From d17f81782b4ce0a50c963ccb0394e0d2ae796ad0 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Mon, 1 Apr 2013 06:20:40 +0000 Subject: [PATCH] in progress --- .../org/forester/archaeopteryx/Configuration.java | 14 +--------- .../src/org/forester/archaeopteryx/TreePanel.java | 28 +++++++++++--------- 2 files changed, 17 insertions(+), 25 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 8cb5414..1f89033 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -1524,18 +1524,6 @@ public final class Configuration { else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; } - else if ( key.equals( "color_orthologous" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [color_orthologous] is deprecated" ); - } - else if ( key.equals( "color_subtree_neighbors" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [color_subtree_neighbors] is deprecated" ); - } - else if ( key.equals( "color_super_orthologous" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [color_super_orthologous] is deprecated" ); - } else if ( key.equals( "mark_nodes_with_box" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [mark_nodes_with_box] is deprecated" ); @@ -1627,7 +1615,7 @@ public final class Configuration { } } else if ( key.equals( "species_color" ) ) { - getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "domain_color" ) ) { getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 8e78667..1a5fc6f 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -689,21 +689,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { - String species = tax.getTaxonomyCode(); - if ( ForesterUtil.isEmpty( species ) ) { - species = tax.getScientificName(); - if ( ForesterUtil.isEmpty( species ) ) { - species = tax.getCommonName(); - } - } - if ( ForesterUtil.isEmpty( species ) ) { + if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { return getTreeColorSet().getTaxonomyColor(); } - // Look in species hash - Color c = getControlPanel().getSpeciesColors().get( species ); + Color c = null; + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() ); + } + if ( c == null && !ForesterUtil.isEmpty( tax.getScientificName() ) ) { + c = getControlPanel().getSpeciesColors().get( tax.getScientificName() ); + } if ( c == null ) { - c = AptxUtil.calculateColorFromString( species ); - getControlPanel().getSpeciesColors().put( species, c ); + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode() ); + getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c ); + } + else { + c = AptxUtil.calculateColorFromString( tax.getScientificName() ); + getControlPanel().getSpeciesColors().put( tax.getScientificName(), c ); + } } return c; } -- 1.7.10.2