X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=3418951a898498a915f6126c6be3474c39caa9e4;hb=f6b29c53c14e1ef16e4cd614c7f9465e0073309e;hp=27e616ac6237df8656e71bce9e37b0407062e570;hpb=236967e4df09b7a3fd6659a8131aa97ef9906a28;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 27e616a..3418951 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -68,13 +68,13 @@ public final class Configuration { } final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, - { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "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" } }; + { "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" }, @@ -114,6 +114,9 @@ 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 // ------------------ @@ -131,7 +134,8 @@ public final class Configuration { { "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" } }; + { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } + , { "Taxonomy Rank", "display", "no" }}; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -161,6 +165,8 @@ 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; + 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 +185,7 @@ 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 +194,18 @@ 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 +213,14 @@ 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 +230,8 @@ 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 +239,7 @@ 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 +250,7 @@ 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 +259,16 @@ 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 +283,7 @@ 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 +296,17 @@ 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 +321,18 @@ 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 + "]" ); } } @@ -546,6 +554,10 @@ 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"; @@ -644,7 +656,7 @@ public final class Configuration { if ( name.equals( "edit_info" ) ) { index = Configuration.display_node_data; ForesterUtil - .printWarningMessage( Constants.PRG_NAME, + .printWarningMessage( AptxConstants.PRG_NAME, "configuration key [edit_info] is deprecated, use [display node data] instead" ); } else if ( name.equals( "display_node_data" ) ) { @@ -653,6 +665,9 @@ 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 +677,9 @@ 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 +688,7 @@ 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 +725,12 @@ public final class Configuration { index = Configuration.select_nodes; } else if ( name.equals( "display_node_popup" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, + 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 +764,7 @@ 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 +775,7 @@ 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 +787,7 @@ 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 +799,7 @@ 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 +811,7 @@ 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 +871,13 @@ 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; @@ -878,7 +896,7 @@ 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 + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "invalid value [" + clickto_name + "] for [default_click_to]" ); default_clickto = 0; } @@ -898,7 +916,7 @@ 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; } @@ -937,7 +955,7 @@ public final class Configuration { } else { setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [phylogeny_graphics_type]" ); } } @@ -970,20 +988,6 @@ 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 ); @@ -991,7 +995,7 @@ public final class Configuration { setPrintLineWidth( f ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "value for [pdf_export_line_width] cannot be zero or negative" ); } } @@ -1017,7 +1021,7 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, + .printWarningMessage( AptxConstants.PRG_NAME, "value for [default_number_of_bootstrap_resamples] cannot be negative" ); } } @@ -1065,22 +1069,14 @@ 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 + 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() ); } @@ -1111,7 +1107,7 @@ public final class Configuration { } else { setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [overview_placement_type]" ); } } @@ -1125,7 +1121,7 @@ public final class Configuration { } else { setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + type_str + "] for [node_label_direction]" ); } } @@ -1135,7 +1131,7 @@ public final class Configuration { setNumberOfDigitsAfterCommaForBranchLengthValue( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + "] for [branch_length_value_digits]" ); } } @@ -1145,7 +1141,7 @@ public final class Configuration { setNumberOfDigitsAfterCommaForConfidenceValues( i ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "illegal value [" + i + "] for [confidence_value_digits]" ); } } @@ -1159,7 +1155,7 @@ public final class Configuration { final boolean r = parseBoolean( ( String ) st.nextElement() ); if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, + .printWarningMessage( AptxConstants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } else { @@ -1182,14 +1178,14 @@ public final class Configuration { } else { ForesterUtil - .printWarningMessage( Constants.PRG_NAME, + .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, + .printWarningMessage( AptxConstants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } } @@ -1245,7 +1241,7 @@ public final class Configuration { setDefaultNodeFill( NodeFill.SOLID ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + fill_str + "] for [default_node_fill]" ); } } @@ -1258,7 +1254,7 @@ public final class Configuration { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + shape_str + "] for [default_node_shape]" ); } } @@ -1307,7 +1303,7 @@ public final class Configuration { setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return]" ); } } @@ -1329,7 +1325,7 @@ public final class Configuration { setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return_on]" ); } } @@ -1384,6 +1380,9 @@ 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; } @@ -1399,7 +1398,7 @@ public final class Configuration { else if ( key.equals( "color_branches" ) ) { key_index = Configuration.use_style; ForesterUtil - .printWarningMessage( Constants.PRG_NAME, + .printWarningMessage( AptxConstants.PRG_NAME, "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" ); } else if ( key.equals( "width_branches" ) ) { @@ -1479,7 +1478,7 @@ 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 ); } } @@ -1499,20 +1498,20 @@ public final class Configuration { .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( "function_color" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, + 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 + 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 +1632,7 @@ 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; } @@ -1802,4 +1794,10 @@ public final class Configuration { static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } + + public boolean isCouldReadConfigFile() { + return _could_read_config_file; + } + + }