X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=3eb403e4fd822b4b45f491659e33caf7baba6946;hb=b0fd64a5d558885627ba7a7295d9ef612fe76cd0;hp=fdaeacb2657618a5f877dd6efd414cce49d39cc4;hpb=081ab5f646bcae3f5192e9c1786e2d68ce015ed8;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index fdaeacb..3eb403e 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -29,8 +29,7 @@ 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.NodeDataField; import org.forester.phylogeny.data.NodeVisualData; import org.forester.phylogeny.data.NodeVisualData.NodeFill; import org.forester.phylogeny.data.NodeVisualData.NodeShape; @@ -41,6 +40,39 @@ import org.forester.util.ForesterUtil; */ final public class Options { + public static enum CLADOGRAM_TYPE { + EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP; + } + + public static enum NODE_LABEL_DIRECTION { + HORIZONTAL, RADIAL; + } + + public static enum PHYLOGENY_GRAPHICS_TYPE { + CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED; + } + + static enum OVERVIEW_PLACEMENT_TYPE { + LOWER_LEFT( "lower left" ), + LOWER_RIGHT( "lower right" ), + UPPER_LEFT( "upper left" ), + UPPER_RIGHT( "upper right" ); + + private final String _name; + + private OVERVIEW_PLACEMENT_TYPE( final String name ) { + _name = name; + } + + @Override + public String toString() { + return _name; + } + + public String toTag() { + return toString().replaceAll( " ", "_" ); + } + } static final double MIN_CONFIDENCE_DEFAULT = 0.0; private boolean _abbreviate_scientific_names; private boolean _allow_errors_in_distance_to_parent; @@ -55,12 +87,13 @@ final public class Options { private NodeVisualData.NodeShape _default_node_shape; private short _default_node_shape_size; private boolean _editable; - private NODE_DATA _ext_desc_data_to_return; + private NodeDataField _ext_desc_data_to_return; private boolean _graphics_export_using_actual_size; private boolean _graphics_export_visible_only; 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 NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_value_style; private boolean _nh_parsing_replace_underscores; @@ -77,20 +110,22 @@ final public class Options { private double _scale_bar_length; private boolean _search_case_sensitive; private boolean _show_annotation_ref_source; - private boolean _show_branch_length_values; private boolean _show_confidence_stddev; + 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; } @@ -98,8 +133,12 @@ final public class Options { return _allow_errors_in_distance_to_parent; } - public boolean isAllowFontSizeChange() { - return true; + final public boolean isLineUpRendarableNodeData() { + return _line_up_renderable_node_data; + } + + final public boolean isRightLineUpDomains() { + return _right_align_domains; } public final boolean isShowAnnotationRefSource() { @@ -122,10 +161,18 @@ 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; } + 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; + } + public final void setShowAnnotationRefSource( final boolean show_annotation_ref_source ) { _show_annotation_ref_source = show_annotation_ref_source; } @@ -134,6 +181,67 @@ final public class Options { _show_domain_labels = show_domain_labels; } + final private void init() { + _default_node_shape = NodeShape.CIRCLE; + _default_node_fill = NodeFill.GRADIENT; + _default_node_shape_size = AptxConstants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; + _internal_number_are_confidence_for_nh_parsing = false; + _show_scale = 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 = AptxConstants.US_LETTER_SIZE_X; + _print_size_y = AptxConstants.US_LETTER_SIZE_Y; + } + else { + _print_size_x = AptxConstants.A4_SIZE_X; + _print_size_y = AptxConstants.A4_SIZE_Y; + } + _min_confidence_value = MIN_CONFIDENCE_DEFAULT; + _print_black_and_white = 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 = AptxConstants.PDF_LINE_WIDTH_DEFAULT; + _show_overview = true; + _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; + _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; + _inverse_search_result = false; + _scale_bar_length = 0.0; + _number_of_digits_after_comma_for_branch_length_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; + _number_of_digits_after_comma_for_confidence_values = AptxConstants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; + _nh_parsing_replace_underscores = false; + _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; + _cladogram_type = AptxConstants.CLADOGRAM_TYPE_DEFAULT; + _show_domain_labels = true; + _show_annotation_ref_source = true; + setAbbreviateScientificTaxonNames( false ); + _color_labels_same_as_parent_branch = false; + _show_confidence_stddev = false; + _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE; + _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 ) { + _number_of_digits_after_comma_for_branch_length_values = number_of_digits_after_comma_for_branch_length_values; + } + + final private 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; + } + final Font getBaseFont() { return _base_font; } @@ -270,8 +378,8 @@ final public class Options { return _search_case_sensitive; } - final boolean isShowBranchLengthValues() { - return _show_branch_length_values; + final boolean isSearchWithRegex() { + return _search_with_regex; } boolean isShowConfidenceStddev() { @@ -282,6 +390,10 @@ 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; } @@ -412,8 +524,8 @@ 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 setSearchWithRegex( final boolean search_with_regex ) { + _search_with_regex = search_with_regex; } void setShowConfidenceStddev( final boolean show_confidence_stddev ) { @@ -424,6 +536,10 @@ final public class Options { _show_default_node_shapes_external = show_default_node_shapes_external; } + 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; + } + void setShowDefaultNodeShapesInternal( final boolean show_default_node_shapes_internal ) { _show_default_node_shapes_internal = show_default_node_shapes_internal; } @@ -440,70 +556,11 @@ final public class Options { _taxonomy_extraction = taxonomy_extraction; } - final private void init() { - _default_node_shape = NodeShape.CIRCLE; - _default_node_fill = NodeFill.GRADIENT; - _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; - _show_branch_length_values = false; - _internal_number_are_confidence_for_nh_parsing = false; - _show_scale = 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; - if ( AptxUtil.isUsOrCanada() ) { - _print_size_x = Constants.US_LETTER_SIZE_X; - _print_size_y = Constants.US_LETTER_SIZE_Y; - } - else { - _print_size_x = Constants.A4_SIZE_X; - _print_size_y = Constants.A4_SIZE_Y; - } - _min_confidence_value = MIN_CONFIDENCE_DEFAULT; - _print_black_and_white = false; - _print_using_actual_size = false; - _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_case_sensitive = false; - _print_line_width = Constants.PDF_LINE_WIDTH_DEFAULT; - _show_overview = true; - _ov_placement = OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT; - _node_label_direction = NODE_LABEL_DIRECTION.HORIZONTAL; - _inverse_search_result = false; - _scale_bar_length = 0.0; - _number_of_digits_after_comma_for_branch_length_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT; - _number_of_digits_after_comma_for_confidence_values = Constants.NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT; - _nh_parsing_replace_underscores = false; - _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; - _cladogram_type = Constants.CLADOGRAM_TYPE_DEFAULT; - _show_domain_labels = true; - _show_annotation_ref_source = true; - setAbbreviateScientificTaxonNames( false ); - _color_labels_same_as_parent_branch = false; - _show_confidence_stddev = true; - _nh_conversion_support_value_style = NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE; - _ext_desc_data_to_return = NODE_DATA.UNKNOWN; - } - - final private void setNumberOfDigitsAfterCommaForBranchLength( 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; - } - - final private 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 final static Options createInstance( final Configuration configuration ) { final Options instance = createDefaultInstance(); 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() ); @@ -558,9 +615,12 @@ final public class Options { } 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; @@ -569,38 +629,4 @@ final public class Options { final static Options createDefaultInstance() { return new Options(); } - - public static enum CLADOGRAM_TYPE { - EXT_NODE_SUM_DEP, NON_LINED_UP, TOTAL_NODE_SUM_DEP; - } - - public static enum NODE_LABEL_DIRECTION { - HORIZONTAL, RADIAL; - } - - public static enum PHYLOGENY_GRAPHICS_TYPE { - CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED; - } - - static enum OVERVIEW_PLACEMENT_TYPE { - LOWER_LEFT( "lower left" ), - LOWER_RIGHT( "lower right" ), - UPPER_LEFT( "upper left" ), - UPPER_RIGHT( "upper right" ); - - private final String _name; - - private OVERVIEW_PLACEMENT_TYPE( final String name ) { - _name = name; - } - - @Override - public String toString() { - return _name; - } - - public String toTag() { - return toString().replaceAll( " ", "_" ); - } - } }