X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FBasicTableParser.java;h=4e5f4b35b6d87beb139ca24c053acb53078a43e7;hb=06b38f91bc061d8ab1dfea3b6238c94c95a30d26;hp=bc369bfad1394b88f167ba82e0491da27d666032;hpb=c4cf3c01b3cbb89d98f29418444287ca8703a781;p=jalview.git

diff --git a/forester/java/src/org/forester/util/BasicTableParser.java b/forester/java/src/org/forester/util/BasicTableParser.java
index bc369bf..4e5f4b3 100644
--- a/forester/java/src/org/forester/util/BasicTableParser.java
+++ b/forester/java/src/org/forester/util/BasicTableParser.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.util;
 
@@ -38,13 +38,13 @@ public class BasicTableParser {
     private BasicTableParser() {
     }
 
-    public static BasicTable<String> parse( final Object source, final String column_delimiter ) throws IOException {
+    public static BasicTable<String> parse( final Object source, final char column_delimiter ) throws IOException {
         return BasicTableParser.parse( source, column_delimiter, false, false, START_OF_COMMENT_LINE_DEFAULT, false )
                 .get( 0 );
     }
 
     public static BasicTable<String> parse( final Object source,
-                                            final String column_delimiter,
+                                            final char column_delimiter,
                                             final boolean use_first_separator_only,
                                             final boolean use_last_separator_only ) throws IOException {
         return BasicTableParser.parse( source,
@@ -56,12 +56,15 @@ public class BasicTableParser {
     }
 
     public static List<BasicTable<String>> parse( final Object source,
-                                                  final String column_delimiter,
+                                                  final char column_delimiter,
                                                   final boolean use_first_separator_only,
                                                   final boolean use_last_separator_only,
                                                   final String start_of_comment_line,
                                                   final boolean tables_separated_by_single_string_line )
             throws IOException {
+        if ( use_first_separator_only && use_last_separator_only ) {
+            throw new IllegalArgumentException();
+        }
         final BufferedReader reader = ForesterUtil.obtainReader( source );
         final List<BasicTable<String>> tables = new ArrayList<BasicTable<String>>();
         BasicTable<String> table = new BasicTable<String>();
@@ -90,16 +93,16 @@ public class BasicTableParser {
                     && ( !use_start_of_comment_line || !line.startsWith( start_of_comment_line ) ) ) {
                 saw_first_table = true;
                 if ( use_last_separator_only ) {
-                    String e[] = line.split( column_delimiter );
+                    final String e[] = line.split( column_delimiter + "" );
                     final StringBuffer rest = new StringBuffer();
-                    for( int i = 0; i < e.length - 1; ++i ) {
+                    for( int i = 0; i < ( e.length - 1 ); ++i ) {
                         rest.append( e[ i ].trim() );
                     }
-                    table.setValue( 0, row, e[ e.length - 1 ] );
-                    table.setValue( 1, row, rest.toString() );
+                    table.setValue( 0, row, rest.toString() );
+                    table.setValue( 1, row, e[ e.length - 1 ] );
                 }
                 else {
-                    final StringTokenizer st = new StringTokenizer( line, column_delimiter );
+                    final StringTokenizer st = new StringTokenizer( line, column_delimiter + "" );
                     int col = 0;
                     if ( st.hasMoreTokens() ) {
                         table.setValue( col++, row, st.nextToken().trim() );
@@ -117,8 +120,8 @@ public class BasicTableParser {
                         }
                     }
                 }
+                ++row;
             }
-            ++row;
         }
         if ( !table.isEmpty() ) {
             tables.add( table );