X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=1914d76082e317b192ec1e49f25d213a7e04c93a;hb=70da437f494b483dac92a488bd3500e5add2e34e;hp=5223e7e4596be1b4091963f7c7a58a1553810845;hpb=e6176aa35853eeaa7ab3a4f2d8a1431d9c76a290;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 5223e7e..1914d76 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -57,20 +57,21 @@ public final class Configuration { final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree(s)", "display" }, - { "Colorize Node(s)", "display" }, { "Change Node Font", "display" }, { "Open Sequence DB", "display" }, - { "Go to PDB", "display" }, { "Open Taxonomy DB", "display" }, { "Blast", "display" }, - { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, - { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, - { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } }; + { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, + { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" }, + { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" }, + { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" }, + { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, + { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" }, + { "Return", "display" }, { "Select Node(s)", "display" } }; final static int display_node_data = 0; final static int collapse_uncollapse = 1; final static int reroot = 2; final static int subtree = 3; final static int swap = 4; - final static int color_subtree = 5; - final static int color_node_font = 6; - final static int change_node_font = 7; + final static int color_node_font = 5; + final static int change_node_font = 6; + final static int color_subtree = 7; final static int open_seq_web = 8; final static int open_pdb_web = 9; final static int open_tax_web = 10; @@ -91,16 +92,16 @@ public final class Configuration { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" }, - { "Use Visual Styles", "display", "no" }, { "Use 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" } }; + { "Visual Styles/Branch Colors", "display", "no" }, { "Branch Widths", "display", "no" }, + { "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; @@ -110,24 +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 @@ -400,6 +400,10 @@ public final class Configuration { getDisplayColors().put( key, color ); } + public void setAddTaxonomyImagesCB( final boolean b ) { + display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no"; + } + public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } @@ -440,6 +444,10 @@ public final class Configuration { display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } + public void setUseStyle( final boolean b ) { + display_options[ use_style ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplayColors( final SortedMap display_colors ) { _display_colors = display_colors; } @@ -464,6 +472,10 @@ public final class Configuration { display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; } + public void setDisplayGeneNames( final boolean b ) { + display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; + } + public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { _display_sequence_relations = display_sequence_relations; } @@ -1525,6 +1537,12 @@ public final class Configuration { else if ( key.equals( "use_visual_styles" ) ) { key_index = Configuration.use_style; } + else if ( key.equals( "color_branches" ) ) { + key_index = Configuration.use_style; + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); + } else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; } @@ -1579,9 +1597,6 @@ 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();