X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=1ec856b67ac49045550cd5f0279008e17b19d4c1;hb=e134764b7eec841cb56a417250f2dd898680f985;hp=f282b9fa5929397c1c16feb34b4c570b595ac2f1;hpb=8479d86d490c841168c9eed1ac80960ce4191c78;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index f282b9f..1ec856b 100644
--- 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;
@@ -29,16 +36,21 @@ public class PAEContactMatrix implements ContactMatrixI
 
   float maxscore;
 
-  @SuppressWarnings("unchecked")
-  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+  private void setRefSeq(SequenceI _refSeq)
   {
     refSeq = _refSeq;
     while (refSeq.getDatasetSequence() != null)
     {
       refSeq = refSeq.getDatasetSequence();
     }
-    // convert the lists to primitive arrays and store
     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"))
     {
@@ -52,30 +64,60 @@ public class PAEContactMatrix implements ContactMatrixI
   }
 
   /**
+   * 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)
+    {
+      if (row.length > maxcol)
+      {
+        maxcol = row.length;
+      }
+      maxscore = row[0];
+      for (float f : row)
+      {
+        if (maxscore < f)
+        {
+          maxscore = f;
+        }
+      }
+    }
+    maxrow = matrix.length;
+    elements = matrix;
+
+  }
+
+  /**
    * parse a sane JSON representation of the pAE
    * 
    * @param pae_obj
    */
+  @SuppressWarnings("unchecked")
   private void parse_version_2_pAE(Map<String, Object> pae_obj)
   {
-    elements = new float[length][length];
     // this is never going to be reached by the integer rounding.. or is it ?
     maxscore = ((Double) MapUtils.getFirst(pae_obj,
             "max_predicted_aligned_error", "max_pae")).floatValue();
-    Iterator<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
-            .getFirst(pae_obj, "predicted_aligned_error", "pae"))
-            .iterator();
+    List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
+            .getFirst(pae_obj, "predicted_aligned_error", "pae"));
+    elements = new float[scoreRows.size()][scoreRows.size()];
     int row = 0, col = 0;
-    while (scoreRows.hasNext())
+    for (List<Long> scoreRow : scoreRows)
     {
-      Iterator<Long> scores = scoreRows.next().iterator();
+      Iterator<Long> scores = scoreRow.iterator();
       while (scores.hasNext())
       {
         Object d = scores.next();
         if (d instanceof Double)
           elements[row][col++] = ((Double) d).longValue();
         else
-          elements[row][col++] = (float) d;
+          elements[row][col++] = (float) ((Long) d).longValue();
       }
       row++;
       col = 0;
@@ -90,6 +132,7 @@ public class PAEContactMatrix implements ContactMatrixI
    * 
    * @param pae_obj
    */
+  @SuppressWarnings("unchecked")
   private void parse_version_1_pAE(Map<String, Object> pae_obj)
   {
     // assume indices are with respect to range defined by _refSeq on the
@@ -98,7 +141,7 @@ public class PAEContactMatrix implements ContactMatrixI
     Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
     Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
             .iterator();
-
+    // assume square matrix
     elements = new float[length][length];
     while (scores.hasNext())
     {
@@ -149,7 +192,6 @@ public class PAEContactMatrix implements ContactMatrixI
         {
           return -1;
         }
-        // TODO Auto-generated method stub
         return elements[_column][column];
       }
     });
@@ -182,12 +224,176 @@ 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";
+
+  @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;
+  }
+
+  @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;
   }
 }