)
+  {
+    if (bs==null) {
+      return Color.white;
+    }
+    Color groupCol=colorMap.get(bs);
+    if (groupCol==null)
+    {
+      return Color.white;
+    }
+    return groupCol;
+  }
+  @Override 
+  public void setColorForGroup(BitSet bs,Color color)
+  {
+    colorMap.put(bs,color);
+  }
 }

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7af8940..29826f0 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -36,7 +36,9 @@ import java.awt.print.PageFormat;
 import java.awt.print.Printable;
 import java.awt.print.PrinterException;
 import java.awt.print.PrinterJob;
+import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -51,8 +53,10 @@ import javax.swing.ToolTipManager;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -993,6 +997,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   void colourGroups(List<BinaryNode> groups)
   {
     AlignmentPanel[] aps = getAssociatedPanels();
+    List<BitSet> colGroups = new ArrayList<>();
+    Map<BitSet,Color> colors=new HashMap();
     for (int i = 0; i < groups.size(); i++)
     {
       Color col = new Color((int) (Math.random() * 255),
@@ -1003,7 +1009,25 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       if (!tp.isColumnWise()) {
         createSeqGroupFor(aps, l, col);
       } else {
-        markColumnsFor(aps,l,col);
+        BitSet gp=createColumnGroupFor(l,col);
+
+        colGroups.add(gp);
+        colors.put(gp, col);
+      }
+    }
+    if (tp.isColumnWise())
+    {
+      AlignmentAnnotation aa = tp.getAssocAnnotation();
+      if (aa!=null) {
+        ContactMatrixI cm = av.getContactMatrix(aa);
+        if (cm!=null)
+        {
+          cm.updateGroups(colGroups);
+          for (BitSet gp:colors.keySet())
+          {
+            cm.setColorForGroup(gp, colors.get(gp));
+          }
+        }
       }
     }
 
@@ -1056,6 +1080,29 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     return false;
   }
+  
+  private BitSet createColumnGroupFor(Vector<BinaryNode> l,
+          Color col)
+  {
+    BitSet gp=new BitSet();
+    for (BinaryNode bn:l)
+    {
+      int colm=-1;
+      if (bn.element()!=null && bn.element()instanceof Integer)
+      { colm = (Integer)bn.element();
+      } else {
+        // parse out from nodename
+      try {
+        colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
+      } catch (Exception e)
+      {
+        continue;
+      }
+      }
+      gp.set(colm);
+    }
+    return gp;
+  }
 
   private void markColumnsFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
           Color col)

diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java
index e1ef021..3df9804 100644 (file)
--- a/src/jalview/io/PContactPredictionFile.java
+++ b/src/jalview/io/PContactPredictionFile.java
@@ -25,6 +25,7 @@ import jalview.datamodel.SequenceI;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 0a2278b..e54f471 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -12,6 +12,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.ContactRange;
 import jalview.datamodel.HiddenColumns;
 import jalview.renderer.api.AnnotationRowRendererI;
@@ -114,6 +115,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
     int column;
     int aaMax = aa_annotations.length - 1;
+    ContactMatrixI cm = viewport.getContactMatrix(_aa);
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -144,6 +146,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
+      Color gpcol = (cm==null) ? Color.white: cm.getColourForGroup(cm.getGroupsFor(column));
       // feature still in development - highlight or omit regions hidden in
       // the alignment - currently marks them as red rows
       boolean maskHiddenCols = false;
@@ -213,7 +216,14 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         {
           col = shade.hidden;
         }
+        if (gpcol!=null && gpcol!=Color.white) {
+          // todo - could overlay group as a transparent rectangle ?
+          col = new Color((int)(((float)(col.getRed()+gpcol.getRed()))/2f),
+                  (int)(((float)(col.getGreen()+gpcol.getGreen()))/2f),
+                  (int)(((float)(col.getBlue()+gpcol.getBlue()))/2f));
+        }
         g.setColor(col);
+        
         if (cgeom.pixels_step > 1)
         {
           g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 5fe27cc..41e677a 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,7 +1,9 @@
 package jalview.ws.datamodel.alphafold;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -309,7 +311,14 @@ public class PAEContactMatrix implements ContactMatrixI
       groups.add(gpset);
     }
   }
-  
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    if (colGroups!=null)
+    {
+      groups=colGroups;
+    }    
+  }
   @Override
   public BitSet getGroupsFor(int column)
   {
@@ -322,6 +331,25 @@ public class PAEContactMatrix implements ContactMatrixI
     return ContactMatrixI.super.getGroupsFor(column);
   }
 
+  HashMap<BitSet,Color> colorMap = new HashMap<>();
+  @Override 
+  public Color getColourForGroup(BitSet bs)
+  {
+    if (bs==null) {
+      return Color.white;
+    }
+    Color groupCol=colorMap.get(bs);
+    if (groupCol==null)
+    {
+      return Color.white;
+    }
+    return groupCol;
+  }
+  @Override 
+  public void setColorForGroup(BitSet bs,Color color)
+  {
+    colorMap.put(bs,color);
+  }
   public void restoreGroups(List<BitSet> newgroups, String treeMethod,
           String tree, double thresh2)
   {