X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConfiguration.java;h=162ac79997486cf5000f376d976eafd7f8a76291;hb=605b9b5326538a70a7afe353368b206516292575;hp=342fcdb7ac73242c40ce8ce50e6dbcf77a517fe0;hpb=7ed03ec00304ef630c043df6696413d0ca7b5583;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 342fcdb..162ac79 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -93,10 +93,11 @@ public final class Configuration { 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 NodeShape _default_node_shape = NodeShape.NONE; 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_instead_of_labels = false; + private boolean _taxonomy_colorize_node_shapes = false; final static int display_as_phylogram = 0; final static int show_node_names = 1; final static int show_tax_code = 2; @@ -106,22 +107,23 @@ public final class Configuration { final static int color_according_to_species = 6; final static int color_branches = 7; final static int width_branches = 8; - final static int show_domain_architectures = 9; - final static int show_binary_characters = 10; - final static int show_binary_character_counts = 11; - final static int show_gene_names = 12; - final static int show_sequence_acc = 13; - final static int display_internal_data = 14; - final static int dynamically_hide_data = 15; - final static int show_taxonomy_scientific_names = 16; - final static int show_taxonomy_common_names = 17; - final static int color_according_to_annotation = 18; - final static int show_property = 19; - 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_custom_node_shapes = 9; + final static int show_domain_architectures = 10; + final static int show_binary_characters = 11; + final static int show_binary_character_counts = 12; + final static int show_gene_names = 13; + final static int show_sequence_acc = 14; + final static int display_internal_data = 15; + final static int dynamically_hide_data = 16; + 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; // ------------------ // Click-to options // ------------------ @@ -153,7 +155,7 @@ public final class Configuration { { "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" }, { "Domains", "nodisplay", "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", "no" }, { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" }, @@ -364,6 +366,7 @@ public final class Configuration { return _cladogram_type; } + private int getClickToIndex( final String name ) { int index = -1; if ( name.equals( "edit_info" ) ) { @@ -1063,6 +1066,9 @@ 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() ) ); + } else if ( key.equals( "default_node_size" ) ) { final short i = parseShort( ( ( String ) st.nextElement() ).trim() ); setDefaultNodeShapeSize( i ); @@ -1100,7 +1106,7 @@ public final class Configuration { } } else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { - setTaxonomyColorizeNodeShapesInsteadOfLabels( parseBoolean( ( String ) st.nextElement() ) ); + setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); } else if ( st.countTokens() >= 2 ) { // counts the tokens that are not // yet retrieved! @@ -1232,6 +1238,9 @@ public final class Configuration { else if ( key.equals( "show_relation_confidence" ) ) { key_index = Configuration.show_relation_confidence; } + else if ( key.equals( "show_custom_node_shapes" ) ) { + key_index = Configuration.show_custom_node_shapes; + } // If we've found the key, set the values if ( key_index >= 0 ) { display_options[ key_index ][ 1 ] = ( String ) st.nextElement(); @@ -1408,11 +1417,19 @@ public final class Configuration { return _default_node_shape_size; } - private void setTaxonomyColorizeNodeShapesInsteadOfLabels( final boolean taxonomy_colorize_node_shapes_instead_of_labels ) { - _taxonomy_colorize_node_shapes_instead_of_labels = taxonomy_colorize_node_shapes_instead_of_labels; + private void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { + _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; } - public boolean isTaxonomyColorizeNodeShapesInsteadOfLabels() { - return _taxonomy_colorize_node_shapes_instead_of_labels; + public boolean isTaxonomyColorizeNodeShapes() { + return _taxonomy_colorize_node_shapes; } + + public boolean isShowDefaultNodeShapes() { + return _show_default_node_shapes; + } + private void setShowDefaultNodeShapes(boolean show_default_node_shapes) { + _show_default_node_shapes =show_default_node_shapes; + } + }