JAL-2872 Undid inference disabling (done in Jalview instead)

[jalview.git] / forester / java / src / org / forester / evoinference / matrix / distance / BasicSymmetricalDistanceMatrix.java

diff --git a/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java b/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java
index fdf2ec4..14d7e97 100644 (file)
--- a/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java
+++ b/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java
@@ -39,18 +39,14 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix {
 
     // NumberFormat                      nf1              = NumberFormat.getInstance();
     private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat( "0.000000" );
-    final double[][]                  _values;
     final String[]                    _identifiers;
+    final double[][]                  _values;
 
     public BasicSymmetricalDistanceMatrix( final int size ) {
         _values = new double[ size ][ size ];
         _identifiers = new String[ size ];
     }
 
-    public final double[][] getValues() {
-        return _values;
-    }
-
     @Override
     public final String getIdentifier( final int i ) {
         return _identifiers[ i ];
@@ -85,6 +81,10 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix {
         return _values[ col ][ row ];
     }
 
+    public final double[][] getValues() {
+        return _values;
+    }
+
     public final void randomize( final long seed ) {
         final java.util.Random r = new java.util.Random( seed );
         for( int j = 0; j < getSize(); ++j ) {
@@ -122,6 +122,21 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix {
         _values[ col ][ row ] = d;
     }
 
+    @Override
+    public final String toString() {
+        return toPhylip().toString();
+    }
+
+    @Override
+    public final StringBuffer toStringBuffer( final Format format ) {
+        switch ( format ) {
+            case PHYLIP:
+                return toPhylip();
+            default:
+                throw new IllegalArgumentException( "Unknown format:" + format );
+        }
+    }
+
     public final void write( final Writer w ) throws IOException {
         w.write( "    " );
         w.write( getSize() + "" );
@@ -179,19 +194,4 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix {
         }
         return sb;
     }
-
-    @Override
-    public final String toString() {
-        return toPhylip().toString();
-    }
-
-    @Override
-    public final StringBuffer toStringBuffer( final Format format ) {
-        switch ( format ) {
-            case PHYLIP:
-                return toPhylip();
-            default:
-                throw new IllegalArgumentException( "Unknown format:" + format );
-        }
-    }
 }