X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=deaaec843c63090e3b9b42e495cc8fb9eeffb331;hb=bc282cbd857f4fb9decdc00b278640bcf146a645;hp=96299a3bc85139756bf4c83c194f4013ce413a93;hpb=4acc1443d8c6c6f47c26a7c57357bdcdad27ecf8;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 96299a3..deaaec8 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -47,6 +47,7 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.data.NodeData.NODE_DATA; import org.forester.phylogeny.data.NodeVisualization; import org.forester.phylogeny.data.NodeVisualization.NodeFill; @@ -56,7 +57,7 @@ import org.forester.util.ForesterUtil; public final class Configuration { public enum EXT_NODE_DATA_RETURN_ON { - CONSOLE, WINODW; + CONSOLE, WINODW, BUFFER_ONLY; } static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static final String WEB_LINK_KEY = "web_link"; @@ -86,7 +87,7 @@ 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 boolean _nh_parsing_extract_pfam_taxonomy_codes = false; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY; 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; @@ -150,6 +151,7 @@ public final class Configuration { 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; // --------------------------- // Display options for trees // --------------------------- @@ -162,7 +164,7 @@ public final class Configuration { final static String display_options[][] = { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, { "Event", "display", "?" }, - { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" }, + { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" }, @@ -178,7 +180,7 @@ public final class Configuration { { "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" } }; + { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -213,9 +215,9 @@ public final class Configuration { private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; - private NODE_DATA _ext_desc_data_to_return = NODE_DATA.NODE_NAME; + private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; private String _label_for_get_ext_descendents_data = ""; - private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.CONSOLE; + private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; private static String DEFAULT_FONT_FAMILY = ""; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { @@ -415,6 +417,9 @@ public final class Configuration { else if ( name.equals( "edit_node_data" ) ) { index = Configuration.edit_node_data; } + else if ( name.equals( "select_nodes" ) ) { + index = Configuration.select_nodes; + } else if ( name.equals( "display_node_popup" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [display_node_popup] is deprecated" ); @@ -625,8 +630,8 @@ public final class Configuration { return _editable; } - boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } boolean isHasWebLink( final String source ) { @@ -920,8 +925,8 @@ public final class Configuration { _editable = editable; } - public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { - _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -1200,7 +1205,7 @@ public final class Configuration { } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); - if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) { + if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); @@ -1209,16 +1214,26 @@ public final class Configuration { setReplaceUnderscoresInNhParsing( r ); } } - else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) { - final boolean e = parseBoolean( ( String ) st.nextElement() ); - if ( e && isReplaceUnderscoresInNhParsing() ) { + else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) { + final String s = ( String ) st.nextElement(); + if ( s.equalsIgnoreCase( "no" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } + else if ( s.equalsIgnoreCase( "yes" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); + } + else if ( s.equalsIgnoreCase( "pfam" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s ); + } + if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } - else { - setExtractPfamTaxonomyCodesInNhParsing( e ); - } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) ); @@ -1315,6 +1330,9 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return]" ); @@ -1338,6 +1356,9 @@ public final class Configuration { else if ( s.equals( "window" ) ) { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); } + else if ( s.equals( "buffer_only" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); + } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return_on]" );