import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
+import org.forester.phylogeny.data.NodeData.NODE_DATA;
import org.forester.phylogeny.data.NodeVisualization;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
public final class Configuration {
+ public enum EXT_NODE_DATA_RETURN_ON {
+ CONSOLE, WINODW;
+ }
static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
private static final String WEB_LINK_KEY = "web_link";
private static final String DISPLAY_COLOR_KEY = "display_color";
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_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;
final static int show_vector_data = 23;
final static int show_taxonomy_images = 24;
final static int show_properties = 25;
- final static int write_confidence_values_sd = 26;
// ------------------
// Click-to options
// ------------------
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 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;
+ final static int get_ext_desc_data = 16;
// ---------------------------
// Display options for trees
// ---------------------------
{ "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
{ "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
{ "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
- { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" },
- { "Confidence StdDev", "display", "no" } };
+ { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
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" } };
+ { "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" }, { "Return", "display" } };
// This option is selected in the dropdown
int default_clickto = Configuration.display_node_data;
// --------------
private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT;
private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
+ private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+ private String _label_for_get_ext_descendents_data = "";
+ private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
private static String DEFAULT_FONT_FAMILY = "";
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
else if ( name.equals( "swap" ) ) {
index = Configuration.swap;
}
+ else if ( name.equals( "sort_descendants" ) ) {
+ index = Configuration.sort_descendents;
+ }
+ else if ( name.equals( "get_ext_descendents_data" ) ) {
+ index = Configuration.get_ext_desc_data;
+ }
else if ( name.equals( "display_sequences" ) ) {
ForesterUtil
.printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
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;
}
return _default_bootstrap_samples;
}
+ public File getpathToLocalMafft() {
+ return _path_to_local_mafft;
+ }
+
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
+ }
+
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
+ }
+
int getDefaultDisplayClicktoOption() {
return default_clickto;
}
private double parseDouble( final String str ) {
double d = 0.0;
try {
- d = Double.parseDouble( str );
+ d = Double.parseDouble( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" );
private float parseFloat( final String str ) {
float f = 0.0f;
try {
- f = Float.parseFloat( str );
+ f = Float.parseFloat( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" );
private int parseInt( final String str ) {
int i = -1;
try {
- i = Integer.parseInt( str );
+ i = Integer.parseInt( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" );
private short parseShort( final String str ) {
short i = -1;
try {
- i = Short.parseShort( str );
+ i = Short.parseShort( str.trim() );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" );
_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 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;
}
* Set a key-value(s) tuple
*/
private void setKeyValue( final StringTokenizer st ) {
- String key = ( String ) st.nextElement();
- key = key.replace( ':', ' ' );
- key = key.trim();
- key = key.toLowerCase();
+ final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase();
+ if ( !st.hasMoreElements() ) {
+ return;
+ }
// Handle single value settings first:
if ( key.equals( "default_click_to" ) ) {
final String clickto_name = ( 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( "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() ) );
}
_use_tabbed_display = parseBoolean( ( String ) st.nextElement() );
}
else if ( key.equals( "overview_width" ) ) {
- final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
+ final short i = parseShort( ( ( String ) st.nextElement() ) );
setOvMaxWidth( i );
}
else if ( key.equals( "overview_height" ) ) {
- final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
+ final short i = parseShort( ( ( String ) st.nextElement() ) );
setOvMaxHeight( i );
}
else if ( key.equals( "overview_placement_type" ) ) {
else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) {
setTaxonomyColorizeNodeShapes( 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" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
+ }
+ else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
+ }
+ else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
+ }
+ else if ( s.equalsIgnoreCase( "user_selected" ) ) {
+ setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ + "] for [ext_descendents_data_to_return]" );
+ }
+ }
+ else if ( 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 {
+ setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
+ }
+ }
+ else if ( 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 if ( s.equals( "window" ) ) {
+ setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW );
+ }
+ else {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
+ + "] for [ext_descendents_data_to_return_on]" );
+ }
+ }
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
int key_index = -1;
}
}
+ private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) {
+ _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
+ }
+
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
+ }
+
public void setMinConfidenceValue( final double min_confidence_value ) {
_min_confidence_value = min_confidence_value;
}
_node_label_direction = node_label_direction;
}
- public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) {
- this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values;
+ public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) {
+ _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values;
}
- public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) {
- this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values;
+ public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
}
private void setOvMaxHeight( final short ov_max_height ) {
public enum UI {
NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN
}
+
+ public NODE_DATA getExtDescNodeDataToReturn() {
+ return _ext_desc_data_to_return;
+ }
+
+ public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
+ public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() {
+ return _ext_node_data_return_on;
+ }
+
+ private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
+ _ext_node_data_return_on = ext_node_data_return_on;
+ }
}
git://source.jalview.org / jalview.git / blobdiff