JAL-2795 finalized method arguments; commited forester matrix changes

diff --git a/forester b/forester
index 09a8c72..d605114 160000 (submodule)
--- a/forester
+++ b/forester
@@ -1 +1 @@
-Subproject commit 09a8c723e9ab220999f25c6be635282f18186be7
+Subproject commit d605114bdf420c6cb680b02bb10ea25f09db769c

diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index fa67e4e..c58b2a9 100644 (file)
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -24,8 +24,8 @@ public class ForesterMatrix implements DistanceMatrix
 
   private String[] identifiers;
 
-  public ForesterMatrix(MatrixI jalviewInputMatrix,
-          Sequence[] matrixSequences)
+  public ForesterMatrix(final MatrixI jalviewInputMatrix,
+          final Sequence[] matrixSequences)
   {
     this.jalviewMatrix = jalviewInputMatrix;
     this.sequences = matrixSequences;
@@ -45,8 +45,8 @@ public class ForesterMatrix implements DistanceMatrix
 
   }
 
-  public ForesterMatrix(MatrixI jalviewInputMatrix,
-          String[] matrixIdentifiers)
+  public ForesterMatrix(final MatrixI jalviewInputMatrix,
+          final String[] matrixIdentifiers)
   {
     this.jalviewMatrix = jalviewInputMatrix;
     this.identifiers = matrixIdentifiers;
@@ -62,13 +62,13 @@ public class ForesterMatrix implements DistanceMatrix
   }
 
   @Override
-  public String getIdentifier(int i)
+  public String getIdentifier(final int i)
   {
     return identifiers[i];
   }
 
   @Override
-  public int getIndex(String identifier)
+  public int getIndex(final String identifier)
   {
     return Arrays.asList(identifiers).indexOf(identifier);
   }
@@ -87,13 +87,13 @@ public class ForesterMatrix implements DistanceMatrix
    * in the parameters is inverted here (as that is how forester demands it)
    */
   @Override
-  public double getValue(int col, int row)
+  public double getValue(final int col, final int row)
   {
     return jalviewMatrix.getValue(row, col);
   }
 
   @Override
-  public void setIdentifier(int i, String identifier)
+  public void setIdentifier(final int i, final String identifier)
   {
     identifiers[i] = identifier;
 
@@ -104,7 +104,7 @@ public class ForesterMatrix implements DistanceMatrix
    * parameters is inverted here (as that is how forester demands it)
    */
   @Override
-  public void setValue(int col, int row, double distance)
+  public void setValue(final int col, final int row, final double distance)
   {
     jalviewMatrix.setValue(row, col, distance);
 
@@ -127,7 +127,7 @@ public class ForesterMatrix implements DistanceMatrix
   }
 
   @Override
-  public void write(Writer w) throws IOException // directly copied from
+  public void write(final Writer w) throws IOException // directly copied from
                                                  // forester
   {
     w.write("    ");