X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=c822ef45a7106288170023af717c070746b6c60d;hb=a06dd69fae641b3f5a8f202b439796df8469abb6;hp=9d7891d312620fbdceded129e4e9ba303f20f3da;hpb=9e40070f757fc662aba39ba6314be4937276ead4;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 9d7891d..c822ef4 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,49 +1,42 @@
 package jalview.ws.datamodel.alphafold;
 
-import java.awt.Color;
-import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-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 java.util.Map.Entry;
 
 import org.json.simple.JSONObject;
 
-import jalview.analysis.AverageDistanceEngine;
-import jalview.bin.Console;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.BinaryNode;
 import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
 import jalview.datamodel.ContactMatrixI;
-import jalview.datamodel.Mapping;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
-import jalview.io.FileParse;
 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 +84,18 @@ 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 +127,6 @@ 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 +135,7 @@ 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];
@@ -209,21 +204,7 @@ 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)
+    if (column < 0 || column >= elements.length)
     {
       return null;
     }
@@ -233,7 +214,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
       @Override
       public int getPosition()
       {
-        return _column;
+        return column;
       }
 
       @Override
@@ -245,12 +226,11 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
       @Override
       public double getContactAt(int mcolumn)
       {
-        int[] column=(toSeq==null) ? new int[] {mcolumn} : toSeq.locateInTo(mcolumn,mcolumn);
-        if (column==null || column[0] < 0 || column[0] >= elements[_column].length)
+        if (mcolumn < 0 || mcolumn >= elements[column].length)
         {
           return -1;
         }
-        return elements[_column][column[0]];
+        return elements[column][mcolumn];
       }
     });
   }
@@ -260,6 +240,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   {
     return elements[_column][i];
   }
+
   @Override
   public float getMin()
   {
@@ -275,17 +256,18 @@ 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();
   }
 
@@ -300,166 +282,49 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   @Override
   public int getWidth()
   {
-    return length;
+    return maxcol;
   }
 
   @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)
-  {
-    if (groups != null)
-    {
-      for (BitSet gp : groups)
-      {
-        if (gp.get(column))
-        {
-          return gp;
-        }
-      }
-    }
-    return ContactMatrixI.super.getGroupsFor(column);
+    return maxrow;
   }
-
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
-  public Color getColourForGroup(BitSet bs)
+  public static void validateContactMatrixFile(String fileName)
+          throws FileFormatException, IOException
   {
-    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;
+  }
 }