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;
+ }
+
+ static enum TRIPLET {
+ FALSE, TRUE, UNKNOWN
+ }
+
+ public enum UI {
+ CROSSPLATFORM, NATIVE, NIMBUS, 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" },
- { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
- { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "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" } };
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
+ { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
+ { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "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" },
+ { "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;
// Click-to options
// ------------------
final static String display_options[][] = {
- { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
- { "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" },
- { "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" },
- { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
- { "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" } };
+ { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
+ { "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" }, { "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" },
+ { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+ { "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" },
+ { "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 short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT;
private SortedMap<String, Color> _display_colors = null;
private boolean _display_sequence_relations = false;
- private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT;
- private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT;
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 = 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 ) {
}
}
+ static String getDefaultFontFamilyName() {
+ return DEFAULT_FONT_FAMILY;
+ }
+
public Configuration() {
this( null, false, false, false );
}
}
}
+ 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;
+ }
+
public String getBaseFontFamilyName() {
return _base_font_family_name;
}
+ int getBaseFontSize() {
+ return _base_font_size;
+ }
+
+ CLADOGRAM_TYPE getCladogramType() {
+ return _cladogram_type;
+ }
+
+ private int getClickToIndex( final String name ) {
+ int index = -1;
+ if ( name.equals( "edit_info" ) ) {
+ index = Configuration.display_node_data;
+ ForesterUtil
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [edit_info] is deprecated, use [display node data] instead" );
+ }
+ else if ( name.equals( "display_node_data" ) ) {
+ index = Configuration.display_node_data;
+ }
+ else if ( name.equals( "collapse_uncollapse" ) ) {
+ index = Configuration.collapse_uncollapse;
+ }
+ else if ( name.equals( "reroot" ) ) {
+ index = Configuration.reroot;
+ }
+ else if ( name.equals( "subtree" ) ) {
+ index = Configuration.subtree;
+ }
+ 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" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "open_seq_web" ) ) {
+ index = Configuration.open_seq_web;
+ }
+ else if ( name.equals( "open_pdb_web" ) ) {
+ index = Configuration.open_pdb_web;
+ }
+ 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;
+ }
+ else if ( name.equals( "copy_subtree" ) ) {
+ index = Configuration.copy_subtree;
+ }
+ else if ( name.equals( "paste_subtree" ) ) {
+ index = Configuration.paste_subtree;
+ }
+ else if ( name.equals( "delete" ) ) {
+ index = Configuration.delete_subtree_or_node;
+ }
+ else if ( name.equals( "add_new_node" ) ) {
+ index = Configuration.add_new_node;
+ }
+ else if ( name.equals( "edit_node_data" ) ) {
+ index = Configuration.edit_node_data;
+ }
+ else if ( name.equals( "select_nodes" ) ) {
+ index = Configuration.select_nodes;
+ }
+ else if ( name.equals( "display_node_popup" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME,
+ "configuration key [display_node_popup] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "custom_option" ) ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
+ return DEPRECATED;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ else if ( name.equals( "change_node_font" ) ) {
+ index = Configuration.change_node_font;
+ }
+ else if ( name.equals( "color_node_font" ) ) {
+ index = Configuration.color_node_font;
+ }
+ else if ( name.equals( "color_subtree" ) ) {
+ index = Configuration.color_subtree;
+ }
+ return index;
+ }
+
+ int getClickToOptionsCount() {
+ return clickto_options.length;
+ }
+
+ String getClickToTitle( final int which ) {
+ return clickto_options[ which ][ 0 ];
+ }
+
public int getDefaultBootstrapSamples() {
return _default_bootstrap_samples;
}
+ int getDefaultDisplayClicktoOption() {
+ return default_clickto;
+ }
+
public NodeFill getDefaultNodeFill() {
return _default_node_fill;
}
return _default_node_shape_size;
}
- public Color getDomainStructureBaseColor() {
- return _domain_structure_base_color;
+ SortedMap<String, Color> getDisplayColors() {
+ return _display_colors;
+ }
+
+ String getDisplayTitle( final int which ) {
+ return display_options[ which ][ 0 ];
}
- public Color getDomainStructureFontColor() {
- return _domain_structure_font_color;
+ Map<String, Color> getDomainColors() {
+ if ( _domain_colors == null ) {
+ _domain_colors = new Hashtable<String, Color>();
+ }
+ return _domain_colors;
}
- public NODE_DATA getExtDescNodeDataToReturn() {
+ public NodeDataField getExtDescNodeDataToReturn() {
return _ext_desc_data_to_return;
}
return _frame_y_size;
}
- public String getLabelForGetExtDescendentsData() {
- return _label_for_get_ext_descendents_data;
+ int getGraphicsExportX() {
+ return _graphics_export_x;
}
- public File getPathToLocalFastme() {
- return _path_to_local_fastme;
+ int getGraphicsExportY() {
+ return _graphics_export_y;
}
- public File getPathToLocalMafft() {
- return _path_to_local_mafft;
+ Color getGuiBackgroundColor() {
+ return _gui_background_color;
}
- public File getPathToLocalRaxml() {
- return _path_to_local_raxml;
+ Color getGuiButtonBackgroundColor() {
+ return _gui_button_background_color;
}
- public boolean isAbbreviateScientificTaxonNames() {
- return _abbreviate_scientific_names;
+ Color getGuiButtonBorderColor() {
+ return _gui_button_border_color;
}
- public boolean isBackgroundColorGradient() {
- return _background_color_gradient;
+ Color getGuiButtonTextColor() {
+ return _gui_button_text_color;
}
- public boolean isColorByTaxonomicGroup() {
- return false;
+ Color getGuiCheckboxAndButtonActiveColor() {
+ return _gui_checkbox_and_button_active_color;
}
- public boolean isColorLabelsSameAsParentBranch() {
- return _color_labels_same_as_parent_branch;
+ Color getGuiCheckboxTextColor() {
+ return _gui_checkbox_text_color;
}
- public boolean isMidpointReroot() {
- return _midpoint_root;
+ Color getGuiMenuBackgroundColor() {
+ return _gui_menu_background_color;
}
- public boolean isShowAnnotationRefSource() {
- return _show_annotation_ref_source;
+ Color getGuiMenuTextColor() {
+ return _gui_menu_text_color;
}
- public boolean isShowDefaultNodeShapesExternal() {
- return _show_default_node_shapes_external;
+ public String getLabelForGetExtDescendentsData() {
+ return _label_for_get_ext_descendents_data;
}
- public boolean isShowDefaultNodeShapesInternal() {
- return _show_default_node_shapes_internal;
+ int getMaxBaseFontSize() {
+ return _max_base_font_size;
}
- public boolean isShowDomainLabels() {
- return _show_domain_labels;
+ int getMinBaseFontSize() {
+ return _min_base_font_size;
}
- public void putDisplayColors( final String key, final Color color ) {
- getDisplayColors().put( key, color );
+ double getMinConfidenceValue() {
+ return _min_confidence_value;
}
- public void setAddTaxonomyImagesCB( final boolean b ) {
- display_options[ show_taxonomy_images ][ 1 ] = b ? "yes" : "no";
+ NODE_LABEL_DIRECTION getNodeLabelDirection() {
+ return _node_label_direction;
}
- public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) {
- _abbreviate_scientific_names = abbreviate_scientific_names;
+ short getNumberOfDigitsAfterCommaForBranchLengthValues() {
+ return _number_of_digits_after_comma_for_branch_length_values;
}
- public void setBackgroundColorGradient( final boolean background_color_gradient ) {
- _background_color_gradient = background_color_gradient;
+ short getNumberOfDigitsAfterCommaForConfidenceValues() {
+ return _number_of_digits_after_comma_for_confidence_values;
}
- public void setBaseFontFamilyName( final String base_font_family_name ) {
- _base_font_family_name = base_font_family_name;
+ short getOvMaxHeight() {
+ return _ov_max_height;
}
- public void setBaseFontSize( final int base_font_size ) {
- _base_font_size = base_font_size;
+ short getOvMaxWidth() {
+ return _ov_max_width;
}
- public void setColorizeBranches( final boolean b ) {
- display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
+ return _ov_placement;
}
- public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
- _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ public File getPathToLocalFastme() {
+ return _path_to_local_fastme;
}
- public void setDefaultNodeFill( final NodeFill default_node_fill ) {
- _default_node_fill = default_node_fill;
+ public File getPathToLocalMafft() {
+ return _path_to_local_mafft;
}
- public void setDefaultNodeShape( final NodeShape default_node_shape ) {
- _default_node_shape = default_node_shape;
- }
-
- public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
- _default_node_shape_size = default_node_shape_size;
- }
-
- public void setDisplayAsPhylogram( final boolean b ) {
- 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;
- }
-
- public void setDisplayConfidenceValues( final boolean b ) {
- display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayInternalData( final boolean b ) {
- display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayNodeNames( final boolean b ) {
- display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplaySequenceAcc( final boolean b ) {
- display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplaySequenceNames( final boolean b ) {
- 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;
- }
-
- public void setDisplaySequenceSymbols( final boolean b ) {
- display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyCode( final boolean b ) {
- display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyCommonNames( final boolean b ) {
- display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyImages( final boolean b ) {
- display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDisplayTaxonomyScientificNames( final boolean b ) {
- display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setDynamicallyHideData( final boolean b ) {
- display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
- }
-
- public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) {
- _ext_desc_data_to_return = ext_desc_data_to_return;
- }
-
- public void setFrameXSize( final int frame_x_size ) {
- _frame_x_size = frame_x_size;
- }
-
- public void setFrameYSize( final int frame_y_size ) {
- _frame_y_size = frame_y_size;
- }
-
- public void setMidpointReroot( final boolean midpoint_root ) {
- _midpoint_root = midpoint_root;
- }
-
- public void setMinConfidenceValue( final double min_confidence_value ) {
- _min_confidence_value = min_confidence_value;
- }
-
- public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
- _node_label_direction = node_label_direction;
- }
-
- 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 ) {
- _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
- }
-
- public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
- _phylogeny_graphics_type = phylogeny_graphics_type;
- }
-
- public void setPrintLineWidth( final float print_line_width ) {
- _print_line_width = print_line_width;
- }
-
- public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
- _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;
- }
-
- public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
- _show_default_node_shapes_external = show_default_node_shapes_external;
- }
-
- public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
- _show_default_node_shapes_internal = show_default_node_shapes_internal;
- }
-
- public void setShowDomainLabels( final boolean show_domain_labels ) {
- _show_domain_labels = show_domain_labels;
- }
-
- public void setShowScale( final boolean show_scale ) {
- _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" );
+ public File getPathToLocalRaxml() {
+ return _path_to_local_raxml;
}
- boolean doDisplayOption( final int which ) {
- return display_options[ which ][ 1 ].equalsIgnoreCase( "display" );
+ PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
+ return _phylogeny_graphics_type;
}
- /**
- * 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( "?" );
+ float getPrintLineWidth() {
+ return _print_line_width;
}
- Map<String, Color> getAnnotationColors() {
- if ( _annotation_colors == null ) {
- _annotation_colors = new Hashtable<String, Color>();
+ Hashtable<String, Color> getSequenceColors() {
+ if ( _sequence_colors == null ) {
+ _sequence_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 ];
+ return _sequence_colors;
}
- Map<String, Color> getDomainColors() {
- if ( _domain_colors == null ) {
- _domain_colors = new Hashtable<String, Color>();
+ Hashtable<String, Color> getSpeciesColors() {
+ if ( _species_colors == null ) {
+ initSpeciesColors();
}
- 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;
+ return _species_colors;
}
- short getOvMaxHeight() {
- return _ov_max_height;
+ final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
+ return _taxonomy_extraction;
}
- short getOvMaxWidth() {
- return _ov_max_width;
+ public double getVectorDataHeight() {
+ return _vector_data_height;
}
- OVERVIEW_PLACEMENT_TYPE getOvPlacement() {
- return _ov_placement;
+ public Color getVectorDataMaxColor() {
+ return _vector_data_max_color;
}
- PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() {
- return _phylogeny_graphics_type;
+ public Color getVectorDataMeanColor() {
+ return _vector_data_mean_color;
}
- float getPrintLineWidth() {
- return _print_line_width;
+ public Color getVectorDataMinColor() {
+ return _vector_data_min_color;
}
- Hashtable<String, Color> getSpeciesColors() {
- if ( _species_colors == null ) {
- _species_colors = new Hashtable<String, Color>();
- }
- return _species_colors;
+ public int getVectorDataWidth() {
+ return _vector_data_width;
}
- Hashtable<String, Color> getSequenceColors() {
- if ( _sequence_colors == null ) {
- _sequence_colors = new Hashtable<String, Color>();
+ 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 ] ) );
}
- return _sequence_colors;
}
- final TAXONOMY_EXTRACTION getTaxonomyExtraction() {
- return _taxonomy_extraction;
+ public boolean isAbbreviateScientificTaxonNames() {
+ return _abbreviate_scientific_names;
}
boolean isAntialiasScreen() {
return _antialias_screen;
}
+ public boolean isBackgroundColorGradient() {
+ return _background_color_gradient;
+ }
+
+ public boolean isColorByTaxonomicGroup() {
+ return false;
+ }
+
+ public boolean isColorLabelsSameAsParentBranch() {
+ return _color_labels_same_as_parent_branch;
+ }
+
/**
* Convenience method.
- *
+ *
* @return true if value in configuration file was 'yes'
*/
boolean isDrawAsPhylogram() {
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;
+ final public boolean isLineUpRendarableNodeData() {
+ return _line_up_renderable_node_data;
}
- /**
- * Only used by ArchaeoptryxE.
- *
- */
- boolean isUseTabbedDisplay() {
- return _use_tabbed_display;
- }
-
- boolean isValidatePhyloXmlAgainstSchema() {
- return _validate_against_phyloxml_xsd_schema;
+ public boolean isMidpointReroot() {
+ return _midpoint_root;
}
- final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) {
- _taxonomy_extraction = taxonomy_extraction;
+ boolean isReplaceUnderscoresInNhParsing() {
+ return _nh_parsing_replace_underscores;
}
-
- private int getClickToIndex( final String name ) {
- int index = -1;
- if ( name.equals( "edit_info" ) ) {
- index = Configuration.display_node_data;
- ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [edit_info] is deprecated, use [display node data] instead" );
- }
- else if ( name.equals( "display_node_data" ) ) {
- index = Configuration.display_node_data;
- }
- else if ( name.equals( "collapse_uncollapse" ) ) {
- index = Configuration.collapse_uncollapse;
- }
- else if ( name.equals( "reroot" ) ) {
- index = Configuration.reroot;
- }
- else if ( name.equals( "subtree" ) ) {
- index = Configuration.subtree;
- }
- 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" );
- return DEPRECATED;
- }
- else if ( name.equals( "open_seq_web" ) ) {
- index = Configuration.open_seq_web;
- }
- else if ( name.equals( "open_pdb_web" ) ) {
- index = Configuration.open_pdb_web;
- }
- 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;
- }
- else if ( name.equals( "copy_subtree" ) ) {
- index = Configuration.copy_subtree;
- }
- else if ( name.equals( "paste_subtree" ) ) {
- index = Configuration.paste_subtree;
- }
- else if ( name.equals( "delete" ) ) {
- index = Configuration.delete_subtree_or_node;
- }
- else if ( name.equals( "add_new_node" ) ) {
- index = Configuration.add_new_node;
- }
- else if ( name.equals( "edit_node_data" ) ) {
- index = Configuration.edit_node_data;
- }
- else if ( name.equals( "select_nodes" ) ) {
- index = Configuration.select_nodes;
- }
- else if ( name.equals( "display_node_popup" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "custom_option" ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" );
- return DEPRECATED;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
- }
- else if ( name.equals( "change_node_font" ) ) {
- index = Configuration.change_node_font;
- }
- else if ( name.equals( "color_node_font" ) ) {
- index = Configuration.color_node_font;
- }
- else if ( name.equals( "color_subtree" ) ) {
- index = Configuration.color_subtree;
+
+ final public boolean isRightLineUpDomains() {
+ return _right_align_domains;
+ }
+
+ public boolean isShowAnnotationRefSource() {
+ return _show_annotation_ref_source;
+ }
+
+ public boolean isShowDefaultNodeShapesExternal() {
+ 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;
+ }
+
+ public boolean isShowDomainLabels() {
+ return _show_domain_labels;
+ }
+
+ boolean isShowOverview() {
+ return _show_overview;
+ }
+
+ boolean isShowScale() {
+ return _show_scale;
+ }
+
+ final boolean isUseNativeUI() {
+ if ( ( _ui == UI.UNKNOWN ) && ForesterUtil.isMac() ) {
+ _ui = UI.NATIVE;
}
- return index;
+ return _ui == UI.NATIVE;
+ }
+
+ /**
+ * Only used by ArchaeoptryxE.
+ *
+ */
+ boolean isUseTabbedDisplay() {
+ return _use_tabbed_display;
+ }
+
+ boolean isValidatePhyloXmlAgainstSchema() {
+ return _validate_against_phyloxml_xsd_schema;
}
private boolean parseBoolean( final String str ) {
}
}
+ public void putDisplayColors( final String key, final Color color ) {
+ getDisplayColors().put( key, color );
+ }
+
/**
* 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;
} while ( line != null );
}
+ 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";
+ }
+
private void setAntialiasScreen( final boolean antialias_screen ) {
_antialias_screen = antialias_screen;
}
+ public void setBackgroundColorGradient( final boolean background_color_gradient ) {
+ _background_color_gradient = background_color_gradient;
+ }
+
+ public void setBaseFontFamilyName( final String base_font_family_name ) {
+ _base_font_family_name = base_font_family_name;
+ }
+
+ public void setBaseFontSize( final int base_font_size ) {
+ _base_font_size = base_font_size;
+ }
+
private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) {
_cladogram_type = cladogram_type;
}
+ public void setColorizeBranches( final boolean b ) {
+ display_options[ use_style ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) {
+ _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch;
+ }
+
private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) {
_default_bootstrap_samples = default_bootstrap_samples;
}
+ public void setDefaultNodeFill( final NodeFill default_node_fill ) {
+ _default_node_fill = default_node_fill;
+ }
+
+ public void setDefaultNodeShape( final NodeShape default_node_shape ) {
+ _default_node_shape = default_node_shape;
+ }
+
+ public void setDefaultNodeShapeSize( final short default_node_shape_size ) {
+ _default_node_shape_size = default_node_shape_size;
+ }
+
+ public void setDisplayAsPhylogram( final boolean b ) {
+ display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayColors( final SortedMap<String, Color> display_colors ) {
+ _display_colors = display_colors;
+ }
+
+ public void setDisplayConfidenceValues( final boolean b ) {
+ 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 setDisplayNodeNames( final boolean b ) {
+ display_options[ show_node_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceAcc( final boolean b ) {
+ display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceNames( final boolean b ) {
+ display_options[ show_seq_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplaySequenceRelations( final boolean display_sequence_relations ) {
+ _display_sequence_relations = display_sequence_relations;
+ }
+
+ public void setDisplaySequenceSymbols( final boolean b ) {
+ display_options[ show_seq_symbols ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCode( final boolean b ) {
+ display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyCommonNames( final boolean b ) {
+ display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyImages( final boolean b ) {
+ display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDisplayTaxonomyScientificNames( final boolean b ) {
+ display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no";
+ }
+
+ public void setDynamicallyHideData( final boolean b ) {
+ display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no";
+ }
+
private void setEditable( final boolean editable ) {
_editable = editable;
}
+ public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) {
+ _ext_desc_data_to_return = ext_desc_data_to_return;
+ }
+
private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) {
_ext_node_data_return_on = ext_node_data_return_on;
}
+ public void setFrameXSize( final int frame_x_size ) {
+ _frame_x_size = frame_x_size;
+ }
+
+ public void setFrameYSize( final int frame_y_size ) {
+ _frame_y_size = frame_y_size;
+ }
+
private void setGraphicsExportX( final int graphics_export_x ) {
_graphics_export_x = graphics_export_x;
}
default_clickto = getClickToIndex( clickto_name );
if ( default_clickto == -1 ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
- + "] for [default_click_to]" );
+ + "] for [default_click_to]" );
default_clickto = 0;
}
else if ( default_clickto == DEPRECATED ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
- + "]" );
+ + "]" );
_ui = UI.UNKNOWN;
}
}
else {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [phylogeny_graphics_type]" );
+ + "] for [phylogeny_graphics_type]" );
}
}
else if ( key.equals( "min_confidence_value" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "value for [pdf_export_line_width] cannot be zero or negative" );
+ "value for [pdf_export_line_width] cannot be zero or negative" );
}
}
else if ( key.equals( "window_initial_size_x" ) ) {
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "value for [default_number_of_bootstrap_resamples] cannot be negative" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
else if ( key.equals( "mafft_local" ) ) {
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 {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [cladogram_type]" );
+ + "] for [cladogram_type]" );
}
}
else if ( key.equals( "non_lined_up_cladogram" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
}
else if ( key.equals( "hide_controls_and_menus" ) ) {
_hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
else {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [overview_placement_type]" );
+ + "] for [overview_placement_type]" );
}
}
else if ( key.equals( "node_label_direction" ) ) {
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [node_label_direction]" );
+ + "] for [node_label_direction]" );
}
}
else if ( key.equals( "branch_length_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [branch_length_value_digits]" );
+ + "] for [branch_length_value_digits]" );
}
}
else if ( key.equals( "confidence_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [confidence_value_digits]" );
+ + "] for [confidence_value_digits]" );
}
}
else if ( key.equals( "allow_editing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
else {
setReplaceUnderscoresInNhParsing( r );
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
- + s
- + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
}
if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
else if ( key.equals( "gui_button_border_color" ) ) {
_gui_button_border_color = Color.decode( ( String ) st.nextElement() );
}
- else if ( key.equals( "domain_structure_font_color" ) ) {
- _domain_structure_font_color = Color.decode( ( String ) st.nextElement() );
- }
- else if ( key.equals( "domain_structure_base_color" ) ) {
- _domain_structure_base_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 {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
- + "] for [default_node_fill]" );
+ + "] for [default_node_fill]" );
}
}
else if ( key.equals( "default_node_shape" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
- + "] for [default_node_shape]" );
+ + "] for [default_node_shape]" );
}
}
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]" );
+ + "] 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 );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return_on]" );
+ + "] 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( "color_branches" ) ) {
key_index = Configuration.use_style;
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
}
else if ( key.equals( "width_branches" ) ) {
key_index = Configuration.width_branches;
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;
}
}
else if ( key.equals( "annotation_color" ) ) {
getAnnotationColors()
- .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [function_color] is deprecated" );
+ "configuration key [function_color] is deprecated" );
}
else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
- + "] in: " + config_filename );
+ + "] in: " + config_filename );
}
}
}
_label_for_get_ext_descendents_data = label_for_get_ext_descendents_data;
}
+ final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) {
+ _line_up_renderable_node_data = line_up_renderable_node_data;
+ }
+
private void setMaxBaseFontSize( final int max_base_font_size ) {
_max_base_font_size = max_base_font_size;
}
+ public void setMidpointReroot( final boolean midpoint_root ) {
+ _midpoint_root = midpoint_root;
+ }
+
private void setMinBaseFontSize( final int min_base_font_size ) {
_min_base_font_size = min_base_font_size;
}
+ public void setMinConfidenceValue( final double min_confidence_value ) {
+ _min_confidence_value = min_confidence_value;
+ }
+
+ public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) {
+ _node_label_direction = node_label_direction;
+ }
+
+ 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 ) {
+ _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values;
+ }
+
private void setOvMaxHeight( final short ov_max_height ) {
_ov_max_height = ov_max_height;
}
_path_to_local_raxml = path_to_local_raxml;
}
- private void setShowAnnotationRefSource( final boolean b ) {
- _show_annotation_ref_source = b;
+ public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) {
+ _phylogeny_graphics_type = phylogeny_graphics_type;
}
- private void setShowOverview( final boolean show_overview ) {
- _show_overview = show_overview;
+ public void setPrintLineWidth( final float print_line_width ) {
+ _print_line_width = print_line_width;
}
- private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
- _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
+ public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) {
+ _nh_parsing_replace_underscores = nh_parsing_replace_underscores;
}
- static String getDefaultFontFamilyName() {
- return DEFAULT_FONT_FAMILY;
+ final public void setRightLineUpDomains( final boolean right_align_domains ) {
+ _right_align_domains = right_align_domains;
}
- public enum EXT_NODE_DATA_RETURN_ON {
- BUFFER_ONLY, CONSOLE, WINODW;
+ private void setShowAnnotationRefSource( final boolean b ) {
+ _show_annotation_ref_source = b;
}
- public enum UI {
- CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
+ public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) {
+ _show_default_node_shapes_external = show_default_node_shapes_external;
}
- static enum TRIPLET {
- FALSE, TRUE, UNKNOWN
+ 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 Color getVectorDataMinColor() {
- return _vector_data_min_color;
+ public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) {
+ _show_default_node_shapes_internal = show_default_node_shapes_internal;
}
- public Color getVectorDataMaxColor() {
- return _vector_data_max_color;
+ public void setShowDomainLabels( final boolean show_domain_labels ) {
+ _show_domain_labels = show_domain_labels;
}
- public Color getVectorDataMeanColor() {
- return _vector_data_mean_color;
+ private void setShowOverview( final boolean show_overview ) {
+ _show_overview = show_overview;
}
- public double getVectorDataHeight() {
- return _vector_data_height;
+ public void setShowScale( final boolean show_scale ) {
+ _show_scale = show_scale;
}
- public int getVectorDataWidth() {
- return _vector_data_width;
+ 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 void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) {
+ _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema;
+ }
+
+ public boolean isAllowThickStrokes() {
+ return _allow_thick_strokes;
}
}