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