X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=cefdbd21b7a68edc6d24bcd9f2fa5d1d1ef3b9b5;hb=d42b7588a34477b24ce97ba75788536e74e6cf86;hp=03494179b8cf0f489f31e7971820eb7a38a8d456;hpb=a939b4c646235d460df3b7b9377ef8d8569caaff;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 0349417..cefdbd2 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -38,12 +38,13 @@ public class PAEContactMatrix implements ContactMatrixI
     }
     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
-    
+
     if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
     {
       parse_version_1_pAE(pae_obj);
@@ -54,32 +55,35 @@ public class PAEContactMatrix implements ContactMatrixI
       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)
+    maxcol = 0;
+    for (float[] row : matrix)
     {
-      if (row.length>maxcol)
+      if (row.length > maxcol)
       {
-        maxcol=row.length;
+        maxcol = row.length;
       }
-      maxscore=row[0];
-      for (float f:row)
+      maxscore = row[0];
+      for (float f : row)
       {
-        if (maxscore<f) {
-          maxscore=f;
+        if (maxscore < f)
+        {
+          maxscore = f;
         }
       }
     }
-    maxrow=matrix.length;
+    maxrow = matrix.length;
     elements = matrix;
-    
+
   }
 
   /**
@@ -90,24 +94,23 @@ public class PAEContactMatrix implements ContactMatrixI
   @SuppressWarnings("unchecked")
   private void parse_version_2_pAE(Map<String, Object> pae_obj)
   {
-    elements = new float[length][length];
     // 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();
-    Iterator<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
-            .getFirst(pae_obj, "predicted_aligned_error", "pae"))
-            .iterator();
+    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;
-    while (scoreRows.hasNext())
+    for (List<Long> scoreRow : scoreRows)
     {
-      Iterator<Long> scores = scoreRows.next().iterator();
+      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) d;
+          elements[row][col++] = (float) ((Long) d).longValue();
       }
       row++;
       col = 0;
@@ -131,7 +134,7 @@ public class PAEContactMatrix implements ContactMatrixI
     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())
     {
@@ -172,7 +175,7 @@ public class PAEContactMatrix implements ContactMatrixI
       @Override
       public int getContactHeight()
       {
-        return maxcol-1;
+        return maxcol - 1;
       }
 
       @Override
@@ -220,20 +223,26 @@ public class PAEContactMatrix implements ContactMatrixI
   @Override
   public String getAnnotLabel()
   {
-    return "pAE Matrix";
+    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";
+  public static final String PAEMATRIX = "PAE_MATRIX";
+
   @Override
   public String getType()
   {
     return PAEMATRIX;
   }
+
   @Override
   public int getWidth()
   {
     return length;
   }
+
   @Override
   public int getHeight()
   {