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: https://sites.google.com/site/cmzmasek/home/software/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, false, START_OF_COMMENT_LINE_DEFAULT, false )
46 public static BasicTable<String> parse( final Object source,
47 final String column_delimiter,
48 final boolean use_first_separator_only,
49 final boolean use_last_separator_only ) throws IOException {
50 return BasicTableParser.parse( source,
52 use_first_separator_only,
53 use_last_separator_only,
54 START_OF_COMMENT_LINE_DEFAULT,
58 public static List<BasicTable<String>> parse( final Object source,
59 final String column_delimiter,
60 final boolean use_first_separator_only,
61 final boolean use_last_separator_only,
62 final String start_of_comment_line,
63 final boolean tables_separated_by_single_string_line )
65 if ( use_first_separator_only && use_last_separator_only ) {
66 throw new IllegalArgumentException();
68 final BufferedReader reader = ForesterUtil.obtainReader( source );
69 final List<BasicTable<String>> tables = new ArrayList<BasicTable<String>>();
70 BasicTable<String> table = new BasicTable<String>();
73 boolean saw_first_table = false;
74 final boolean use_start_of_comment_line = !( ForesterUtil.isEmpty( start_of_comment_line ) );
75 while ( ( line = reader.readLine() ) != null ) {
77 if ( !ForesterUtil.isEmpty( line )
78 && ( ( ( line.charAt( 0 ) == '"' ) && ( line.charAt( line.length() - 1 ) == '"' ) && ( ForesterUtil
79 .countChars( line, '"' ) == 2 ) ) || ( ( line.charAt( 0 ) == '\'' )
80 && ( line.charAt( line.length() - 1 ) == '\'' ) && ( ForesterUtil.countChars( line, '\'' ) == 2 ) ) ) ) {
81 line = line.substring( 1, line.length() - 1 ).trim();
84 && ( ForesterUtil.isEmpty( line ) || ( tables_separated_by_single_string_line && ( line
85 .indexOf( column_delimiter ) < 0 ) ) ) ) {
86 if ( !table.isEmpty() ) {
89 table = new BasicTable<String>();
92 else if ( !ForesterUtil.isEmpty( line )
93 && ( !use_start_of_comment_line || !line.startsWith( start_of_comment_line ) ) ) {
94 saw_first_table = true;
95 if ( use_last_separator_only ) {
96 final String e[] = line.split( column_delimiter );
97 final StringBuffer rest = new StringBuffer();
98 for( int i = 0; i < ( e.length - 1 ); ++i ) {
99 rest.append( e[ i ].trim() );
101 table.setValue( 0, row, rest.toString() );
102 table.setValue( 1, row, e[ e.length - 1 ] );
105 final StringTokenizer st = new StringTokenizer( line, column_delimiter );
107 if ( st.hasMoreTokens() ) {
108 table.setValue( col++, row, st.nextToken().trim() );
110 if ( use_first_separator_only ) {
111 final StringBuffer rest = new StringBuffer();
112 while ( st.hasMoreTokens() ) {
113 rest.append( st.nextToken() );
115 table.setValue( col++, row, rest.toString() );
118 while ( st.hasMoreTokens() ) {
119 table.setValue( col++, row, st.nextToken().trim() );
126 if ( !table.isEmpty() ) {