in progress...

[jalview.git] / forester / java / src / org / forester / util / BasicTableParser.java

diff --git a/forester/java/src/org/forester/util/BasicTableParser.java b/forester/java/src/org/forester/util/BasicTableParser.java
index 59e5cd2..8d7f887 100644 (file)
--- 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;
 
@@ -38,26 +38,33 @@ public class BasicTableParser {
     private BasicTableParser() {
     }
 
-    public static BasicTable<String> parse( final Object source, final String column_delimiter ) throws IOException {
-        return BasicTableParser.parse( source, column_delimiter, false, START_OF_COMMENT_LINE_DEFAULT, false ).get( 0 );
+    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 boolean use_first_separator_only ) throws IOException {
+                                            final char column_delimiter,
+                                            final boolean use_first_separator_only,
+                                            final boolean use_last_separator_only ) throws IOException {
         return BasicTableParser.parse( source,
                                        column_delimiter,
                                        use_first_separator_only,
+                                       use_last_separator_only,
                                        START_OF_COMMENT_LINE_DEFAULT,
                                        false ).get( 0 );
     }
 
     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 {
+                                                          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>();
@@ -67,18 +74,12 @@ public class BasicTableParser {
         final boolean use_start_of_comment_line = !( ForesterUtil.isEmpty( start_of_comment_line ) );
         while ( ( line = reader.readLine() ) != null ) {
             line = line.trim();
-            if ( !ForesterUtil.isEmpty( line) && 
-                    
-                    
-                     (( line.charAt( 0 ) == '"' && line.charAt( line.length() -1 ) == '"' && ForesterUtil.countChars( line, '"' ) == 2 ) 
-                             
-                             ||
-                             
-                             
-                      ( line.charAt( 0 ) == '\'' && line.charAt( line.length() -1 ) == '\'' && ForesterUtil.countChars( line, '\'' ) == 2  ) ) ) {
-                line = line.substring( 1, line.length() -1  ).trim();
+            if ( !ForesterUtil.isEmpty( line )
+                    && ( ( ( line.charAt( 0 ) == '"' ) && ( line.charAt( line.length() - 1 ) == '"' ) && ( ForesterUtil
+                            .countChars( line, '"' ) == 2 ) ) || ( ( line.charAt( 0 ) == '\'' )
+                                    && ( line.charAt( line.length() - 1 ) == '\'' ) && ( ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) ) {
+                line = line.substring( 1, line.length() - 1 ).trim();
             }
-            
             if ( saw_first_table
                     && ( ForesterUtil.isEmpty( line ) || ( tables_separated_by_single_string_line && ( line
                             .indexOf( column_delimiter ) < 0 ) ) ) ) {
@@ -91,22 +92,33 @@ public class BasicTableParser {
             else if ( !ForesterUtil.isEmpty( line )
                     && ( !use_start_of_comment_line || !line.startsWith( start_of_comment_line ) ) ) {
                 saw_first_table = true;
-                final StringTokenizer st = new StringTokenizer( line, column_delimiter );
-                int col = 0;
-                if ( st.hasMoreTokens() ) {
-                    table.setValue( col++, row, st.nextToken().trim() );
-                }
-                if ( !use_first_separator_only ) {
-                    while ( st.hasMoreTokens() ) {
-                        table.setValue( col++, row, st.nextToken().trim() );
+                if ( use_last_separator_only ) {
+                    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() );
                     }
+                    table.setValue( 0, row, rest.toString() );
+                    table.setValue( 1, row, e[ e.length - 1 ] );
                 }
                 else {
-                    final StringBuffer rest = new StringBuffer();
-                    while ( st.hasMoreTokens() ) {
-                        rest.append( st.nextToken() );
+                    final StringTokenizer st = new StringTokenizer( line, column_delimiter + "" );
+                    int col = 0;
+                    if ( st.hasMoreTokens() ) {
+                        table.setValue( col++, row, st.nextToken().trim() );
+                    }
+                    if ( use_first_separator_only ) {
+                        final StringBuffer rest = new StringBuffer();
+                        while ( st.hasMoreTokens() ) {
+                            rest.append( st.nextToken() );
+                        }
+                        table.setValue( col++, row, rest.toString() );
+                    }
+                    else {
+                        while ( st.hasMoreTokens() ) {
+                            table.setValue( col++, row, st.nextToken().trim() );
+                        }
                     }
-                    table.setValue( col++, row, rest.toString().trim() );
                 }
                 ++row;
             }