From cf3e8343ced61a995515cb96e2c638f26dc813b9 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 18 Jul 2023 16:17:12 +0100
Subject: [PATCH] JAL-3855 PAE matrices are transposed on import from JSON so
 returned contact vectors correspond to errors predicted
 when superposing at a given column position

---
 .../ws/datamodel/alphafold/PAEContactMatrix.java   |   36 ++++++++++++++++----
 1 file changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index c822ef4..22884f1 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -21,6 +21,21 @@ 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
 {
@@ -129,17 +144,18 @@ public class PAEContactMatrix extends
         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;
@@ -180,7 +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();
@@ -194,13 +210,17 @@ 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)
   {
@@ -235,6 +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)
   {
-- 
1.7.10.2