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 0aef757..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;
@@ -115,30 +115,30 @@ 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( "Query                        : " + query );
             System.out.print( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
-                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeConfidence() ) ) {
-                System.out.println( "\t(" + res.getGreatestCommonCladeConfidence() + ")" );
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
             }
             else {
                 System.out.println();
             }
             System.out.print( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
-                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpConfidence() ) ) {
-                System.out.println( "\t(" + res.getGreatestCommonCladeUpConfidence() + ")" );
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
             }
             else {
                 System.out.println();
             }
             System.out.print( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
-                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownConfidence() ) ) {
-                System.out.println( "\t(" + res.getGreatestCommonCladeDownConfidence() + ")" );
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
             }
             else {
                 System.out.println();