X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=36961368037c529b8aa1ffb642b5df01e7d21a8e;hb=814c97be10a4c55b0bb642668f9ef8e1f80d5a6c;hp=8ec94abeb10270f98b19f8ea6dfac6abbfd0b996;hpb=54d8e3a926c3cf3477199c8b85aca478230e223c;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 8ec94ab..3696136 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -67,32 +67,32 @@ public final class Configuration { FALSE, TRUE, UNKNOWN } final static String clickto_options[][] = { - { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" }, - { "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" } }; + { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, + { "Go to Sub/Supertree", "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" } , { "Uncollapse All", "display" }, { "Order Subtree", "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" } }; + { "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; @@ -114,24 +114,28 @@ public final class Configuration { final static int sort_descendents = 18; final static int get_ext_desc_data = 19; final static int select_nodes = 20; + final static int uncollapse_all = 21; + final static int order_subtree = 22; + // ------------------ // 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" }, { "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" } }; + { "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" } + , { "Taxonomy Rank", "display", "no" }, { "Show External Data", "display", "yes" }}; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -161,6 +165,9 @@ public final class Configuration { final static int show_gene_names = 26; final static int show_mol_seqs = 27; final static int write_branch_length_values = 28; + final static int show_tax_rank = 29; + final static int display_external_data = 30; + static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static Hashtable _sequence_colors; private static Hashtable _annotation_colors; @@ -179,7 +186,7 @@ public final class Configuration { String config_filename; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; - String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; + String default_config_filename = AptxConstants.DEFAULT_CONFIGURATION_FILE_NAME; // -------------- // Color set // -------------- @@ -188,18 +195,18 @@ public final class Configuration { // Fonts // ------- TreeFontSet tree_font_set; - boolean verbose = Constants.VERBOSE_DEFAULT; + boolean verbose = AptxConstants.VERBOSE_DEFAULT; private boolean _abbreviate_scientific_names = false; private boolean _antialias_screen = true; private boolean _background_color_gradient = false; private String _base_font_family_name = ""; private int _base_font_size = -1; - private CLADOGRAM_TYPE _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; + private CLADOGRAM_TYPE _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT; private boolean _color_labels_same_as_parent_branch = false; private int _default_bootstrap_samples = -1; private NodeFill _default_node_fill = NodeFill.SOLID; private NodeShape _default_node_shape = NodeShape.RECTANGLE; - private short _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; + private short _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; private SortedMap _display_colors = null; private boolean _display_sequence_relations = false; private boolean _editable = true; @@ -207,16 +214,14 @@ public final class Configuration { private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; private int _frame_x_size; private int _frame_y_size; - private int _graphics_export_x = -1; - private int _graphics_export_y = -1; - private Color _gui_background_color = Constants.GUI_BACKGROUND_DEFAULT; - private Color _gui_button_background_color = Constants.BUTTON_BACKGROUND_COLOR_DEFAULT; - private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; - private Color _gui_button_text_color = Constants.BUTTON_TEXT_COLOR_DEFAULT; - private Color _gui_checkbox_and_button_active_color = Constants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; - private Color _gui_checkbox_text_color = Constants.CHECKBOX_TEXT_COLOR_DEFAULT; - private Color _gui_menu_background_color = Constants.MENU_BACKGROUND_COLOR_DEFAULT; - private Color _gui_menu_text_color = Constants.MENU_TEXT_COLOR_DEFAULT; + private Color _gui_background_color = AptxConstants.GUI_BACKGROUND_DEFAULT; + private Color _gui_button_background_color = AptxConstants.BUTTON_BACKGROUND_COLOR_DEFAULT; + private Color _gui_button_border_color = AptxConstants.BUTTON_BORDER_COLOR_DEFAULT; + private Color _gui_button_text_color = AptxConstants.BUTTON_TEXT_COLOR_DEFAULT; + private Color _gui_checkbox_and_button_active_color = AptxConstants.CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT; + private Color _gui_checkbox_text_color = AptxConstants.CHECKBOX_TEXT_COLOR_DEFAULT; + private Color _gui_menu_background_color = AptxConstants.MENU_BACKGROUND_COLOR_DEFAULT; + private Color _gui_menu_text_color = AptxConstants.MENU_TEXT_COLOR_DEFAULT; private boolean _hide_controls_and_menus = false; private boolean _internal_number_are_confidence_for_nh_parsing = false; private String _label_for_get_ext_descendents_data = ""; @@ -226,8 +231,8 @@ public final class Configuration { private double _min_confidence_value = Options.MIN_CONFIDENCE_DEFAULT; private boolean _nh_parsing_replace_underscores = false; private NODE_LABEL_DIRECTION _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; - private short _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; - private short _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; + private short _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; + private short _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; private short _ov_max_height = 80; private short _ov_max_width = 80; private OVERVIEW_PLACEMENT_TYPE _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; @@ -235,7 +240,7 @@ public final class Configuration { private File _path_to_local_mafft = null; private File _path_to_local_raxml = null; private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - private float _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; + private float _print_line_width = AptxConstants.PDF_LINE_WIDTH_DEFAULT; private boolean _show_annotation_ref_source = true; private boolean _show_default_node_shapes_external = false; private boolean _show_default_node_shapes_for_marked_nodes = false; @@ -246,7 +251,7 @@ public final class Configuration { private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; - private boolean _validate_against_phyloxml_xsd_schema = Constants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; + private boolean _validate_against_phyloxml_xsd_schema = AptxConstants.VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT; private Color _vector_data_min_color = Color.BLUE; private Color _vector_data_max_color = Color.YELLOW; private Color _vector_data_mean_color = Color.WHITE; @@ -255,15 +260,16 @@ public final class Configuration { private boolean _line_up_renderable_node_data = true; private boolean _right_align_domains = false; private boolean _allow_thick_strokes = false; + private boolean _could_read_config_file = false; static { - for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { + for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) { if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { DEFAULT_FONT_FAMILY = font_name; break; } } if ( ForesterUtil.isEmpty( DEFAULT_FONT_FAMILY ) ) { - DEFAULT_FONT_FAMILY = Constants.DEFAULT_FONT_CHOICES[ Constants.DEFAULT_FONT_CHOICES.length - 1 ]; + DEFAULT_FONT_FAMILY = AptxConstants.DEFAULT_FONT_CHOICES[ AptxConstants.DEFAULT_FONT_CHOICES.length - 1 ]; } } @@ -278,6 +284,7 @@ public final class Configuration { else { config_filename = cf; } + _could_read_config_file = false; setDisplayColors( new TreeMap() ); config_filename = config_filename.trim(); URL u = null; @@ -290,16 +297,17 @@ public final class Configuration { final BufferedReader bf = new BufferedReader( isr ); readConfig( bf ); bf.close(); - ForesterUtil.programMessage( Constants.PRG_NAME, "successfully read from configuration url [" + ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url [" + config_filename + "]" ); + _could_read_config_file = true; } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e.getLocalizedMessage() ); } } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration url [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration url [" + config_filename + "]" ); } } @@ -314,17 +322,18 @@ public final class Configuration { final BufferedReader bf = new BufferedReader( new FileReader( f ) ); readConfig( bf ); bf.close(); + _could_read_config_file = true; } catch ( final Exception e ) { if ( verbose ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from [" + config_filename + "]: " + e ); } } } else { if ( verbose ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "cannot find or open configuration file [" + config_filename + "]" ); } } @@ -518,6 +527,10 @@ public final class Configuration { public void setDisplayInternalData( final boolean b ) { display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } + + public void setDisplayExternalData( final boolean b ) { + display_options[ display_external_data ][ 2 ] = b ? "yes" : "no"; + } public void setDisplayMultipleSequenceAlignment( final boolean b ) { display_options[ show_mol_seqs ][ 2 ] = b ? "yes" : "no"; @@ -546,6 +559,10 @@ public final class Configuration { public void setDisplayTaxonomyCode( final boolean b ) { display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; } + + public void setDisplayTaxonomyRank( final boolean b ) { + display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no"; + } public void setDisplayTaxonomyCommonNames( final boolean b ) { display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; @@ -644,8 +661,8 @@ public final class Configuration { 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" ); + .printWarningMessage( AptxConstants.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; @@ -653,6 +670,9 @@ public final class Configuration { else if ( name.equals( "collapse_uncollapse" ) ) { index = Configuration.collapse_uncollapse; } + else if ( name.equals( "uncollapse_all" ) ) { + index = Configuration.uncollapse_all; + } else if ( name.equals( "reroot" ) ) { index = Configuration.reroot; } @@ -662,6 +682,9 @@ public final class Configuration { else if ( name.equals( "swap" ) ) { index = Configuration.swap; } + else if ( name.equals( "order_subtree" ) ) { + index = Configuration.order_subtree; + } else if ( name.equals( "sort_descendants" ) ) { index = Configuration.sort_descendents; } @@ -670,7 +693,7 @@ public final class Configuration { } else if ( name.equals( "display_sequences" ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); + .printWarningMessage( AptxConstants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); return DEPRECATED; } else if ( name.equals( "open_seq_web" ) ) { @@ -707,12 +730,12 @@ public final class Configuration { index = Configuration.select_nodes; } else if ( name.equals( "display_node_popup" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [display_node_popup] is deprecated" ); + ForesterUtil.printWarningMessage( AptxConstants.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" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "configuration key [custom_option] is deprecated" ); return DEPRECATED; } else if ( name.equals( "color_subtree" ) ) { @@ -746,7 +769,7 @@ public final class Configuration { return false; } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse boolean value from [" + str + "]" ); return false; } } @@ -757,7 +780,7 @@ public final class Configuration { d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse double from [" + str + "]" ); d = 0.0; } return d; @@ -769,7 +792,7 @@ public final class Configuration { f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse float from [" + str + "]" ); f = 0.0f; } return f; @@ -781,7 +804,7 @@ public final class Configuration { i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse integer from [" + str + "]" ); i = -1; } return i; @@ -793,7 +816,7 @@ public final class Configuration { i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse short from [" + str + "]" ); i = -1; } return i; @@ -853,13 +876,13 @@ public final class Configuration { _ext_node_data_return_on = ext_node_data_return_on; } - private void setGraphicsExportX( final int graphics_export_x ) { - _graphics_export_x = graphics_export_x; - } + //private void setGraphicsExportX( final int graphics_export_x ) { + // _graphics_export_x = graphics_export_x; + //} - private void setGraphicsExportY( final int graphics_export_y ) { - _graphics_export_y = graphics_export_y; - } + //private void setGraphicsExportY( final int graphics_export_y ) { + // _graphics_export_y = graphics_export_y; + //} private void setInternalNumberAreConfidenceForNhParsing( final boolean internal_number_are_confidence_for_nh_parsing ) { _internal_number_are_confidence_for_nh_parsing = internal_number_are_confidence_for_nh_parsing; @@ -878,8 +901,8 @@ public final class Configuration { final String clickto_name = ( String ) st.nextElement(); default_clickto = getClickToIndex( clickto_name ); if ( default_clickto == -1 ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name - + "] for [default_click_to]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name + + "] for [default_click_to]" ); default_clickto = 0; } else if ( default_clickto == DEPRECATED ) { @@ -898,8 +921,8 @@ public final class Configuration { _ui = UI.UNKNOWN; } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str - + "]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "could not parse yes/no/? value from [" + my_str + + "]" ); _ui = UI.UNKNOWN; } } @@ -937,8 +960,8 @@ public final class Configuration { } else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [phylogeny_graphics_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [phylogeny_graphics_type]" ); } } else if ( key.equals( "min_confidence_value" ) ) { @@ -970,20 +993,6 @@ public final class Configuration { setMaxBaseFontSize( i ); } } - else if ( key.equals( "graphics_export_x" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - final int i = parseInt( str ); - if ( i > 0 ) { - setGraphicsExportX( i ); - } - } - else if ( key.equals( "graphics_export_y" ) ) { - final String str = ( ( String ) st.nextElement() ).trim(); - final int i = parseInt( str ); - if ( i > 0 ) { - setGraphicsExportY( i ); - } - } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final float f = parseFloat( str ); @@ -991,8 +1000,8 @@ public final class Configuration { setPrintLineWidth( f ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "value for [pdf_export_line_width] cannot be zero or negative" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "value for [pdf_export_line_width] cannot be zero or negative" ); } } else if ( key.equals( "window_initial_size_x" ) ) { @@ -1017,8 +1026,8 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "value for [default_number_of_bootstrap_resamples] cannot be negative" ); + .printWarningMessage( AptxConstants.PRG_NAME, + "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } else if ( key.equals( "mafft_local" ) ) { @@ -1065,22 +1074,14 @@ public final class Configuration { if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.NON_LINED_UP.toString() ) ) { setCladogramType( Options.CLADOGRAM_TYPE.NON_LINED_UP ); } - else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP.toString() ) ) { - setCladogramType( Options.CLADOGRAM_TYPE.EXT_NODE_SUM_DEP ); - } - else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP.toString() ) ) { - setCladogramType( Options.CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP ); + else if ( type_str.equalsIgnoreCase( Options.CLADOGRAM_TYPE.LINED_UP.toString() ) ) { + setCladogramType( Options.CLADOGRAM_TYPE.LINED_UP ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [cladogram_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] 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" ); - } else if ( key.equals( "hide_controls_and_menus" ) ) { _hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() ); } @@ -1111,8 +1112,8 @@ public final class Configuration { } else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [overview_placement_type]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [overview_placement_type]" ); } } else if ( key.equals( "node_label_direction" ) ) { @@ -1125,8 +1126,8 @@ public final class Configuration { } else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str - + "] for [node_label_direction]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + + "] for [node_label_direction]" ); } } else if ( key.equals( "branch_length_value_digits" ) ) { @@ -1135,8 +1136,8 @@ public final class Configuration { setNumberOfDigitsAfterCommaForBranchLengthValue( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [branch_length_value_digits]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + + "] for [branch_length_value_digits]" ); } } else if ( key.equals( "confidence_value_digits" ) ) { @@ -1145,8 +1146,8 @@ public final class Configuration { setNumberOfDigitsAfterCommaForConfidenceValues( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i - + "] for [confidence_value_digits]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + + "] for [confidence_value_digits]" ); } } else if ( key.equals( "allow_editing" ) ) { @@ -1159,8 +1160,8 @@ 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( AptxConstants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } else { setReplaceUnderscoresInNhParsing( r ); @@ -1182,15 +1183,15 @@ 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( AptxConstants.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( AptxConstants.PRG_NAME, + "attempt to extract taxonomies and replace underscores at the same time" ); } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { @@ -1245,8 +1246,8 @@ public final class Configuration { setDefaultNodeFill( NodeFill.SOLID ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str - + "] for [default_node_fill]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str + + "] for [default_node_fill]" ); } } else if ( key.equals( "default_node_shape" ) ) { @@ -1258,8 +1259,8 @@ public final class Configuration { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str - + "] for [default_node_shape]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str + + "] for [default_node_shape]" ); } } else if ( key.equals( "midpoint_reroot" ) ) { @@ -1307,8 +1308,8 @@ public final class Configuration { setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); } } else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) { @@ -1329,8 +1330,8 @@ public final class Configuration { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s - + "] for [ext_descendents_data_to_return_on]" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); } } else if ( key.equals( "vector_data_min_color" ) ) { @@ -1384,6 +1385,9 @@ public final class Configuration { else if ( key.equals( "show_taxonomy_code" ) ) { key_index = Configuration.show_tax_code; } + else if ( key.equals( "show_taxonomy_rank" ) ) { + key_index = Configuration.show_tax_rank; + } else if ( key.equals( "write_confidence_values" ) ) { key_index = Configuration.write_confidence_values; } @@ -1399,8 +1403,8 @@ 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( AptxConstants.PRG_NAME, + "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); } else if ( key.equals( "width_branches" ) ) { key_index = Configuration.width_branches; @@ -1435,6 +1439,9 @@ public final class Configuration { else if ( key.equals( "display_internal_data" ) ) { key_index = Configuration.display_internal_data; } + else if ( key.equals( "display_external_data" ) ) { + key_index = Configuration.display_external_data; + } else if ( key.equals( "dynamically_hide_data" ) ) { key_index = Configuration.dynamically_hide_data; } @@ -1479,7 +1486,7 @@ public final class Configuration { // Deprecated. } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown click-to option: " + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown click-to option: " + click_to_name ); } } @@ -1496,23 +1503,23 @@ 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" ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, + "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 ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + + "] in: " + config_filename ); } } } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key + "] in: " + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown configuration key [" + key + "] in: " + config_filename ); } } @@ -1633,14 +1640,7 @@ public final class Configuration { return _domain_colors; } - int getGraphicsExportX() { - return _graphics_export_x; - } - - int getGraphicsExportY() { - return _graphics_export_y; - } - + Color getGuiBackgroundColor() { return _gui_background_color; } @@ -1673,6 +1673,10 @@ public final class Configuration { return _gui_menu_text_color; } + static int getGuiFontSize() { + return 11; + } + int getMaxBaseFontSize() { return _max_base_font_size; } @@ -1802,4 +1806,10 @@ public final class Configuration { static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } + + public boolean isCouldReadConfigFile() { + return _could_read_config_file; + } + + }