JAL-629 Better formatting of Arg.Opt options in usage statement

[jalview.git] / src / jalview / ws / datamodel / alphafold / PAEContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 87ccab6..1ec856b 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;
@@ -222,17 +224,18 @@ public class PAEContactMatrix implements ContactMatrixI
   @Override
   public String getAnnotDescr()
   {
-    return "Predicted Alignment Error for " + refSeq.getName();
+    return "Predicted Alignment Error"
+            + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
   }
 
   @Override
   public String getAnnotLabel()
   {
     StringBuilder label = new StringBuilder("PAE Matrix");
-    if (this.getReferenceSeq() != null)
-    {
-      label.append(":").append(this.getReferenceSeq().getDisplayId(false));
-    }
+    // if (this.getReferenceSeq() != null)
+    // {
+    // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+    // }
     return label.toString();
   }
 
@@ -255,33 +258,50 @@ public class PAEContactMatrix implements ContactMatrixI
   {
     return length;
   }
-  List<BitSet> groups=null;
+
+  List<BitSet> groups = null;
+
   @Override
   public boolean hasGroups()
   {
-    return groups!=null;
+    return groups != null;
   }
-  String newick=null;
-  public String getNewickString()
+
+  String newick = null;
+
+  @Override
+  public String getNewick()
   {
     return newick;
   }
+
+  @Override
+  public boolean hasTree()
+  {
+    return newick != null && newick.length() > 0;
+  }
+
   boolean abs;
+
   double thresh;
-  String treeType=null;
-  public void makeGroups(float thresh,boolean abs)
+
+  String treeType = null;
+
+  public void makeGroups(float thresh, boolean abs)
   {
-    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
+    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+            this);
     double height = clusterer.findHeight(clusterer.getTopNode());
-    newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
+    newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true)
+            .print();
     treeType = "UPGMA";
-    Console.trace("Newick string\n"+newick);
+    Console.trace("Newick string\n" + newick);
 
     List<BinaryNode> nodegroups;
     if (abs ? height > thresh : 0 < thresh && thresh < 1)
     {
       float cut = abs ? (float) (thresh / height) : thresh;
-      Console.debug("Threshold "+cut+" for height="+height);
+      Console.debug("Threshold " + cut + " for height=" + height);
 
       nodegroups = clusterer.groupNodes(cut);
     }
@@ -290,24 +310,34 @@ public class PAEContactMatrix implements ContactMatrixI
       nodegroups = new ArrayList<BinaryNode>();
       nodegroups.add(clusterer.getTopNode());
     }
-    this.abs=abs;
-    this.thresh=thresh;
+    this.abs = abs;
+    this.thresh = thresh;
     groups = new ArrayList<>();
-    for (BinaryNode root:nodegroups)
+    for (BinaryNode root : nodegroups)
     {
-      BitSet gpset=new BitSet();
-      for (BinaryNode leaf:clusterer.findLeaves(root))
+      BitSet gpset = new BitSet();
+      for (BinaryNode leaf : clusterer.findLeaves(root))
       {
-        gpset.set((Integer)leaf.element());
+        gpset.set((Integer) leaf.element());
       }
       groups.add(gpset);
     }
   }
-  
+
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    if (colGroups != null)
+    {
+      groups = colGroups;
+    }
+  }
+
   @Override
   public BitSet getGroupsFor(int column)
   {
-    for (BitSet gp:groups) {
+    for (BitSet gp : groups)
+    {
       if (gp.get(column))
       {
         return gp;
@@ -316,24 +346,51 @@ 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)
   {
-    treeType=treeMethod;
+    treeType = treeMethod;
     groups = newgroups;
-    thresh=thresh2;
-    newick =tree;
-    
+    thresh = thresh2;
+    newick = tree;
+
   }
+
   @Override
-  public boolean hasCutHeight() {
-    return groups!=null && thresh!=0;
+  public boolean hasCutHeight()
+  {
+    return groups != null && thresh != 0;
   }
+
   @Override
   public double getCutHeight()
   {
     return thresh;
   }
+
   @Override
   public String getTreeMethod()
   {