From 6612399dae19a3e895a6cec6c61efa0799ec8bc3 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 11 Jan 2012 23:52:53 +0000 Subject: [PATCH] in progress --- forester/java/src/org/forester/archaeopteryx/Constants.java | 4 ++-- .../src/org/forester/archaeopteryx/MainFrameApplication.java | 10 ++++++++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 81eea48..7edf5b0 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -41,8 +41,8 @@ public final class Constants { public final static boolean __SNAPSHOT_RELEASE = false; // TODO remove me public final static boolean __SYNTH_LF = false; // TODO remove me public final static String PRG_NAME = "Archaeopteryx"; - final static String VERSION = "0.968 beta BG"; - final static String PRG_DATE = "2012.01.03"; + final static String VERSION = "0.969 beta BG"; + final static String PRG_DATE = "2012.01.11"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Verdana", "Tahoma", "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index 20c775d..f717323 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -910,10 +910,10 @@ public final class MainFrameApplication extends MainFrame { _tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) ); customizeJMenuItem( _collapse_species_specific_subtrees ); _tools_menu - .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold" ) ); + .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) ); customizeJMenuItem( _collapse_below_threshold ); _collapse_below_threshold - .setToolTipText( "To permanently collapse branches without at least one support value above a given threshold" ); + .setToolTipText( "To collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" ); _tools_menu.addSeparator(); _tools_menu .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) ); @@ -1103,8 +1103,14 @@ public final class MainFrameApplication extends MainFrame { phy.hashIDs(); phy.recalculateNumberOfExternalDescendants( true ); getCurrentTreePanel().resetNodeIdToDistToLeafMap(); + getCurrentTreePanel().updateSetOfCollapsedExternalNodes( phy ); + getCurrentTreePanel().calculateLongestExtNodeInfo(); + getCurrentTreePanel().setNodeInPreorderToNull(); + getCurrentTreePanel().recalculateMaxDistanceToRoot(); + getCurrentTreePanel().resetPreferredSize(); getCurrentTreePanel().setEdited( true ); getCurrentTreePanel().repaint(); + repaint(); } if ( to_be_removed.size() > 0 ) { JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size() -- 1.7.10.2