X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=1ec856b67ac49045550cd5f0279008e17b19d4c1;hb=e134764b7eec841cb56a417250f2dd898680f985;hp=e61af44a14f2b05986ea7531d349c66fadd1f097;hpb=b5ea0bbb85bef19c50fb4341bda9e9da9ef09b13;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index e61af44..1ec856b 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,80 +1,197 @@
 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;
 import jalview.datamodel.ContactMatrixI;
-import jalview.datamodel.ContactRange;
 import jalview.datamodel.SequenceI;
+import jalview.util.MapUtils;
 
 public class PAEContactMatrix implements ContactMatrixI
 {
 
-  SequenceI refSeq=null;
-  int maxrow=0,maxcol=0;
-  int[] indices1,indices2;
+  SequenceI refSeq = null;
+
+  /**
+   * the length that refSeq is expected to be (excluding gaps, of course)
+   */
+  int length;
+
+  int maxrow = 0, maxcol = 0;
+
+  int[] indices1, indices2;
+
   float[][] elements;
+
   float maxscore;
-  
-  @SuppressWarnings("unchecked")
-  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws Exception
+
+  private void setRefSeq(SequenceI _refSeq)
   {
     refSeq = _refSeq;
-    while (refSeq.getDatasetSequence()!=null)
+    while (refSeq.getDatasetSequence() != null)
     {
-      refSeq=refSeq.getDatasetSequence();
+      refSeq = refSeq.getDatasetSequence();
     }
+    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
-    int length = _refSeq.getEnd()-_refSeq.getStart()+1;
-    
-    // assume indices are with respect to range defined by _refSeq on the dataset refSeq
-    Iterator<Long> rows = ((List<Long>)pae_obj.get("residue1")).iterator();
-    Iterator<Long> cols = ((List<Long>)pae_obj.get("residue2")).iterator();
-    Iterator<Double> scores = ((List<Double>)pae_obj.get("distance")).iterator();
-    
-    elements=new float[length][length];
-    while (scores.hasNext()) {
-      float escore=scores.next().floatValue();
-      int row=rows.next().intValue();
-      int col=cols.next().intValue();
-      if (maxrow<row)
+
+    if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
+    {
+      parse_version_1_pAE(pae_obj);
+      return;
+    }
+    else
+    {
+      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)
+    {
+      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)
+  {
+    // 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();
+    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;
+    for (List<Long> scoreRow : scoreRows)
+    {
+      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) ((Long) d).longValue();
+      }
+      row++;
+      col = 0;
+    }
+    maxcol = length;
+    maxrow = length;
+  }
+
+  /**
+   * v1 format got ditched 28th July 2022 see
+   * https://alphafold.ebi.ac.uk/faq#:~:text=We%20updated%20the%20PAE%20JSON%20file%20format%20on%2028th%20July%202022
+   * 
+   * @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
+    // dataset refSeq
+    Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
+    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())
+    {
+      float escore = scores.next().floatValue();
+      int row = rows.next().intValue();
+      int col = cols.next().intValue();
+      if (maxrow < row)
       {
-        maxrow=row;
+        maxrow = row;
       }
-      if (maxcol<col)
+      if (maxcol < col)
       {
-        maxcol=col;
+        maxcol = col;
       }
-      elements[row-1][col-1]=escore;
+      elements[row - 1][col - 1] = escore;
     }
-    
-    maxscore = ((Double) pae_obj.get("max_predicted_aligned_error")).floatValue();
+
+    maxscore = ((Double) MapUtils.getFirst(pae_obj,
+            "max_predicted_aligned_error", "max_pae")).floatValue();
   }
 
   @Override
   public ContactListI getContactList(final int _column)
   {
-    
-    return new ContactListImpl(new ContactListProviderI() 
+    if (_column < 0 || _column >= elements.length)
+    {
+      return null;
+    }
+
+    return new ContactListImpl(new ContactListProviderI()
     {
       @Override
+      public int getPosition()
+      {
+        return _column;
+      }
+
+      @Override
       public int getContactHeight()
       {
-        return maxcol-1;
+        return maxcol - 1;
       }
-      
+
       @Override
       public double getContactAt(int column)
       {
-        if (column<0 || column>=elements[_column].length)
+        if (column < 0 || column >= elements[_column].length)
         {
           return -1;
         }
-        // TODO Auto-generated method stub
         return elements[_column][column];
       }
     });
@@ -95,7 +212,7 @@ public class PAEContactMatrix implements ContactMatrixI
   @Override
   public boolean hasReferenceSeq()
   {
-    return (refSeq!=null);
+    return (refSeq != null);
   }
 
   @Override
@@ -104,4 +221,179 @@ public class PAEContactMatrix implements ContactMatrixI
     return refSeq;
   }
 
+  @Override
+  public String getAnnotDescr()
+  {
+    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));
+    // }
+    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;
+  }
 }