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;
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";
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;
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
// ---------------------------
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" },
{ "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;
// --------------
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 ) {
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" );
return _editable;
}
- boolean isExtractPfamTaxonomyCodesInNhParsing() {
- return _nh_parsing_extract_pfam_taxonomy_codes;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
boolean isHasWebLink( final String source ) {
_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 ) {
}
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" );
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() ) );
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]" );
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]" );