X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=a5ce9a0e3a76e0dd4018367208a6a4cf151b69bb;hb=5d5099b75d2653cedf49bb98308dcb94202ed16e;hp=48071bdb8f8a1ea7f8dfcf4757403f3cb2f88aca;hpb=7f98aeaa190d77fd40dcf80d55faedcace024d6f;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 48071bd..a5ce9a0 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,9 +1,14 @@
 package jalview.ws.datamodel.alphafold;
 
+import java.util.ArrayList;
+import java.util.BitSet;
 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;
@@ -38,12 +43,13 @@ 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);
@@ -54,32 +60,35 @@ 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;
-    
+
   }
 
   /**
@@ -94,11 +103,10 @@ 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())
@@ -107,7 +115,7 @@ 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;
@@ -172,7 +180,7 @@ public class PAEContactMatrix implements ContactMatrixI
       @Override
       public int getContactHeight()
       {
-        return maxcol-1;
+        return maxcol - 1;
       }
 
       @Override
@@ -214,29 +222,122 @@ 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;
+  @Override
+  public boolean hasGroups()
+  {
+    return groups!=null;
+  }
+  String newick=null;
+  @Override
+  public String getNewick()
+  {
+    return newick;
+  }
+  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 BitSet getGroupsFor(int column)
+  {
+    for (BitSet gp:groups) {
+      if (gp.get(column))
+      {
+        return gp;
+      }
+    }
+    return ContactMatrixI.super.getGroupsFor(column);
+  }
+
+  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;
+  }
 }