X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=ce072e06a0477b8b3245154dae6548758618a568;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=d48d539d60e599430bf81a5c27c8a9c97ad4b864;hpb=4080955a4825b990ebfb1df6208ee1728bea360c;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index d48d539..ce072e0 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -23,6 +23,8 @@ import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
 import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceI;
@@ -33,17 +35,22 @@ import jalview.util.MapList;
 import jalview.util.MapUtils;
 import jalview.ws.dbsources.EBIAlfaFold;
 
-public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
+public class PAEContactMatrix extends
+        MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
 {
+
+
   int maxrow = 0, maxcol = 0;
 
+
   float[][] elements;
 
   float maxscore;
 
 
   @SuppressWarnings("unchecked")
-  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws FileFormatException
+  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+          throws FileFormatException
   {
     setRefSeq(_refSeq);
     // convert the lists to primitive arrays and store
@@ -91,15 +98,18 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
 
   /**
    * new matrix with specific mapping to a reference sequence
+   * 
    * @param newRefSeq
    * @param newFromMapList
    * @param elements2
+   * @param grps2
    */
-  public PAEContactMatrix(SequenceI newRefSeq,
-          MapList newFromMapList, float[][] elements2)
+  public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
+          float[][] elements2, GroupSet grps2)
   {
-    this(newRefSeq,elements2);
+    this(newRefSeq, elements2);
     toSeq = newFromMapList;
+    grps = grps2;
   }
 
   /**
@@ -131,7 +141,6 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
       while (scores.hasNext())
       {
         Object d = scores.next();
-
         if (d instanceof Double)
         {
           elements[row][col++] = ((Double) d).longValue();
@@ -140,7 +149,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
         {
           elements[row][col++] = (float) ((Long) d).longValue();
         }
-        
+
         if (maxscore < elements[row][col - 1])
         {
           maxscore = elements[row][col - 1];
@@ -209,20 +218,6 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   @Override
   public ContactListI getContactList(final int column)
   {
-//    final int _column;
-//    if (toSeq != null)
-//    {
-//      int[] word = toSeq.locateInTo(column, column);
-//      if (word == null)
-//      {
-//        return null;
-//      }
-//      _column = word[0];
-//    }
-//    else
-//    {
-//      _column = column;
-//    }
     if (column < 0 || column >= elements.length)
     {
       return null;
@@ -259,6 +254,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   {
     return elements[_column][i];
   }
+
   @Override
   public float getMin()
   {
@@ -274,17 +270,18 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   @Override
   public String getAnnotDescr()
   {
-    return "Predicted Alignment Error"+((refSeq==null) ? "" : (" 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));
-    //}
+    // if (this.getReferenceSeq() != null)
+    // {
+    // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+    // }
     return label.toString();
   }
 
@@ -307,158 +304,41 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   {
     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)
+  public static void validateContactMatrixFile(String fileName)
+          throws FileFormatException, IOException
   {
-    if (groups != null)
-    {
-      for (BitSet gp : groups)
-      {
-        if (gp.get(column))
-        {
-          return gp;
-        }
-      }
-    }
-    return 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)
+    FileInputStream infile = null;
+    try
     {
-      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;
-  }
-
-  public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
-  {
-    FileInputStream infile=null;
-    try {
       infile = new FileInputStream(new File(fileName));
     } catch (Throwable t)
     {
-      new IOException("Couldn't open "+fileName,t);      
+      new IOException("Couldn't open " + fileName, t);
     }
-    
-    
-    JSONObject paeDict=null;
-    try {
+    JSONObject paeDict = null;
+    try
+    {
       paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
     } catch (Throwable t)
     {
-      new FileFormatException("Couldn't parse "+fileName+" as a JSON dict or array containing a dict");
+      new FileFormatException("Couldn't parse " + fileName
+              + " as a JSON dict or array containing a dict");
     }
-    
-    PAEContactMatrix matrix = new PAEContactMatrix(new SequenceDummy("Predicted"), (Map<String,Object>)paeDict);
-    if (matrix.getWidth()<=0)
+
+    PAEContactMatrix matrix = new PAEContactMatrix(
+            new SequenceDummy("Predicted"), (Map<String, Object>) paeDict);
+    if (matrix.getWidth() <= 0)
     {
-      throw new FileFormatException("No data in PAE matrix read from '"+fileName+"'");
+      throw new FileFormatException(
+              "No data in PAE matrix read from '" + fileName + "'");
     }
   }
-
   @Override
-  protected PAEContactMatrix newMappableContactMatrix(
-          SequenceI newRefSeq, MapList newFromMapList)
+  protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+          MapList newFromMapList)
   {
-      return new PAEContactMatrix(newRefSeq, newFromMapList,
-              elements);
-  } 
+    PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+            elements, new GroupSet(grps));
+    return pae;
+  }
 }