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
26 package org.forester.util;
28 import java.io.IOException;
29 import java.util.HashMap;
32 public class BasicTable<E> {
36 private Map<String, Map<String, E>> _rows;
42 // Returns -1 if not found, IllegalArgumentException if not unique.
43 public int findRow( final String first_col_value ) throws IllegalArgumentException {
45 for( int i = 0; i < this.getNumberOfRows(); ++i ) {
46 if ( getValueAsString( 0, i ).equals( first_col_value ) ) {
48 throw new IllegalArgumentException( "\"" + first_col_value + "\" is not unique" );
56 public Map<String, E> getColumnsAsMap( final int key_col, final int value_col ) throws IllegalArgumentException {
57 final Map<String, E> map = new HashMap<String, E>();
58 for( int row = 0; row < getNumberOfRows(); ++row ) {
59 final String key = ( String ) getValue( key_col, row );
60 final E value = getValue( value_col, row );
61 if ( ( key != null ) && ( value != null ) ) {
62 if ( map.containsKey( key ) ) {
63 throw new IllegalArgumentException( "attempt to use non-unique table value as key [" + key + "]" );
65 map.put( key, value );
71 public Map<String, Double> getColumnsAsMapDouble( final int key_col, final int value_col )
72 throws IllegalArgumentException, IOException {
73 final Map<String, Double> map = new HashMap<String, Double>();
74 for( int row = 0; row < getNumberOfRows(); ++row ) {
75 final String key = ( String ) getValue( key_col, row );
78 value = Double.parseDouble( getValueAsString( value_col, row ) );
80 catch ( final NumberFormatException e ) {
81 throw new IOException( e );
84 if ( map.containsKey( key ) ) {
85 throw new IllegalArgumentException( "attempt to use non-unique table value as key [" + key + "]" );
87 map.put( key, value );
93 public int getNumberOfColumns() {
97 public int getNumberOfRows() {
101 public final String getRowAsString( final int row, final String separator ) {
102 final StringBuilder sb = new StringBuilder();
103 for( int col = 0; col < getNumberOfColumns(); ++col ) {
104 sb.append( getValue( col, row ).toString() );
105 if ( col < ( getNumberOfColumns() - 1 ) ) {
106 sb.append( separator );
109 return sb.toString();
112 public E getValue( final int col, final int row ) throws IllegalArgumentException {
113 if ( ( row > ( getNumberOfRows() - 1 ) ) || ( row < 0 ) ) {
114 throw new IllegalArgumentException( "value for row (" + row + ") is out of range [number of rows: "
115 + getNumberOfRows() + "]" );
117 else if ( ( col >= getNumberOfColumns() ) || ( row < 0 ) ) {
118 throw new IllegalArgumentException( "value for column (" + col + ") is out of range [number of columns: "
119 + getNumberOfColumns() + "]" );
121 final Map<String, E> row_map = getRow( row );
122 if ( ( row_map == null ) || ( row_map.size() < 1 ) ) {
125 return row_map.get( "" + col );
128 public String getValueAsString( final int col, final int row ) throws IllegalArgumentException {
129 if ( getValue( col, row ) != null ) {
130 return getValue( col, row ).toString();
135 public boolean isEmpty() {
136 return getNumberOfRows() <= 0;
139 public void setValue( final int col, final int row, final E value ) {
140 if ( ( row < 0 ) || ( col < 0 ) ) {
141 throw new IllegalArgumentException( "attempt to use negative values for row or column" );
143 if ( row > ( getNumberOfRows() - 1 ) ) {
146 if ( col > ( getNumberOfColumns() - 1 ) ) {
149 final String row_key = "" + row;
150 Map<String, E> row_map = null;
151 if ( getRows().containsKey( row_key ) ) {
152 row_map = getRows().get( row_key );
155 row_map = new HashMap<String, E>();
156 getRows().put( row_key, row_map );
158 row_map.put( "" + col, value );
162 public String toString() {
163 final StringBuilder sb = new StringBuilder();
164 for( int row = 0; row < getNumberOfRows(); ++row ) {
165 for( int col = 0; col < getNumberOfColumns(); ++col ) {
166 sb.append( getValue( col, row ) );
167 if ( col < ( getNumberOfColumns() - 1 ) ) {
171 if ( row < ( getNumberOfRows() - 1 ) ) {
172 sb.append( ForesterUtil.LINE_SEPARATOR );
175 return sb.toString();
178 private Map<String, E> getRow( final int row ) {
179 return getRows().get( "" + row );
182 private Map<String, Map<String, E>> getRows() {
186 private void init() {
187 _rows = new HashMap<String, Map<String, E>>();
192 private void setMaxCol( final int max_col ) {
196 private void setMaxRow( final int max_row ) {