X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=80f0861edbc70c95b5ea370b26e36488c29c15fc;hb=a32f4076b5b309b4dcc0852d6283a2bd18785f28;hp=b533aa6000c3212131d508de54134042619b416c;hpb=3b5c2fab212d221196ed1734ee9c623f45310bb7;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index b533aa6..80f0861 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -29,11 +29,10 @@ import java.awt.Font; import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE; -import org.forester.phylogeny.data.NodeData; -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; +import org.forester.phylogeny.data.NodeDataField; +import org.forester.phylogeny.data.NodeVisualData; +import org.forester.phylogeny.data.NodeVisualData.NodeFill; +import org.forester.phylogeny.data.NodeVisualData.NodeShape; import org.forester.util.ForesterUtil; /* @@ -42,68 +41,75 @@ import org.forester.util.ForesterUtil; final public class Options { static final double MIN_CONFIDENCE_DEFAULT = 0.0; - private boolean _color_by_taxonomic_group; - private boolean _show_branch_length_values; - private boolean _internal_number_are_confidence_for_nh_parsing; - private boolean _show_scale; - private boolean _show_overview; - private boolean _antialias_screen; + private boolean _abbreviate_scientific_names; + private boolean _allow_errors_in_distance_to_parent; private boolean _antialias_print; + private boolean _antialias_screen; + private boolean _background_color_gradient; + private Font _base_font; + private CLADOGRAM_TYPE _cladogram_type; + private boolean _color_by_taxonomic_group; + private boolean _color_labels_same_as_parent_branch; + private NodeVisualData.NodeFill _default_node_fill; + private NodeVisualData.NodeShape _default_node_shape; + private short _default_node_shape_size; + private boolean _editable; + private NodeDataField _ext_desc_data_to_return; + private boolean _graphics_export_using_actual_size; private boolean _graphics_export_visible_only; - private int _print_size_x; - private int _print_size_y; + private boolean _internal_number_are_confidence_for_nh_parsing; + private boolean _inverse_search_result; + private boolean _match_whole_terms_only; + private boolean _search_with_regex; private double _min_confidence_value; - private boolean _print_black_and_white; - private boolean _print_using_actual_size; - private boolean _graphics_export_using_actual_size; - private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type; - private CLADOGRAM_TYPE _cladogram_type; - private OVERVIEW_PLACEMENT_TYPE _ov_placement; + private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style; + private boolean _nh_parsing_replace_underscores; private NODE_LABEL_DIRECTION _node_label_direction; - private Font _base_font; - private boolean _match_whole_terms_only; - private boolean _search_case_sensitive; + private short _number_of_digits_after_comma_for_branch_length_values; + private short _number_of_digits_after_comma_for_confidence_values; + private OVERVIEW_PLACEMENT_TYPE _ov_placement; + private PHYLOGENY_GRAPHICS_TYPE _phylogeny_graphics_type; + private boolean _print_black_and_white; private float _print_line_width; - private boolean _inverse_search_result; + private int _print_size_x; + private int _print_size_y; + private boolean _print_using_actual_size; private double _scale_bar_length; - private short _number_of_digits_after_comma_for_confidence_values; - private short _number_of_digits_after_comma_for_branch_length_values; - private boolean _nh_parsing_replace_underscores; - private TAXONOMY_EXTRACTION _taxonomy_extraction; - private boolean _editable; - private boolean _background_color_gradient; - private boolean _show_domain_labels; + private boolean _search_case_sensitive; private boolean _show_annotation_ref_source; - private boolean _color_labels_same_as_parent_branch; - private boolean _abbreviate_scientific_names; - private NodeVisualization.NodeShape _default_node_shape; - private NodeVisualization.NodeFill _default_node_fill; - private short _default_node_shape_size; - private boolean _taxonomy_colorize_node_shapes; - private boolean _show_default_node_shapes_internal; - private boolean _show_default_node_shapes_external; private boolean _show_confidence_stddev; - private NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style; - private NODE_DATA _ext_desc_data_to_return; + private boolean _show_default_node_shapes_for_marked_nodes; + private boolean _show_default_node_shapes_external; + private boolean _show_default_node_shapes_internal; + private boolean _show_domain_labels; + private boolean _show_overview; + private boolean _show_scale; + private TAXONOMY_EXTRACTION _taxonomy_extraction; + private boolean _line_up_renderable_node_data; + private boolean _right_align_domains; private Options() { init(); } - public NodeData.NODE_DATA getExtDescNodeDataToReturn() { + public NodeDataField getExtDescNodeDataToReturn() { return _ext_desc_data_to_return; } - public final boolean isShowDomainLabels() { - return _show_domain_labels; + public boolean isAllowErrorsInDistanceToParent() { + return _allow_errors_in_distance_to_parent; } public final boolean isShowAnnotationRefSource() { return _show_annotation_ref_source; } - public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) { - _show_annotation_ref_source = show_annotation_ref_source; + public final boolean isShowDomainLabels() { + return _show_domain_labels; + } + + public final void setAllowErrorsInDistanceToParent( final boolean allow_errors_in_distance_to_parent ) { + _allow_errors_in_distance_to_parent = allow_errors_in_distance_to_parent; } public void setBackgroundColorGradient( final boolean background_color_gradient ) { @@ -114,10 +120,14 @@ final public class Options { _color_labels_same_as_parent_branch = color_labels_same_as_parent_branch; } - public void setExtDescNodeDataToReturn( final NODE_DATA ext_desc_data_to_return ) { + public void setExtDescNodeDataToReturn( final NodeDataField ext_desc_data_to_return ) { _ext_desc_data_to_return = ext_desc_data_to_return; } + public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) { + _show_annotation_ref_source = show_annotation_ref_source; + } + public void setShowDomainLabels( final boolean show_domain_labels ) { _show_domain_labels = show_domain_labels; } @@ -210,6 +220,10 @@ final public class Options { return _background_color_gradient; } + final boolean isColorByTaxonomicGroup() { + return _color_by_taxonomic_group; + } + final boolean isColorLabelsSameAsParentBranch() { return _color_labels_same_as_parent_branch; } @@ -238,6 +252,10 @@ final public class Options { return _match_whole_terms_only; } + final boolean isSearchWithRegex() { + return _search_with_regex; + } + final boolean isPrintBlackAndWhite() { return _print_black_and_white; } @@ -254,14 +272,6 @@ final public class Options { return _search_case_sensitive; } - final boolean isShowBranchLengthValues() { - return _show_branch_length_values; - } - - final boolean isColorByTaxonomicGroup() { - return _color_by_taxonomic_group; - } - boolean isShowConfidenceStddev() { return _show_confidence_stddev; } @@ -270,6 +280,10 @@ final public class Options { return _show_default_node_shapes_external; } + boolean isShowDefaultNodeShapesForMarkedNodes() { + return _show_default_node_shapes_for_marked_nodes; + } + boolean isShowDefaultNodeShapesInternal() { return _show_default_node_shapes_internal; } @@ -282,10 +296,6 @@ final public class Options { return _show_scale; } - boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } @@ -306,6 +316,10 @@ final public class Options { _cladogram_type = cladogram_type; } + final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) { + _color_by_taxonomic_group = color_by_taxonomic_group; + } + final void setDefaultNodeFill( final NodeFill default_node_fill ) { _default_node_fill = default_node_fill; } @@ -348,6 +362,10 @@ final public class Options { _match_whole_terms_only = search_whole_words_only; } + final void setSearchWithRegex( final boolean search_with_regex ) { + _search_with_regex = search_with_regex; + } + final void setMinConfidenceValue( final double min_confidence_value ) { _min_confidence_value = min_confidence_value; } @@ -400,14 +418,6 @@ final public class Options { _search_case_sensitive = search_case_sensitive; } - final void setShowBranchLengthValues( final boolean show_branch_length_values ) { - _show_branch_length_values = show_branch_length_values; - } - - final void setColorByTaxonomicGroup( final boolean color_by_taxonomic_group ) { - _color_by_taxonomic_group = color_by_taxonomic_group; - } - void setShowConfidenceStddev( final boolean show_confidence_stddev ) { _show_confidence_stddev = show_confidence_stddev; } @@ -420,6 +430,10 @@ final public class Options { _show_default_node_shapes_internal = show_default_node_shapes_internal; } + void setShowDefaultNodeShapesForMarkedNodes( final boolean show_default_node_shapes_for_marked_nodes ) { + _show_default_node_shapes_for_marked_nodes = show_default_node_shapes_for_marked_nodes; + } + final void setShowOverview( final boolean show_overview ) { _show_overview = show_overview; } @@ -428,10 +442,6 @@ final public class Options { _show_scale = show_scale; } - void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { _taxonomy_extraction = taxonomy_extraction; } @@ -440,17 +450,16 @@ final public class Options { _default_node_shape = NodeShape.CIRCLE; _default_node_fill = NodeFill.GRADIENT; _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; - _taxonomy_colorize_node_shapes = false; - _show_branch_length_values = false; _internal_number_are_confidence_for_nh_parsing = false; _show_scale = false; - _antialias_screen = false; + _antialias_screen = true; _antialias_print = true; _graphics_export_visible_only = false; _editable = true; _background_color_gradient = false; _show_default_node_shapes_internal = false; _show_default_node_shapes_external = false; + _show_default_node_shapes_for_marked_nodes = false; if ( AptxUtil.isUsOrCanada() ) { _print_size_x = Constants.US_LETTER_SIZE_X; _print_size_y = Constants.US_LETTER_SIZE_Y; @@ -461,11 +470,12 @@ final public class Options { } _min_confidence_value = MIN_CONFIDENCE_DEFAULT; _print_black_and_white = false; - _print_using_actual_size = false; + _print_using_actual_size = true; _graphics_export_using_actual_size = true; _phylogeny_graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; _base_font = new Font( Configuration.getDefaultFontFamilyName(), Font.PLAIN, 10 ); _match_whole_terms_only = false; + _search_with_regex = false; _search_case_sensitive = false; _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; _show_overview = true; @@ -482,9 +492,11 @@ final public class Options { _show_annotation_ref_source = true; setAbbreviateScientificTaxonNames( false ); _color_labels_same_as_parent_branch = false; - _show_confidence_stddev = true; + _show_confidence_stddev = false; _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE; - _ext_desc_data_to_return = NODE_DATA.UNKNOWN; + _ext_desc_data_to_return = NodeDataField.UNKNOWN; + _line_up_renderable_node_data = true; + _right_align_domains = false; } final private void setNumberOfDigitsAfterCommaForBranchLength( final short number_of_digits_after_comma_for_branch_length_values ) { @@ -500,7 +512,6 @@ final public class Options { if ( configuration != null ) { instance.setAntialiasScreen( configuration.isAntialiasScreen() ); instance.setShowScale( configuration.isShowScale() ); - instance.setShowBranchLengthValues( configuration.isShowBranchLengthValues() ); instance.setShowOverview( configuration.isShowOverview() ); instance.setColorByTaxonomicGroup( configuration.isColorByTaxonomicGroup() ); instance.setCladogramType( configuration.getCladogramType() ); @@ -553,12 +564,15 @@ final public class Options { if ( configuration.getDefaultNodeShapeSize() >= 0 ) { instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() ); } - instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() ); instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() ); instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() ); + instance.setShowDefaultNodeShapesForMarkedNodes( configuration.isShowDefaultNodeShapesForMarkedNodes() ); if ( configuration.getExtDescNodeDataToReturn() != null ) { instance.setExtDescNodeDataToReturn( configuration.getExtDescNodeDataToReturn() ); } + instance.setRightLineUpDomains( configuration.isRightLineUpDomains() ); + instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() ); + instance.setAllowErrorsInDistanceToParent( false ); } return instance; } @@ -568,7 +582,7 @@ final public class Options { } public static enum CLADOGRAM_TYPE { - NON_LINED_UP, EXT_NODE_SUM_DEP, TOTAL_NODE_SUM_DEP; + EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP; } public static enum NODE_LABEL_DIRECTION { @@ -576,14 +590,14 @@ final public class Options { } public static enum PHYLOGENY_GRAPHICS_TYPE { - RECTANGULAR, TRIANGULAR, EURO_STYLE, ROUNDED, CONVEX, CURVED, UNROOTED, CIRCULAR; + CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED; } static enum OVERVIEW_PLACEMENT_TYPE { - UPPER_LEFT( "upper left" ), - UPPER_RIGHT( "upper right" ), LOWER_LEFT( "lower left" ), - LOWER_RIGHT( "lower right" ); + LOWER_RIGHT( "lower right" ), + UPPER_LEFT( "upper left" ), + UPPER_RIGHT( "upper right" ); private final String _name; @@ -601,7 +615,19 @@ final public class Options { } } - public boolean isAllowFontSizeChange() { - return true; + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; + } + + final public boolean isRightLineUpDomains() { + return _right_align_domains; + } + + final public void setLineUpRendarableNodeData( final boolean line_up_renderable_node_data ) { + _line_up_renderable_node_data = line_up_renderable_node_data; + } + + final public void setRightLineUpDomains( final boolean right_align_domains ) { + _right_align_domains = right_align_domains; } }