From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 18 Sep 2012 02:21:45 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8bf76b660ffee22c50db603d6771a24138676e63;p=jalview.git

in progress
---

diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java
index 4f77bde..be7c164 100644
--- a/forester/java/src/org/forester/application/decorator.java
+++ b/forester/java/src/org/forester/application/decorator.java
@@ -47,33 +47,32 @@ import org.forester.util.ForesterUtil;
 
 public final class decorator {
 
-    private static final String  SEQUENCE_NAME_FIELD                    = "s";
-    private static final String  TAXONOMY_CODE_FIELD                    = "c";
-    private static final String  TAXONOMY_SCIENTIFIC_NAME_FIELD         = "sn";
-    private static final String  DS_FILED                               = "d";
-    private static final String  SEQUENCE_ANNOTATION_DESC               = "a";
-    private static final String  NODE_NAME_FIELD                        = "n";
-    final static private String  PICKY_OPTION                           = "p";
-    final static private String  FIELD_OPTION                           = "f";
-    final static private String  TRIM_AFTER_TILDE_OPTION                = "t";
-    final static private String  MOVE_DOMAIN_NUMBER_OPTION              = "mdn";       // Hidden expert option.
-    final static private String  TREE_NAME_OPTION                       = "pn";
-    final static private String  TREE_ID_OPTION                         = "pi";
-    final static private String  TREE_DESC_OPTION                       = "pd";
-    final static private String  EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
-    final static private String  PROCESS_NAME_INTELLIGENTLY_OPTION      = "x";
-    final static private String  PROCESS_SIMILAR_TO_OPTION              = "xs";
-    final static private String  CUT_NAME_AFTER_FIRST_SPACE_OPTION      = "c";
-    final static private String  ALLOW_REMOVAL_OF_CHARS_OPTION          = "r";
-    final static private String  ADVANCED_TABLE_OPTION                  = "table";
-    final static private String  KEY_COLUMN                             = "k";
-    final static private String  VALUE_COLUMN                           = "v";
-    final static private String  MAPPING_FILE_SEPARATOR_OPTION          = "s";
-    final static private String  MAPPING_FILE_SEPARATOR_DEFAULT         = ":";
-    final static private boolean USE_FIRST_SEPARATOR_ONLY               = true;
-    final static private String  PRG_NAME                               = "decorator";
-    final static private String  PRG_VERSION                            = "1.11";
-    final static private String  PRG_DATE                               = "2012.09.15";
+    private static final String SEQUENCE_NAME_FIELD                    = "s";
+    private static final String TAXONOMY_CODE_FIELD                    = "c";
+    private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD         = "sn";
+    private static final String DS_FILED                               = "d";
+    private static final String SEQUENCE_ANNOTATION_DESC               = "a";
+    private static final String NODE_NAME_FIELD                        = "n";
+    final static private String PICKY_OPTION                           = "p";
+    final static private String FIELD_OPTION                           = "f";
+    final static private String TRIM_AFTER_TILDE_OPTION                = "t";
+    final static private String MOVE_DOMAIN_NUMBER_OPTION              = "mdn";       // Hidden expert option.
+    final static private String TREE_NAME_OPTION                       = "pn";
+    final static private String TREE_ID_OPTION                         = "pi";
+    final static private String TREE_DESC_OPTION                       = "pd";
+    final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
+    final static private String PROCESS_NAME_INTELLIGENTLY_OPTION      = "x";
+    final static private String PROCESS_SIMILAR_TO_OPTION              = "xs";
+    final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION      = "c";
+    final static private String ALLOW_REMOVAL_OF_CHARS_OPTION          = "r";
+    final static private String ADVANCED_TABLE_OPTION                  = "table";
+    final static private String KEY_COLUMN                             = "k";
+    final static private String VALUE_COLUMN                           = "v";
+    final static private String MAPPING_FILE_SEPARATOR_OPTION          = "s";
+    final static private String MAPPING_FILE_SEPARATOR_DEFAULT         = ":";
+    final static private String PRG_NAME                               = "decorator";
+    final static private String PRG_VERSION                            = "1.11";
+    final static private String PRG_DATE                               = "2012.09.15";
 
     private static void argumentsError() {
         System.out.println();
@@ -320,7 +319,6 @@ public final class decorator {
                 ForesterUtil.fatalError( decorator.PRG_NAME,
                                          "failed to read [" + mapping_infile + "] [" + e.getMessage() + "]" );
             }
-            System.out.println( mapping_table.toString() );
             if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
             }
diff --git a/forester/java/src/org/forester/util/BasicTableParser.java b/forester/java/src/org/forester/util/BasicTableParser.java
index 6592f17..63e7e13 100644
--- a/forester/java/src/org/forester/util/BasicTableParser.java
+++ b/forester/java/src/org/forester/util/BasicTableParser.java
@@ -93,7 +93,7 @@ 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 ) {
                         rest.append( e[ i ].trim() );