From 8fce85002e6f6a5957dc95662c6a3d80fcce8e82 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 6 Mar 2023 20:43:45 +0000
Subject: [PATCH] JAL-629 Fix null AlignPanel. More descriptive label of pAE
 Matrix allows 'Add reference annotation' to be enabled for
 subsequent PDB+PAE files.

---
 src/jalview/datamodel/ContactMapHolder.java        |    2 +-
 src/jalview/gui/StructureChooser.java              |    2 +-
 .../ws/datamodel/alphafold/PAEContactMatrix.java   |   45 ++++++++++++--------
 3 files changed, 29 insertions(+), 20 deletions(-)

diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java
index 5849374..a555a17 100644
--- a/src/jalview/datamodel/ContactMapHolder.java
+++ b/src/jalview/datamodel/ContactMapHolder.java
@@ -44,7 +44,7 @@ public class ContactMapHolder implements ContactMapHolderI
     aa.graphMin = cm.getMin();
     aa.graphMax = cm.getMax();
     aa.editable = false;
-    aa.calcId=cm.getType();
+    aa.calcId = cm.getType();
 
     contactmaps.put(aa.annotationId, cm);
     // TODO: contact matrices could be intra or inter - more than one refseq
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 29551b8..3fce931 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1276,7 +1276,7 @@ public class StructureChooser extends GStructureChooser
             selectedSequence = userSelectedSeq;
           String pdbFilename = selectedPdbFileName;
 
-          StructureChooser.openStructureFileForSequence(ssm, sc, null,
+          StructureChooser.openStructureFileForSequence(ssm, sc, ap,
                   selectedSequence, true, pdbFilename, tft, paeFilename);
         }
         SwingUtilities.invokeLater(new Runnable()
diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 48071bd..d1a2e9d 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;
-    
+
   }
 
   /**
@@ -94,11 +98,10 @@ public class PAEContactMatrix implements ContactMatrixI
     maxscore = ((Double) MapUtils.getFirst(pae_obj,
             "max_predicted_aligned_error", "max_pae")).floatValue();
     List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
-            .getFirst(pae_obj, "predicted_aligned_error", "pae"))
-            ;
+            .getFirst(pae_obj, "predicted_aligned_error", "pae"));
     elements = new float[scoreRows.size()][scoreRows.size()];
     int row = 0, col = 0;
-    for (List<Long> scoreRow:scoreRows)
+    for (List<Long> scoreRow : scoreRows)
     {
       Iterator<Long> scores = scoreRow.iterator();
       while (scores.hasNext())
@@ -107,7 +110,7 @@ public class PAEContactMatrix implements ContactMatrixI
         if (d instanceof Double)
           elements[row][col++] = ((Double) d).longValue();
         else
-          elements[row][col++] = (float) ((Long)d).longValue();
+          elements[row][col++] = (float) ((Long) d).longValue();
       }
       row++;
       col = 0;
@@ -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()
   {
-- 
1.7.10.2