JAL-3855 PAE matrices are transposed on import from JSON so returned contact vectors...

[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 b29c0d5..22884f1 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -1,49 +1,54 @@
 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.GroupSet;
-import jalview.datamodel.GroupSetI;
-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;
 
+/**
+ * routines and class for holding predicted alignment error matrices as produced
+ * by alphafold et al.
+ * 
+ * getContactList(column) returns the vector of predicted alignment errors for
+ * reference position given by column getElementAt(column, i) returns the
+ * predicted superposition error for the ith position when column is used as
+ * reference
+ * 
+ * Many thanks to Ora Schueler Furman for noticing that earlier development
+ * versions did not show the PAE oriented correctly
+ *
+ * @author jprocter
+ *
+ */
 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
@@ -137,20 +142,20 @@ public class PAEContactMatrix extends
       while (scores.hasNext())
       {
         Object d = scores.next();
-
         if (d instanceof Double)
         {
-          elements[row][col++] = ((Double) d).longValue();
+          elements[col][row] = ((Double) d).longValue();
         }
         else
         {
-          elements[row][col++] = (float) ((Long) d).longValue();
+          elements[col][row] = (float) ((Long) d).longValue();
         }
 
-        if (maxscore < elements[row][col - 1])
+        if (maxscore < elements[col][row])
         {
-          maxscore = elements[row][col - 1];
+          maxscore = elements[col][row];
         }
+        col++;
       }
       row++;
       col = 0;
@@ -191,7 +196,7 @@ public class PAEContactMatrix extends
     cols = ((List<Long>) pae_obj.get("residue2")).iterator();
     Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
             .iterator();
-    elements = new float[maxrow][maxcol];
+    elements = new float[maxcol][maxrow];
     while (scores.hasNext())
     {
       float escore = scores.next().floatValue();
@@ -205,30 +210,20 @@ public class PAEContactMatrix extends
       {
         maxcol = col;
       }
-      elements[row - 1][col - 1] = escore;
+      elements[col - 1][row-1] = escore;
     }
 
     maxscore = ((Double) MapUtils.getFirst(pae_obj,
             "max_predicted_aligned_error", "max_pae")).floatValue();
   }
 
+  /**
+   * getContactList(column) @returns the vector of predicted alignment errors
+   * for reference position given by column
+   */
   @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;
@@ -260,6 +255,10 @@ public class PAEContactMatrix extends
     });
   }
 
+  /**
+   * getElementAt(column, i) @returns the predicted superposition error for the
+   * ith position when column is used as reference
+   */
   @Override
   protected double getElementAt(int _column, int i)
   {
@@ -307,15 +306,14 @@ public class PAEContactMatrix extends
   @Override
   public int getWidth()
   {
-    return length;
+    return maxcol;
   }
 
   @Override
   public int getHeight()
   {
-    return length;
+    return maxrow;
   }
-
   public static void validateContactMatrixFile(String fileName)
           throws FileFormatException, IOException
   {
@@ -327,7 +325,6 @@ public class PAEContactMatrix extends
     {
       new IOException("Couldn't open " + fileName, t);
     }
-
     JSONObject paeDict = null;
     try
     {
@@ -346,7 +343,6 @@ public class PAEContactMatrix extends
               "No data in PAE matrix read from '" + fileName + "'");
     }
   }
-
   @Override
   protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
           MapList newFromMapList)