Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

[jalview.git] / src / jalview / ws / datamodel / alphafold / PAEContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index b29c0d5..ce072e0 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -38,12 +38,16 @@ import jalview.ws.dbsources.EBIAlfaFold;
 public class PAEContactMatrix extends
         MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
 {
+
+
   int maxrow = 0, maxcol = 0;
 
+
   float[][] elements;
 
   float maxscore;
 
+
   @SuppressWarnings("unchecked")
   public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
           throws FileFormatException
@@ -137,7 +141,6 @@ public class PAEContactMatrix extends
       while (scores.hasNext())
       {
         Object d = scores.next();
-
         if (d instanceof Double)
         {
           elements[row][col++] = ((Double) d).longValue();
@@ -215,20 +218,6 @@ public class PAEContactMatrix extends
   @Override
   public ContactListI getContactList(final int column)
   {
-    // final int _column;
-    // if (toSeq != null)
-    // {
-    // int[] word = toSeq.locateInTo(column, column);
-    // if (word == null)
-    // {
-    // return null;
-    // }
-    // _column = word[0];
-    // }
-    // else
-    // {
-    // _column = column;
-    // }
     if (column < 0 || column >= elements.length)
     {
       return null;
@@ -315,7 +304,6 @@ public class PAEContactMatrix extends
   {
     return length;
   }
-
   public static void validateContactMatrixFile(String fileName)
           throws FileFormatException, IOException
   {
@@ -327,7 +315,6 @@ public class PAEContactMatrix extends
     {
       new IOException("Couldn't open " + fileName, t);
     }
-
     JSONObject paeDict = null;
     try
     {
@@ -346,7 +333,6 @@ public class PAEContactMatrix extends
               "No data in PAE matrix read from '" + fileName + "'");
     }
   }
-
   @Override
   protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
           MapList newFromMapList)