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 d1a2e9d..1ec856b 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,9 +1,16 @@
 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;
 
+import jalview.analysis.AverageDistanceEngine;
+import jalview.bin.Console;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
@@ -217,15 +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));
+    StringBuilder label = new StringBuilder("PAE Matrix");
+    // if (this.getReferenceSeq() != null)
+    // {
+    // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+    // }
     return label.toString();
   }
 
@@ -248,4 +258,142 @@ public class PAEContactMatrix implements ContactMatrixI
   {
     return length;
   }
+
+  List<BitSet> groups = null;
+
+  @Override
+  public boolean hasGroups()
+  {
+    return groups != null;
+  }
+
+  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)
+  {
+    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+            this);
+    double height = clusterer.findHeight(clusterer.getTopNode());
+    newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true)
+            .print();
+    treeType = "UPGMA";
+    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);
+
+      nodegroups = clusterer.groupNodes(cut);
+    }
+    else
+    {
+      nodegroups = new ArrayList<BinaryNode>();
+      nodegroups.add(clusterer.getTopNode());
+    }
+    this.abs = abs;
+    this.thresh = thresh;
+    groups = new ArrayList<>();
+    for (BinaryNode root : nodegroups)
+    {
+      BitSet gpset = new BitSet();
+      for (BinaryNode leaf : clusterer.findLeaves(root))
+      {
+        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)
+    {
+      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 void restoreGroups(List<BitSet> newgroups, String treeMethod,
+          String tree, double thresh2)
+  {
+    treeType = treeMethod;
+    groups = newgroups;
+    thresh = thresh2;
+    newick = tree;
+
+  }
+
+  @Override
+  public boolean hasCutHeight()
+  {
+    return groups != null && thresh != 0;
+  }
+
+  @Override
+  public double getCutHeight()
+  {
+    return thresh;
+  }
+
+  @Override
+  public String getTreeMethod()
+  {
+    return treeType;
+  }
 }