From 59f8f1014e5ef09bf93c8a2cabe11b846012a521 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 24 Jun 2022 17:11:34 +0100
Subject: [PATCH] JAL-2349 JAL-3855 resolve sequence position for contact
 lookup and catch out bound contact requests

---
 src/jalview/renderer/ContactMapRenderer.java       |    8 +-
 .../ws/datamodel/alphafold/PAEContactMatrix.java   |   78 +++++++++++---------
 2 files changed, 50 insertions(+), 36 deletions(-)

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index c9198ed..aaa8a61 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -61,9 +61,11 @@ public class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
-      /*
-       * {profile type, #values, total count, char1, pct1, char2, pct2...}
-       */
+      if (_aa.sequenceRef != null)
+      {
+        // get the sequence position for the column
+        column = _aa.sequenceRef.findPosition(column) - 1;
+      }
       ContactListI contacts = viewport.getContactList(_aa, column);
       if (contacts == null)
       {
diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index e61af44..af8dfc3 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -8,69 +8,81 @@ import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
 import jalview.datamodel.ContactMatrixI;
-import jalview.datamodel.ContactRange;
 import jalview.datamodel.SequenceI;
 
 public class PAEContactMatrix implements ContactMatrixI
 {
 
-  SequenceI refSeq=null;
-  int maxrow=0,maxcol=0;
-  int[] indices1,indices2;
+  SequenceI refSeq = null;
+
+  int maxrow = 0, maxcol = 0;
+
+  int[] indices1, indices2;
+
   float[][] elements;
+
   float maxscore;
-  
+
   @SuppressWarnings("unchecked")
-  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws Exception
+  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+          throws Exception
   {
     refSeq = _refSeq;
-    while (refSeq.getDatasetSequence()!=null)
+    while (refSeq.getDatasetSequence() != null)
     {
-      refSeq=refSeq.getDatasetSequence();
+      refSeq = refSeq.getDatasetSequence();
     }
     // convert the lists to primitive arrays and store
-    int length = _refSeq.getEnd()-_refSeq.getStart()+1;
-    
-    // assume indices are with respect to range defined by _refSeq on the dataset refSeq
-    Iterator<Long> rows = ((List<Long>)pae_obj.get("residue1")).iterator();
-    Iterator<Long> cols = ((List<Long>)pae_obj.get("residue2")).iterator();
-    Iterator<Double> scores = ((List<Double>)pae_obj.get("distance")).iterator();
-    
-    elements=new float[length][length];
-    while (scores.hasNext()) {
-      float escore=scores.next().floatValue();
-      int row=rows.next().intValue();
-      int col=cols.next().intValue();
-      if (maxrow<row)
+    int length = _refSeq.getEnd() - _refSeq.getStart() + 1;
+
+    // assume indices are with respect to range defined by _refSeq on the
+    // dataset refSeq
+    Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
+    Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
+    Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
+            .iterator();
+
+    elements = new float[length][length];
+    while (scores.hasNext())
+    {
+      float escore = scores.next().floatValue();
+      int row = rows.next().intValue();
+      int col = cols.next().intValue();
+      if (maxrow < row)
       {
-        maxrow=row;
+        maxrow = row;
       }
-      if (maxcol<col)
+      if (maxcol < col)
       {
-        maxcol=col;
+        maxcol = col;
       }
-      elements[row-1][col-1]=escore;
+      elements[row - 1][col - 1] = escore;
     }
-    
-    maxscore = ((Double) pae_obj.get("max_predicted_aligned_error")).floatValue();
+
+    maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
+            .floatValue();
   }
 
   @Override
   public ContactListI getContactList(final int _column)
   {
-    
-    return new ContactListImpl(new ContactListProviderI() 
+    if (_column < 0 || _column >= elements.length)
+    {
+      return null;
+    }
+
+    return new ContactListImpl(new ContactListProviderI()
     {
       @Override
       public int getContactHeight()
       {
-        return maxcol-1;
+        return maxcol - 1;
       }
-      
+
       @Override
       public double getContactAt(int column)
       {
-        if (column<0 || column>=elements[_column].length)
+        if (column < 0 || column >= elements[_column].length)
         {
           return -1;
         }
@@ -95,7 +107,7 @@ public class PAEContactMatrix implements ContactMatrixI
   @Override
   public boolean hasReferenceSeq()
   {
-    return (refSeq!=null);
+    return (refSeq != null);
   }
 
   @Override
-- 
1.7.10.2