forester/java/src/org/forester/clade_analysis/CladeAnalysisDemo.java

   1
   2 package org.forester.clade_analysis;
   3
   4 import java.io.File;
   5
   6 import org.forester.io.parsers.PhylogenyParser;
   7 import org.forester.io.parsers.util.ParserUtils;
   8 import org.forester.phylogeny.Phylogeny;
   9 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  10 import org.forester.phylogeny.factories.PhylogenyFactory;
  11 import org.forester.util.ForesterUtil;
  12
  13 public class CladeAnalysisDemo {
  14
  15     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
  16             + "test_data" + ForesterUtil.getFileSeparator();
  17
  18     public static void main( final String[] args ) {
  19         boolean failed = false;
  20
  21         if ( !testCladeAnalysis1() ) {
  22             System.out.println( "Demo 1 failed" );
  23             failed = true;
  24         }
  25         if ( !testCladeAnalysis2() ) {
  26             System.out.println( "Demo 2 failed" );
  27             failed = true;
  28         }
  29
  30         if ( !testCladeAnalysis3() ) {
  31             System.out.println( "Demo 3 failed" );
  32             failed = true;
  33         }
  34
  35         if ( !testCladeAnalysis4() ) {
  36             System.out.println( "Demo 4 failed" );
  37             failed = true;
  38         }
  39
  40         if ( !testCladeAnalysis5() ) {
  41             System.out.println( "Demo 5 failed" );
  42             failed = true;
  43         }
  44
  45         if ( !testCladeAnalysis6() ) {
  46             System.out.println( "Demo 6 failed" );
  47             failed = true;
  48         }
  49
  50         if ( !testCladeAnalysis7() ) {
  51             System.out.println( "Demo 7 failed" );
  52             failed = true;
  53         }
  54
  55         if ( !testCladeAnalysis8() ) {
  56             System.out.println( "Demo 8 failed" );
  57             failed = true;
  58         }
  59
  60         if ( !testCladeAnalysis9() ) {
  61             System.out.println( "Demo 9 failed" );
  62             failed = true;
  63         }
  64
  65
  66         if ( !failed ) {
  67             System.out.println( "OK" );
  68         }
  69         else {
  70             System.out.println( "NOT OK" );
  71         }
  72     }
  73
  74
  75
  76
  77
  78
  79
  80     private static boolean testCladeAnalysis1() {
  81         try {
  82             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_1.xml" );
  83             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  84             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
  85             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
  86             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
  87
  88             System.out.println( "DEMO 1:" );
  89             System.out.println( "+++++++" );
  90             System.out.print( res.toString() );
  91             System.out.println( "------------------------- " );
  92             System.out.println();
  93         }
  94         catch ( final Exception e ) {
  95             e.printStackTrace( System.out );
  96             return false;
  97         }
  98         return true;
  99     }
 100
 101     private static boolean testCladeAnalysis2() {
 102         try {
 103             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_2.xml" );
 104             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 105             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 106             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 107             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 108
 109             System.out.println( "DEMO 1:" );
 110             System.out.println( "+++++++" );
 111             System.out.print( res.toString() );
 112             System.out.println( "------------------------- " );
 113             System.out.println();
 114         }
 115         catch ( final Exception e ) {
 116             e.printStackTrace( System.out );
 117             return false;
 118         }
 119         return true;
 120     }
 121
 122     private static boolean testCladeAnalysis3() {
 123         try {
 124             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_3.xml" );
 125             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 126             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 127             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 128             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 129
 130             System.out.println( "DEMO 3:" );
 131             System.out.println( "+++++++" );
 132             System.out.print( res.toString() );
 133             System.out.println( "------------------------- " );
 134             System.out.println();
 135         }
 136         catch ( final Exception e ) {
 137             e.printStackTrace( System.out );
 138             return false;
 139         }
 140         return true;
 141     }
 142
 143
 144     private static boolean testCladeAnalysis4() {
 145         try {
 146             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_4.xml" );
 147             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 148             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 149             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 150             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 151
 152             System.out.println( "DEMO 4:" );
 153             System.out.println( "+++++++" );
 154             System.out.print( res.toString() );
 155             System.out.println( "------------------------- " );
 156             System.out.println();
 157         }
 158         catch ( final Exception e ) {
 159             e.printStackTrace( System.out );
 160             return false;
 161         }
 162         return true;
 163     }
 164
 165     private static boolean testCladeAnalysis5() {
 166         try {
 167             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_5.xml" );
 168             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 169             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 170             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 171             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 172
 173             System.out.println( "DEMO 5:" );
 174             System.out.println( "+++++++" );
 175             System.out.print( res.toString() );
 176             System.out.println( "------------------------- " );
 177             System.out.println();
 178         }
 179         catch ( final Exception e ) {
 180             e.printStackTrace( System.out );
 181             return false;
 182         }
 183         return true;
 184     }
 185
 186     private static boolean testCladeAnalysis6() {
 187         try {
 188             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_6.xml" );
 189             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 190             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 191             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 192             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 193
 194             System.out.println( "DEMO 6:" );
 195             System.out.println( "+++++++" );
 196             System.out.print( res.toString() );
 197             System.out.println( "------------------------- " );
 198             System.out.println();
 199         }
 200         catch ( final Exception e ) {
 201             e.printStackTrace( System.out );
 202             return false;
 203         }
 204         return true;
 205     }
 206
 207     private static boolean testCladeAnalysis7() {
 208         try {
 209             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_7.xml" );
 210             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 211             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 212             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 213             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 214
 215             System.out.println( "DEMO 7:" );
 216             System.out.println( "+++++++" );
 217             System.out.print( res.toString() );
 218             System.out.println( "------------------------- " );
 219             System.out.println();
 220         }
 221         catch ( final Exception e ) {
 222             e.printStackTrace( System.out );
 223             return false;
 224         }
 225         return true;
 226     }
 227
 228     private static boolean testCladeAnalysis8() {
 229         try {
 230             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_8.xml" );
 231             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 232             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 233             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 234             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 235
 236             System.out.println( "DEMO 8:" );
 237             System.out.println( "+++++++" );
 238             System.out.print( res.toString() );
 239             System.out.println( "------------------------- " );
 240             System.out.println();
 241         }
 242         catch ( final Exception e ) {
 243             e.printStackTrace( System.out );
 244             return false;
 245         }
 246         return true;
 247     }
 248
 249     private static boolean testCladeAnalysis9() {
 250         try {
 251             final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_9.xml" );
 252             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 253             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
 254             final Phylogeny p1 = factory.create( in, pp )[ 0 ];
 255             ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
 256
 257             System.out.println( "DEMO 9:" );
 258             System.out.println( "+++++++" );
 259             System.out.print( res.toString() );
 260             System.out.println( "------------------------- " );
 261             System.out.println();
 262         }
 263         catch ( final Exception e ) {
 264             e.printStackTrace( System.out );
 265             return false;
 266         }
 267         return true;
 268     }
 269
 270
 271 }