X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=1ec856b67ac49045550cd5f0279008e17b19d4c1;hb=e134764b7eec841cb56a417250f2dd898680f985;hp=30c77d287ac150b74eb65fdbda054cd6c8f68427;hpb=7420ce36f2b43280ef610e3743960207e4c2dbe3;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 30c77d2..1ec856b 100644
--- 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;
@@ -43,12 +45,13 @@ public class PAEContactMatrix implements ContactMatrixI
     }
     length = _refSeq.getEnd() - _refSeq.getStart() + 1;
   }
+
   @SuppressWarnings("unchecked")
   public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
   {
     setRefSeq(_refSeq);
     // convert the lists to primitive arrays and store
-    
+
     if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
     {
       parse_version_1_pAE(pae_obj);
@@ -59,32 +62,35 @@ public class PAEContactMatrix implements ContactMatrixI
       parse_version_2_pAE(pae_obj);
     }
   }
+
   /**
    * construct a sequence associated PAE matrix directly from a float array
+   * 
    * @param _refSeq
    * @param matrix
    */
   public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
   {
     setRefSeq(_refSeq);
-    maxcol=0;
-    for (float[] row:matrix)
+    maxcol = 0;
+    for (float[] row : matrix)
     {
-      if (row.length>maxcol)
+      if (row.length > maxcol)
       {
-        maxcol=row.length;
+        maxcol = row.length;
       }
-      maxscore=row[0];
-      for (float f:row)
+      maxscore = row[0];
+      for (float f : row)
       {
-        if (maxscore<f) {
-          maxscore=f;
+        if (maxscore < f)
+        {
+          maxscore = f;
         }
       }
     }
-    maxrow=matrix.length;
+    maxrow = matrix.length;
     elements = matrix;
-    
+
   }
 
   /**
@@ -99,11 +105,10 @@ public class PAEContactMatrix implements ContactMatrixI
     maxscore = ((Double) MapUtils.getFirst(pae_obj,
             "max_predicted_aligned_error", "max_pae")).floatValue();
     List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
-            .getFirst(pae_obj, "predicted_aligned_error", "pae"))
-            ;
+            .getFirst(pae_obj, "predicted_aligned_error", "pae"));
     elements = new float[scoreRows.size()][scoreRows.size()];
     int row = 0, col = 0;
-    for (List<Long> scoreRow:scoreRows)
+    for (List<Long> scoreRow : scoreRows)
     {
       Iterator<Long> scores = scoreRow.iterator();
       while (scores.hasNext())
@@ -112,7 +117,7 @@ public class PAEContactMatrix implements ContactMatrixI
         if (d instanceof Double)
           elements[row][col++] = ((Double) d).longValue();
         else
-          elements[row][col++] = (float) ((Long)d).longValue();
+          elements[row][col++] = (float) ((Long) d).longValue();
       }
       row++;
       col = 0;
@@ -177,7 +182,7 @@ public class PAEContactMatrix implements ContactMatrixI
       @Override
       public int getContactHeight()
       {
-        return maxcol-1;
+        return maxcol - 1;
       }
 
       @Override
@@ -219,55 +224,84 @@ 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()
   {
-    return "pAE Matrix";
+    StringBuilder label = new StringBuilder("PAE Matrix");
+    // if (this.getReferenceSeq() != null)
+    // {
+    // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+    // }
+    return label.toString();
   }
 
-  public static final String PAEMATRIX="PAE_MATRIX";
+  public static final String PAEMATRIX = "PAE_MATRIX";
+
   @Override
   public String getType()
   {
     return PAEMATRIX;
   }
+
   @Override
   public int getWidth()
   {
     return length;
   }
+
   @Override
   public int getHeight()
   {
     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;
   }
-  public void makeGroups(float thresh,boolean abs)
+
+  @Override
+  public boolean hasTree()
   {
-    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
-    double height = clusterer.findHeight(clusterer.getTopNode());
-    newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
+    return newick != null && newick.length() > 0;
+  }
+
+  boolean abs;
+
+  double thresh;
 
-    Console.trace("Newick string\n"+newick);
+  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);
+      Console.debug("Threshold " + cut + " for height=" + height);
 
       nodegroups = clusterer.groupNodes(cut);
     }
@@ -276,23 +310,34 @@ public class PAEContactMatrix implements ContactMatrixI
       nodegroups = new ArrayList<BinaryNode>();
       nodegroups.add(clusterer.getTopNode());
     }
-
+    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;
@@ -300,4 +345,55 @@ 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;
+    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;
+  }
 }