forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   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.
  13 //
  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.
  18 //
  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
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.phylogeny.data;
  27
  28 import java.awt.Graphics;
  29 import java.io.IOException;
  30 import java.io.Writer;
  31 import java.util.ArrayList;
  32
  33 import org.forester.io.writers.PhylogenyWriter;
  34 import org.forester.util.ForesterUtil;
  35
  36 public final class PhylogenyDataUtil {
  37
  38     /** Value of -99.0 is used as default value. */
  39     public final static double BRANCH_LENGTH_DEFAULT = -1024.0;
  40
  41     public static void appendClose( final Writer w, final String element_name ) throws IOException {
  42         w.write( "</" );
  43         w.write( element_name );
  44         w.write( ">" );
  45     }
  46
  47     public static void appendElement( final Writer w, final String element_name, final String value )
  48             throws IOException {
  49         appendOpen( w, element_name );
  50         w.write( replaceIllegalXmlCharacters( value ) );
  51         appendClose( w, element_name );
  52     }
  53
  54     public static void appendElement( final Writer w,
  55                                       final String element_name,
  56                                       final String value,
  57                                       final String indentation ) throws IOException {
  58         w.write( ForesterUtil.LINE_SEPARATOR );
  59         w.write( indentation );
  60         w.write( PhylogenyWriter.PHYLO_XML_INTENDATION_BASE );
  61         // Something like this replacement needs to be done in a more systematic manner.
  62         appendElement( w, element_name, value );
  63     }
  64
  65     public static void appendElement( final Writer w,
  66                                       final String element_name,
  67                                       final String value,
  68                                       final String attribute_name,
  69                                       final String attribute_value ) throws IOException {
  70         appendOpen( w, element_name, attribute_name, attribute_value );
  71         w.write( replaceIllegalXmlCharacters( value ) );
  72         appendClose( w, element_name );
  73     }
  74
  75     public static void appendElement( final Writer w,
  76                                       final String element_name,
  77                                       final String value,
  78                                       final String attribute_name,
  79                                       final String attribute_value,
  80                                       final String indentation ) throws IOException {
  81         w.write( ForesterUtil.LINE_SEPARATOR );
  82         w.write( indentation );
  83         w.write( PhylogenyWriter.PHYLO_XML_INTENDATION_BASE );
  84         appendOpen( w, element_name, attribute_name, attribute_value );
  85         w.write( replaceIllegalXmlCharacters( value ) );
  86         appendClose( w, element_name );
  87     }
  88
  89     public static void appendElement( final Writer w,
  90                                       final String element_name,
  91                                       final String value,
  92                                       final String attribute1_name,
  93                                       final String attribute1_value,
  94                                       final String attribute2_name,
  95                                       final String attribute2_value,
  96                                       final String indentation ) throws IOException {
  97         w.write( ForesterUtil.LINE_SEPARATOR );
  98         w.write( indentation );
  99         w.write( PhylogenyWriter.PHYLO_XML_INTENDATION_BASE );
 100         appendOpen( w, element_name, attribute1_name, attribute1_value, attribute2_name, attribute2_value );
 101         w.write( replaceIllegalXmlCharacters( value ) );
 102         appendClose( w, element_name );
 103     }
 104
 105     public static void appendElement( final Writer w,
 106                                       final String element_name,
 107                                       final String value,
 108                                       final String attribute1_name,
 109                                       final String attribute1_value,
 110                                       final String attribute2_name,
 111                                       final String attribute2_value ) throws IOException {
 112         appendOpen( w, element_name, attribute1_name, attribute1_value, attribute2_name, attribute2_value );
 113         w.write( replaceIllegalXmlCharacters( value ) );
 114         appendClose( w, element_name );
 115     }
 116
 117     public static void appendElement( final Writer w,
 118                                       final String element_name,
 119                                       final String attribute1_name,
 120                                       final String attribute1_value,
 121                                       final String attribute2_name,
 122                                       final String attribute2_value,
 123                                       final String attribute3_name,
 124                                       final String attribute3_value,
 125                                       final String attribute4_name,
 126                                       final String attribute4_value,
 127                                       final String indentation ) throws IOException {
 128         w.write( ForesterUtil.LINE_SEPARATOR );
 129         w.write( indentation );
 130         appendOpen( w,
 131                     element_name,
 132                     attribute1_name,
 133                     attribute1_value,
 134                     attribute2_name,
 135                     attribute2_value,
 136                     attribute3_name,
 137                     attribute3_value,
 138                     attribute4_name,
 139                     attribute4_value );
 140         appendClose( w, element_name );
 141     }
 142
 143     public static void appendElement( final Writer w,
 144                                       final String element_name,
 145                                       final String value,
 146                                       final String attribute1_name,
 147                                       final String attribute1_value,
 148                                       final String attribute2_name,
 149                                       final String attribute2_value,
 150                                       final String attribute3_name,
 151                                       final String attribute3_value,
 152                                       final String attribute4_name,
 153                                       final String attribute4_value,
 154                                       final String attribute5_name,
 155                                       final String attribute5_value,
 156                                       final String indentation ) throws IOException {
 157         w.write( ForesterUtil.LINE_SEPARATOR );
 158         w.write( indentation );
 159         w.write( PhylogenyWriter.PHYLO_XML_INTENDATION_BASE );
 160         appendOpen( w,
 161                     element_name,
 162                     attribute1_name,
 163                     attribute1_value,
 164                     attribute2_name,
 165                     attribute2_value,
 166                     attribute3_name,
 167                     attribute3_value,
 168                     attribute4_name,
 169                     attribute4_value,
 170                     attribute5_name,
 171                     attribute5_value );
 172         w.write( replaceIllegalXmlCharacters( value ) );
 173         appendClose( w, element_name );
 174     }
 175
 176     public static void appendOpen( final Writer w, final String element_name ) throws IOException {
 177         w.write( "<" );
 178         w.write( element_name );
 179         w.write( ">" );
 180     }
 181
 182     public static void appendOpen( final Writer w,
 183                                    final String element_name,
 184                                    final String attribute_name,
 185                                    final String attribute_value ) throws IOException {
 186         w.write( "<" );
 187         w.write( element_name );
 188         if ( !ForesterUtil.isEmpty( attribute_value ) ) {
 189             w.write( " " );
 190             w.write( attribute_name );
 191             w.write( "=\"" );
 192             w.write( attribute_value );
 193             w.write( "\"" );
 194         }
 195         w.write( ">" );
 196     }
 197
 198     public static void appendOpen( final Writer w,
 199                                    final String element_name,
 200                                    final String attribute1_name,
 201                                    final String attribute1_value,
 202                                    final String attribute2_name,
 203                                    final String attribute2_value ) throws IOException {
 204         w.write( "<" );
 205         w.write( element_name );
 206         if ( !ForesterUtil.isEmpty( attribute1_value ) ) {
 207             w.write( " " );
 208             w.write( attribute1_name );
 209             w.write( "=\"" );
 210             w.write( attribute1_value );
 211             w.write( "\"" );
 212         }
 213         if ( !ForesterUtil.isEmpty( attribute2_value ) ) {
 214             w.write( " " );
 215             w.write( attribute2_name );
 216             w.write( "=\"" );
 217             w.write( attribute2_value );
 218             w.write( "\"" );
 219         }
 220         w.write( ">" );
 221     }
 222
 223     public static void appendOpen( final Writer w,
 224                                    final String element_name,
 225                                    final String attribute1_name,
 226                                    final String attribute1_value,
 227                                    final String attribute2_name,
 228                                    final String attribute2_value,
 229                                    final String attribute3_name,
 230                                    final String attribute3_value ) throws IOException {
 231         w.write( "<" );
 232         w.write( element_name );
 233         if ( !ForesterUtil.isEmpty( attribute1_value ) ) {
 234             w.write( " " );
 235             w.write( attribute1_name );
 236             w.write( "=\"" );
 237             w.write( attribute1_value );
 238             w.write( "\"" );
 239         }
 240         if ( !ForesterUtil.isEmpty( attribute2_value ) ) {
 241             w.write( " " );
 242             w.write( attribute2_name );
 243             w.write( "=\"" );
 244             w.write( attribute2_value );
 245             w.write( "\"" );
 246         }
 247         if ( !ForesterUtil.isEmpty( attribute2_value ) ) {
 248             w.write( " " );
 249             w.write( attribute3_name );
 250             w.write( "=\"" );
 251             w.write( attribute3_value );
 252             w.write( "\"" );
 253         }
 254         w.write( ">" );
 255     }
 256
 257     public static void appendOpen( final Writer w,
 258                                    final String element_name,
 259                                    final String attribute1_name,
 260                                    final String attribute1_value,
 261                                    final String attribute2_name,
 262                                    final String attribute2_value,
 263                                    final String attribute3_name,
 264                                    final String attribute3_value,
 265                                    final String attribute4_name,
 266                                    final String attribute4_value ) throws IOException {
 267         w.write( "<" );
 268         w.write( element_name );
 269         if ( !ForesterUtil.isEmpty( attribute1_value ) ) {
 270             w.write( " " );
 271             w.write( attribute1_name );
 272             w.write( "=\"" );
 273             w.write( attribute1_value );
 274             w.write( "\"" );
 275         }
 276         if ( !ForesterUtil.isEmpty( attribute2_value ) ) {
 277             w.write( " " );
 278             w.write( attribute2_name );
 279             w.write( "=\"" );
 280             w.write( attribute2_value );
 281             w.write( "\"" );
 282         }
 283         if ( !ForesterUtil.isEmpty( attribute3_value ) ) {
 284             w.write( " " );
 285             w.write( attribute3_name );
 286             w.write( "=\"" );
 287             w.write( attribute3_value );
 288             w.write( "\"" );
 289         }
 290         if ( !ForesterUtil.isEmpty( attribute4_value ) ) {
 291             w.write( " " );
 292             w.write( attribute4_name );
 293             w.write( "=\"" );
 294             w.write( attribute4_value );
 295             w.write( "\"" );
 296         }
 297         w.write( ">" );
 298     }
 299
 300     public static void appendOpen( final Writer w,
 301                                    final String element_name,
 302                                    final String attribute1_name,
 303                                    final String attribute1_value,
 304                                    final String attribute2_name,
 305                                    final String attribute2_value,
 306                                    final String attribute3_name,
 307                                    final String attribute3_value,
 308                                    final String attribute4_name,
 309                                    final String attribute4_value,
 310                                    final String attribute5_name,
 311                                    final String attribute5_value ) throws IOException {
 312         w.write( "<" );
 313         w.write( element_name );
 314         if ( !ForesterUtil.isEmpty( attribute1_value ) ) {
 315             w.write( " " );
 316             w.write( attribute1_name );
 317             w.write( "=\"" );
 318             w.write( attribute1_value );
 319             w.write( "\"" );
 320         }
 321         if ( !ForesterUtil.isEmpty( attribute2_value ) ) {
 322             w.write( " " );
 323             w.write( attribute2_name );
 324             w.write( "=\"" );
 325             w.write( attribute2_value );
 326             w.write( "\"" );
 327         }
 328         if ( !ForesterUtil.isEmpty( attribute3_value ) ) {
 329             w.write( " " );
 330             w.write( attribute3_name );
 331             w.write( "=\"" );
 332             w.write( attribute3_value );
 333             w.write( "\"" );
 334         }
 335         if ( !ForesterUtil.isEmpty( attribute4_value ) ) {
 336             w.write( " " );
 337             w.write( attribute4_name );
 338             w.write( "=\"" );
 339             w.write( attribute4_value );
 340             w.write( "\"" );
 341         }
 342         if ( !ForesterUtil.isEmpty( attribute5_value ) ) {
 343             w.write( " " );
 344             w.write( attribute5_name );
 345             w.write( "=\"" );
 346             w.write( attribute5_value );
 347             w.write( "\"" );
 348         }
 349         w.write( ">" );
 350     }
 351
 352     /**
 353      * Creates a deep copy of ArrayList of PhylogenyData objects.
 354      *
 355      * @param list
 356      *            an ArrayList of PhylogenyData objects
 357      * @return a deep copy of ArrayList list
 358      */
 359     public static ArrayList<PhylogenyData> copy( final ArrayList<PhylogenyData> list ) {
 360         final ArrayList<PhylogenyData> l = new ArrayList<PhylogenyData>( list.size() );
 361         for( int i = 0; i < list.size(); ++i ) {
 362             l.add( ( list.get( i ) ).copy() );
 363         }
 364         return l;
 365     }
 366
 367     public static void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics g ) {
 368         g.drawLine( org.forester.util.ForesterUtil.roundToInt( x1 ),
 369                     org.forester.util.ForesterUtil.roundToInt( y1 ),
 370                     org.forester.util.ForesterUtil.roundToInt( x2 ),
 371                     org.forester.util.ForesterUtil.roundToInt( y2 ) );
 372     }
 373
 374     public static String replaceIllegalXmlCharacters( final String value ) {
 375         String v = value.replaceAll( "&", "&amp;" );
 376         v = v.replaceAll( "<", "&lt;" );
 377         v = v.replaceAll( ">", "&gt;" );
 378         v = v.replaceAll( "'", "&apos;" );
 379         v = v.replaceAll( "\"", "&quot;" );
 380         return v;
 381     }
 382 }