From 04275071ecc44e04eaf6006397eae0b86514cc75 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 10 Jan 2013 18:30:08 +0000 Subject: [PATCH] messed up at the moment --- .../org/forester/archaeopteryx/Configuration.java | 921 ++++++++++---------- .../src/org/forester/archaeopteryx/MainPanel.java | 2 +- .../org/forester/archaeopteryx/TreeFontSet.java | 110 +-- .../src/org/forester/archaeopteryx/TreePanel.java | 35 +- .../phylogeny/data/RenderableVector.java | 107 +-- 5 files changed, 620 insertions(+), 555 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 8fe8076..e647804 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -56,9 +56,6 @@ import org.forester.util.ForesterUtil; public final class Configuration { - public enum EXT_NODE_DATA_RETURN_ON { - CONSOLE, WINODW, BUFFER_ONLY; - } static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema"; private static final String WEB_LINK_KEY = "web_link"; private static final String DISPLAY_COLOR_KEY = "display_color"; @@ -73,6 +70,8 @@ public final class Configuration { private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; private String _base_font_family_name = ""; private int _base_font_size = -1; + private int _min_base_font_size = 2; + private int _max_base_font_size = 20; private int _graphics_export_x = -1; private int _graphics_export_y = -1; private short _ov_max_width = 80; @@ -300,271 +299,413 @@ public final class Configuration { } } - private void createWebLink( final String url_str, final String desc, final String source_identifier ) { - WebLink weblink = null; - boolean ex = false; - try { - weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); - } - catch ( final MalformedURLException e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); - ex = true; - } - if ( !ex && ( weblink != null ) ) { - getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); - } + public String getBaseFontFamilyName() { + return _base_font_family_name; } - boolean displaySequenceRelations() { - return _display_sequence_relations; + public int getDefaultBootstrapSamples() { + return _default_bootstrap_samples; } - boolean doCheckOption( final int which ) { - return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) - || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); + public NodeFill getDefaultNodeFill() { + return _default_node_fill; } - boolean doDisplayClickToOption( final int which ) { - return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + public NodeShape getDefaultNodeShape() { + return _default_node_shape; } - boolean doDisplayOption( final int which ) { - return display_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + public short getDefaultNodeShapeSize() { + return _default_node_shape_size; } - /** - * Will attempt to use the phylogeny to determine whether to check - * this or not (e.g. phylogram) - * - */ - boolean doGuessCheckOption( final int which ) { - return display_options[ which ][ 2 ].equals( "?" ); + public Color getDomainStructureBaseColor() { + return _domain_structure_base_color; } - Map getAnnotationColors() { - if ( _annotation_colors == null ) { - _annotation_colors = new Hashtable(); - } - return _annotation_colors; + public Color getDomainStructureFontColor() { + return _domain_structure_font_color; } - public String getBaseFontFamilyName() { - return _base_font_family_name; + public NODE_DATA getExtDescNodeDataToReturn() { + return _ext_desc_data_to_return; } - int getBaseFontSize() { - return _base_font_size; + public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { + return _ext_node_data_return_on; } - CLADOGRAM_TYPE getCladogramType() { - return _cladogram_type; + public int getFrameXSize() { + return _frame_x_size; } - private int getClickToIndex( final String name ) { - int index = -1; - if ( name.equals( "edit_info" ) ) { - index = Configuration.display_node_data; - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, - "configuration key [edit_info] is deprecated, use [display node data] instead" ); - } - else if ( name.equals( "display_node_data" ) ) { - index = Configuration.display_node_data; - } - else if ( name.equals( "collapse_uncollapse" ) ) { - index = Configuration.collapse_uncollapse; - } - else if ( name.equals( "reroot" ) ) { - index = Configuration.reroot; - } - else if ( name.equals( "subtree" ) ) { - index = Configuration.subtree; - } - else if ( name.equals( "swap" ) ) { - index = Configuration.swap; - } - else if ( name.equals( "sort_descendants" ) ) { - index = Configuration.sort_descendents; - } - else if ( name.equals( "get_ext_descendents_data" ) ) { - index = Configuration.get_ext_desc_data; - } - else if ( name.equals( "display_sequences" ) ) { - ForesterUtil - .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "open_seq_web" ) ) { - index = Configuration.open_seq_web; - } - else if ( name.equals( "open_tax_web" ) ) { - index = Configuration.open_tax_web; - } - else if ( name.equals( "blast" ) ) { - index = Configuration.blast; - } - else if ( name.equals( "cut_subtree" ) ) { - index = Configuration.cut_subtree; - } - else if ( name.equals( "copy_subtree" ) ) { - index = Configuration.copy_subtree; - } - else if ( name.equals( "paste_subtree" ) ) { - index = Configuration.paste_subtree; - } - else if ( name.equals( "delete" ) ) { - index = Configuration.delete_subtree_or_node; - } - else if ( name.equals( "add_new_node" ) ) { - index = Configuration.add_new_node; - } - else if ( name.equals( "edit_node_data" ) ) { - index = Configuration.edit_node_data; - } - else if ( name.equals( "select_nodes" ) ) { - index = Configuration.select_nodes; - } - else if ( name.equals( "display_node_popup" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, - "configuration key [display_node_popup] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "custom_option" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); - return DEPRECATED; - } - else if ( name.equals( "color_subtree" ) ) { - index = Configuration.color_subtree; - } - else if ( name.equals( "go_to_swiss_prot" ) ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); - return DEPRECATED; - } - return index; + public int getFrameYSize() { + return _frame_y_size; } - int getClickToOptionsCount() { - return clickto_options.length; + public String getLabelForGetExtDescendentsData() { + return _label_for_get_ext_descendents_data; } - String getClickToTitle( final int which ) { - return clickto_options[ which ][ 0 ]; + public File getPathToLocalClustalOmega() { + return _path_to_local_clustalo; } - public int getDefaultBootstrapSamples() { - return _default_bootstrap_samples; + public File getPathToLocalFastme() { + return _path_to_local_fastme; } public File getpathToLocalMafft() { return _path_to_local_mafft; } - public File getPathToLocalFastme() { - return _path_to_local_fastme; - } - public File getPathToLocalRaxml() { return _path_to_local_raxml; } - int getDefaultDisplayClicktoOption() { - return default_clickto; + public boolean isAbbreviateScientificTaxonNames() { + return _abbreviate_scientific_names; } - public NodeFill getDefaultNodeFill() { - return _default_node_fill; + public boolean isBackgroundColorGradient() { + return _background_color_gradient; } - public NodeShape getDefaultNodeShape() { - return _default_node_shape; + public boolean isColorLabelsSameAsParentBranch() { + return _color_labels_same_as_parent_branch; } - public short getDefaultNodeShapeSize() { - return _default_node_shape_size; + public boolean isShowDefaultNodeShapesExternal() { + return _show_default_node_shapes_external; } - SortedMap getDisplayColors() { - return _display_colors; + public boolean isShowDefaultNodeShapesInternal() { + return _show_default_node_shapes_internal; } - String getDisplayTitle( final int which ) { - return display_options[ which ][ 0 ]; + public boolean isShowDomainLabels() { + return _show_domain_labels; } - Map getDomainColors() { - if ( _domain_colors == null ) { - _domain_colors = new Hashtable(); - } - return _domain_colors; + public boolean isTaxonomyColorizeNodeShapes() { + return _taxonomy_colorize_node_shapes; } - public Color getDomainStructureBaseColor() { - return _domain_structure_base_color; + public void putDisplayColors( final String key, final Color color ) { + getDisplayColors().put( key, color ); } - public Color getDomainStructureFontColor() { - return _domain_structure_font_color; + public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { + _abbreviate_scientific_names = abbreviate_scientific_names; } - int getGraphicsExportX() { - return _graphics_export_x; + public void setBackgroundColorGradient( final boolean background_color_gradient ) { + _background_color_gradient = background_color_gradient; } - int getGraphicsExportY() { - return _graphics_export_y; + public void setBaseFontFamilyName( final String base_font_family_name ) { + _base_font_family_name = base_font_family_name; } - Color getGuiBackgroundColor() { - return _gui_background_color; + public void setBaseFontSize( final int base_font_size ) { + _base_font_size = base_font_size; } - Color getGuiButtonBackgroundColor() { - return _gui_button_background_color; + private void setMaxBaseFontSize( final int max_base_font_size ) { + _max_base_font_size = max_base_font_size; } - Color getGuiButtonBorderColor() { - return _gui_button_border_color; + private void setMinBaseFontSize( final int min_base_font_size ) { + _min_base_font_size = min_base_font_size; } - Color getGuiButtonTextColor() { - return _gui_button_text_color; + public void setColorizeBranches( final boolean b ) { + display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; } - Color getGuiCheckboxAndButtonActiveColor() { - return _gui_checkbox_and_button_active_color; + public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { + _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } - Color getGuiCheckboxTextColor() { - return _gui_checkbox_text_color; + public void setDefaultNodeFill( final NodeFill default_node_fill ) { + _default_node_fill = default_node_fill; } - Color getGuiMenuBackgroundColor() { - return _gui_menu_background_color; + public void setDefaultNodeShape( final NodeShape default_node_shape ) { + _default_node_shape = default_node_shape; } - Color getGuiMenuTextColor() { - return _gui_menu_text_color; + public void setDefaultNodeShapeSize( final short default_node_shape_size ) { + _default_node_shape_size = default_node_shape_size; } - double getMinConfidenceValue() { - return _min_confidence_value; + public void setDisplayAsPhylogram( final boolean b ) { + display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; } - NODE_LABEL_DIRECTION getNodeLabelDirection() { - return _node_label_direction; + public void setDisplayColors( final SortedMap display_colors ) { + _display_colors = display_colors; } - short getNumberOfDigitsAfterCommaForBranchLengthValues() { - return _number_of_digits_after_comma_for_branch_length_values; + public void setDisplayConfidenceValues( final boolean b ) { + display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; } - short getNumberOfDigitsAfterCommaForConfidenceValues() { - return _number_of_digits_after_comma_for_confidence_values; + public void setDisplayInternalData( final boolean b ) { + display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; } - short getOvMaxHeight() { - return _ov_max_height; - } + public void setDisplayNodeNames( final boolean b ) { + display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; + } + + 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"; + } + + public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + _ext_desc_data_to_return = ext_desc_data_to_return; + } + + public void setFrameXSize( final int frame_x_size ) { + _frame_x_size = frame_x_size; + } + + public void setFrameYSize( final int frame_y_size ) { + _frame_y_size = frame_y_size; + } + + public void setMinConfidenceValue( final double min_confidence_value ) { + _min_confidence_value = min_confidence_value; + } + + public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { + _node_label_direction = node_label_direction; + } + + public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) { + _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; + } + + public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { + _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; + } + + public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) { + _path_to_local_clustalo = path_to_local_clustalo; + } + + public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { + _phylogeny_graphics_type = phylogeny_graphics_type; + } + + public void setPrintLineWidth( final float print_line_width ) { + _print_line_width = print_line_width; + } + + public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { + _nh_parsing_replace_underscores = nh_parsing_replace_underscores; + } + + public void setShowBranchLengthValues( final boolean show_branch_length_values ) { + _show_branch_length_values = show_branch_length_values; + } + + public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { + _show_default_node_shapes_external = show_default_node_shapes_external; + } + + public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { + _show_default_node_shapes_internal = show_default_node_shapes_internal; + } + + public void setShowDomainLabels( final boolean show_domain_labels ) { + _show_domain_labels = show_domain_labels; + } + + public void setShowScale( final boolean show_scale ) { + _show_scale = show_scale; + } + + public void setTaxonomyColorize( final boolean b ) { + display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; + } + + public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { + _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; + } + + public void setUseBranchesWidths( final boolean b ) { + display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; + } + + boolean displaySequenceRelations() { + return _display_sequence_relations; + } + + boolean doCheckOption( final int which ) { + return ( display_options[ which ][ 2 ].equalsIgnoreCase( "yes" ) ) + || ( display_options[ which ][ 2 ].equalsIgnoreCase( "true" ) ); + } + + boolean doDisplayClickToOption( final int which ) { + return clickto_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + } + + boolean doDisplayOption( final int which ) { + return display_options[ which ][ 1 ].equalsIgnoreCase( "display" ); + } + + /** + * Will attempt to use the phylogeny to determine whether to check + * this or not (e.g. phylogram) + * + */ + boolean doGuessCheckOption( final int which ) { + return display_options[ which ][ 2 ].equals( "?" ); + } + + Map getAnnotationColors() { + if ( _annotation_colors == null ) { + _annotation_colors = new Hashtable(); + } + return _annotation_colors; + } + + int getBaseFontSize() { + return _base_font_size; + } + + int getMinBaseFontSize() { + return _min_base_font_size; + } + + int getMaxBaseFontSize() { + return _max_base_font_size; + } + + CLADOGRAM_TYPE getCladogramType() { + return _cladogram_type; + } + + int getClickToOptionsCount() { + return clickto_options.length; + } + + String getClickToTitle( final int which ) { + return clickto_options[ which ][ 0 ]; + } + + int getDefaultDisplayClicktoOption() { + return default_clickto; + } + + SortedMap getDisplayColors() { + return _display_colors; + } + + String getDisplayTitle( final int which ) { + return display_options[ which ][ 0 ]; + } + + Map getDomainColors() { + if ( _domain_colors == null ) { + _domain_colors = new Hashtable(); + } + return _domain_colors; + } + + int getGraphicsExportX() { + return _graphics_export_x; + } + + int getGraphicsExportY() { + return _graphics_export_y; + } + + Color getGuiBackgroundColor() { + return _gui_background_color; + } + + Color getGuiButtonBackgroundColor() { + return _gui_button_background_color; + } + + Color getGuiButtonBorderColor() { + return _gui_button_border_color; + } + + Color getGuiButtonTextColor() { + return _gui_button_text_color; + } + + Color getGuiCheckboxAndButtonActiveColor() { + return _gui_checkbox_and_button_active_color; + } + + Color getGuiCheckboxTextColor() { + return _gui_checkbox_text_color; + } + + Color getGuiMenuBackgroundColor() { + return _gui_menu_background_color; + } + + Color getGuiMenuTextColor() { + return _gui_menu_text_color; + } + + double getMinConfidenceValue() { + return _min_confidence_value; + } + + NODE_LABEL_DIRECTION getNodeLabelDirection() { + return _node_label_direction; + } + + short getNumberOfDigitsAfterCommaForBranchLengthValues() { + return _number_of_digits_after_comma_for_branch_length_values; + } + + short getNumberOfDigitsAfterCommaForConfidenceValues() { + return _number_of_digits_after_comma_for_confidence_values; + } + + short getOvMaxHeight() { + return _ov_max_height; + } short getOvMaxWidth() { return _ov_max_width; @@ -589,12 +730,8 @@ public final class Configuration { return _species_colors; } - TreeColorSet getTreeColorSet() { - return null; - } - - TreeFontSet getTreeFontSet() { - return null; + final TAXONOMY_EXTRACTION getTaxonomyExtraction() { + return _taxonomy_extraction; } WebLink getWebLink( final String source ) { @@ -605,22 +742,10 @@ public final class Configuration { return _weblinks; } - public boolean isAbbreviateScientificTaxonNames() { - return _abbreviate_scientific_names; - } - boolean isAntialiasScreen() { return _antialias_screen; } - public boolean isBackgroundColorGradient() { - return _background_color_gradient; - } - - public boolean isColorLabelsSameAsParentBranch() { - return _color_labels_same_as_parent_branch; - } - /** * Convenience method. * @@ -634,10 +759,6 @@ public final class Configuration { return _editable; } - final TAXONOMY_EXTRACTION getTaxonomyExtraction() { - return _taxonomy_extraction; - } - boolean isHasWebLink( final String source ) { return getWebLinks().containsKey( source ); } @@ -662,47 +783,137 @@ public final class Configuration { return _show_branch_length_values; } - public boolean isShowDefaultNodeShapesExternal() { - return _show_default_node_shapes_external; + boolean isShowOverview() { + return _show_overview; } - public boolean isShowDefaultNodeShapesInternal() { - return _show_default_node_shapes_internal; + boolean isShowScale() { + return _show_scale; } - public boolean isShowDomainLabels() { - return _show_domain_labels; + final boolean isUseNativeUI() { + if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { + _ui = UI.NATIVE; + } + return _ui == UI.NATIVE; } - boolean isShowOverview() { - return _show_overview; + /** + * Only used by ArchaeoptryxE. + * + */ + boolean isUseTabbedDisplay() { + return _use_tabbed_display; } - boolean isShowScale() { - return _show_scale; + boolean isValidatePhyloXmlAgainstSchema() { + return _validate_against_phyloxml_xsd_schema; } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; + final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { + _taxonomy_extraction = taxonomy_extraction; } - final boolean isUseNativeUI() { - if ( ( _ui == UI.UNKNOWN ) && AptxUtil.isMac() && AptxUtil.isJava15() ) { - _ui = UI.NATIVE; + void setWebLinks( final SortedMap weblinks ) { + _weblinks = weblinks; + } + + private void createWebLink( final String url_str, final String desc, final String source_identifier ) { + WebLink weblink = null; + boolean ex = false; + try { + weblink = new WebLink( new URL( url_str.trim() ), desc.trim(), source_identifier.trim() ); + } + catch ( final MalformedURLException e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not create URL from [" + url_str + "]" ); + ex = true; + } + if ( !ex && ( weblink != null ) ) { + getWebLinks().put( weblink.getSourceIdentifier().toLowerCase(), weblink ); + } + } + + private int getClickToIndex( final String name ) { + int index = -1; + if ( name.equals( "edit_info" ) ) { + index = Configuration.display_node_data; + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, + "configuration key [edit_info] is deprecated, use [display node data] instead" ); + } + else if ( name.equals( "display_node_data" ) ) { + index = Configuration.display_node_data; + } + else if ( name.equals( "collapse_uncollapse" ) ) { + index = Configuration.collapse_uncollapse; + } + else if ( name.equals( "reroot" ) ) { + index = Configuration.reroot; + } + else if ( name.equals( "subtree" ) ) { + index = Configuration.subtree; + } + else if ( name.equals( "swap" ) ) { + index = Configuration.swap; + } + else if ( name.equals( "sort_descendants" ) ) { + index = Configuration.sort_descendents; + } + else if ( name.equals( "get_ext_descendents_data" ) ) { + index = Configuration.get_ext_desc_data; + } + else if ( name.equals( "display_sequences" ) ) { + ForesterUtil + .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "open_seq_web" ) ) { + index = Configuration.open_seq_web; + } + else if ( name.equals( "open_tax_web" ) ) { + index = Configuration.open_tax_web; + } + else if ( name.equals( "blast" ) ) { + index = Configuration.blast; + } + else if ( name.equals( "cut_subtree" ) ) { + index = Configuration.cut_subtree; + } + else if ( name.equals( "copy_subtree" ) ) { + index = Configuration.copy_subtree; + } + else if ( name.equals( "paste_subtree" ) ) { + index = Configuration.paste_subtree; + } + else if ( name.equals( "delete" ) ) { + index = Configuration.delete_subtree_or_node; + } + else if ( name.equals( "add_new_node" ) ) { + index = Configuration.add_new_node; + } + else if ( name.equals( "edit_node_data" ) ) { + index = Configuration.edit_node_data; + } + else if ( name.equals( "select_nodes" ) ) { + index = Configuration.select_nodes; + } + else if ( name.equals( "display_node_popup" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, + "configuration key [display_node_popup] is deprecated" ); + return DEPRECATED; + } + else if ( name.equals( "custom_option" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [custom_option] is deprecated" ); + return DEPRECATED; } - return _ui == UI.NATIVE; - } - - /** - * Only used by ArchaeoptryxE. - * - */ - boolean isUseTabbedDisplay() { - return _use_tabbed_display; - } - - boolean isValidatePhyloXmlAgainstSchema() { - return _validate_against_phyloxml_xsd_schema; + else if ( name.equals( "color_subtree" ) ) { + index = Configuration.color_subtree; + } + else if ( name.equals( "go_to_swiss_prot" ) ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [go_to_swiss_prot] is deprecated" ); + return DEPRECATED; + } + return index; } private boolean parseBoolean( final String str ) { @@ -780,10 +991,6 @@ public final class Configuration { } } - public void putDisplayColors( final String key, final Color color ) { - getDisplayColors().put( key, color ); - } - /** * read each line of config file, process non-comment lines * @throws IOException @@ -805,136 +1012,24 @@ public final class Configuration { } while ( line != null ); } - public void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { - _abbreviate_scientific_names = abbreviate_scientific_names; - } - private void setAntialiasScreen( final boolean antialias_screen ) { _antialias_screen = antialias_screen; } - public void setBackgroundColorGradient( final boolean background_color_gradient ) { - _background_color_gradient = background_color_gradient; - } - - public void setBaseFontFamilyName( final String base_font_family_name ) { - _base_font_family_name = base_font_family_name; - } - - public void setBaseFontSize( final int base_font_size ) { - _base_font_size = base_font_size; - } - private void setCladogramType( final CLADOGRAM_TYPE cladogram_type ) { _cladogram_type = cladogram_type; } - public void setColorizeBranches( final boolean b ) { - display_options[ color_branches ][ 2 ] = b ? "yes" : "no"; - } - - public void setColorLabelsSameAsParentBranch( final boolean color_labels_same_as_parent_branch ) { - _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; - } - private void setDefaultBootstrapSamples( final int default_bootstrap_samples ) { _default_bootstrap_samples = default_bootstrap_samples; } - private void setPathToLocalMafft( final File path_to_local_mafft ) { - _path_to_local_mafft = path_to_local_mafft; - } - - private void setPathToLocalFastme( final File path_to_local_fastme ) { - _path_to_local_fastme = path_to_local_fastme; - } - - private void setPathToLocalRaxml( final File path_to_local_raxml ) { - _path_to_local_raxml = path_to_local_raxml; - } - - public File getPathToLocalClustalOmega() { - return _path_to_local_clustalo; - } - - public void setPathToLocalClustalOmega( final File path_to_local_clustalo ) { - _path_to_local_clustalo = path_to_local_clustalo; - } - - public void setDefaultNodeFill( final NodeFill default_node_fill ) { - _default_node_fill = default_node_fill; - } - - public void setDefaultNodeShape( final NodeShape default_node_shape ) { - _default_node_shape = default_node_shape; - } - - public void setDefaultNodeShapeSize( final short default_node_shape_size ) { - _default_node_shape_size = default_node_shape_size; - } - - public void setDisplayAsPhylogram( final boolean b ) { - display_options[ display_as_phylogram ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayColors( final SortedMap display_colors ) { - _display_colors = display_colors; - } - - public void setDisplayConfidenceValues( final boolean b ) { - display_options[ write_confidence_values ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayInternalData( final boolean b ) { - display_options[ display_internal_data ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayNodeNames( final boolean b ) { - display_options[ show_node_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplaySequenceAcc( final boolean b ) { - display_options[ show_sequence_acc ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplaySequenceNames( final boolean b ) { - display_options[ show_gene_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplaySequenceRelations( final boolean display_sequence_relations ) { - _display_sequence_relations = display_sequence_relations; - } - - public void setDisplaySequenceSymbols( final boolean b ) { - display_options[ show_gene_symbols ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyCode( final boolean b ) { - display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyCommonNames( final boolean b ) { - display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyImages( final boolean b ) { - display_options[ show_taxonomy_images ][ 2 ] = b ? "yes" : "no"; - } - - public void setDisplayTaxonomyScientificNames( final boolean b ) { - display_options[ show_taxonomy_scientific_names ][ 2 ] = b ? "yes" : "no"; - } - - public void setDynamicallyHideData( final boolean b ) { - display_options[ dynamically_hide_data ][ 2 ] = b ? "yes" : "no"; - } - private void setEditable( final boolean editable ) { _editable = editable; } - final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { - _taxonomy_extraction = taxonomy_extraction; + private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { + _ext_node_data_return_on = ext_node_data_return_on; } private void setGraphicsExportX( final int graphics_export_x ) { @@ -1040,6 +1135,20 @@ public final class Configuration { setBaseFontSize( i ); } } + else if ( key.equals( "font_size_min" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 0 ) { + setMinBaseFontSize( i ); + } + } + else if ( key.equals( "font_size_max" ) ) { + final String size_str = ( ( String ) st.nextElement() ).trim(); + final int i = parseInt( size_str ); + if ( i > 1 ) { + setMaxBaseFontSize( i ); + } + } else if ( key.equals( "graphics_export_x" ) ) { final String str = ( ( String ) st.nextElement() ).trim(); final int i = parseInt( str ); @@ -1604,26 +1713,6 @@ public final class Configuration { _label_for_get_ext_descendents_data = label_for_get_ext_descendents_data; } - public String getLabelForGetExtDescendentsData() { - return _label_for_get_ext_descendents_data; - } - - public void setMinConfidenceValue( final double min_confidence_value ) { - _min_confidence_value = min_confidence_value; - } - - public void setNodeLabelDirection( final NODE_LABEL_DIRECTION node_label_direction ) { - _node_label_direction = node_label_direction; - } - - public void setNumberOfDigitsAfterCommaForBranchLengthValue( final short number_of_digits_after_comma_for_branch_length_values ) { - _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; - } - - public void setNumberOfDigitsAfterCommaForConfidenceValues( final short number_of_digits_after_comma_for_confidence_values ) { - _number_of_digits_after_comma_for_confidence_values = number_of_digits_after_comma_for_confidence_values; - } - private void setOvMaxHeight( final short ov_max_height ) { _ov_max_height = ov_max_height; } @@ -1636,103 +1725,39 @@ public final class Configuration { _ov_placement = ov_placement; } - public void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE phylogeny_graphics_type ) { - _phylogeny_graphics_type = phylogeny_graphics_type; - } - - public void setPrintLineWidth( final float print_line_width ) { - _print_line_width = print_line_width; - } - - public void setReplaceUnderscoresInNhParsing( final boolean nh_parsing_replace_underscores ) { - _nh_parsing_replace_underscores = nh_parsing_replace_underscores; - } - - public void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; - } - - public void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { - _show_default_node_shapes_internal = show_default_node_shapes_internal; + private void setPathToLocalFastme( final File path_to_local_fastme ) { + _path_to_local_fastme = path_to_local_fastme; } - public void setShowDefaultNodeShapesExternal( final boolean show_default_node_shapes_external ) { - _show_default_node_shapes_external = show_default_node_shapes_external; + private void setPathToLocalMafft( final File path_to_local_mafft ) { + _path_to_local_mafft = path_to_local_mafft; } - public void setShowDomainLabels( final boolean show_domain_labels ) { - _show_domain_labels = show_domain_labels; + private void setPathToLocalRaxml( final File path_to_local_raxml ) { + _path_to_local_raxml = path_to_local_raxml; } private void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } - public void setShowScale( final boolean show_scale ) { - _show_scale = show_scale; - } - - public void setTaxonomyColorize( final boolean b ) { - display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; - } - - public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - - public void setUseBranchesWidths( final boolean b ) { - display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; - } - private void setValidatePhyloXmlAgainstSchema( final boolean validate_against_phyloxml_xsd_schema ) { _validate_against_phyloxml_xsd_schema = validate_against_phyloxml_xsd_schema; } - void setWebLinks( final SortedMap weblinks ) { - _weblinks = weblinks; - } - static String getDefaultFontFamilyName() { return DEFAULT_FONT_FAMILY; } - static enum TRIPLET { - TRUE, FALSE, UNKNOWN + public enum EXT_NODE_DATA_RETURN_ON { + CONSOLE, WINODW, BUFFER_ONLY; } public enum UI { NATIVE, CROSSPLATFORM, NIMBUS, UNKNOWN } - public NODE_DATA getExtDescNodeDataToReturn() { - return _ext_desc_data_to_return; - } - - public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { - _ext_desc_data_to_return = ext_desc_data_to_return; - } - - public EXT_NODE_DATA_RETURN_ON getExtNodeDataReturnOn() { - return _ext_node_data_return_on; - } - - private void setExtNodeDataReturnOn( final EXT_NODE_DATA_RETURN_ON ext_node_data_return_on ) { - _ext_node_data_return_on = ext_node_data_return_on; - } - - public int getFrameXSize() { - return _frame_x_size; - } - - public int getFrameYSize() { - return _frame_y_size; - } - - public void setFrameXSize( final int frame_x_size ) { - _frame_x_size = frame_x_size; - } - - public void setFrameYSize( final int frame_y_size ) { - _frame_y_size = frame_y_size; + static enum TRIPLET { + TRUE, FALSE, UNKNOWN } } diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java index 885e378..f59a3d4 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java @@ -222,7 +222,7 @@ public class MainPanel extends JPanel implements ComponentListener { // Do nothing. } - private Configuration getConfiguration() { + Configuration getConfiguration() { return _configuration; } diff --git a/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java b/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java index a3c136d..d21e0b8 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java @@ -28,7 +28,6 @@ package org.forester.archaeopteryx; -import java.awt.Component; import java.awt.Font; import java.awt.FontMetrics; @@ -37,11 +36,12 @@ import java.awt.FontMetrics; */ public final class TreeFontSet { + final static float SMALL_FONTS_BASE = 8; private final static String DEFAULT_FONT = "Verdana"; private final static float FONT_SIZE_CHANGE_STEP = 1.0f; static final int BOLD_AND_ITALIC = Font.BOLD + Font.ITALIC; // the owner (needed to get font metrics) - private final Component _owner; + private final MainPanel _owner; // The fonts private Font _small_font; private Font _large_font; @@ -62,14 +62,26 @@ public final class TreeFontSet { // hold font measurements int _small_max_descent = 0; int _small_max_ascent = 0; + private final int _min; + private final int _max; - TreeFontSet( final Component owner ) { + TreeFontSet( final MainPanel owner ) { _owner = owner; + _min = _owner.getConfiguration().getMinBaseFontSize(); + _max = _owner.getConfiguration().getMinBaseFontSize(); setBaseFont( new Font( DEFAULT_FONT, Font.PLAIN, 10 ) ); } - void decreaseFontSize() { - if ( _large_font.getSize() > 0 ) { + public Font getSmallFont() { + return _small_font; + } + + public Font getSmallFontSystem() { + return _small_font_system; + } + + void decreaseFontSize( final int min ) { + if ( _large_font.getSize() >= min ) { _small_font = _small_font.deriveFont( _small_font.getSize() - FONT_SIZE_CHANGE_STEP ); _large_font = _large_font.deriveFont( _large_font.getSize() - FONT_SIZE_CHANGE_STEP ); _small_italic_font = _small_italic_font.deriveFont( _small_italic_font.getSize() - FONT_SIZE_CHANGE_STEP ); @@ -78,10 +90,6 @@ public final class TreeFontSet { } } - void reset() { - _large_font_system = _large_font; - } - Font getBaseFont() { return _base_font; } @@ -90,10 +98,6 @@ public final class TreeFontSet { return _large_font; } - private Font getLargeFontSystem() { - return _large_font_system; - } - Font getLargeItalicFont() { return _large_italic_font; } @@ -102,14 +106,6 @@ public final class TreeFontSet { return _large_italic_font_system; } - public Font getSmallFont() { - return _small_font; - } - - public Font getSmallFontSystem() { - return _small_font_system; - } - Font getSmallItalicFont() { return _small_italic_font; } @@ -126,23 +122,6 @@ public final class TreeFontSet { setupFontMetrics(); } - private void intializeFonts() { - final int small_size = getBaseFont().getSize() - 1; - int italic = Font.ITALIC; - if ( getBaseFont().getStyle() == Font.BOLD ) { - italic = italic + Font.BOLD; - } - _small_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size ); - _large_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() ); - _small_italic_font = new Font( getBaseFont().getFontName(), italic, small_size ); - _large_italic_font = new Font( getBaseFont().getFontName(), italic, getBaseFont().getSize() ); - _small_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size ); - _large_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() ); - _small_italic_font_system = new Font( getBaseFont().getFontName(), italic, small_size ); - _large_italic_font_system = new Font( getBaseFont().getFontName(), italic, getBaseFont().getSize() ); - setupFontMetrics(); - } - void largeFonts() { _small_font = _small_font.deriveFont( 12f ); _large_font = _large_font.deriveFont( 14f ); @@ -159,27 +138,20 @@ public final class TreeFontSet { setupFontMetrics(); } + void reset() { + _large_font_system = _large_font; + } + void setBaseFont( final Font base_font ) { _base_font = base_font; intializeFonts(); } - private void setupFontMetrics() { - _fm_small = _owner.getFontMetrics( _small_font ); - _fm_large = _owner.getFontMetrics( _large_font ); - _fm_small_italic = _owner.getFontMetrics( _small_italic_font ); - _fm_small_italic_bold = _owner.getFontMetrics( _small_italic_font.deriveFont( Font.BOLD ) ); - _fm_large_italic = _owner.getFontMetrics( _large_italic_font ); - _fm_large_italic_bold = _owner.getFontMetrics( _large_italic_font.deriveFont( Font.BOLD ) ); - _small_max_descent = _fm_small.getMaxDescent(); - _small_max_ascent = _fm_small.getMaxAscent() + 1; - } - void smallFonts() { - _small_font = _small_font.deriveFont( 7f ); - _large_font = _large_font.deriveFont( 8f ); - _small_italic_font = _small_italic_font.deriveFont( 7f ); - _large_italic_font = _large_italic_font.deriveFont( 8f ); + _small_font = _small_font.deriveFont( SMALL_FONTS_BASE - 1 ); + _large_font = _large_font.deriveFont( SMALL_FONTS_BASE ); + _small_italic_font = _small_italic_font.deriveFont( SMALL_FONTS_BASE - 1 ); + _large_italic_font = _large_italic_font.deriveFont( SMALL_FONTS_BASE ); setupFontMetrics(); } @@ -198,4 +170,36 @@ public final class TreeFontSet { _large_italic_font = _large_italic_font.deriveFont( 6f ); setupFontMetrics(); } + + private Font getLargeFontSystem() { + return _large_font_system; + } + + private void intializeFonts() { + final int small_size = getBaseFont().getSize() - 1; + int italic = Font.ITALIC; + if ( getBaseFont().getStyle() == Font.BOLD ) { + italic = italic + Font.BOLD; + } + _small_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size ); + _large_font = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() ); + _small_italic_font = new Font( getBaseFont().getFontName(), italic, small_size ); + _large_italic_font = new Font( getBaseFont().getFontName(), italic, getBaseFont().getSize() ); + _small_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), small_size ); + _large_font_system = new Font( getBaseFont().getFontName(), getBaseFont().getStyle(), getBaseFont().getSize() ); + _small_italic_font_system = new Font( getBaseFont().getFontName(), italic, small_size ); + _large_italic_font_system = new Font( getBaseFont().getFontName(), italic, getBaseFont().getSize() ); + setupFontMetrics(); + } + + private void setupFontMetrics() { + _fm_small = _owner.getFontMetrics( _small_font ); + _fm_large = _owner.getFontMetrics( _large_font ); + _fm_small_italic = _owner.getFontMetrics( _small_italic_font ); + _fm_small_italic_bold = _owner.getFontMetrics( _small_italic_font.deriveFont( Font.BOLD ) ); + _fm_large_italic = _owner.getFontMetrics( _large_italic_font ); + _fm_large_italic_bold = _owner.getFontMetrics( _large_italic_font.deriveFont( Font.BOLD ) ); + _small_max_descent = _fm_small.getMaxDescent(); + _small_max_ascent = _fm_small.getMaxAscent() + 1; + } } diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 4c1529f..1a4fef3 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -404,7 +404,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getControlPanel().displayedPhylogenyMightHaveChanged( true ); } else { - getTreeFontSet().decreaseFontSize(); + getTreeFontSet().decreaseFontSize( 1 ); getControlPanel().displayedPhylogenyMightHaveChanged( true ); } } @@ -525,7 +525,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( recalc_longest_ext_node_info ) { calculateLongestExtNodeInfo(); while ( ( getLongestExtNodeInfo() > ( x * 0.67 ) ) && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize(); + getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize() ); calculateLongestExtNodeInfo(); } } @@ -574,6 +574,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } _circ_max_depth = max_depth; setUpUrtFactor(); + // + if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + int dynamic_hiding_factor = calcDynamicHidingFactor(); + if ( dynamic_hiding_factor > 1 ) { + while ( dynamic_hiding_factor > 1 + && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) { + getTreeFontSet().decreaseFontSize( 1 ); + dynamic_hiding_factor = calcDynamicHidingFactor(); + } + } + else { + while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) { + getTreeFontSet().increaseFontSize(); + dynamic_hiding_factor = calcDynamicHidingFactor(); + } + } + } + // } } @@ -816,6 +835,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { msg += "colorized one subtree"; } + setEdited( true ); JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Completed (" + rank + ")", @@ -1114,6 +1134,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee PhylogenyMethods.midpointRoot( _phylogeny ); resetNodeIdToDistToLeafMap(); setArrowCursor(); + setEdited( true ); repaint(); } @@ -1512,7 +1533,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee // Position starting Y of tree _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) + ( TreePanel.MOVE / 2.0f ) ); - final int dynamic_hiding_factor = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ); + final int dynamic_hiding_factor = calcDynamicHidingFactor(); if ( getControlPanel().isDynamicallyHideData() ) { if ( dynamic_hiding_factor > 1 ) { getControlPanel().setDynamicHidingIsOn( true ); @@ -1648,6 +1669,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + private final int calcDynamicHidingFactor() { + return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) ); + } + final void recalculateMaxDistanceToRoot() { _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); } @@ -1700,6 +1725,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setNodeInPreorderToNull(); resetPreferredSize(); getMainPanel().adjustJScrollPane(); + setEdited( true ); repaint(); if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { getControlPanel().showWhole(); @@ -1986,6 +2012,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( _control_panel.getColorBranchesCb() != null ) { _control_panel.getColorBranchesCb().setSelected( true ); } + setEdited( true ); setArrowCursor(); repaint(); } @@ -2954,7 +2981,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize(); + getMainPanel().getTreeFontSet().decreaseFontSize( 1 ); getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } else if ( plusPressed( e.getKeyCode() ) ) { diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java index df16b75..cc0d772 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java @@ -34,6 +34,7 @@ import java.io.IOException; import java.io.Writer; import java.util.List; +import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.Configuration; import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.data.PhylogenyData; @@ -54,26 +55,6 @@ public final class RenderableVector implements RenderablePhylogenyData { private double _mean; private static RenderableVector _instance = null; - public static RenderableVector createInstance( final List values, - final DescriptiveStatistics stats, - final Configuration configuration ) { - if ( _instance == null ) { - _instance = new RenderableVector(); - } - _instance.setRenderingHeight( DEFAULT_HEIGHT ); - _instance._values = values; - _instance._configuration = configuration; - _instance._min = stats.getMin(); - _instance._max = stats.getMax(); - _instance._mean = stats.arithmeticMean(); - return _instance; - } - - @Override - public Object clone() { - throw new NoSuchMethodError(); - } - private RenderableVector() { _values = null; _configuration = null; @@ -89,10 +70,35 @@ public final class RenderableVector implements RenderablePhylogenyData { return asSimpleText(); } + @Override + public Object clone() { + throw new NoSuchMethodError(); + } + + @Override + public PhylogenyData copy() { + throw new NoSuchMethodError(); + } + + @Override + public Dimension getOriginalSize() { + return new Dimension( getTotalLength(), ( int ) getRenderingHeight() ); + } + + @Override + public Object getParameter() { + return null; + } + public double getRenderingFactorWidth() { return _rendering_factor_width; } + @Override + public Dimension getRenderingSize() { + return getOriginalSize(); + } + public int getTotalLength() { return ( int ) ( _values.size() * getRenderingHeight() ); } @@ -118,8 +124,9 @@ public final class RenderableVector implements RenderablePhylogenyData { } } - private Color calculateColor( final double v ) { - return ForesterUtil.calcColor( v, _min, _max, _mean, Color.MAGENTA, Color.GREEN, Color.WHITE ); + @Override + public void setParameter( final double parameter ) { + throw new NoSuchMethodError(); } public void setRenderingFactorWidth( final double rendering_factor_width ) { @@ -127,46 +134,48 @@ public final class RenderableVector implements RenderablePhylogenyData { } @Override - public StringBuffer toNHX() { - throw new NoSuchMethodError(); - } - - @Override - public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException { - throw new NoSuchMethodError(); + public void setRenderingHeight( final double height ) { + _height = height; } @Override - public PhylogenyData copy() { + public StringBuffer toNHX() { throw new NoSuchMethodError(); } @Override - public Dimension getOriginalSize() { - return new Dimension( getTotalLength(), ( int ) getRenderingHeight() ); - } - - @Override - public Object getParameter() { - return null; - } - - @Override - public Dimension getRenderingSize() { - return getOriginalSize(); - } - - @Override - public void setParameter( final double parameter ) { + public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException { throw new NoSuchMethodError(); } - @Override - public void setRenderingHeight( final double height ) { - _height = height; + private Color calculateColor( final double v ) { + return ForesterUtil.calcColor( v, _min, _max, _mean, Color.MAGENTA, Color.GREEN, Color.WHITE ); } private double getRenderingHeight() { return _height; } + + public static RenderableVector createInstance( final List values, + final DescriptiveStatistics stats, + final Configuration configuration ) { + if ( _instance == null ) { + _instance = new RenderableVector(); + } + _instance.setRenderingHeight( DEFAULT_HEIGHT ); + _instance._values = values; + _instance._configuration = configuration; + if ( stats.getN() > 0 ) { + _instance._min = stats.getMin(); + _instance._max = stats.getMax(); + _instance._mean = stats.arithmeticMean(); + } + else { + _instance._min = 0; + _instance._max = 0; + _instance._mean = 0; + AptxUtil.printWarningMessage( "Archaeopteryx", "creating renderable vector with empty statistics" ); + } + return _instance; + } } -- 1.7.10.2