X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2FSymmetricalDistanceMatrixParser.java;h=03f66df33f14b9afa8eb371af50875ef594ba519;hb=2b1c49af616eb01a99a69daf8f703f494b1a5a7e;hp=991329be3ad8761f120c4c5aea4155b38cc00052;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java b/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java
index 991329b..03f66df 100644
--- a/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java
+++ b/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java
@@ -98,7 +98,12 @@ public class SymmetricalDistanceMatrixParser {
 
     public DistanceMatrix[] parse( final Object source ) throws IOException {
         reset();
-        final List<BasicTable<String>> tables = BasicTableParser.parse( source, VALUE_SEPARATOR, false, COMMENT, true );
+        final List<BasicTable<String>> tables = BasicTableParser.parse( source,
+                                                                        VALUE_SEPARATOR,
+                                                                        false,
+                                                                        false,
+                                                                        COMMENT,
+                                                                        true );
         final DistanceMatrix[] distance_matrices = new DistanceMatrix[ tables.size() ];
         int i = 0;
         for( final BasicTable<String> table : tables ) {
@@ -137,7 +142,7 @@ public class SymmetricalDistanceMatrixParser {
             throw new IOException( "illegal format for distance [" + table_value + "] at [" + ( col - 1 ) + ", " + row
                     + "]" );
         }
-        distance_matrix.setValue( col - 1 + col_offset, row, d );
+        distance_matrix.setValue( ( col - 1 ) + col_offset, row, d );
     }
 
     private DistanceMatrix transform( final BasicTable<String> table ) throws IllegalArgumentException, IOException {
@@ -149,7 +154,7 @@ public class SymmetricalDistanceMatrixParser {
         if ( table.getNumberOfColumns() == table.getNumberOfRows() ) {
             first_line_is_size = true;
         }
-        else if ( table.getNumberOfColumns() != table.getNumberOfRows() + 1 ) {
+        else if ( table.getNumberOfColumns() != ( table.getNumberOfRows() + 1 ) ) {
             throw new IllegalArgumentException( "attempt to create distance matrix with illegal dimensions [columns: "
                     + table.getNumberOfColumns() + ", rows: " + table.getNumberOfRows() + "]" );
         }
@@ -158,7 +163,7 @@ public class SymmetricalDistanceMatrixParser {
         if ( first_line_is_size ) {
             start_row = 1;
         }
-        for( int row = 0; row < table.getNumberOfRows() - start_row; row++ ) {
+        for( int row = 0; row < ( table.getNumberOfRows() - start_row ); row++ ) {
             distance_matrix.setIdentifier( row, table.getValue( 0, row + start_row ) );
             switch ( getInputMatrixType() ) {
                 case LOWER_TRIANGLE: