From df3da405342b96c6630e280a2ac407864ac3a62f Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 22 Feb 2023 14:23:15 +0000
Subject: [PATCH] JAL-3858 construct a PAE direct from float array

---
 .../ws/datamodel/alphafold/PAEContactMatrix.java   |   41 +++++++++++++++++---
 1 file changed, 36 insertions(+), 5 deletions(-)

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 79ad458..58a4a83 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -29,17 +29,21 @@ public class PAEContactMatrix implements ContactMatrixI
 
   float maxscore;
 
-  @SuppressWarnings("unchecked")
-  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+  private void setRefSeq(SequenceI _refSeq)
   {
     refSeq = _refSeq;
     while (refSeq.getDatasetSequence() != null)
     {
       refSeq = refSeq.getDatasetSequence();
     }
-    // convert the lists to primitive arrays and store
     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);
@@ -50,12 +54,39 @@ 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)
+    {
+      if (row.length>maxcol)
+      {
+        maxcol=row.length;
+      }
+      maxscore=row[0];
+      for (float f:row)
+      {
+        if (maxscore<f) {
+          maxscore=f;
+        }
+      }
+    }
+    maxrow=matrix.length;
+    
+  }
 
   /**
    * parse a sane JSON representation of the pAE
    * 
    * @param pae_obj
    */
+  @SuppressWarnings("unchecked")
   private void parse_version_2_pAE(Map<String, Object> pae_obj)
   {
     elements = new float[length][length];
@@ -86,6 +117,7 @@ public class PAEContactMatrix implements ContactMatrixI
    * 
    * @param pae_obj
    */
+  @SuppressWarnings("unchecked")
   private void parse_version_1_pAE(Map<String, Object> pae_obj)
   {
     // assume indices are with respect to range defined by _refSeq on the
@@ -145,7 +177,6 @@ public class PAEContactMatrix implements ContactMatrixI
         {
           return -1;
         }
-        // TODO Auto-generated method stub
         return elements[_column][column];
       }
     });
-- 
1.7.10.2