X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=3db44f7a8b113188ab4b1a196462c204b7dbb88a;hb=a2e1b38bab7e593d79946c24e653776e6d796e00;hp=bf2851162247af65d0ba21095bb5a1128dc196c2;hpb=2153d77fe476de9ceeb3b1e7fb3438c2ce373963;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index bf28511..3db44f7 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -68,13 +68,13 @@ public final class Configuration { } final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, + { "Go to Sub/Supertree", "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" }, - { "List Node Data", "display" }, { "Select Node(s)", "display" } }; + { "List Node Data", "display" }, { "Select Node(s)", "display" } , { "Uncollapse All", "display" }, { "Order Subtree", "display" }, }; private final static String DEFAULT_SPECIES_COLORS[][] = { { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" }, { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" }, @@ -114,6 +114,9 @@ public final class Configuration { final static int sort_descendents = 18; final static int get_ext_desc_data = 19; final static int select_nodes = 20; + final static int uncollapse_all = 21; + final static int order_subtree = 22; + // ------------------ // Click-to options // ------------------ @@ -131,7 +134,8 @@ public final class Configuration { { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" }, { "Gene Name", "display", "yes" }, - { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } }; + { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } + , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "display", "yes" }}; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -161,6 +165,9 @@ public final class Configuration { final static int show_gene_names = 26; final static int show_mol_seqs = 27; final static int write_branch_length_values = 28; + final static int show_tax_rank = 29; + final static int display_external_data = 30; + static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static Hashtable _sequence_colors; private static Hashtable _annotation_colors; @@ -520,6 +527,10 @@ public final class Configuration { public void setDisplayInternalData( final boolean b ) { display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } + + public void setDisplayExternalData( final boolean b ) { + display_options[ display_external_data ][ 2 ] = b ? "yes" : "no"; + } public void setDisplayMultipleSequenceAlignment( final boolean b ) { display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no"; @@ -548,6 +559,10 @@ public final class Configuration { public void setDisplayTaxonomyCode( final boolean b ) { display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; } + + public void setDisplayTaxonomyRank( final boolean b ) { + display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no"; + } public void setDisplayTaxonomyCommonNames( final boolean b ) { display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; @@ -655,6 +670,9 @@ public final class Configuration { else if ( name.equals( "collapse_uncollapse" ) ) { index = Configuration.collapse_uncollapse; } + else if ( name.equals( "uncollapse_all" ) ) { + index = Configuration.uncollapse_all; + } else if ( name.equals( "reroot" ) ) { index = Configuration.reroot; } @@ -664,6 +682,9 @@ public final class Configuration { else if ( name.equals( "swap" ) ) { index = Configuration.swap; } + else if ( name.equals( "order_subtree" ) ) { + index = Configuration.order_subtree; + } else if ( name.equals( "sort_descendants" ) ) { index = Configuration.sort_descendents; } @@ -972,20 +993,6 @@ public final class Configuration { setMaxBaseFontSize( i ); } } - else if ( key.equals( "graphics_export_x" ) ) { - // final String str = ( ( String ) st.nextElement() ).trim(); - // final int i = parseInt( str ); - // if ( i > 0 ) { - // setGraphicsExportX( i ); - // } - } - else if ( key.equals( "graphics_export_y" ) ) { - //final String str = ( ( String ) st.nextElement() ).trim(); - // final int i = parseInt( str ); - //if ( i > 0 ) { - // setGraphicsExportY( i ); - //} - } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final float f = parseFloat( str ); @@ -1067,22 +1074,14 @@ public final class Configuration { if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP ); } - else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) { - setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - } - else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) { - setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); + else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.LINED_UP.toString() ) ) { + setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP ); } else { ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [cladogram_type]" ); } } - else if ( key.equals( "non_lined_up_cladogram" ) ) { - ForesterUtil - .printWarningMessage( AptxConstants.PRG_NAME, - "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" ); - } else if ( key.equals( "hide_controls_and_menus" ) ) { _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() ); } @@ -1386,6 +1385,9 @@ public final class Configuration { else if ( key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; } + else if ( key.equals( "show_taxonomy_rank" ) ) { + key_index = Configuration.show_tax_rank; + } else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; } @@ -1437,6 +1439,9 @@ public final class Configuration { else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } + else if ( key.equals( "display_external_data" ) ) { + key_index = Configuration.display_external_data; + } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } @@ -1668,6 +1673,10 @@ public final class Configuration { return _gui_menu_text_color; } + static int getGuiFontSize() { + return 11; + } + int getMaxBaseFontSize() { return _max_base_font_size; } @@ -1726,7 +1735,7 @@ public final class Configuration { return _species_colors; } - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + public final TAXONOMY_EXTRACTION getTaxonomyExtraction() { return _taxonomy_extraction; } @@ -1755,11 +1764,11 @@ public final class Configuration { return _hide_controls_and_menus; } - boolean isInternalNumberAreConfidenceForNhParsing() { + public boolean isInternalNumberAreConfidenceForNhParsing() { return _internal_number_are_confidence_for_nh_parsing; } - boolean isReplaceUnderscoresInNhParsing() { + public boolean isReplaceUnderscoresInNhParsing() { return _nh_parsing_replace_underscores; } @@ -1786,7 +1795,7 @@ public final class Configuration { return _use_tabbed_display; } - boolean isValidatePhyloXmlAgainstSchema() { + public boolean isValidatePhyloXmlAgainstSchema() { return _validate_against_phyloxml_xsd_schema; } @@ -1803,4 +1812,10 @@ public final class Configuration { } + public String getConfigFilename() { + return config_filename; + } + + + }