X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=c578e05d66214e3a99da0ac7f905a2a574dc4980;hb=aec065f948a075773794133f102ea19eb1d59f64;hp=7b440a8d0ecf7a360ecf8efe0fe062dfea74c90d;hpb=37cb4c1bc15ea30a6f64953d5e23e09694083f06;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 7b440a8..c578e05 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -34,7 +34,6 @@ import java.io.File; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.net.MalformedURLException; import java.net.URL; import java.util.Arrays; import java.util.Hashtable; @@ -56,23 +55,20 @@ import org.forester.util.ForesterUtil; public final class Configuration { - public enum EXT_NODE_DATA_RETURN_ON { - CONSOLE, WINODW, BUFFER_ONLY; - } static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; - private static final String WEB_LINK_KEY = "web_link"; private static final String DISPLAY_COLOR_KEY = "display_color"; private static final int DEPRECATED = -2; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; private boolean _hide_controls_and_menus = false; private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - private SortedMap _weblinks = null; private SortedMap _display_colors = null; private boolean _antialias_screen = true; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; private String _base_font_family_name = ""; private int _base_font_size = -1; + private int _min_base_font_size = 2; + private int _max_base_font_size = 20; private int _graphics_export_x = -1; private int _graphics_export_y = -1; private short _ov_max_width = 80; @@ -87,7 +83,7 @@ public final class Configuration { private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; private boolean _editable = true; private boolean _nh_parsing_replace_underscores = false; - private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT; private boolean _internal_number_are_confidence_for_nh_parsing = false; private boolean _display_sequence_relations = false; private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; @@ -95,16 +91,16 @@ public final class Configuration { private boolean _show_domain_labels = true; private boolean _abbreviate_scientific_names = false; private boolean _color_labels_same_as_parent_branch = false; - private boolean _show_default_node_shapes = false; - private NodeShape _default_node_shape = NodeShape.CIRCLE; - private NodeFill _default_node_fill = NodeFill.GRADIENT; + private boolean _show_default_node_shapes_internal = false; + private boolean _show_default_node_shapes_external = false; + private NodeShape _default_node_shape = NodeShape.RECTANGLE; + private NodeFill _default_node_fill = NodeFill.SOLID; private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private boolean _taxonomy_colorize_node_shapes = false; private int _default_bootstrap_samples = -1; private File _path_to_local_mafft = null; private File _path_to_local_fastme = null; private File _path_to_local_raxml = null; - private File _path_to_local_clustalo = null; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -245,7 +241,6 @@ public final class Configuration { else { config_filename = cf; } - setWebLinks( new TreeMap() ); setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -299,325 +294,439 @@ public final class Configuration { } } - private void createWebLink( final String url_str, final String desc, final String source_identifier ) { - WebLink weblink = null; - boolean ex = false; - try { - weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); - } - catch ( final MalformedURLException e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); - ex = true; - } - if ( !ex && ( weblink != null ) ) { - getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); - } - } - - boolean displaySequenceRelations() { - return _display_sequence_relations; + public String getBaseFontFamilyName() { + return _base_font_family_name; } - boolean doCheckOption( final int which ) { - return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) - || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); + public int getDefaultBootstrapSamples() { + return _default_bootstrap_samples; } - boolean doDisplayClickToOption( final int which ) { - return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + public NodeFill getDefaultNodeFill() { + return _default_node_fill; } - boolean doDisplayOption( final int which ) { - return display_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + public NodeShape getDefaultNodeShape() { + return _default_node_shape; } - /** - * Will attempt to use the phylogeny to determine whether to check - * this or not (e.g. phylogram) - * - */ - boolean doGuessCheckOption( final int which ) { - return display_options[ which ][ 2 ].equals( "?" ); + public short getDefaultNodeShapeSize() { + return _default_node_shape_size; } - Map getAnnotationColors() { - if ( _annotation_colors == null ) { - _annotation_colors = new Hashtable(); - } - return _annotation_colors; + public Color getDomainStructureBaseColor() { + return _domain_structure_base_color; } - public String getBaseFontFamilyName() { - return _base_font_family_name; + public Color getDomainStructureFontColor() { + return _domain_structure_font_color; } - int getBaseFontSize() { - return _base_font_size; + public NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; } - CLADOGRAM_TYPE getCladogramType() { - return _cladogram_type; + public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { + return _ext_node_data_return_on; } - 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_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( "go_to_swiss_prot" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); - return DEPRECATED; - } - return index; + public int getFrameXSize() { + return _frame_x_size; } - int getClickToOptionsCount() { - return clickto_options.length; + public int getFrameYSize() { + return _frame_y_size; } - String getClickToTitle( final int which ) { - return clickto_options[ which ][ 0 ]; + public String getLabelForGetExtDescendentsData() { + return _label_for_get_ext_descendents_data; } - public int getDefaultBootstrapSamples() { - return _default_bootstrap_samples; + public File getPathToLocalFastme() { + return _path_to_local_fastme; } public File getpathToLocalMafft() { return _path_to_local_mafft; } - public File getPathToLocalFastme() { - return _path_to_local_fastme; - } - public File getPathToLocalRaxml() { return _path_to_local_raxml; } - int getDefaultDisplayClicktoOption() { - return default_clickto; + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; } - public NodeFill getDefaultNodeFill() { - return _default_node_fill; + public boolean isBackgroundColorGradient() { + return _background_color_gradient; } - public NodeShape getDefaultNodeShape() { - return _default_node_shape; + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; } - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; } - SortedMap getDisplayColors() { - return _display_colors; + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; } - String getDisplayTitle( final int which ) { - return display_options[ which ][ 0 ]; + public boolean isShowDomainLabels() { + return _show_domain_labels; } - Map getDomainColors() { - if ( _domain_colors == null ) { - _domain_colors = new Hashtable(); - } - return _domain_colors; + public boolean isTaxonomyColorizeNodeShapes() { + return _taxonomy_colorize_node_shapes; } - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; + public void putDisplayColors( final String key, final Color color ) { + getDisplayColors().put( key, color ); } - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; + public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { + _abbreviate_scientific_names = abbreviate_scientific_names; } - int getGraphicsExportX() { - return _graphics_export_x; + public void setBackgroundColorGradient( final boolean background_color_gradient ) { + _background_color_gradient = background_color_gradient; } - int getGraphicsExportY() { - return _graphics_export_y; + public void setBaseFontFamilyName( final String base_font_family_name ) { + _base_font_family_name = base_font_family_name; } - Color getGuiBackgroundColor() { - return _gui_background_color; + public void setBaseFontSize( final int base_font_size ) { + _base_font_size = base_font_size; } - Color getGuiButtonBackgroundColor() { - return _gui_button_background_color; + private void setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; } - Color getGuiButtonBorderColor() { - return _gui_button_border_color; + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; } - Color getGuiButtonTextColor() { - return _gui_button_text_color; + public void setColorizeBranches( final boolean b ) { + display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; } - Color getGuiCheckboxAndButtonActiveColor() { - return _gui_checkbox_and_button_active_color; + public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } - Color getGuiCheckboxTextColor() { - return _gui_checkbox_text_color; + public void setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; } - Color getGuiMenuBackgroundColor() { - return _gui_menu_background_color; + public void setDefaultNodeShape( final NodeShape default_node_shape ) { + _default_node_shape = default_node_shape; } - Color getGuiMenuTextColor() { - return _gui_menu_text_color; + public void setDefaultNodeShapeSize( final short default_node_shape_size ) { + _default_node_shape_size = default_node_shape_size; } - double getMinConfidenceValue() { - return _min_confidence_value; + public void setDisplayAsPhylogram( final boolean b ) { + display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } - NODE_LABEL_DIRECTION getNodeLabelDirection() { - return _node_label_direction; + public void setDisplayColors( final SortedMap display_colors ) { + _display_colors = display_colors; } - short getNumberOfDigitsAfterCommaForBranchLengthValues() { - return _number_of_digits_after_comma_for_branch_length_values; + public void setDisplayConfidenceValues( final boolean b ) { + display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; } - short getNumberOfDigitsAfterCommaForConfidenceValues() { - return _number_of_digits_after_comma_for_confidence_values; + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } - short getOvMaxHeight() { - return _ov_max_height; + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; } - short getOvMaxWidth() { - return _ov_max_width; + public void setDisplaySequenceAcc( final boolean b ) { + display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; } - OVERVIEW_PLACEMENT_TYPE getOvPlacement() { - return _ov_placement; + public void setDisplaySequenceNames( final boolean b ) { + display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; } - PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _phylogeny_graphics_type; + public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { + _display_sequence_relations = display_sequence_relations; } - float getPrintLineWidth() { - return _print_line_width; + public void setDisplaySequenceSymbols( final boolean b ) { + display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; } - Hashtable getSpeciesColors() { - if ( _species_colors == null ) { - _species_colors = new Hashtable(); + 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 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; + } + + public void setTaxonomyColorize( final boolean b ) { + display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; + } + + public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { + _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + } + + public void setUseBranchesWidths( final boolean b ) { + display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; + } + + 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 _species_colors; + return _annotation_colors; } - TreeColorSet getTreeColorSet() { - return null; + int getBaseFontSize() { + return _base_font_size; } - TreeFontSet getTreeFontSet() { - return null; + int getMinBaseFontSize() { + return _min_base_font_size; } - WebLink getWebLink( final String source ) { - return getWebLinks().get( source ); + int getMaxBaseFontSize() { + return _max_base_font_size; } - Map getWebLinks() { - return _weblinks; + CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; } - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; + int getClickToOptionsCount() { + return clickto_options.length; } - boolean isAntialiasScreen() { - return _antialias_screen; + String getClickToTitle( final int which ) { + return clickto_options[ which ][ 0 ]; } - public boolean isBackgroundColorGradient() { - return _background_color_gradient; + int getDefaultDisplayClicktoOption() { + return default_clickto; } - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; + 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; + } + + 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; + } + + double getMinConfidenceValue() { + return _min_confidence_value; + } + + NODE_LABEL_DIRECTION getNodeLabelDirection() { + return _node_label_direction; + } + + short getNumberOfDigitsAfterCommaForBranchLengthValues() { + return _number_of_digits_after_comma_for_branch_length_values; + } + + short getNumberOfDigitsAfterCommaForConfidenceValues() { + return _number_of_digits_after_comma_for_confidence_values; + } + + short getOvMaxHeight() { + return _ov_max_height; + } + + short getOvMaxWidth() { + return _ov_max_width; + } + + OVERVIEW_PLACEMENT_TYPE getOvPlacement() { + return _ov_placement; + } + + PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _phylogeny_graphics_type; + } + + float getPrintLineWidth() { + return _print_line_width; + } + + Hashtable getSpeciesColors() { + if ( _species_colors == null ) { + _species_colors = new Hashtable(); + } + return _species_colors; + } + + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; + } + + boolean isAntialiasScreen() { + if ( AptxUtil.isMac() ) { + // Apple Macintosh graphics are slow, turn off anti-alias. + return false; + } + return _antialias_screen; } /** @@ -633,14 +742,6 @@ public final class Configuration { return _editable; } - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { - return _taxonomy_extraction; - } - - boolean isHasWebLink( final String source ) { - return getWebLinks().containsKey( source ); - } - /** * Only used by ArchaeoptryxE. * @@ -661,14 +762,6 @@ public final class Configuration { return _show_branch_length_values; } - public boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; - } - - public boolean isShowDomainLabels() { - return _show_domain_labels; - } - boolean isShowOverview() { return _show_overview; } @@ -677,27 +770,110 @@ public final class Configuration { return _show_scale; } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { + if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() ) { _ui = UI.NATIVE; } - return _ui == UI.NATIVE; - } - - /** - * Only used by ArchaeoptryxE. - * - */ - boolean isUseTabbedDisplay() { - return _use_tabbed_display; - } - - boolean isValidatePhyloXmlAgainstSchema() { - return _validate_against_phyloxml_xsd_schema; + return _ui == UI.NATIVE; + } + + /** + * Only used by ArchaeoptryxE. + * + */ + boolean isUseTabbedDisplay() { + return _use_tabbed_display; + } + + boolean isValidatePhyloXmlAgainstSchema() { + return _validate_against_phyloxml_xsd_schema; + } + + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; + } + + 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_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( "go_to_swiss_prot" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); + return DEPRECATED; + } + return index; } private boolean parseBoolean( final String str ) { @@ -775,10 +951,6 @@ 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 @@ -800,136 +972,24 @@ public final class Configuration { } while ( line != null ); } - public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; - } - 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[ color_branches ][ 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; } - private void setPathToLocalMafft( final File path_to_local_mafft ) { - _path_to_local_mafft = path_to_local_mafft; - } - - private void setPathToLocalFastme( final File path_to_local_fastme ) { - _path_to_local_fastme = path_to_local_fastme; - } - - private void setPathToLocalRaxml( final File path_to_local_raxml ) { - _path_to_local_raxml = path_to_local_raxml; - } - - public File getPathToLocalClustalOmega() { - return _path_to_local_clustalo; - } - - public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) { - _path_to_local_clustalo = path_to_local_clustalo; - } - - public void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; - } - - 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 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_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_gene_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; } - final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { - _taxonomy_extraction = taxonomy_extraction; + private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { + _ext_node_data_return_on = ext_node_data_return_on; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -1035,6 +1095,20 @@ public final class Configuration { setBaseFontSize( i ); } } + else if ( key.equals( "font_size_min" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 0 ) { + setMinBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_max" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 1 ) { + setMaxBaseFontSize( i ); + } + } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); @@ -1086,12 +1160,6 @@ public final class Configuration { "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } - else if ( key.equals( "clustalo_local" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - if ( !ForesterUtil.isEmpty( str ) ) { - setPathToLocalClustalOmega( new File( str ) ); - } - } else if ( key.equals( "mafft_local" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); if ( !ForesterUtil.isEmpty( str ) ) { @@ -1243,10 +1311,10 @@ public final class Configuration { setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); } else if ( s.equalsIgnoreCase( "yes" ) ) { - setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED ); } else if ( s.equalsIgnoreCase( "pfam" ) ) { - setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT ); } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, @@ -1292,7 +1360,18 @@ public final class Configuration { _domain_structure_base_color = Color.decode( ( String ) st.nextElement() ); } else if ( key.equals( "show_default_node_shapes" ) ) { - setShowDefaultNodeShapes( parseBoolean( ( ( String ) st.nextElement() ).trim() ) ); + 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( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); @@ -1338,6 +1417,9 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { setExtDescNodeDataToReturn( NODE_DATA.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 ); } @@ -1561,17 +1643,6 @@ public final class Configuration { else if ( key.equals( DISPLAY_COLOR_KEY ) ) { putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } - else if ( key.equals( WEB_LINK_KEY ) ) { - if ( st.countTokens() == 3 ) { - createWebLink( ( String ) st.nextElement(), - ( String ) st.nextElement(), - ( String ) st.nextElement() ); - } - else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "illegal format in configuration file for key [" + key + "]" ); - } - } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); @@ -1588,26 +1659,6 @@ public final class Configuration { _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } - public String getLabelForGetExtDescendentsData() { - return _label_for_get_ext_descendents_data; - } - - public void setMinConfidenceValue( final double min_confidence_value ) { - _min_confidence_value = min_confidence_value; - } - - 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; } @@ -1620,99 +1671,39 @@ public final class Configuration { _ov_placement = ov_placement; } - 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; + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; } - public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = show_default_node_shapes; + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; } - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; } private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } - public void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; - } - - public void setTaxonomyColorize( final boolean b ) { - display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; - } - - public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - - public void setUseBranchesWidths( final boolean b ) { - display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; - } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; - } - static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } - static enum TRIPLET { - TRUE, FALSE, UNKNOWN + public enum EXT_NODE_DATA_RETURN_ON { + CONSOLE, WINODW, BUFFER_ONLY; } public enum UI { NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } - public NODE_DATA getExtDescNodeDataToReturn() { - return _ext_desc_data_to_return; - } - - public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { - _ext_desc_data_to_return = ext_desc_data_to_return; - } - - public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { - return _ext_node_data_return_on; - } - - private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { - _ext_node_data_return_on = ext_node_data_return_on; - } - - public int getFrameXSize() { - return _frame_x_size; - } - - public int getFrameYSize() { - return _frame_y_size; - } - - 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; + static enum TRIPLET { + TRUE, FALSE, UNKNOWN } }