private boolean _use_tabbed_display = false;
private boolean _hide_controls_and_menus = false;
private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT;
+ private File _mafft = null;
+ private File _clustalo = null;
+ private File _fastme = null;
private SortedMap<String, WebLink> _weblinks = null;
private SortedMap<String, Color> _display_colors = null;
private boolean _antialias_screen = true;
_ui = UI.UNKNOWN;
}
}
+ else if ( key.equals( "path_to_mafft" ) ) {
+ setPathToMafft( new File( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "path_to_clustalo" ) ) {
+ setPathToClustalOmega( new File( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "path_to_fastme" ) ) {
+ setPathToFastME( new File( ( String ) st.nextElement() ) );
+ }
+ else if ( key.equals( "path_to_mafft" ) ) {
+ setPathToMafft( new File( ( String ) st.nextElement() ) );
+ }
else if ( key.equals( VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA ) ) {
setValidatePhyloXmlAgainstSchema( parseBoolean( ( String ) st.nextElement() ) );
}
return DEFAULT_FONT_FAMILY;
}
+ public File getPathToMafft() {
+ return _mafft;
+ }
+
+ public File getPathToClustalOmega() {
+ return _clustalo;
+ }
+
+ public File getPathToFastME() {
+ return _fastme;
+ }
+
+ public void setPathToMafft( final File mafft ) {
+ _mafft = mafft;
+ }
+
+ public void setPathToClustalOmega( final File clustalo ) {
+ _clustalo = clustalo;
+ }
+
+ public void setPathToFastME( final File fastme ) {
+ _fastme = fastme;
+ }
+
static enum TRIPLET {
TRUE, FALSE, UNKNOWN
}