import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
-import org.forester.phylogeny.data.NodeData.NODE_DATA;
+import org.forester.phylogeny.data.NodeDataField;
import org.forester.phylogeny.data.NodeVisualData;
import org.forester.phylogeny.data.NodeVisualData.NodeFill;
import org.forester.phylogeny.data.NodeVisualData.NodeShape;
public final class Configuration {
+ public enum EXT_NODE_DATA_RETURN_ON {
+ BUFFER_ONLY, CONSOLE, WINODW;
+ }
+
+ public enum UI {
+ CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ }
+
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
+ }
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
{ "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
{ "Open Taxonomy DB", "display" }, { "Launch 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" }, { "Select Node(s)", "display" } };
+ { "List Node Data", "display" }, { "Select Node(s)", "display" } };
+ private final static String DEFAULT_SPECIES_COLORS[][] = {
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
final static int display_node_data = 0;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
{ "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
{ "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
{ "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
- { "Branch Widths", "display", "no" }, { "Protein Domains", "display", "no" },
+ { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
{ "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
{ "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
{ "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
{ "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
{ "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
{ "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
- { "Properties", "display", "no" }, { "Gene Name", "display", "yes" } };
+ { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
+ { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
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_taxonomy_images = 24;
final static int show_properties = 25;
final static int show_gene_names = 26;
+ final static int show_mol_seqs = 27;
+ final static int write_branch_length_values = 28;
static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
private static Hashtable<String, Color> _sequence_colors;
private static Hashtable<String, Color> _annotation_colors;
private SortedMap<String, Color> _display_colors = null;
private boolean _display_sequence_relations = false;
private boolean _editable = true;
- private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN;
+ private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
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 PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT;
private boolean _show_annotation_ref_source = true;
- private boolean _show_branch_length_values = false;
private boolean _show_default_node_shapes_external = false;
+ private boolean _show_default_node_shapes_for_marked_nodes = false;
private boolean _show_default_node_shapes_internal = false;
private boolean _show_domain_labels = true;
private boolean _show_overview = true;
private Color _vector_data_mean_color = Color.WHITE;
private double _vector_data_height = 12;
private int _vector_data_width = 120;
- private boolean _line_up_renderable_node_data;
- private boolean _right_align_domains;
-
+ private boolean _line_up_renderable_node_data = true;
+ private boolean _right_align_domains = false;
+ private boolean _allow_thick_strokes = false;
static {
for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) {
if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
return _default_node_shape_size;
}
- public NODE_DATA getExtDescNodeDataToReturn() {
+ public NodeDataField getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
return _path_to_local_raxml;
}
+ public double getVectorDataHeight() {
+ return _vector_data_height;
+ }
+
+ public Color getVectorDataMaxColor() {
+ return _vector_data_max_color;
+ }
+
+ public Color getVectorDataMeanColor() {
+ return _vector_data_mean_color;
+ }
+
+ public Color getVectorDataMinColor() {
+ return _vector_data_min_color;
+ }
+
+ public int getVectorDataWidth() {
+ return _vector_data_width;
+ }
+
public boolean isAbbreviateScientificTaxonNames() {
return _abbreviate_scientific_names;
}
+ public boolean isAllowThickStrokes() {
+ return _allow_thick_strokes;
+ }
+
public boolean isBackgroundColorGradient() {
return _background_color_gradient;
}
return _color_labels_same_as_parent_branch;
}
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
+ }
+
public boolean isMidpointReroot() {
return _midpoint_root;
}
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
+ }
+
public boolean isShowAnnotationRefSource() {
return _show_annotation_ref_source;
}
return _show_default_node_shapes_external;
}
+ public boolean isShowDefaultNodeShapesForMarkedNodes() {
+ return _show_default_node_shapes_for_marked_nodes;
+ }
+
public boolean isShowDefaultNodeShapesInternal() {
return _show_default_node_shapes_internal;
}
getDisplayColors().put( key, color );
}
- public void setAddTaxonomyImagesCB( final boolean b ) {
- display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
- }
-
public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
_abbreviate_scientific_names = abbreviate_scientific_names;
}
+ public void setAddTaxonomyImagesCB( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
+ }
+
public void setBackgroundColorGradient( final boolean background_color_gradient ) {
_background_color_gradient = background_color_gradient;
}
display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
}
- public void setUseStyle( final boolean b ) {
- display_options[ use_style ][ 2 ] = b ? "yes" : "no";
- }
-
public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
_display_colors = display_colors;
}
display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
}
+ public void setDisplayGeneNames( final boolean b ) {
+ display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
+ }
+
public void setDisplayInternalData( final boolean b ) {
display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
}
+ public void setDisplayMultipleSequenceAlignment( final boolean b ) {
+ display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no";
+ }
+
public void setDisplayNodeNames( final boolean b ) {
display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
}
display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
}
- public void setDisplayGeneNames( final boolean b ) {
- display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no";
- }
-
public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
_display_sequence_relations = display_sequence_relations;
}
display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
}
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
+ public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
_ext_desc_data_to_return = ext_desc_data_to_return;
}
_frame_y_size = frame_y_size;
}
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
+ }
+
public void setMidpointReroot( final boolean midpoint_root ) {
_midpoint_root = midpoint_root;
}
_nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
- public void setShowBranchLengthValues( final boolean show_branch_length_values ) {
- _show_branch_length_values = show_branch_length_values;
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
}
public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
_show_default_node_shapes_external = show_default_node_shapes_external;
}
+ public void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) {
+ _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes;
+ }
+
public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
_show_default_node_shapes_internal = show_default_node_shapes_internal;
}
_show_scale = show_scale;
}
- boolean displaySequenceRelations() {
- return _display_sequence_relations;
- }
-
- boolean doCheckOption( final int which ) {
- return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
- || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
- }
-
- boolean doDisplayClickToOption( final int which ) {
- return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
- }
-
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
- }
-
- /**
- * Will attempt to use the phylogeny to determine whether to check
- * this or not (e.g. phylogram)
- *
- */
- boolean doGuessCheckOption( final int which ) {
- return display_options[ which ][ 2 ].equals( "?" );
- }
-
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
- }
- return _annotation_colors;
- }
-
- int getBaseFontSize() {
- return _base_font_size;
- }
-
- CLADOGRAM_TYPE getCladogramType() {
- return _cladogram_type;
- }
-
- int getClickToOptionsCount() {
- return clickto_options.length;
- }
-
- String getClickToTitle( final int which ) {
- return clickto_options[ which ][ 0 ];
- }
-
- int getDefaultDisplayClicktoOption() {
- return default_clickto;
- }
-
- SortedMap<String, Color> getDisplayColors() {
- return _display_colors;
- }
-
- String getDisplayTitle( final int which ) {
- return display_options[ which ][ 0 ];
- }
-
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
- }
- return _domain_colors;
- }
-
- int getGraphicsExportX() {
- return _graphics_export_x;
- }
-
- int getGraphicsExportY() {
- return _graphics_export_y;
- }
-
- Color getGuiBackgroundColor() {
- return _gui_background_color;
- }
-
- Color getGuiButtonBackgroundColor() {
- return _gui_button_background_color;
- }
-
- Color getGuiButtonBorderColor() {
- return _gui_button_border_color;
- }
-
- Color getGuiButtonTextColor() {
- return _gui_button_text_color;
- }
-
- Color getGuiCheckboxAndButtonActiveColor() {
- return _gui_checkbox_and_button_active_color;
- }
-
- Color getGuiCheckboxTextColor() {
- return _gui_checkbox_text_color;
- }
-
- Color getGuiMenuBackgroundColor() {
- return _gui_menu_background_color;
- }
-
- Color getGuiMenuTextColor() {
- return _gui_menu_text_color;
- }
-
- int getMaxBaseFontSize() {
- return _max_base_font_size;
- }
-
- int getMinBaseFontSize() {
- return _min_base_font_size;
- }
-
- double getMinConfidenceValue() {
- return _min_confidence_value;
- }
-
- NODE_LABEL_DIRECTION getNodeLabelDirection() {
- return _node_label_direction;
- }
-
- short getNumberOfDigitsAfterCommaForBranchLengthValues() {
- return _number_of_digits_after_comma_for_branch_length_values;
- }
-
- short getNumberOfDigitsAfterCommaForConfidenceValues() {
- return _number_of_digits_after_comma_for_confidence_values;
- }
-
- short getOvMaxHeight() {
- return _ov_max_height;
- }
-
- short getOvMaxWidth() {
- return _ov_max_width;
- }
-
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
- }
-
- PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _phylogeny_graphics_type;
- }
-
- float getPrintLineWidth() {
- return _print_line_width;
- }
-
- Hashtable<String, Color> getSpeciesColors() {
- if ( _species_colors == null ) {
- _species_colors = new Hashtable<String, Color>();
- }
- return _species_colors;
- }
-
- Hashtable<String, Color> getSequenceColors() {
- if ( _sequence_colors == null ) {
- _sequence_colors = new Hashtable<String, Color>();
- }
- return _sequence_colors;
- }
-
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
- }
-
- boolean isAntialiasScreen() {
- if ( ForesterUtil.isMac() ) {
- //Apple Macintosh graphics are slow, turn off anti-alias.
- return false;
- }
- return _antialias_screen;
- }
-
- /**
- * Convenience method.
- *
- * @return true if value in configuration file was 'yes'
- */
- boolean isDrawAsPhylogram() {
- return doCheckOption( display_as_phylogram );
- }
-
- boolean isEditable() {
- return _editable;
- }
-
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isHideControlPanelAndMenubar() {
- return _hide_controls_and_menus;
- }
-
- boolean isInternalNumberAreConfidenceForNhParsing() {
- return _internal_number_are_confidence_for_nh_parsing;
- }
-
- boolean isReplaceUnderscoresInNhParsing() {
- return _nh_parsing_replace_underscores;
- }
-
- boolean isShowBranchLengthValues() {
- return _show_branch_length_values;
- }
-
- boolean isShowOverview() {
- return _show_overview;
- }
-
- boolean isShowScale() {
- return _show_scale;
- }
-
- final boolean isUseNativeUI() {
- if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
- _ui = UI.NATIVE;
- }
- return _ui == UI.NATIVE;
- }
-
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isUseTabbedDisplay() {
- return _use_tabbed_display;
- }
-
- boolean isValidatePhyloXmlAgainstSchema() {
- return _validate_against_phyloxml_xsd_schema;
- }
-
- final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
+ public void setUseStyle( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
}
private int getClickToIndex( final String name ) {
else if ( name.equals( "color_subtree" ) ) {
index = Configuration.color_subtree;
}
- return index;
+ return index;
+ }
+
+ private final void initSpeciesColors() {
+ _species_colors = new Hashtable<String, Color>();
+ for( final String[] s : DEFAULT_SPECIES_COLORS ) {
+ _species_colors.put( s[ 0 ], Color.decode( s[ 1 ] ) );
+ }
}
private boolean parseBoolean( final String str ) {
/**
* read each line of config file, process non-comment lines
- * @throws IOException
+ * @throws IOException
*/
private void readConfig( final BufferedReader conf_in ) throws IOException {
String line;
else if ( key.equals( "show_overview" ) ) {
setShowOverview( parseBoolean( ( String ) st.nextElement() ) );
}
- else if ( key.equals( "show_branch_length_values" ) ) {
- setShowBranchLengthValues( parseBoolean( ( String ) st.nextElement() ) );
- }
else if ( key.equals( "background_gradient" ) ) {
setBackgroundColorGradient( parseBoolean( ( String ) st.nextElement() ) );
}
else if ( key.equals( "gui_button_border_color" ) ) {
_gui_button_border_color = Color.decode( ( String ) st.nextElement() );
}
-
- else if ( key.equals( "show_default_node_shapes" ) ) {
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [show_default_node_shapes] is deprecated, use [show_default_node_shapes_internal] and [show_default_node_shapes_external] instead" );
- final boolean b = parseBoolean( ( ( String ) st.nextElement() ).trim() );
- setShowDefaultNodeShapesInternal( b );
- setShowDefaultNodeShapesExternal( b );
- }
else if ( key.equals( "show_default_node_shapes_internal" ) ) {
setShowDefaultNodeShapesInternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
}
else if ( key.equals( "show_default_node_shapes_external" ) ) {
setShowDefaultNodeShapesExternal( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
}
+ else if ( key.equals( "show_node_shapes_for_nodes_with_vis_data" ) ) {
+ setShowDefaultNodeShapesForMarkedNodes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) );
+ }
else if ( key.equals( "default_node_size" ) ) {
final short i = parseShort( ( ( String ) st.nextElement() ).trim() );
setDefaultNodeShapeSize( i );
else if ( key.equals( "midpoint_reroot" ) ) {
setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
}
- else if ( key.equals( "ext_descendents_data_to_return" ) ) {
+ else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
if ( s.equalsIgnoreCase( "node_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
}
else if ( s.equalsIgnoreCase( "sequence_acc" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_ACC );
}
else if ( s.equalsIgnoreCase( "sequence_mol_seq_fasta" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ_FASTA );
- }
- else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );
}
else if ( s.equalsIgnoreCase( "sequence_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_NAME );
}
else if ( s.equalsIgnoreCase( "gene_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.GENE_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.GENE_NAME );
}
else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL );
+ setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_SYMBOL );
}
else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_SCIENTIFIC_NAME );
}
else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE );
- }
- else if ( s.equalsIgnoreCase( "taxonomy_common_name" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_COMM0N_NAME );
+ setExtDescNodeDataToReturn( NodeDataField.TAXONOMY_CODE );
}
else if ( s.equalsIgnoreCase( "user_selected" ) ) {
- setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN );
+ setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );
+ }
+ else if ( s.equalsIgnoreCase( "domains" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );
+ }
+ else if ( s.equalsIgnoreCase( "domains_collapsed" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );
+ }
+ else if ( s.equalsIgnoreCase( "seq_annotations" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );
+ }
+ else if ( s.equalsIgnoreCase( "go_term_ids" ) ) {
+ setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );
}
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" ) ) {
+ else if ( key.equals( "list_node_data_custom_label" ) || 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 {
+ if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
}
}
- else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
+ else if ( key.equals( "list_node_data_in" ) || 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 );
+ "] for [ext_descendents_data_to_return_on]" );
}
}
-
else if ( key.equals( "vector_data_min_color" ) ) {
_vector_data_min_color = Color.decode( ( String ) st.nextElement() );
}
else if ( key.equals( "vector_data_mean_color" ) ) {
_vector_data_mean_color = Color.decode( ( String ) st.nextElement() );
}
-
else if ( key.equals( "vector_data_width" ) ) {
_vector_data_width = parseShort( ( String ) st.nextElement() );
if ( _vector_data_width < 1 ) {
_vector_data_height = 12;
}
}
-
else if ( key.equals( "line_up_renderable_data" ) ) {
setLineUpRendarableNodeData( parseBoolean( ( String ) st.nextElement() ) );
}
-
else if ( key.equals( "right_align_domain_architectures" ) ) {
setRightLineUpDomains( parseBoolean( ( String ) st.nextElement() ) );
}
-
-
+ else if ( key.equals( "allow_thick_strokes" ) ) {
+ _allow_thick_strokes = parseBoolean( ( String ) st.nextElement() );
+ }
else if ( st.countTokens() >= 2 ) { // counts the tokens that are not
// yet retrieved!
int key_index = -1;
else if ( key.equals( "write_confidence_values" ) ) {
key_index = Configuration.write_confidence_values;
}
+ else if ( key.equals( "write_branch_length_values" ) ) {
+ key_index = Configuration.write_branch_length_values;
+ }
else if ( key.equals( "write_events" ) ) {
key_index = Configuration.write_events;
}
else if ( key.equals( "show_domain_architectures" ) ) {
key_index = Configuration.show_domain_architectures;
}
+ else if ( key.equals( "show_msa" ) ) {
+ key_index = Configuration.show_mol_seqs;
+ }
else if ( key.equals( "show_annotations" ) ) {
key_index = Configuration.show_annotation;
}
_validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
}
- static String getDefaultFontFamilyName() {
- return DEFAULT_FONT_FAMILY;
+ boolean displaySequenceRelations() {
+ return _display_sequence_relations;
}
- public enum EXT_NODE_DATA_RETURN_ON {
- BUFFER_ONLY, CONSOLE, WINODW;
+ boolean doCheckOption( final int which ) {
+ return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) )
+ || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) );
}
- public enum UI {
- CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ boolean doDisplayClickToOption( final int which ) {
+ return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" );
}
- static enum TRIPLET {
- FALSE, TRUE, UNKNOWN
+ boolean doDisplayOption( final int which ) {
+ return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
}
- public Color getVectorDataMinColor() {
- return _vector_data_min_color;
+ /**
+ * Will attempt to use the phylogeny to determine whether to check
+ * this or not (e.g. phylogram)
+ *
+ */
+ boolean doGuessCheckOption( final int which ) {
+ return display_options[ which ][ 2 ].equals( "?" );
}
- public Color getVectorDataMaxColor() {
- return _vector_data_max_color;
+ Map<String, Color> getAnnotationColors() {
+ if ( _annotation_colors == null ) {
+ _annotation_colors = new Hashtable<String, Color>();
+ }
+ return _annotation_colors;
}
- public Color getVectorDataMeanColor() {
- return _vector_data_mean_color;
+ int getBaseFontSize() {
+ return _base_font_size;
}
- public double getVectorDataHeight() {
- return _vector_data_height;
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
}
- public int getVectorDataWidth() {
- return _vector_data_width;
+ int getClickToOptionsCount() {
+ return clickto_options.length;
}
-
- final public boolean isLineUpRendarableNodeData() {
-
- return _line_up_renderable_node_data;
+
+ String getClickToTitle( final int which ) {
+ return clickto_options[ which ][ 0 ];
}
-
- final public boolean isRightLineUpDomains() {
-
- return _right_align_domains;
+
+ int getDefaultDisplayClicktoOption() {
+ return default_clickto;
}
-
- final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data) {
-
- _line_up_renderable_node_data = line_up_renderable_node_data;
+
+ SortedMap<String, Color> getDisplayColors() {
+ return _display_colors;
}
-
- final public void setRightLineUpDomains( final boolean right_align_domains ) {
-
- _right_align_domains = right_align_domains;
+
+ String getDisplayTitle( final int which ) {
+ return display_options[ which ][ 0 ];
+ }
+
+ Map<String, Color> getDomainColors() {
+ if ( _domain_colors == null ) {
+ _domain_colors = new Hashtable<String, Color>();
+ }
+ return _domain_colors;
+ }
+
+ int getGraphicsExportX() {
+ return _graphics_export_x;
+ }
+
+ int getGraphicsExportY() {
+ return _graphics_export_y;
+ }
+
+ Color getGuiBackgroundColor() {
+ return _gui_background_color;
+ }
+
+ Color getGuiButtonBackgroundColor() {
+ return _gui_button_background_color;
+ }
+
+ Color getGuiButtonBorderColor() {
+ return _gui_button_border_color;
+ }
+
+ Color getGuiButtonTextColor() {
+ return _gui_button_text_color;
+ }
+
+ Color getGuiCheckboxAndButtonActiveColor() {
+ return _gui_checkbox_and_button_active_color;
+ }
+
+ Color getGuiCheckboxTextColor() {
+ return _gui_checkbox_text_color;
+ }
+
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
+ }
+
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
+ }
+
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
+ }
+
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
+ }
+
+ double getMinConfidenceValue() {
+ return _min_confidence_value;
+ }
+
+ NODE_LABEL_DIRECTION getNodeLabelDirection() {
+ return _node_label_direction;
+ }
+
+ short getNumberOfDigitsAfterCommaForBranchLengthValues() {
+ return _number_of_digits_after_comma_for_branch_length_values;
+ }
+
+ short getNumberOfDigitsAfterCommaForConfidenceValues() {
+ return _number_of_digits_after_comma_for_confidence_values;
+ }
+
+ short getOvMaxHeight() {
+ return _ov_max_height;
+ }
+
+ short getOvMaxWidth() {
+ return _ov_max_width;
+ }
+
+ OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
+ return _ov_placement;
+ }
+
+ PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _phylogeny_graphics_type;
+ }
+
+ float getPrintLineWidth() {
+ return _print_line_width;
+ }
+
+ Hashtable<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_colors = new Hashtable<String, Color>();
+ }
+ return _sequence_colors;
+ }
+
+ Hashtable<String, Color> getSpeciesColors() {
+ if ( _species_colors == null ) {
+ initSpeciesColors();
+ }
+ return _species_colors;
+ }
+
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
+ }
+
+ boolean isAntialiasScreen() {
+ return _antialias_screen;
+ }
+
+ /**
+ * Convenience method.
+ *
+ * @return true if value in configuration file was 'yes'
+ */
+ boolean isDrawAsPhylogram() {
+ return doCheckOption( display_as_phylogram );
+ }
+
+ boolean isEditable() {
+ return _editable;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isHideControlPanelAndMenubar() {
+ return _hide_controls_and_menus;
+ }
+
+ boolean isInternalNumberAreConfidenceForNhParsing() {
+ return _internal_number_are_confidence_for_nh_parsing;
+ }
+
+ boolean isReplaceUnderscoresInNhParsing() {
+ return _nh_parsing_replace_underscores;
+ }
+
+ boolean isShowOverview() {
+ return _show_overview;
+ }
+
+ boolean isShowScale() {
+ return _show_scale;
+ }
+
+ final boolean isUseNativeUI() {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
+ _ui = UI.NATIVE;
+ }
+ return _ui == UI.NATIVE;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isUseTabbedDisplay() {
+ return _use_tabbed_display;
+ }
+
+ boolean isValidatePhyloXmlAgainstSchema() {
+ return _validate_against_phyloxml_xsd_schema;
+ }
+
+ final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
+ _taxonomy_extraction = taxonomy_extraction;
+ }
+
+ static String getDefaultFontFamilyName() {
+ return DEFAULT_FONT_FAMILY;
}
-
-
}