X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=80f0861edbc70c95b5ea370b26e36488c29c15fc;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=4d961641cf3c8c4dc8dbc18ea4d2560c3a9030c2;hpb=bf4f34e0511813622f68e54ffb783e4e6d92bfa4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 4d96164..80f0861 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -29,13 +29,11 @@ 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; import org.forester.util.ForesterUtil; -import org.omg.stub.java.rmi._Remote_Stub; /* * This is to hold changeable options. @@ -56,12 +54,13 @@ 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; @@ -78,22 +77,22 @@ 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 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; } @@ -101,10 +100,6 @@ final public class Options { return _allow_errors_in_distance_to_parent; } - public boolean isAllowFontSizeChange() { - return true; - } - public final boolean isShowAnnotationRefSource() { return _show_annotation_ref_source; } @@ -125,7 +120,7 @@ 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; } @@ -257,6 +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; } @@ -273,10 +272,6 @@ final public class Options { return _search_case_sensitive; } - final boolean isShowBranchLengthValues() { - return _show_branch_length_values; - } - boolean isShowConfidenceStddev() { return _show_confidence_stddev; } @@ -285,6 +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; } @@ -363,6 +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; } @@ -415,10 +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; - } - void setShowConfidenceStddev( final boolean show_confidence_stddev ) { _show_confidence_stddev = show_confidence_stddev; } @@ -431,6 +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; } @@ -447,7 +450,6 @@ final public class Options { _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; @@ -457,6 +459,7 @@ final public class Options { _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; @@ -472,6 +475,7 @@ final public class Options { _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; @@ -488,10 +492,10 @@ 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; - _line_up_renderable_node_data = false; + _ext_desc_data_to_return = NodeDataField.UNKNOWN; + _line_up_renderable_node_data = true; _right_align_domains = false; } @@ -508,7 +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() ); @@ -563,12 +566,12 @@ 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.setRightLineUpDomains( configuration.isRightLineUpDomains() ); + instance.setLineUpRendarableNodeData( configuration.isLineUpRendarableNodeData() ); instance.setAllowErrorsInDistanceToParent( false ); } return instance; @@ -613,23 +616,18 @@ final public class Options { } 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 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; } - }