From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 19 Feb 2013 23:34:43 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=670062d012a2654b8874ee1ea865f4869dc705f1;hp=5b893ccab7622dabfc46de996331cc88b6fe0eff;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index 17dbf7e..d5c30a3 100644
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -280,11 +280,6 @@ public final class gsdi {
                 + "ms" );
         System.out.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
         log_writer.println( "Mapping based on                         : " + gsdii.getTaxCompBase() );
-        if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {
-            final GSDIR gsdir = ( GSDIR ) gsdii;
-            System.out.println( "Duplications sum statistics              : " + gsdir.getMinDuplicationsSum() );
-            log_writer.println( "Duplications sum statistics              : " + gsdir.getMinDuplicationsSum() );
-        }
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
             if ( base_algorithm == ALGORITHM.GSDIR ) {
diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 084bae9..b8e4a1a 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -1196,6 +1196,7 @@ public final class MainFrameApplication extends MainFrame {
         _mainpanel.getTabbedPane().setSelectedIndex( selected );
         showWhole();
         _mainpanel.getCurrentTreePanel().setEdited( true );
+        final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
         if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
             JOptionPane.showMessageDialog( this,
                                            "Duplications: " + gsdi.getDuplicationsSum() + "\n"
@@ -1204,7 +1205,8 @@ public final class MainFrameApplication extends MainFrame {
                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
                                                    + "Stripped gene tree nodes: "
                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n",
+                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",
                                            "GSDI successfully completed",
                                            JOptionPane.WARNING_MESSAGE );
         }
@@ -1216,7 +1218,8 @@ public final class MainFrameApplication extends MainFrame {
                                                    + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
                                                    + "Stripped gene tree nodes: "
                                                    + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n",
+                                                   + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",
                                            "GSDI successfully completed",
                                            JOptionPane.INFORMATION_MESSAGE );
         }
@@ -1267,21 +1270,26 @@ public final class MainFrameApplication extends MainFrame {
         _mainpanel.getTabbedPane().setSelectedIndex( selected );
         showWhole();
         _mainpanel.getCurrentTreePanel().setEdited( true );
+        final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
         if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
             JOptionPane.showMessageDialog( this,
-                                           "Duplications: " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
-                                                   + gsdir.getSpeciationsSum() + "\n" + "Stripped gene tree nodes: "
+                                           "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+                                                   + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+                                                   + "Stripped gene tree nodes: "
                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n",
+                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",
                                            "GSDIR successfully completed",
                                            JOptionPane.WARNING_MESSAGE );
         }
         else {
             JOptionPane.showMessageDialog( this,
-                                           "Duplications: " + gsdir.getMinDuplicationsSum() + "\n" + "Speciations: "
-                                                   + gsdir.getSpeciationsSum() + "\n" + "Stripped gene tree nodes: "
+                                           "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+                                                   + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+                                                   + "Stripped gene tree nodes: "
                                                    + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
-                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n",
+                                                   + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+                                                   + "Number of polytomies in species tree used: " + poly + "\n",
                                            "GSDIR successfully completed",
                                            JOptionPane.INFORMATION_MESSAGE );
         }