2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.util;
28 import java.io.BufferedReader;
29 import java.io.IOException;
30 import java.util.ArrayList;
31 import java.util.List;
32 import java.util.StringTokenizer;
34 public class BasicTableParser {
36 private final static String START_OF_COMMENT_LINE_DEFAULT = "#";
38 private BasicTableParser() {
41 public static BasicTable<String> parse( final Object source, final String column_delimiter ) throws IOException {
42 return BasicTableParser.parse( source, column_delimiter, false, START_OF_COMMENT_LINE_DEFAULT, false ).get( 0 );
45 public static BasicTable<String> parse( final Object source,
46 final String column_delimiter,
47 final boolean use_first_separator_only ) throws IOException {
48 return BasicTableParser.parse( source,
50 use_first_separator_only,
51 START_OF_COMMENT_LINE_DEFAULT,
55 public static List<BasicTable<String>> parse( final Object source,
56 final String column_delimiter,
57 final boolean use_first_separator_only,
58 final String start_of_comment_line,
59 final boolean tables_separated_by_single_string_line )
61 final BufferedReader reader = ForesterUtil.obtainReader( source );
62 final List<BasicTable<String>> tables = new ArrayList<BasicTable<String>>();
63 BasicTable<String> table = new BasicTable<String>();
66 boolean saw_first_table = false;
67 final boolean use_start_of_comment_line = !( ForesterUtil.isEmpty( start_of_comment_line ) );
68 while ( ( line = reader.readLine() ) != null ) {
70 if ( !ForesterUtil.isEmpty( line) &&
73 (( line.charAt( 0 ) == '"' && line.charAt( line.length() -1 ) == '"' && ForesterUtil.countChars( line, '"' ) == 2 )
78 ( line.charAt( 0 ) == '\'' && line.charAt( line.length() -1 ) == '\'' && ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) {
79 line = line.substring( 1, line.length() -1 ).trim();
83 && ( ForesterUtil.isEmpty( line ) || ( tables_separated_by_single_string_line && ( line
84 .indexOf( column_delimiter ) < 0 ) ) ) ) {
85 if ( !table.isEmpty() ) {
88 table = new BasicTable<String>();
91 else if ( !ForesterUtil.isEmpty( line )
92 && ( !use_start_of_comment_line || !line.startsWith( start_of_comment_line ) ) ) {
93 saw_first_table = true;
94 final StringTokenizer st = new StringTokenizer( line, column_delimiter );
96 if ( st.hasMoreTokens() ) {
97 table.setValue( col++, row, st.nextToken().trim() );
99 if ( !use_first_separator_only ) {
100 while ( st.hasMoreTokens() ) {
101 table.setValue( col++, row, st.nextToken().trim() );
105 final StringBuffer rest = new StringBuffer();
106 while ( st.hasMoreTokens() ) {
107 rest.append( st.nextToken() );
109 table.setValue( col++, row, rest.toString().trim() );
114 if ( !table.isEmpty() ) {