X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=8fe80766f93e1c6e575dd266707412b5504c4365;hb=790ebe51ea3e7fcafc91057f4842453a1c351b61;hp=3562e10536b6a61bbbb3571a3a94460fe3ecfac7;hpb=5a6b799447987d651276b06c1330b22836420ded;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 3562e10..8fe8076 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -47,6 +47,8 @@ import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.OVERVIEW_PLACEMENT_TYPE; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.phylogeny.data.NodeData.NODE_DATA; import org.forester.phylogeny.data.NodeVisualization; import org.forester.phylogeny.data.NodeVisualization.NodeFill; import org.forester.phylogeny.data.NodeVisualization.NodeShape; @@ -54,8 +56,8 @@ import org.forester.util.ForesterUtil; public final class Configuration { - public enum UI { - NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN + 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"; @@ -85,7 +87,7 @@ 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 boolean _nh_parsing_extract_pfam_taxonomy_codes = false; + private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY; 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; @@ -93,12 +95,17 @@ 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 int _default_bootstrap_samples = -1; - private boolean _show_default_node_shapes = false; + private boolean _show_default_node_shapes_internal = false; + private boolean _show_default_node_shapes_external = false; private NodeShape _default_node_shape = NodeShape.CIRCLE; private NodeFill _default_node_fill = NodeFill.GRADIENT; 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; @@ -119,12 +126,12 @@ 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 // ------------------ @@ -136,13 +143,16 @@ public final class Configuration { final static int color_subtree = 5; final static int open_seq_web = 6; final static int open_tax_web = 7; - final static int cut_subtree = 8; - final static int copy_subtree = 9; - final static int paste_subtree = 10; - final static int delete_subtree_or_node = 11; - final static int add_new_node = 12; - final static int edit_node_data = 13; - final static int blast = 14; + final static int blast = 8; + final static int cut_subtree = 9; + final static int copy_subtree = 10; + final static int paste_subtree = 11; + final static int delete_subtree_or_node = 12; + final static int add_new_node = 13; + final static int edit_node_data = 14; + final static int sort_descendents = 15; + final static int get_ext_desc_data = 16; + final static int select_nodes = 17; // --------------------------- // Display options for trees // --------------------------- @@ -154,23 +164,25 @@ public final class Configuration { String default_config_filename = Constants.DEFAULT_CONFIGURATION_FILE_NAME; 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" }, - { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "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", "yes" }, - { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" }, - { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" } }; + { "Annotation", "nodisplay", "no" }, { "Confidence Values", "display", "?" }, + { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" }, + { "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" }, + { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" }, + { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, + { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" }, + { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" }, + { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" }, + { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" }, + { "Properties", "nodisplay", "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" }, - { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, - { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Blast", "display" } }; + { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" }, + { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, + { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, + { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -205,10 +217,15 @@ public final class Configuration { private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; + private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + private String _label_for_get_ext_descendents_data = ""; + 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 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; } @@ -218,7 +235,11 @@ 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; } @@ -264,13 +285,17 @@ 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 + "]" ); + } } } } @@ -290,38 +315,6 @@ 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; } @@ -390,6 +383,12 @@ public final class Configuration { 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" ); @@ -401,6 +400,9 @@ public final class Configuration { 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; } @@ -419,6 +421,9 @@ public final class Configuration { 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" ); @@ -446,10 +451,38 @@ public final class Configuration { return clickto_options[ which ][ 0 ]; } + public int getDefaultBootstrapSamples() { + return _default_bootstrap_samples; + } + + 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 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; } @@ -465,6 +498,14 @@ 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; } @@ -473,8 +514,36 @@ 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() { @@ -536,6 +605,10 @@ public final class Configuration { return _weblinks; } + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; + } + boolean isAntialiasScreen() { return _antialias_screen; } @@ -544,6 +617,10 @@ public final class Configuration { return _background_color_gradient; } + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; + } + /** * Convenience method. * @@ -557,8 +634,8 @@ public final class Configuration { return _editable; } - boolean isExtractPfamTaxonomyCodesInNhParsing() { - return _nh_parsing_extract_pfam_taxonomy_codes; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } boolean isHasWebLink( final String source ) { @@ -585,6 +662,18 @@ public final class Configuration { return _show_branch_length_values; } + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; + } + + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; + } + + public boolean isShowDomainLabels() { + return _show_domain_labels; + } + boolean isShowOverview() { return _show_overview; } @@ -593,8 +682,12 @@ 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; @@ -629,7 +722,7 @@ public final class Configuration { private double parseDouble( final String str ) { double d = 0.0; try { - d = Double.parseDouble( str ); + d = Double.parseDouble( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse double from [" + str + "]" ); @@ -641,7 +734,7 @@ public final class Configuration { private float parseFloat( final String str ) { float f = 0.0f; try { - f = Float.parseFloat( str ); + f = Float.parseFloat( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse float from [" + str + "]" ); @@ -653,7 +746,7 @@ public final class Configuration { private int parseInt( final String str ) { int i = -1; try { - i = Integer.parseInt( str ); + i = Integer.parseInt( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse integer from [" + str + "]" ); @@ -665,7 +758,7 @@ public final class Configuration { private short parseShort( final String str ) { short i = -1; try { - i = Short.parseShort( str ); + i = Short.parseShort( str.trim() ); } catch ( final Exception e ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse short from [" + str + "]" ); @@ -680,13 +773,17 @@ 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 @@ -708,6 +805,10 @@ 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; } @@ -716,44 +817,124 @@ 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; + } + + 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; } - void setDisplayColors( final SortedMap display_colors ) { + 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 ) { - _nh_parsing_extract_pfam_taxonomy_codes = nh_parsing_extract_pfam_taxonomy_codes; + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -764,10 +945,6 @@ 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; } @@ -776,10 +953,10 @@ public final class Configuration { * Set a key-value(s) tuple */ private void setKeyValue( final StringTokenizer st ) { - String key = ( String ) st.nextElement(); - key = key.replace( ':', ' ' ); - key = key.trim(); - key = key.toLowerCase(); + final String key = ( ( String ) st.nextElement() ).replace( ':', ' ' ).trim().toLowerCase(); + if ( !st.hasMoreElements() ) { + return; + } // Handle single value settings first: if ( key.equals( "default_click_to" ) ) { final String clickto_name = ( String ) st.nextElement(); @@ -859,17 +1036,23 @@ public final class Configuration { else if ( key.equals( "font_size" ) ) { final String size_str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( size_str ); - setBaseFontSize( i ); + if ( i > 0 ) { + setBaseFontSize( i ); + } } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportX( i ); + if ( i > 0 ) { + setGraphicsExportX( i ); + } } else if ( key.equals( "graphics_export_y" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); - setGraphicsExportY( i ); + if ( i > 0 ) { + setGraphicsExportY( i ); + } } else if ( key.equals( "pdf_export_line_width" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); @@ -882,6 +1065,20 @@ public final class Configuration { "value for [pdf_export_line_width] cannot be zero or negative" ); } } + else if ( key.equals( "window_initial_size_x" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameXSize( i ); + } + } + else if ( key.equals( "window_initial_size_y" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( str ); + if ( i > 0 ) { + setFrameYSize( i ); + } + } else if ( key.equals( "default_number_of_bootstrap_resamples" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); @@ -894,6 +1091,30 @@ 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 ) ) { + setPathToLocalMafft( new File( str ) ); + } + } + else if ( key.equals( "fastme_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalFastme( new File( str ) ); + } + } + else if ( key.equals( "raxml_local" ) ) { + final String str = ( ( String ) st.nextElement() ).trim(); + if ( !ForesterUtil.isEmpty( str ) ) { + setPathToLocalRaxml( new File( str ) ); + } + } else if ( key.equals( "show_scale" ) ) { setShowScale( parseBoolean( ( String ) st.nextElement() ) ); } @@ -943,11 +1164,11 @@ public final class Configuration { _use_tabbed_display = parseBoolean( ( String ) st.nextElement() ); } else if ( key.equals( "overview_width" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxWidth( i ); } else if ( key.equals( "overview_height" ) ) { - final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); + final short i = parseShort( ( ( String ) st.nextElement() ) ); setOvMaxHeight( i ); } else if ( key.equals( "overview_placement_type" ) ) { @@ -1012,7 +1233,7 @@ public final class Configuration { } else if ( key.equals( "replace_underscores_in_nh_parsing" ) ) { final boolean r = parseBoolean( ( String ) st.nextElement() ); - if ( r && isExtractPfamTaxonomyCodesInNhParsing() ) { + if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); @@ -1021,16 +1242,26 @@ public final class Configuration { setReplaceUnderscoresInNhParsing( r ); } } - else if ( key.equals( "extract_taxonomy_codes_in_nh_parsing" ) ) { - final boolean e = parseBoolean( ( String ) st.nextElement() ); - if ( e && isReplaceUnderscoresInNhParsing() ) { + else if ( key.equals( "taxonomy_extraction_in_nh_parsing" ) ) { + final String s = ( String ) st.nextElement(); + if ( s.equalsIgnoreCase( "no" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO ); + } + else if ( s.equalsIgnoreCase( "yes" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES ); + } + else if ( s.equalsIgnoreCase( "pfam" ) ) { + setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, + "unknown value for \"taxonomy_extraction_in_nh_parsing\": " + s ); + } + if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) { ForesterUtil .printWarningMessage( Constants.PRG_NAME, "attempt to extract taxonomies and replace underscores at the same time" ); } - else { - setExtractPfamTaxonomyCodesInNhParsing( e ); - } } else if ( key.equals( "internal_labels_are_confidence_values" ) ) { setInternalNumberAreConfidenceForNhParsing( parseBoolean( ( String ) st.nextElement() ) ); @@ -1066,7 +1297,18 @@ 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() ); @@ -1104,6 +1346,63 @@ public final class Configuration { else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); } + else if ( key.equals( "ext_descendents_data_to_return" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( s.equalsIgnoreCase( "node_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.NODE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_acc" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_ACC ); + } + else if ( s.equalsIgnoreCase( "sequence_mol_seq" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_MOL_SEQ ); + } + else if ( s.equalsIgnoreCase( "sequence_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_NAME ); + } + else if ( s.equalsIgnoreCase( "sequence_symbol" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.SEQUENCE_SYMBOL ); + } + else if ( s.equalsIgnoreCase( "taxonomy_scientific_name" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_SCIENTIFIC_NAME ); + } + else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); + } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return]" ); + } + } + else if ( key.equals( "label_for_get_ext_descendents_data" ) ) { + final String s = ( ( String ) st.nextElement() ).trim(); + if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s + + "] for [label_for_get_ext_descendents_data]" ); + } + else { + setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) ); + } + } + else if ( key.equals( "ext_descendents_data_to_return_on" ) ) { + final String s = ( ( String ) st.nextElement() ).trim().toLowerCase(); + if ( s.equals( "console" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE ); + } + else if ( s.equals( "window" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.WINODW ); + } + else if ( s.equals( "buffer_only" ) ) { + setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ); + } + else { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + + "] for [ext_descendents_data_to_return_on]" ); + } + } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! int key_index = -1; @@ -1225,12 +1524,12 @@ 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; } @@ -1276,7 +1575,7 @@ 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 ) { @@ -1301,20 +1600,28 @@ public final class Configuration { } } - private void setMinConfidenceValue( final double min_confidence_value ) { + private void setLabelForGetExtDescendentsData( final String label_for_get_ext_descendents_data ) { + _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; } - 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 ) { - this._number_of_digits_after_comma_for_branch_length_values = _number_of_digits_after_comma_for_branch_length_values; + 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; } - private 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; + 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 ) { @@ -1329,103 +1636,103 @@ 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; } - private void setShowOverview( final boolean show_overview ) { - _show_overview = show_overview; + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; } - private void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; + public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { - _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; + private void setShowOverview( final boolean show_overview ) { + _show_overview = show_overview; } - static String getDefaultFontFamilyName() { - return DEFAULT_FONT_FAMILY; + public void setShowScale( final boolean show_scale ) { + _show_scale = show_scale; } - static enum TRIPLET { - TRUE, FALSE, UNKNOWN + public void setTaxonomyColorize( final boolean b ) { + display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; } - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; + public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { + _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; } - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; + public void setUseBranchesWidths( final boolean b ) { + display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; } - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; + private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { + _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - public boolean isShowDomainLabels() { - return _show_domain_labels; + void setWebLinks( final SortedMap weblinks ) { + _weblinks = weblinks; } - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; + static String getDefaultFontFamilyName() { + return DEFAULT_FONT_FAMILY; } - public NodeShape getDefaultNodeShape() { - return _default_node_shape; + static enum TRIPLET { + TRUE, FALSE, UNKNOWN } - private void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; + public enum UI { + NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } - private void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; + public NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; } - public NodeFill getDefaultNodeFill() { - return _default_node_fill; + public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; } - private void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; + public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { + return _ext_node_data_return_on; } - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; + 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 setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + public int getFrameXSize() { + return _frame_x_size; } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; + public int getFrameYSize() { + return _frame_y_size; } - public boolean isShowDefaultNodeShapes() { - return _show_default_node_shapes; + public void setFrameXSize( final int frame_x_size ) { + _frame_x_size = frame_x_size; } - private void setShowDefaultNodeShapes( final boolean show_default_node_shapes ) { - _show_default_node_shapes = show_default_node_shapes; + public void setFrameYSize( final int frame_y_size ) { + _frame_y_size = frame_y_size; } }