X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=adb0f402486c57dfa4cee9a4cd0ccb38dd76204c;hb=a32f4076b5b309b4dcc0852d6283a2bd18785f28;hp=271bdfa73ca6a9d685dc6939682deda7f06a1d88;hpb=187777133416c347dd7da371d7edf7ce20ebe56b;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 271bdfa..adb0f40 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -47,7 +47,7 @@ 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.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; @@ -55,15 +55,44 @@ import org.forester.util.ForesterUtil; 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; @@ -89,19 +118,20 @@ public final class Configuration { // 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; @@ -129,6 +159,8 @@ public final class Configuration { 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 _sequence_colors; private static Hashtable _annotation_colors; @@ -171,7 +203,7 @@ public final class Configuration { private SortedMap _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; @@ -205,8 +237,8 @@ public final class Configuration { 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; @@ -220,6 +252,9 @@ public final class Configuration { 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 ) { @@ -232,6 +267,10 @@ public final class Configuration { } } + static String getDefaultFontFamilyName() { + return DEFAULT_FONT_FAMILY; + } + public Configuration() { this( null, false, false, false ); } @@ -296,14 +335,158 @@ public final class Configuration { } } + 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 getAnnotationColors() { + if ( _annotation_colors == null ) { + _annotation_colors = new Hashtable(); + } + 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; } @@ -316,7 +499,22 @@ public final class Configuration { return _default_node_shape_size; } - public NODE_DATA getExtDescNodeDataToReturn() { + SortedMap getDisplayColors() { + return _display_colors; + } + + String getDisplayTitle( final int which ) { + return display_options[ which ][ 0 ]; + } + + Map getDomainColors() { + if ( _domain_colors == null ) { + _domain_colors = new Hashtable(); + } + return _domain_colors; + } + + public NodeDataField getExtDescNodeDataToReturn() { return _ext_desc_data_to_return; } @@ -332,398 +530,153 @@ public final class Configuration { 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 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 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" ) ); + public File getPathToLocalMafft() { + return _path_to_local_mafft; } - 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 getAnnotationColors() { - if ( _annotation_colors == null ) { - _annotation_colors = new Hashtable(); + Hashtable getSequenceColors() { + if ( _sequence_colors == null ) { + _sequence_colors = new Hashtable(); } - 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 getDisplayColors() { - return _display_colors; - } - - String getDisplayTitle( final int which ) { - return display_options[ which ][ 0 ]; + return _sequence_colors; } - Map getDomainColors() { - if ( _domain_colors == null ) { - _domain_colors = new Hashtable(); + Hashtable 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 getSpeciesColors() { - if ( _species_colors == null ) { - _species_colors = new Hashtable(); - } - return _species_colors; + public int getVectorDataWidth() { + return _vector_data_width; } - Hashtable getSequenceColors() { - if ( _sequence_colors == null ) { - _sequence_colors = new Hashtable(); + private final void initSpeciesColors() { + _species_colors = new Hashtable(); + 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() { @@ -734,9 +687,21 @@ public final class Configuration { 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() { @@ -759,134 +724,67 @@ public final class Configuration { 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; - } - - final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { - _taxonomy_extraction = taxonomy_extraction; + public boolean isMidpointReroot() { + return _midpoint_root; } - 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; + boolean isReplaceUnderscoresInNhParsing() { + return _nh_parsing_replace_underscores; + } + + 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 ) { @@ -964,9 +862,13 @@ public final class Configuration { } } + 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; @@ -985,26 +887,138 @@ public final class Configuration { } 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 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; } @@ -1031,7 +1045,7 @@ public final class Configuration { 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 ) { @@ -1051,7 +1065,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str - + "]" ); + + "]" ); _ui = UI.UNKNOWN; } } @@ -1090,7 +1104,7 @@ public final class Configuration { 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" ) ) { @@ -1144,7 +1158,7 @@ public final class Configuration { } 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" ) ) { @@ -1169,8 +1183,8 @@ public final class Configuration { } 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" ) ) { @@ -1197,9 +1211,6 @@ public final class Configuration { 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() ) ); } @@ -1228,13 +1239,13 @@ public final class Configuration { } 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() ); @@ -1267,7 +1278,7 @@ public final class Configuration { 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" ) ) { @@ -1281,7 +1292,7 @@ public final class Configuration { 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" ) ) { @@ -1291,7 +1302,7 @@ public final class Configuration { } 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" ) ) { @@ -1301,7 +1312,7 @@ public final class Configuration { } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [confidence_value_digits]" ); + + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { @@ -1314,8 +1325,8 @@ public final class Configuration { 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 ); @@ -1337,15 +1348,15 @@ public final class Configuration { } 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" ) ) { @@ -1375,21 +1386,15 @@ public final class Configuration { 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 ); @@ -1407,7 +1412,7 @@ public final class Configuration { } 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" ) ) { @@ -1420,63 +1425,65 @@ public final class Configuration { } 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 ); @@ -1489,10 +1496,9 @@ public final class Configuration { } 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() ); } @@ -1502,7 +1508,6 @@ public final class Configuration { 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 ) { @@ -1515,7 +1520,15 @@ public final class Configuration { _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; @@ -1540,6 +1553,9 @@ public final class Configuration { 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; } @@ -1549,8 +1565,8 @@ public final class Configuration { 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; @@ -1558,6 +1574,9 @@ public final class Configuration { 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; } @@ -1643,18 +1662,18 @@ public final class Configuration { } 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 ); } } } @@ -1668,14 +1687,38 @@ public final class Configuration { _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; } @@ -1700,51 +1743,63 @@ public final class Configuration { _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; } }