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;
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
// ------------------
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
// ---------------------------
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;
// --------------
}
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 ) {
}
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 ) {
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;
}
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() ) );
}
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 );
}
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 );
}
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;
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;
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;
}
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;
}
}
}
+ 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;
}
public void setMidpointReroot( final boolean midpoint_root ) {
_midpoint_root = midpoint_root;
}
+
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ public boolean isColorByTaxonomicGroup() {
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff