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.NodeDataField;
import org.forester.phylogeny.data.NodeVisualData;
import org.forester.phylogeny.data.NodeVisualData.NodeFill;
import org.forester.phylogeny.data.NodeVisualData.NodeShape;
CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
}
final static String clickto_options[][] = {
- { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
- { "Go to Sub-/Super-Tree", "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" },
- { "Return", "display" }, { "Select Node(s)", "display" } };
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Go to Sub-/Super-Tree", "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" } };
private final static String DEFAULT_SPECIES_COLORS[][] = {
- { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
- { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
- { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
- { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
- { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
- { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
- { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
- { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
- { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
- { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
- { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
- { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
- { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
- { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
- { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
- { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
- { "PORGI", "0x918E00" } };
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
final static int display_node_data = 0;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
// Click-to options
// ------------------
final static String display_options[][] = {
- { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
- { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
- { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
- { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
- { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
- { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "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" },
- { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
- { "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" } };
+ { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
+ { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
+ { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
+ { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
+ { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
+ { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "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" },
+ { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
+ { "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" } };
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
private SortedMap<String, Color> _display_colors = null;
private boolean _display_sequence_relations = false;
private boolean _editable = true;
- private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+ private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
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 _vector_data_width = 120;
private boolean _line_up_renderable_node_data = true;
private boolean _right_align_domains = false;
+ private boolean _allow_thick_strokes = false;
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
/**
* Will attempt to use the phylogeny to determine whether to check
* this or not (e.g. phylogram)
- *
+ *
*/
boolean doGuessCheckOption( final int which ) {
return display_options[ which ][ 2 ].equals( "?" );
if ( name.equals( "edit_info" ) ) {
index = Configuration.display_node_data;
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [edit_info] is deprecated, use [display node data] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [edit_info] is deprecated, use [display node data] instead" );
}
else if ( name.equals( "display_node_data" ) ) {
index = Configuration.display_node_data;
}
else if ( name.equals( "display_sequences" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
+ .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "open_seq_web" ) ) {
}
else if ( name.equals( "display_node_popup" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
+ "configuration key [display_node_popup] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "custom_option" ) ) {
return _domain_colors;
}
- public NODE_DATA getExtDescNodeDataToReturn() {
+ public NodeDataField getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
/**
* Convenience method.
- *
+ *
* @return true if value in configuration file was 'yes'
*/
boolean isDrawAsPhylogram() {
/**
* read each line of config file, process non-comment lines
- * @throws IOException
+ * @throws IOException
*/
private void readConfig( final BufferedReader conf_in ) throws IOException {
String line;
_editable = editable;
}
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
_ext_desc_data_to_return = ext_desc_data_to_return;
}
default_clickto = getClickToIndex( clickto_name );
if ( default_clickto == -1 ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
- + "] for [default_click_to]" );
+ + "] for [default_click_to]" );
default_clickto = 0;
}
else if ( default_clickto == DEPRECATED ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
- + "]" );
+ + "]" );
_ui = UI.UNKNOWN;
}
}
else {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [phylogeny_graphics_type]" );
+ + "] for [phylogeny_graphics_type]" );
}
}
else if ( key.equals( "min_confidence_value" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "value for [pdf_export_line_width] cannot be zero or negative" );
+ "value for [pdf_export_line_width] cannot be zero or negative" );
}
}
else if ( key.equals( "window_initial_size_x" ) ) {
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "value for [default_number_of_bootstrap_resamples] cannot be negative" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
else if ( key.equals( "mafft_local" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [cladogram_type]" );
+ + "] for [cladogram_type]" );
}
}
else if ( key.equals( "non_lined_up_cladogram" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
+ .printWarningMessage( Constants.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 {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [overview_placement_type]" );
+ + "] for [overview_placement_type]" );
}
}
else if ( key.equals( "node_label_direction" ) ) {
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [node_label_direction]" );
+ + "] for [node_label_direction]" );
}
}
else if ( key.equals( "branch_length_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [branch_length_value_digits]" );
+ + "] for [branch_length_value_digits]" );
}
}
else if ( key.equals( "confidence_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [confidence_value_digits]" );
+ + "] for [confidence_value_digits]" );
}
}
else if ( key.equals( "allow_editing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
else {
setReplaceUnderscoresInNhParsing( r );
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
- + s
- + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
}
if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
- + "] for [default_node_fill]" );
+ + "] for [default_node_fill]" );
}
}
else if ( key.equals( "default_node_shape" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
- + "] for [default_node_shape]" );
+ + "] for [default_node_shape]" );
}
}
else if ( key.equals( "midpoint_reroot" ) ) {
setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
}
- else if ( key.equals( "ext_descendents_data_to_return" ) ) {
+ else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
if ( s.equalsIgnoreCase( "node_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
}
else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC );
}
else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
- }
- else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
}
else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME );
}
else if ( s.equalsIgnoreCase( "gene_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.GENE_NAME );
}
else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL );
}
else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME );
}
else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
- }
- else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE );
}
else if ( s.equalsIgnoreCase( "user_selected" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
+ setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ else if ( s.equalsIgnoreCase( "domains" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
+ }
+ else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
+ }
+ else if ( s.equalsIgnoreCase( "seq_annotations" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
+ }
+ else if ( s.equalsIgnoreCase( "go_term_ids" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return]" );
+ + "] for [ext_descendents_data_to_return]" );
}
}
- else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
+ else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
- if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
- + "] for [label_for_get_ext_descendents_data]" );
- }
- else {
+ if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
}
}
- else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
+ else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) {
final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
if ( s.equals( "console" ) ) {
setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return_on]" );
+ + "] for [ext_descendents_data_to_return_on]" );
}
}
else if ( key.equals( "vector_data_min_color" ) ) {
else if ( key.equals( "right_align_domain_architectures" ) ) {
setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
}
+ else if ( key.equals( "allow_thick_strokes" ) ) {
+ _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
+ }
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
int key_index = -1;
else if ( key.equals( "color_branches" ) ) {
key_index = Configuration.use_style;
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
}
else if ( key.equals( "width_branches" ) ) {
key_index = Configuration.width_branches;
}
else if ( key.equals( "annotation_color" ) ) {
getAnnotationColors()
- .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [function_color] is deprecated" );
+ "configuration key [function_color] is deprecated" );
}
else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
- + "] in: " + config_filename );
+ + "] in: " + config_filename );
}
}
}
private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
_validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
+
+ public boolean isAllowThickStrokes() {
+ return _allow_thick_strokes;
+ }
}
git://source.jalview.org / jalview.git / blobdiff