X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=689fde7c60926f2f4e2ebf00bc6dce23d66618d2;hb=36cad5d7aee97eedcf1e42889ba4a1384b887777;hp=1f890332be14be1d92879c95f9c8c15aa103adf1;hpb=d17f81782b4ce0a50c963ccb0394e0d2ae796ad0;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 1f89033..689fde7 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -83,12 +83,13 @@ public final class Configuration { private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; private boolean _editable = true; private boolean _nh_parsing_replace_underscores = false; - private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; private boolean _internal_number_are_confidence_for_nh_parsing = false; private boolean _display_sequence_relations = false; private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; private boolean _background_color_gradient = false; private boolean _show_domain_labels = true; + private boolean _show_annotation_ref_source = true; private boolean _abbreviate_scientific_names = false; private boolean _color_labels_same_as_parent_branch = false; private boolean _show_default_node_shapes_internal = false; @@ -114,19 +115,20 @@ public final class Configuration { 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_gene_names = 13; + 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_gene_symbols = 20; + 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; // ------------------ // Click-to options // ------------------ @@ -137,17 +139,18 @@ public final class Configuration { final static int swap = 4; final static int color_subtree = 5; final static int open_seq_web = 6; - final static int open_tax_web = 7; - final static int blast = 8; - final static int cut_subtree = 9; - final static int copy_subtree = 10; - final static int paste_subtree = 11; - final static int delete_subtree_or_node = 12; - final static int add_new_node = 13; - final static int edit_node_data = 14; - final static int sort_descendents = 15; - final static int get_ext_desc_data = 16; - final static int select_nodes = 17; + final static int open_pdb_web = 7; + final static int open_tax_web = 8; + final static int blast = 9; + final static int cut_subtree = 10; + final static int copy_subtree = 11; + final static int paste_subtree = 12; + final static int delete_subtree_or_node = 13; + final static int add_new_node = 14; + final static int edit_node_data = 15; + final static int sort_descendents = 16; + final static int get_ext_desc_data = 17; + final static int select_nodes = 18; // --------------------------- // Display options for trees // --------------------------- @@ -159,25 +162,26 @@ public final class Configuration { String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; final static String display_options[][] = { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, - { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, - { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" }, - { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" }, - { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" }, + { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, + { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "yes" }, + { "Use Branch Colors", "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 Acc", "display", "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" }, - { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" }, + { "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" } }; + { "Properties", "nodisplay", "no" }, { "Gene Name", "display", "yes" } }; final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" }, - { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "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" } }; + { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, + { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" }, { "Open 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" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -456,7 +460,7 @@ public final class Configuration { } public void setDisplaySequenceNames( final boolean b ) { - display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; + display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no"; } public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { @@ -464,7 +468,7 @@ public final class Configuration { } public void setDisplaySequenceSymbols( final boolean b ) { - display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; + display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no"; } public void setDisplayTaxonomyCode( final boolean b ) { @@ -723,8 +727,8 @@ public final class Configuration { } boolean isAntialiasScreen() { - if ( AptxUtil.isMac() ) { - // Apple Macintosh graphics are slow, turn off anti-alias. + if ( ForesterUtil.isMac() ) { + //Apple Macintosh graphics are slow, turn off anti-alias. return false; } return _antialias_screen; @@ -772,7 +776,7 @@ public final class Configuration { } final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) { + if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; @@ -831,6 +835,9 @@ public final class Configuration { else if ( name.equals( "open_seq_web" ) ) { index = Configuration.open_seq_web; } + else if ( name.equals( "open_pdb_web" ) ) { + index = Configuration.open_pdb_web; + } else if ( name.equals( "open_tax_web" ) ) { index = Configuration.open_tax_web; } @@ -1193,6 +1200,9 @@ public final class Configuration { else if ( key.equals( "show_domain_labels" ) ) { setShowDomainLabels( parseBoolean( ( String ) st.nextElement() ) ); } + else if ( key.equals( "show_seq_annotation_ref_sources" ) ) { + setShowAnnotationRefSource( parseBoolean( ( String ) st.nextElement() ) ); + } else if ( key.equals( "abbreviate_scientific_names" ) ) { setAbbreviateScientificTaxonNames( parseBoolean( ( String ) st.nextElement() ) ); } @@ -1307,15 +1317,21 @@ public final class Configuration { if ( s.equalsIgnoreCase( "no" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } - else if ( s.equalsIgnoreCase( "yes" ) ) { + else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } - else if ( s.equalsIgnoreCase( "pfam" ) ) { + else if ( s.equalsIgnoreCase( "pfam_strict" ) ) { setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } + else if ( s.equalsIgnoreCase( "aggressive" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE ); + } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s ); + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + + s + + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" ); } if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil @@ -1426,6 +1442,9 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "sequence_name" ) ) { setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); } + else if ( s.equalsIgnoreCase( "gene_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME ); + } else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); } @@ -1435,6 +1454,9 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); } + else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME ); + } else if ( s.equalsIgnoreCase( "user_selected" ) ) { setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); } @@ -1472,13 +1494,8 @@ public final class Configuration { else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; - if ( key.equals( "use_real_br_lengths" ) || key.equals( "phylogram" ) ) { + if ( key.equals( "phylogram" ) ) { key_index = Configuration.display_as_phylogram; - if ( key.equals( "use_real_br_lengths" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [use_real_br_lengths] is deprecated, use [phylogram] instead" ); - } } else if ( key.equals( "rollover" ) ) { key_index = Configuration.node_data_popup; @@ -1489,34 +1506,14 @@ public final class Configuration { else if ( key.equals( "show_node_names" ) ) { key_index = Configuration.show_node_names; } - else if ( key.equals( "show_taxonomy" ) || key.equals( "show_taxonomy_code" ) ) { + else if ( key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; - if ( key.equals( "show_taxonomy" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [show_taxonomy] is deprecated, use [show_taxonomy_code] instead" ); - } } - else if ( key.equals( "write_br_length_values" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [write_br_length_values] is deprecated" ); - key_index = DEPRECATED; - } - else if ( key.equals( "write_bootstrap_values" ) || key.equals( "write_confidence_values" ) ) { + else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; - if ( key.equals( "write_bootstrap_values" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [write_bootstrap_values] is deprecated, use [write_confidence_values] instead" ); - } } - else if ( key.equals( "write_events" ) || key.equals( "write_dup_spec" ) ) { + else if ( key.equals( "write_events" ) ) { key_index = Configuration.write_events; - if ( key.equals( "write_dup_spec" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [write_dup_spec] is deprecated, use [write_events] instead" ); - } } else if ( key.equals( "color_branches" ) ) { key_index = Configuration.color_branches; @@ -1524,11 +1521,6 @@ public final class Configuration { else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; } - else if ( key.equals( "mark_nodes_with_box" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [mark_nodes_with_box] is deprecated" ); - key_index = DEPRECATED; - } else if ( key.equals( "show_domain_architectures" ) ) { key_index = Configuration.show_domain_architectures; } @@ -1541,31 +1533,24 @@ public final class Configuration { else if ( key.equals( "show_binary_character_counts" ) ) { key_index = Configuration.show_binary_character_counts; } + else if ( key.equals( "show_seq_names" ) ) { + key_index = Configuration.show_seq_names; + } else if ( key.equals( "show_gene_names" ) ) { key_index = Configuration.show_gene_names; } - else if ( key.equals( "show_gene_symbols" ) ) { - key_index = Configuration.show_gene_symbols; + else if ( key.equals( "show_seq_symbols" ) ) { + key_index = Configuration.show_seq_symbols; } - else if ( key.equals( "show_sequence_acc" ) ) { + else if ( key.equals( "show_seq_acc" ) ) { key_index = Configuration.show_sequence_acc; } - else if ( key.equals( "show_node_ids" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [show_node_ids] is deprecated" ); - key_index = DEPRECATED; - } else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } - else if ( key.equals( "show_taxonomy_names" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [show_taxonomy_names] is deprecated" ); - key_index = DEPRECATED; - } else if ( key.equals( "show_taxonomy_scientific_names" ) ) { key_index = Configuration.show_taxonomy_scientific_names; } @@ -1615,7 +1600,8 @@ public final class Configuration { } } else if ( key.equals( "species_color" ) ) { - getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ), 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() ) ); @@ -1643,6 +1629,10 @@ public final class Configuration { } } + private void setShowAnnotationRefSource( final boolean b ) { + _show_annotation_ref_source = b; + } + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } @@ -1702,4 +1692,12 @@ public final class Configuration { public void setMidpointReroot( final boolean midpoint_root ) { _midpoint_root = midpoint_root; } + + public boolean isShowAnnotationRefSource() { + return _show_annotation_ref_source; + } + + public boolean isColorByTaxonomicGroup() { + return false; + } }