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;
private boolean _show_domain_labels = true;
private boolean _abbreviate_scientific_names = false;
private boolean _color_labels_same_as_parent_branch = false;
- private int _default_bootstrap_samples = -1;
private boolean _show_default_node_shapes = false;
private NodeShape _default_node_shape = NodeShape.CIRCLE;
private NodeFill _default_node_fill = NodeFill.GRADIENT;
private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
private boolean _taxonomy_colorize_node_shapes = false;
+ private int _default_bootstrap_samples = -1;
+ private File _path_to_local_mafft = null;
+ private File _path_to_local_kalign = null;
+ private File _path_to_local_fastme = null;
+ private File _path_to_local_raxml = null;
+ private File _path_to_local_clustalo = null;
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
return _default_bootstrap_samples;
}
+ public File getpathToLocalMafft() {
+ return _path_to_local_mafft;
+ }
+
+ public File getPathToLocalKalign() {
+ return _path_to_local_kalign;
+ }
+
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
+ }
+
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
+ }
+
int getDefaultDisplayClicktoOption() {
return default_clickto;
}
_default_bootstrap_samples = default_bootstrap_samples;
}
+ private void setPathToLocalMafft( final File path_to_local_mafft ) {
+ _path_to_local_mafft = path_to_local_mafft;
+ }
+
+ private void setPathToLocalKalign( final File path_to_local_kalign ) {
+ _path_to_local_kalign = path_to_local_kalign;
+ }
+
+ private void setPathToLocalFastme( final File path_to_local_fastme ) {
+ _path_to_local_fastme = path_to_local_fastme;
+ }
+
+ private void setPathToLocalRaxml( final File path_to_local_raxml ) {
+ _path_to_local_raxml = path_to_local_raxml;
+ }
+
+ public File getPathToLocalClustalOmega() {
+ return _path_to_local_clustalo;
+ }
+
+ public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) {
+ _path_to_local_clustalo = path_to_local_clustalo;
+ }
+
public void setDefaultNodeFill( final NodeFill default_node_fill ) {
_default_node_fill = default_node_fill;
}
_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() ) );
}
"value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
+ else if ( key.equals( "clustalo_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalClustalOmega( new File( str ) );
+ }
+ }
+ else if ( key.equals( "mafft_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalMafft( new File( str ) );
+ }
+ }
+ else if ( key.equals( "kalign_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalKalign( new File( str ) );
+ }
+ }
+ else if ( key.equals( "fastme_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalFastme( new File( str ) );
+ }
+ }
+ else if ( key.equals( "raxml_local" ) ) {
+ final String str = ( ( String ) st.nextElement() ).trim();
+ if ( !ForesterUtil.isEmpty( str ) ) {
+ setPathToLocalRaxml( new File( str ) );
+ }
+ }
else if ( key.equals( "show_scale" ) ) {
setShowScale( 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
}