JAL-4090 JAL-1551 spotlessApply

[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 dcd2022..397a84b 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -41,7 +41,6 @@ public class PAEContactMatrix extends
         MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
 {
 
-
   @SuppressWarnings("unchecked")
   public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
           throws FileFormatException
@@ -68,7 +67,7 @@ public class PAEContactMatrix extends
    */
   public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
   {
-    mappedMatrix=new FloatContactMatrix(matrix);
+    mappedMatrix = new FloatContactMatrix(matrix);
     setRefSeq(_refSeq);
   }
 
@@ -83,7 +82,7 @@ public class PAEContactMatrix extends
   public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
           float[][] elements2, GroupSet grps2)
   {
-    this(newRefSeq, new FloatContactMatrix(elements2,grps2));
+    this(newRefSeq, new FloatContactMatrix(elements2, grps2));
     toSeq = newFromMapList;
   }
 
@@ -93,6 +92,7 @@ public class PAEContactMatrix extends
     mappedMatrix = floatContactMatrix;
     setRefSeq(_refSeq);
   }
+
   public PAEContactMatrix(SequenceI _refSeq, MapList newFromMapList,
           ContactMatrixI floatContactMatrix)
   {
@@ -100,7 +100,7 @@ public class PAEContactMatrix extends
     setRefSeq(_refSeq);
     toSeq = newFromMapList;
   }
-  
+
   @Override
   protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
           MapList newFromMapList)
@@ -155,7 +155,7 @@ public class PAEContactMatrix extends
       row++;
       col = 0;
     }
-    mappedMatrix=new FloatContactMatrix(elements);
+    mappedMatrix = new FloatContactMatrix(elements);
   }
 
   /**
@@ -172,8 +172,8 @@ public class PAEContactMatrix extends
     Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
     Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
     // two pass - to allocate the elements array
-    
-    int maxrow=-1,maxcol=-1;
+
+    int maxrow = -1, maxcol = -1;
     while (rows.hasNext())
     {
       int row = rows.next().intValue();
@@ -206,10 +206,10 @@ public class PAEContactMatrix extends
       {
         maxcol = col;
       }
-      elements[col - 1][row-1] = escore;
+      elements[col - 1][row - 1] = escore;
     }
 
-    mappedMatrix=new FloatContactMatrix(elements);
+    mappedMatrix = new FloatContactMatrix(elements);
   }
 
   @Override
@@ -238,7 +238,6 @@ public class PAEContactMatrix extends
     return PAEMATRIX;
   }
 
-
   public static void validateContactMatrixFile(String fileName)
           throws FileFormatException, IOException
   {
@@ -268,11 +267,13 @@ public class PAEContactMatrix extends
               "No data in PAE matrix read from '" + fileName + "'");
     }
   }
+
   @Override
   public boolean equals(Object obj)
   {
     return super.equals(obj);
   }
+
   @Override
   public int hashCode()
   {