in progress...

diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisDemo.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisDemo.java
new file mode 100644 (file)
index 0000000..60e2dfb
--- /dev/null
+++ b/forester/java/src/org/forester/clade_analysis/CladeAnalysisDemo.java
@@ -0,0 +1,271 @@
+
+package org.forester.clade_analysis;
+
+import java.io.File;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.ForesterUtil;
+
+public class CladeAnalysisDemo {
+
+    private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
+            + "test_data" + ForesterUtil.getFileSeparator();
+
+    public static void main( final String[] args ) {
+        boolean failed = false;
+       
+        if ( !testCladeAnalysis1() ) {
+            System.out.println( "Demo 1 failed" );
+            failed = true;
+        }
+        if ( !testCladeAnalysis2() ) {
+            System.out.println( "Demo 2 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis3() ) {
+            System.out.println( "Demo 3 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis4() ) {
+            System.out.println( "Demo 4 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis5() ) {
+            System.out.println( "Demo 5 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis6() ) {
+            System.out.println( "Demo 6 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis7() ) {
+            System.out.println( "Demo 7 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis8() ) {
+            System.out.println( "Demo 8 failed" );
+            failed = true;
+        }
+        
+        if ( !testCladeAnalysis9() ) {
+            System.out.println( "Demo 9 failed" );
+            failed = true;
+        }
+     
+       
+        if ( !failed ) {
+            System.out.println( "OK" );
+        }
+        else {
+            System.out.println( "NOT OK" );
+        }
+    }
+
+
+    
+    
+
+    
+
+    private static boolean testCladeAnalysis1() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_1.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 1:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis2() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_2.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 1:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis3() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_3.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 3:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+
+    
+    private static boolean testCladeAnalysis4() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_4.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 4:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis5() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_5.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 5:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis6() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_6.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 6:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis7() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_7.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 7:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis8() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_8.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 8:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+    
+    private static boolean testCladeAnalysis9() {
+        try {
+            final File in = new File( PATH_TO_TEST_DATA + "cladinator_demo_9.xml" );
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( in, true );
+            final Phylogeny p1 = factory.create( in, pp )[ 0 ];
+            ResultMulti res = AnalysisMulti.execute( p1, 0.5 );
+            
+            System.out.println( "DEMO 9:" );
+            System.out.println( "+++++++" );
+            System.out.print( res.toString() );
+            System.out.println( "------------------------- " );
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+
+ 
+}