}
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" },
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
// ------------------
{ "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;
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<String, Color> _sequence_colors;
private static Hashtable<String, Color> _annotation_colors;
private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
private int _frame_x_size;
private int _frame_y_size;
- private int _graphics_export_x = -1;
- private int _graphics_export_y = -1;
private Color _gui_background_color = AptxConstants.GUI_BACKGROUND_DEFAULT;
private Color _gui_button_background_color = AptxConstants.BUTTON_BACKGROUND_COLOR_DEFAULT;
private Color _gui_button_border_color = AptxConstants.BUTTON_BORDER_COLOR_DEFAULT;
private boolean _line_up_renderable_node_data = true;
private boolean _right_align_domains = false;
private boolean _allow_thick_strokes = false;
+ private boolean _could_read_config_file = false;
static {
for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
else {
config_filename = cf;
}
+ _could_read_config_file = false;
setDisplayColors( new TreeMap<String, Color>() );
config_filename = config_filename.trim();
URL u = null;
bf.close();
ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url ["
+ config_filename + "]" );
+ _could_read_config_file = true;
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from ["
final BufferedReader bf = new BufferedReader( new FileReader( f ) );
readConfig( bf );
bf.close();
+ _could_read_config_file = true;
}
catch ( final Exception e ) {
if ( verbose ) {
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";
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";
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;
}
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;
}
_ext_node_data_return_on = ext_node_data_return_on;
}
- private void setGraphicsExportX( final int graphics_export_x ) {
- _graphics_export_x = graphics_export_x;
- }
+ //private void setGraphicsExportX( final int graphics_export_x ) {
+ // _graphics_export_x = graphics_export_x;
+ //}
- private void setGraphicsExportY( final int graphics_export_y ) {
- _graphics_export_y = graphics_export_y;
- }
+ //private void setGraphicsExportY( final int graphics_export_y ) {
+ // _graphics_export_y = graphics_export_y;
+ //}
private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) {
_internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing;
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 );
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() );
}
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;
}
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;
}
return _domain_colors;
}
- int getGraphicsExportX() {
- return _graphics_export_x;
- }
-
- int getGraphicsExportY() {
- return _graphics_export_y;
- }
-
+
Color getGuiBackgroundColor() {
return _gui_background_color;
}
return _gui_menu_text_color;
}
+ static int getGuiFontSize() {
+ return 11;
+ }
+
int getMaxBaseFontSize() {
return _max_base_font_size;
}
return _species_colors;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ public final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
return _taxonomy_extraction;
}
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;
}
return _use_tabbed_display;
}
- boolean isValidatePhyloXmlAgainstSchema() {
+ public boolean isValidatePhyloXmlAgainstSchema() {
return _validate_against_phyloxml_xsd_schema;
}
static String getDefaultFontFamilyName() {
return DEFAULT_FONT_FAMILY;
}
+
+ public boolean isCouldReadConfigFile() {
+ return _could_read_config_file;
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff