X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=e7c0c2c25544d837fbf78c516b7493a55adfa15c;hb=f1b184dc6eeaa1d9868bdec364e959a73e9cba80;hp=0eead289ffae9f24c057b6276f5c0ce4391460cb;hpb=ebc019e52cc784faa96c1360f23e0d4b8c12ecf5;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 0eead28..e7c0c2c 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -45,17 +45,15 @@ import java.util.TreeMap; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; -import org.forester.archaeopteryx.Options.NodeFill; -import org.forester.archaeopteryx.Options.NodeShape; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.phylogeny.data.NodeVisualization; +import org.forester.phylogeny.data.NodeVisualization.NodeFill; +import org.forester.phylogeny.data.NodeVisualization.NodeShape; import org.forester.util.ForesterUtil; public final class Configuration { - public enum UI { - NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN - } 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"; @@ -118,12 +116,12 @@ public final class Configuration { final static int show_taxonomy_scientific_names = 17; final static int show_taxonomy_common_names = 18; final static int color_according_to_annotation = 19; - final static int show_property = 20; - final static int show_gene_symbols = 21; - final static int node_data_popup = 22; - final static int show_relation_confidence = 23; - final static int show_vector_data = 24; - final static int show_taxonomy_images = 25; + final static int show_gene_symbols = 20; + final static int node_data_popup = 21; + final static int show_relation_confidence = 22; + final static int show_vector_data = 23; + final static int show_taxonomy_images = 24; + final static int show_properties = 25; // ------------------ // Click-to options // ------------------ @@ -154,22 +152,22 @@ public final class Configuration { final static String display_options[][] = { { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" }, { "Annotation", "nodisplay", "no" }, { "Confidence Value", "display", "?" }, { "Event", "display", "?" }, - { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" }, - { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes" }, + { "Taxonomy Colorize", "display", "no" }, { "Colorize Branches", "display", "no" }, + { "Use Branch-Widths", "display", "no" }, { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" }, - { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "no" }, + { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" }, { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" }, - { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "no" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" }, - { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" } }; + { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" }, + { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" }, + { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } }; final static String clickto_options[][] = { { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" }, { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" }, - { "Open Sequence Web", "nodisplay" }, { "Open Taxonomy Web", "nodisplay" }, { "Cut Subtree", "display" }, + { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } }; + { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "nodisplay" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -207,7 +205,7 @@ public final class Configuration { private static String DEFAULT_FONT_FAMILY = ""; static { for( final String font_name : Constants.DEFAULT_FONT_CHOICES ) { - if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) { DEFAULT_FONT_FAMILY = font_name; break; } @@ -217,7 +215,11 @@ public final class Configuration { } } - Configuration( final String cf, final boolean is_url, final boolean is_applet ) { + public Configuration() { + this( null, false, false, false ); + } + + public Configuration( final String cf, final boolean is_url, final boolean is_applet, final boolean verbose ) { if ( ForesterUtil.isEmpty( cf ) ) { config_filename = default_config_filename; } @@ -263,13 +265,17 @@ public final class Configuration { bf.close(); } catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" - + config_filename + "]: " + e ); + if ( verbose ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "failed to read configuration from [" + + config_filename + "]: " + e ); + } } } else { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" - + config_filename + "]" ); + if ( verbose ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "cannot find or open configuration file [" + + config_filename + "]" ); + } } } } @@ -289,38 +295,6 @@ public final class Configuration { } } - Color getGuiBackgroundColor() { - return _gui_background_color; - } - - Color getGuiCheckboxTextColor() { - return _gui_checkbox_text_color; - } - - Color getGuiCheckboxAndButtonActiveColor() { - return _gui_checkbox_and_button_active_color; - } - - Color getGuiButtonTextColor() { - return _gui_button_text_color; - } - - Color getGuiButtonBackgroundColor() { - return _gui_button_background_color; - } - - Color getGuiMenuBackgroundColor() { - return _gui_menu_background_color; - } - - Color getGuiMenuTextColor() { - return _gui_menu_text_color; - } - - Color getGuiButtonBorderColor() { - return _gui_button_border_color; - } - boolean displaySequenceRelations() { return _display_sequence_relations; } @@ -445,10 +419,26 @@ public final class Configuration { return clickto_options[ which ][ 0 ]; } + public int getDefaultBootstrapSamples() { + return _default_bootstrap_samples; + } + int getDefaultDisplayClicktoOption() { return default_clickto; } + public NodeFill getDefaultNodeFill() { + return _default_node_fill; + } + + public NodeShape getDefaultNodeShape() { + return _default_node_shape; + } + + public short getDefaultNodeShapeSize() { + return _default_node_shape_size; + } + SortedMap getDisplayColors() { return _display_colors; } @@ -464,6 +454,14 @@ public final class Configuration { return _domain_colors; } + public Color getDomainStructureBaseColor() { + return _domain_structure_base_color; + } + + public Color getDomainStructureFontColor() { + return _domain_structure_font_color; + } + int getGraphicsExportX() { return _graphics_export_x; } @@ -472,8 +470,36 @@ public final class Configuration { return _graphics_export_y; } - public int getDefaultBootstrapSamples() { - return _default_bootstrap_samples; + 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() { @@ -535,6 +561,10 @@ public final class Configuration { return _weblinks; } + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; + } + boolean isAntialiasScreen() { return _antialias_screen; } @@ -543,6 +573,10 @@ public final class Configuration { return _background_color_gradient; } + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; + } + /** * Convenience method. * @@ -584,6 +618,14 @@ 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; } @@ -592,8 +634,12 @@ public final class Configuration { return _show_scale; } + public boolean isTaxonomyColorizeNodeShapes() { + return _taxonomy_colorize_node_shapes; + } + final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && Util.isMac() && Util.isJava15() ) { + if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { _ui = UI.NATIVE; } return _ui == UI.NATIVE; @@ -679,13 +725,17 @@ public final class Configuration { final String[] fonts = font_str.split( ",+" ); for( String font : fonts ) { font = font.replace( '_', ' ' ).trim(); - if ( Arrays.binarySearch( Util.getAvailableFontFamiliesSorted(), font ) >= 0 ) { + if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font ) >= 0 ) { setBaseFontFamilyName( font ); break; } } } + 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 @@ -707,6 +757,10 @@ 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; } @@ -715,43 +769,103 @@ public final class Configuration { _background_color_gradient = background_color_gradient; } - private void setBaseFontFamilyName( final String base_font_family_name ) { + public void setBaseFontFamilyName( final String base_font_family_name ) { _base_font_family_name = base_font_family_name; } - private void setBaseFontSize( final int base_font_size ) { + public void setBaseFontSize( final int base_font_size ) { _base_font_size = base_font_size; } - private void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { + _cladogram_type = cladogram_type; } - private void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; + public void setColorizeBranches( final boolean b ) { + display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; } - private void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + 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 setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { - _cladogram_type = cladogram_type; + private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { + _default_bootstrap_samples = default_bootstrap_samples; + } + + public void setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; } - void setDisplayColors( final SortedMap display_colors ) { + 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; } - private void setDisplaySequenceRelations( final boolean display_sequence_relations ) { + 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; } - private void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { + public void setExtractPfamTaxonomyCodesInNhParsing( final boolean nh_parsing_extract_pfam_taxonomy_codes ) { _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; } @@ -763,10 +877,6 @@ public final class Configuration { _graphics_export_y = graphics_export_y; } - private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { - _default_bootstrap_samples = default_bootstrap_samples; - } - 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; } @@ -1073,13 +1183,13 @@ public final class Configuration { } else if ( key.equals( "default_node_fill" ) ) { final String fill_str = ( ( String ) st.nextElement() ).trim(); - if ( fill_str.equalsIgnoreCase( Options.NodeFill.NONE.toString() ) ) { + if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.NONE.toString() ) ) { setDefaultNodeFill( NodeFill.NONE ); } - else if ( fill_str.equalsIgnoreCase( Options.NodeFill.GRADIENT.toString() ) ) { + else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.GRADIENT.toString() ) ) { setDefaultNodeFill( NodeFill.GRADIENT ); } - else if ( fill_str.equalsIgnoreCase( Options.NodeFill.SOLID.toString() ) ) { + else if ( fill_str.equalsIgnoreCase( NodeVisualization.NodeFill.SOLID.toString() ) ) { setDefaultNodeFill( NodeFill.SOLID ); } else { @@ -1089,10 +1199,10 @@ public final class Configuration { } else if ( key.equals( "default_node_shape" ) ) { final String shape_str = ( ( String ) st.nextElement() ).trim(); - if ( shape_str.equalsIgnoreCase( Options.NodeShape.CIRCLE.toString() ) ) { + if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.CIRCLE.toString() ) ) { setDefaultNodeShape( NodeShape.CIRCLE ); } - else if ( shape_str.equalsIgnoreCase( Options.NodeShape.RECTANGLE.toString() ) ) { + else if ( shape_str.equalsIgnoreCase( NodeVisualization.NodeShape.RECTANGLE.toString() ) ) { setDefaultNodeShape( NodeShape.RECTANGLE ); } else { @@ -1224,12 +1334,12 @@ public final class Configuration { else if ( key.equals( "color_according_to_annotation" ) ) { key_index = Configuration.color_according_to_annotation; } - else if ( key.equals( "show_property" ) ) { - key_index = Configuration.show_property; - } else if ( key.equals( "show_vector_data" ) ) { key_index = Configuration.show_vector_data; } + else if ( key.equals( "show_properties" ) ) { + key_index = Configuration.show_properties; + } else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } @@ -1275,7 +1385,7 @@ public final class Configuration { "configuration key [function_color] is deprecated" ); } else if ( key.equals( DISPLAY_COLOR_KEY ) ) { - getDisplayColors().put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); + putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) ); } else if ( key.equals( WEB_LINK_KEY ) ) { if ( st.countTokens() == 3 ) { @@ -1300,19 +1410,19 @@ public final class Configuration { } } - private void setMinConfidenceValue( final double min_confidence_value ) { + public void setMinConfidenceValue( final double min_confidence_value ) { _min_confidence_value = min_confidence_value; } - void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { + public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { _node_label_direction = node_label_direction; } - private void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) { + public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short _number_of_digits_after_comma_for_branch_length_values ) { this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values; } - private void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) { + public void setNumberOfDigitsAfterCommaForConfidenceValues( final short _number_of_digits_after_comma_for_confidence_values ) { this._number_of_digits_after_comma_for_confidence_values = _number_of_digits_after_comma_for_confidence_values; } @@ -1328,30 +1438,50 @@ public final class Configuration { _ov_placement = ov_placement; } - void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { + public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { _phylogeny_graphics_type = phylogeny_graphics_type; } - private void setPrintLineWidth( final float print_line_width ) { + public void setPrintLineWidth( final float print_line_width ) { _print_line_width = print_line_width; } - private void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { + public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { _nh_parsing_replace_underscores = nh_parsing_replace_underscores; } - private void setShowBranchLengthValues( final boolean show_branch_length_values ) { + public void setShowBranchLengthValues( final boolean show_branch_length_values ) { _show_branch_length_values = show_branch_length_values; } + public void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { + _show_default_node_shapes = show_default_node_shapes; + } + + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; + } + private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } - private void setShowScale( final boolean show_scale ) { + 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; } @@ -1368,63 +1498,7 @@ public final class Configuration { TRUE, FALSE, UNKNOWN } - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; - } - - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; - } - - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; - } - - public boolean isShowDomainLabels() { - return _show_domain_labels; - } - - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; - } - - public NodeShape getDefaultNodeShape() { - return _default_node_shape; - } - - private void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; - } - - private void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; - } - - public NodeFill getDefaultNodeFill() { - return _default_node_fill; - } - - private void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; - } - - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; - } - - private void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - - public boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; - } - - private void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = show_default_node_shapes; + public enum UI { + NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } }