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;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
final static int subtree = 3;
- final static int swap = 4;
+ final static int swap = 4;
final static int color_subtree = 5;
final static int open_seq_web = 6;
final static int open_tax_web = 7;
- final static int cut_subtree = 8;
- final static int copy_subtree = 9;
- final static int paste_subtree = 10;
- final static int delete_subtree_or_node = 11;
- final static int add_new_node = 12;
- final static int edit_node_data = 13;
- final static int blast = 14;
- final static int sort_descendents = 15;
-
-
+ final static int blast = 8;
+ final static int cut_subtree = 9;
+ final static int copy_subtree = 10;
+ final static int paste_subtree = 11;
+ final static int delete_subtree_or_node = 12;
+ final static int add_new_node = 13;
+ final static int edit_node_data = 14;
+ final static int sort_descendents = 15;
// ---------------------------
// Display options for trees
// ---------------------------
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
{ "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
- { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" },
- { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
- { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" }, { "Sort Descendants", "display" } };
+ { "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" } };
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
// --------------
else if ( name.equals( "open_tax_web" ) ) {
index = Configuration.open_tax_web;
}
+ else if ( name.equals( "blast" ) ) {
+ index = Configuration.blast;
+ }
else if ( name.equals( "cut_subtree" ) ) {
index = Configuration.cut_subtree;
}
_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
}