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 TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT;
+ private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO;
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;
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 boolean _midpoint_root = false;
private static String DEFAULT_FONT_FAMILY = "";
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
}
boolean isAntialiasScreen() {
- if ( AptxUtil.isMac() ) {
- // Apple Macintosh graphics are slow, turn off anti-alias.
+ if ( ForesterUtil.isMac() ) {
+ //Apple Macintosh graphics are slow, turn off anti-alias.
return false;
}
return _antialias_screen;
}
final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
_ui = UI.NATIVE;
}
return _ui == UI.NATIVE;
else if ( name.equals( "color_subtree" ) ) {
index = Configuration.color_subtree;
}
- else if ( name.equals( "go_to_swiss_prot" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" );
- return DEPRECATED;
- }
return index;
}
if ( s.equalsIgnoreCase( "no" ) ) {
setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
}
- else if ( s.equalsIgnoreCase( "yes" ) ) {
+ else if ( s.equalsIgnoreCase( "pfam_relaxed" ) ) {
setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
}
- else if ( s.equalsIgnoreCase( "pfam" ) ) {
+ else if ( s.equalsIgnoreCase( "pfam_strict" ) ) {
setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
}
+ else if ( s.equalsIgnoreCase( "aggressive" ) ) {
+ setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
else {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s );
+ ForesterUtil
+ .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
else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) );
}
+ else if ( key.equals( "midpoint_reroot" ) ) {
+ setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
+ }
else if ( key.equals( "ext_descendents_data_to_return" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
if ( s.equalsIgnoreCase( "node_name" ) ) {
else if ( key.equals( "width_branches" ) ) {
key_index = Configuration.width_branches;
}
- else if ( key.equals( "color_orthologous" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_orthologous] is deprecated" );
- }
- else if ( key.equals( "color_subtree_neighbors" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_subtree_neighbors] is deprecated" );
- }
- else if ( key.equals( "color_super_orthologous" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_super_orthologous] is deprecated" );
- }
else if ( key.equals( "mark_nodes_with_box" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
"configuration key [mark_nodes_with_box] is deprecated" );
}
}
else if ( key.equals( "species_color" ) ) {
- getSpeciesColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ getSpeciesColors().put( ( ( String ) st.nextElement() ).replace( '_', ' ' ),
+ Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "domain_color" ) ) {
getDomainColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
static enum TRIPLET {
TRUE, FALSE, UNKNOWN
}
+
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
+ }
+
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
+ }
}