in progress...

[jalview.git] / forester / java / src / org / forester / application / cladinator.java

diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java
index 5a31966..daf0224 100644 (file)
--- a/forester/java/src/org/forester/application/cladinator.java
+++ b/forester/java/src/org/forester/application/cladinator.java
@@ -31,8 +31,8 @@ import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.forester.clade_analysis.Analysis;
-import org.forester.clade_analysis.Result;
+import org.forester.clade_analysis.AnalysisSingle;
+import org.forester.clade_analysis.ResultSingle;
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
@@ -115,23 +115,34 @@ public final class cladinator {
                 System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
                 System.exit( -1 );
             }
-            final Result res = Analysis.execute( p, query, separator );
+            final ResultSingle res = AnalysisSingle.execute( p, query, separator );
             System.out.println();
             System.out.println( "Result:" );
-            System.out.println( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
-            System.out.println( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
-            System.out.println( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
-            
-            if ( !ForesterUtil.isEmpty( res.getGreatestCommonCladeConfidence() ) ) {
-                System.out.println( "Greatest Common Clade Conf   : " + res.getGreatestCommonCladeConfidence() );
+            System.out.println( "Query                        : " + query );
+            System.out.print( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
+            if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
             }
-            if ( !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpConfidence() ) ) {
-                System.out.println( "Greatest Common Clade Up Conf: " + res.getGreatestCommonCladeUpConfidence() );
+            else {
+                System.out.println();
+            }
+            System.out.print( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
+            if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
             }
-            if ( !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownConfidence() ) ) {
-                System.out.println( "Greatest Common Clade Down Conf: " + res.getGreatestCommonCladeDownConfidence() );
+            else {
+                System.out.println();
+            }
+            System.out.print( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
+            if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
+            }
+            else {
+                System.out.println();
             }
-            
             System.out.println( "Least Encompassing Clade size: " + res.getLeastEncompassingCladeSize()
                     + " external nodes" );
             final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize();