JAL-2349 allow PAE or other contact matrices to hold a coordinate mapping allowing...

[jalview.git] / src / jalview / ws / datamodel / alphafold / PAEContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 22dd7fb..9d7891d 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -11,51 +11,36 @@ 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.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 implements ContactMatrixI
+public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
 {
-
-  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;
 
-  private void setRefSeq(SequenceI _refSeq)
-  {
-    refSeq = _refSeq;
-    while (refSeq.getDatasetSequence() != null)
-    {
-      refSeq = refSeq.getDatasetSequence();
-    }
-    length = _refSeq.getEnd() - _refSeq.getStart() + 1;
-  }
 
   @SuppressWarnings("unchecked")
   public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws FileFormatException
@@ -105,6 +90,19 @@ public class PAEContactMatrix implements ContactMatrixI
   }
 
   /**
+   * new matrix with specific mapping to a reference sequence
+   * @param newRefSeq
+   * @param newFromMapList
+   * @param elements2
+   */
+  public PAEContactMatrix(SequenceI newRefSeq,
+          MapList newFromMapList, float[][] elements2)
+  {
+    this(newRefSeq,elements2);
+    toSeq = newFromMapList;
+  }
+
+  /**
    * parse a sane JSON representation of the pAE
    * 
    * @param pae_obj
@@ -209,8 +207,22 @@ public class PAEContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public ContactListI getContactList(final int _column)
+  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;
@@ -231,18 +243,24 @@ public class PAEContactMatrix implements ContactMatrixI
       }
 
       @Override
-      public double getContactAt(int column)
+      public double getContactAt(int mcolumn)
       {
-        if (column < 0 || column >= elements[_column].length)
+        int[] column=(toSeq==null) ? new int[] {mcolumn} : toSeq.locateInTo(mcolumn,mcolumn);
+        if (column==null || column[0] < 0 || column[0] >= elements[_column].length)
         {
           return -1;
         }
-        return elements[_column][column];
+        return elements[_column][column[0]];
       }
     });
   }
 
   @Override
+  protected double getElementAt(int _column, int i)
+  {
+    return elements[_column][i];
+  }
+  @Override
   public float getMin()
   {
     return 0;
@@ -255,18 +273,6 @@ public class PAEContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
-  {
-    return (refSeq != null);
-  }
-
-  @Override
-  public SequenceI getReferenceSeq()
-  {
-    return refSeq;
-  }
-
-  @Override
   public String getAnnotDescr()
   {
     return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
@@ -367,10 +373,14 @@ public class PAEContactMatrix implements ContactMatrixI
   @Override
   public BitSet getGroupsFor(int column)
   {
-    for (BitSet gp:groups) {
-      if (gp.get(column))
+    if (groups != null)
+    {
+      for (BitSet gp : groups)
       {
-        return gp;
+        if (gp.get(column))
+        {
+          return gp;
+        }
       }
     }
     return ContactMatrixI.super.getGroupsFor(column);
@@ -443,5 +453,13 @@ public class PAEContactMatrix implements ContactMatrixI
     {
       throw new FileFormatException("No data in PAE matrix read from '"+fileName+"'");
     }
+  }
+
+  @Override
+  protected PAEContactMatrix newMappableContactMatrix(
+          SequenceI newRefSeq, MapList newFromMapList)
+  {
+      return new PAEContactMatrix(newRefSeq, newFromMapList,
+              elements);
   } 
 }