From 670062d012a2654b8874ee1ea865f4869dc705f1 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 19 Feb 2013 23:34:43 +0000 Subject: [PATCH] inprogress --- .../java/src/org/forester/application/gsdi.java | 5 ---- .../archaeopteryx/MainFrameApplication.java | 24 +++++++++++++------- 2 files changed, 16 insertions(+), 13 deletions(-) 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 ); } -- 1.7.10.2