From d6ce4feec3a9ed8074eba81a328cb018a08f2400 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 16 Apr 2014 19:57:25 +0000 Subject: [PATCH] inprogress --- .../org/forester/archaeopteryx/Configuration.java | 56 +++++++++----------- 1 file changed, 26 insertions(+), 30 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index d933682..aa3da2c 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -93,15 +93,15 @@ public final class Configuration { { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" }, - { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" }, - { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, - { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" }, - { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, - { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, - { "Colorize by Annotation", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, - { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, - { "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" } }; + { "Protein Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, + { "Binary Char Counts", "nodisplay", "no" }, { "Seq Name", "display", "yes" }, + { "Seq Accession", "display", "no" }, { "Show Internal Data", "display", "yes" }, + { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" }, + { "Taxonomy Common", "display", "no" }, { "Colorize by Annotation", "nodisplay", "no" }, + { "Seq Symbol", "display", "yes" }, { "Rollover", "display", "yes" }, + { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" }, + { "Taxonomy Images", "display", "no" }, { "Properties", "nodisplay", "no" }, + { "Gene Name", "display", "yes" } }; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -111,24 +111,23 @@ public final class Configuration { final static int color_according_to_species = 6; final static int use_style = 7; final static int width_branches = 8; - final static int show_custom_node_shapes = 9; - final static int show_domain_architectures = 10; - final static int show_binary_characters = 11; - final static int show_binary_character_counts = 12; - final static int show_seq_names = 13; - final static int show_sequence_acc = 14; - final static int display_internal_data = 15; - final static int dynamically_hide_data = 16; - final static int show_taxonomy_scientific_names = 17; - final static int show_taxonomy_common_names = 18; - final static int color_according_to_annotation = 19; - final static int show_seq_symbols = 20; - final static int node_data_popup = 21; - final static int show_relation_confidence = 22; - final static int show_vector_data = 23; - final static int show_taxonomy_images = 24; - final static int show_properties = 25; - final static int show_gene_names = 26; + final static int show_domain_architectures = 9; + final static int show_binary_characters = 10; + final static int show_binary_character_counts = 11; + final static int show_seq_names = 12; + final static int show_sequence_acc = 13; + final static int display_internal_data = 14; + final static int dynamically_hide_data = 15; + final static int show_taxonomy_scientific_names = 16; + final static int show_taxonomy_common_names = 17; + final static int color_according_to_annotation = 18; + final static int show_seq_symbols = 19; + final static int node_data_popup = 20; + final static int show_relation_confidence = 21; + final static int show_vector_data = 22; + final static int show_taxonomy_images = 23; + final static int show_properties = 24; + final static int show_gene_names = 25; static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; // ---------------- // Function colors @@ -1586,9 +1585,6 @@ public final class Configuration { else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } - else if ( key.equals( "show_custom_node_shapes" ) ) { - key_index = Configuration.show_custom_node_shapes; - } // If we've found the key, set the values if ( key_index >= 0 ) { display_options[ key_index ][ 1 ] = ( String ) st.nextElement(); -- 1.7.10.2