MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );
}
else if ( o == _cycle_node_fill_mi ) {
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );
+ MainFrame.cycleNodeFill( getOptions() );
}
else if ( o == _cycle_node_shape_mi ) {
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );
+ MainFrame.cycleNodeShape( getOptions() );
}
else if ( o == _non_lined_up_cladograms_rbmi ) {
updateOptions( getOptions() );
CROSSPLATFORM, NATIVE, NIMBUS, UNKNOWN
}
final static String clickto_options[][] = {
- { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
- { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
- { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
- { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
- { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
- { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
- { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
- { "Return", "display" }, { "Select Node(s)", "display" } };
+ { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
+ { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
+ { "Colorize Node(s)", "display" }, { "Change Node Font(s)", "display" },
+ { "Colorize Subtree(s)", "display" }, { "Open Sequence DB", "display" }, { "Open PDB", "display" },
+ { "Open Taxonomy DB", "display" }, { "Launch BLAST", "display" }, { "Cut Subtree", "display" },
+ { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
+ { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
+ { "List Node Data", "display" }, { "Select Node(s)", "display" } };
private final static String DEFAULT_SPECIES_COLORS[][] = {
- { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
- { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
- { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
- { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
- { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
- { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
- { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
- { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
- { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
- { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
- { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
- { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
- { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
- { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
- { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
- { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
- { "PORGI", "0x918E00" } };
+ { "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
+ { "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
+ { "PANTR", "0xCC2400" }, { "MOUSE", "0xFF7F00" }, { "RAT", "0xFFEF00" }, { "MONDO", "0xEE9A49" },
+ { "ORNAN", "0xCD853F" }, { "XENLA", "0x6BAA23" }, { "XENTR", "0x6BAA23" }, { "CHICK", "0xFFC125" },
+ { "FUGRU", "0x0000FF" }, { "BRARE", "0x0000DD" }, { "DANRE", "0x0000BB" }, { "TETNG", "0x0000AA" },
+ { "ORYLA", "0x000088" }, { "GASAC", "0x000066" }, { "CAEEL", "0x666699" }, { "CAEBR", "0xB0B0B0" },
+ { "DROME", "0x663366" }, { "DROPS", "0x996699" }, { "APIME", "0x7A7700" }, { "AEDAE", "0x8C5900" },
+ { "TRICA", "0x918E00" }, { "NEMVE", "0x0066CC" }, { "HYDVU", "0x3399FF" }, { "LUBBA", "0xF7B5CB" },
+ { "GEOCY", "0xF5A0BD" }, { "AMPQE", "0x009966" }, { "SUBDO", "0xC790B9" }, { "MONBE", "0xFC0FC0" },
+ { "DICPU", "0xFFCC33" }, { "DICDI", "0xFFCC00" }, { "ENTHI", "0x5959AB" }, { "ARATH", "0x00FF00" },
+ { "POPTR", "0x006400" }, { "VITVI", "0x00CD00" }, { "GLYMA", "0x00FF7F" }, { "ORYSA", "0x008B00" },
+ { "ORYSJ", "0x008C00" }, { "SORBI", "0x00EE76" }, { "SELMO", "0x238E23" }, { "PHYPA", "0x09F911" },
+ { "OSTLU", "0x7FFF00" }, { "OSTTA", "0x7FFF00" }, { "OSTRC", "0x7FFF00" }, { "MICPU", "0x66CD00" },
+ { "MIC99", "0x66CD00" }, { "CHLRE", "0xB3EE3A" }, { "VOLCA", "0xC0FF3E" }, { "CHLSP", "0x6B8E23" },
+ { "CYAME", "0xD02090" }, { "YEAST", "0xAAAAAA" }, { "BACFR", "0xFF0000" }, { "BACTN", "0xFFFF00" },
+ { "MYXXD", "0x0000FF" }, { "STIAU", "0x00FFFF" }, { "BACOV", "0x8C5900" }, { "BACUN", "0x66CD00" },
+ { "PORGI", "0x918E00" } };
final static int display_node_data = 0;
final static int collapse_uncollapse = 1;
final static int reroot = 2;
// Click-to options
// ------------------
final static String display_options[][] = {
- { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
- { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
- { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
- { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
- { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
- { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
- { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
- { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
- { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
- { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
- { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
- { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
- { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
- { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
+ { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
+ { "Seq Annotations", "display", "no" }, { "Confidence Values", "display", "?" },
+ { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "no" },
+ { "Colorize by Sequence", "display", "no" }, { "Visual Styles/Branch Colors", "display", "no" },
+ { "Branch Widths", "display", "no" }, { "Domain Architectures", "display", "no" },
+ { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
+ { "Seq Name", "display", "yes" }, { "Seq Accession", "display", "no" },
+ { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
+ { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
+ { "Colorize by Annotation", "display", "no" }, { "Seq Symbol", "display", "yes" },
+ { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
+ { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
+ { "Properties", "display", "no" }, { "Gene Name", "display", "yes" },
+ { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" } };
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
private SortedMap<String, Color> _display_colors = null;
private boolean _display_sequence_relations = false;
private boolean _editable = true;
- private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
+ private NodeDataField _ext_desc_data_to_return = NodeDataField.UNKNOWN;
private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW;
private int _frame_x_size;
private int _frame_y_size;
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" );
+ .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( "display_sequences" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
+ .printWarningMessage( Constants.PRG_NAME, "configuration key [display_sequences] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "open_seq_web" ) ) {
}
else if ( name.equals( "display_node_popup" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [display_node_popup] is deprecated" );
+ "configuration key [display_node_popup] is deprecated" );
return DEPRECATED;
}
else if ( name.equals( "custom_option" ) ) {
default_clickto = getClickToIndex( clickto_name );
if ( default_clickto == -1 ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "invalid value [" + clickto_name
- + "] for [default_click_to]" );
+ + "] for [default_click_to]" );
default_clickto = 0;
}
else if ( default_clickto == DEPRECATED ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not parse yes/no/? value from [" + my_str
- + "]" );
+ + "]" );
_ui = UI.UNKNOWN;
}
}
else {
setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [phylogeny_graphics_type]" );
+ + "] for [phylogeny_graphics_type]" );
}
}
else if ( key.equals( "min_confidence_value" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "value for [pdf_export_line_width] cannot be zero or negative" );
+ "value for [pdf_export_line_width] cannot be zero or negative" );
}
}
else if ( key.equals( "window_initial_size_x" ) ) {
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "value for [default_number_of_bootstrap_resamples] cannot be negative" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "value for [default_number_of_bootstrap_resamples] cannot be negative" );
}
}
else if ( key.equals( "mafft_local" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [cladogram_type]" );
+ + "] for [cladogram_type]" );
}
}
else if ( key.equals( "non_lined_up_cladogram" ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [non_lined_up_cladogram] is deprecated, use [cladogram_type] instead" );
}
else if ( key.equals( "hide_controls_and_menus" ) ) {
_hide_controls_and_menus = parseBoolean( ( String ) st.nextElement() );
else {
setOvPlacement( OVERVIEW_PLACEMENT_TYPE.UPPER_LEFT );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [overview_placement_type]" );
+ + "] for [overview_placement_type]" );
}
}
else if ( key.equals( "node_label_direction" ) ) {
else {
setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL );
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + type_str
- + "] for [node_label_direction]" );
+ + "] for [node_label_direction]" );
}
}
else if ( key.equals( "branch_length_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [branch_length_value_digits]" );
+ + "] for [branch_length_value_digits]" );
}
}
else if ( key.equals( "confidence_value_digits" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + i
- + "] for [confidence_value_digits]" );
+ + "] for [confidence_value_digits]" );
}
}
else if ( key.equals( "allow_editing" ) ) {
final boolean r = parseBoolean( ( String ) st.nextElement() );
if ( r && ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
else {
setReplaceUnderscoresInNhParsing( r );
}
else {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
- + s
- + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "unknown value for \"taxonomy_extraction_in_nh_parsing\": "
+ + s
+ + " (must be either: no, pfam_relaxed, pfam_strict, or aggressive)" );
}
if ( ( getTaxonomyExtraction() != TAXONOMY_EXTRACTION.NO ) && isReplaceUnderscoresInNhParsing() ) {
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "attempt to extract taxonomies and replace underscores at the same time" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "attempt to extract taxonomies and replace underscores at the same time" );
}
}
else if ( key.equals( "internal_labels_are_confidence_values" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + fill_str
- + "] for [default_node_fill]" );
+ + "] for [default_node_fill]" );
}
}
else if ( key.equals( "default_node_shape" ) ) {
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + shape_str
- + "] for [default_node_shape]" );
+ + "] for [default_node_shape]" );
}
}
else if ( key.equals( "midpoint_reroot" ) ) {
setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) );
}
- else if ( key.equals( "ext_descendents_data_to_return" ) ) {
+ else if ( key.equals( "list_node_data_field" ) || key.equals( "ext_descendents_data_to_return" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
if ( s.equalsIgnoreCase( "node_name" ) ) {
setExtDescNodeDataToReturn( NodeDataField.NODE_NAME );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return]" );
+ + "] for [ext_descendents_data_to_return]" );
}
}
- else if ( key.equals( "label_for_get_ext_descendents_data" ) ) {
+ else if ( key.equals( "list_node_data_custom_label" ) || key.equals( "label_for_get_ext_descendents_data" ) ) {
final String s = ( ( String ) st.nextElement() ).trim();
- if ( ForesterUtil.isEmpty( s ) || ( s.length() < 2 ) ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "illegal value [" + s
- + "] for [label_for_get_ext_descendents_data]" );
- }
- else {
+ if ( !ForesterUtil.isEmpty( s ) && ( s.length() > 1 ) ) {
setLabelForGetExtDescendentsData( s.replaceAll( "_", " " ) );
}
}
- else if ( key.equals( "ext_descendents_data_to_return_on" ) ) {
+ else if ( key.equals( "list_node_data_in" ) || key.equals( "ext_descendents_data_to_return_on" ) ) {
final String s = ( ( String ) st.nextElement() ).trim().toLowerCase();
if ( s.equals( "console" ) ) {
setExtNodeDataReturnOn( EXT_NODE_DATA_RETURN_ON.CONSOLE );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s
- + "] for [ext_descendents_data_to_return_on]" );
+ + "] for [ext_descendents_data_to_return_on]" );
}
}
else if ( key.equals( "vector_data_min_color" ) ) {
else if ( key.equals( "color_branches" ) ) {
key_index = Configuration.use_style;
ForesterUtil
- .printWarningMessage( Constants.PRG_NAME,
- "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
+ .printWarningMessage( Constants.PRG_NAME,
+ "configuration key [color_branches] is deprecated, use [use_visual_styles] instead" );
}
else if ( key.equals( "width_branches" ) ) {
key_index = Configuration.width_branches;
}
else if ( key.equals( "annotation_color" ) ) {
getAnnotationColors()
- .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
+ .put( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else if ( key.equals( "function_color" ) ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME,
- "configuration key [function_color] is deprecated" );
+ "configuration key [function_color] is deprecated" );
}
else if ( key.equals( DISPLAY_COLOR_KEY ) ) {
putDisplayColors( ( String ) st.nextElement(), Color.decode( ( String ) st.nextElement() ) );
}
else {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown configuration key [" + key
- + "] in: " + config_filename );
+ + "] in: " + config_filename );
}
}
}
public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.9901 beta";
- final static String PRG_DATE = "141118";
+ final static String VERSION = "0.9902 beta";
+ final static String PRG_DATE = "141219";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
"Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
_sequence_colors = sequence_colors;
}
-
void setupControls() {
// The tree display options:
setupDisplayCheckboxes();
_get_ext_desc_data = cb_index;
if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
addClickToOption( Configuration.get_ext_desc_data, getConfiguration()
- .getLabelForGetExtDescendentsData() );
+ .getLabelForGetExtDescendentsData() );
}
else {
- final String s = getOptions().getExtDescNodeDataToReturn().toString();
- final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s;
- addClickToOption( Configuration.get_ext_desc_data, label );
+
+ addClickToOption( Configuration.get_ext_desc_data,
+ getConfiguration().getClickToTitle( Configuration.get_ext_desc_data ) );
}
+
if ( default_option == Configuration.get_ext_desc_data ) {
selected_index = cb_index;
}
MainFrame.cycleOverview( getOptions(), getCurrentTreePanel() );\r
}\r
else if ( o == _cycle_node_fill_mi ) {\r
- MainFrame.cycleNodeFill( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeFill( getOptions() );\r
}\r
else if ( o == _cycle_node_shape_mi ) {\r
- MainFrame.cycleNodeShape( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeShape( getOptions() );\r
}\r
else if ( o == _cycle_data_return ) {\r
- MainFrame.cycleNodeDataReturn( getOptions(), getCurrentTreePanel() );\r
+ MainFrame.cycleNodeDataReturn( getOptions(), getConfiguration() );\r
}\r
else if ( o == _screen_antialias_cbmi ) {\r
updateOptions( getOptions() );\r
return label;\r
}\r
\r
- static void cycleNodeFill( final Options op, final TreePanel tree_panel ) {\r
+ static void cycleNodeFill( final Options op ) {\r
switch ( op.getDefaultNodeFill() ) {\r
case GRADIENT:\r
op.setDefaultNodeFill( NodeFill.SOLID );\r
}\r
}\r
\r
- static void cycleNodeShape( final Options op, final TreePanel tree_panel ) {\r
+ static void cycleNodeShape( final Options op ) {\r
switch ( op.getDefaultNodeShape() ) {\r
case CIRCLE:\r
op.setDefaultNodeShape( NodeShape.RECTANGLE );\r
}\r
}\r
\r
- static void cycleNodeDataReturn( final Options op, final TreePanel tree_panel ) {\r
+ private static void cycleNodeDataReturn( final Options op, Configuration conf ) {\r
switch ( op.getExtDescNodeDataToReturn() ) {\r
case UNKNOWN:\r
op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_ALL );\r
op.setExtDescNodeDataToReturn( NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN );\r
break;\r
case DOMAINS_COLLAPSED_PER_PROTEIN:\r
+ op.setExtDescNodeDataToReturn( NodeDataField.SEQ_ANNOTATIONS );\r
+ break;\r
+ case SEQ_ANNOTATIONS:\r
op.setExtDescNodeDataToReturn( NodeDataField.GO_TERM_IDS );\r
break;\r
case GO_TERM_IDS:\r
op.setExtDescNodeDataToReturn( NodeDataField.SEQUENCE_MOL_SEQ_FASTA );\r
break;\r
+ case SEQUENCE_MOL_SEQ_FASTA:\r
+ if ( conf != null && conf.getExtDescNodeDataToReturn() != null\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_ALL\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQ_ANNOTATIONS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.GO_TERM_IDS\r
+ && conf.getExtDescNodeDataToReturn() != NodeDataField.SEQUENCE_MOL_SEQ_FASTA\r
+ ) {\r
+ op.setExtDescNodeDataToReturn( conf.getExtDescNodeDataToReturn() );\r
+ }\r
+ else {\r
+ op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
+ }\r
+ break; \r
default:\r
op.setExtDescNodeDataToReturn( NodeDataField.UNKNOWN );\r
}\r
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
MainFrame.setTextNodeSizeMenuItem( _choose_node_size_mi, getOptions() );
- MainFrame.setCycleDataReturnMenuItem( _cycle_data_return, getOptions() );
+
try {
getMainPanel().getControlPanel().setVisibilityOfDomainStrucureCB();
getMainPanel().getControlPanel().setVisibilityOfX();
calculateScaleDistance();
FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() );
FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration
- .getNumberOfDigitsAfterCommaForBranchLengthValues() );
+ .getNumberOfDigitsAfterCommaForBranchLengthValues() );
}
@Override
return;
}
int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE )
- * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
+ * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO );
if ( max_length < 40 ) {
max_length = 40;
}
}
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString() );
+ .getGainedCharactersAsStringBuffer().toString() );
}
if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null )
&& ( node.getNodeData().getVector().size() > 0 ) ) {
}
catch ( final NumberFormatException e ) {
JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str
- + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
+ + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE );
return;
}
int i = -1;
catch ( final NumberFormatException e ) {
JOptionPane.showMessageDialog( this,
"Could not parse \"" + index_str
- + "\" into index for vector data",
+ + "\" into index for vector data",
"Problem with Vector Data",
JOptionPane.ERROR_MESSAGE );
return;
if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) {
if ( SPECIAL_DOMAIN_COLORING ) {
rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
- .getDomainArchitecture(), node.getName() );
+ .getDomainArchitecture(), node.getName() );
}
else {
rds = new RenderableDomainArchitecture( node.getNodeData().getSequence()
- .getDomainArchitecture() );
+ .getDomainArchitecture() );
}
node.getNodeData().getSequence().setDomainArchitecture( rds );
}
return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) )
&& ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) )
&& ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y
- + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
+ + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) );
}
final boolean inOvRectangle( final MouseEvent e ) {
return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) )
&& ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) )
&& ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY()
- + getOvRectangle().getHeight() + 1 ) ) );
+ + getOvRectangle().getHeight() + 1 ) ) );
}
final boolean isApplet() {
y = max_y;
}
getMainPanel().getCurrentScrollPane().getViewport()
- .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
+ .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) );
setInOvRect( true );
repaint();
}
if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
g.setColor( getColorForFoundNode( c ) );
drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary()
- - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
}
}
else {
if ( !to_graphics_file ) {
g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y
- + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
+ + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) );
g.fill( r );
}
else {
}
// Position starting Y of tree
_phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() )
- + ( TreePanel.MOVE / 2.0f ) );
+ + ( TreePanel.MOVE / 2.0f ) );
final int dynamic_hiding_factor = calcDynamicHidingFactor();
if ( getControlPanel().isDynamicallyHideData() ) {
if ( dynamic_hiding_factor > 1 ) {
y_pos + radius_ov,
( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ),
- g );
+ g );
g.setTransform( _at );
paintOvRectangle( g );
}
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil
- .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
+ .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() );
}
else {
if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil.roundToInt( getXdistance()
- * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
+ * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) );
}
else {
x = TreePanel.MOVE
+ getLongestExtNodeInfo()
+ ForesterUtil.roundToInt( getXdistance()
- * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
+ * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) );
}
}
setPreferredSize( new Dimension( x, y ) );
return ( ( x >= ( getOvVirtualRectangle().x - 1 ) )
&& ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) )
&& ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y
- + getOvVirtualRectangle().height + 1 ) ) );
+ + getOvVirtualRectangle().height + 1 ) ) );
}
final private boolean inOvVirtualRectangle( final MouseEvent e ) {
&& ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
- .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
- .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
return true;
}
else {
}
return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) )
|| ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node
- .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
+ .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) );
}
final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) {
return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) )
|| ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) )
|| ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect()
- .getMaxX() + 20 ) ) );
+ .getMaxX() + 20 ) ) );
}
final private boolean isNonLinedUpCladogram() {
_node_popup_menu_items = new JMenuItem[ clickto_names.size() ];
for( int i = 0; i < clickto_names.size(); i++ ) {
final String title = clickto_names.get( i );
-
_node_popup_menu_items[ i ] = new JMenuItem( title );
if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
final String id = isCanOpenSeqWeb( node );
else {
_node_popup_menu_items[ i ].setEnabled( false );
}
- //
}
- else if ( title.equals( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) {
- System.out.println( ">>>>>>>>>>>>>>>>>>" + title );//TODO
- _node_popup_menu_items[ i ].setText( "horsehit" );
- //TODO
+ else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ]
+ .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": "
+ + getOptions().getExtDescNodeDataToReturn().toString() );
}
-
-
else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
}
AptxUtil.launchWebBrowser( new URI( uri_str ),
isApplet(),
isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
AptxUtil.launchWebBrowser( new URI( uri_str ),
isApplet(),
isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
AptxUtil.launchWebBrowser( new URI( uri_str ),
isApplet(),
isApplet() ? obtainApplet() : null,
- "_aptx_tax" );
+ "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
if ( !node.isRoot() ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
+ .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet().getSmallMaxDescent(), g );
+ - getTreeFontSet().getSmallMaxDescent(), g );
}
}
final float dx = x2 - x1;
final float dy = y2 - y1;
_cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
+ + ( dy * 0.8f ), x2, y2 );
( g ).draw( _cubic_curve );
}
else {
final float dx = x2 - x1;
final float dy = y2 - y1;
_cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1
- + ( dy * 0.8f ), x2, y2 );
+ + ( dy * 0.8f ), x2, y2 );
g.draw( _cubic_curve );
}
else {
not_first = true;
}
sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
if ( getOptions().isShowConfidenceStddev() ) {
if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
sb.append( "(" );
sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
sb.append( ")" );
}
}
final String conf_str = sb.toString();
TreePanel.drawString( conf_str,
parent_x
- + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
- .stringWidth( conf_str ) ) / 2 ),
- ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
- g );
+ + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
+ .stringWidth( conf_str ) ) / 2 ),
+ ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
+ g );
}
}
g.setColor( Color.BLUE );
}
TreePanel
- .drawString( gained,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
- ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
- g );
+ .drawString( gained,
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
+ ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
+ g );
g.setColor( getTreeColorSet().getLostCharactersColor() );
TreePanel
- .drawString( lost,
- parent_x
- + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
- ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
- g );
+ .drawString( lost,
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
+ ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
+ g );
}
}
|| ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
|| ( getOptions().isShowDefaultNodeShapesForMarkedNodes()
&& ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData()
- .getNodeVisualData().isEmpty() ) )
- || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
- .getNodeData().getNodeVisualData().getNodeColor() != null )
- || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
- || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
- .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
- .isDuplication()
- || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
- .isSpeciationOrDuplication() ) ) ) {
+ .getNodeVisualData().isEmpty() ) )
+ || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
+ .getNodeData().getNodeVisualData().getNodeColor() != null )
+ || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
+ || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
+ .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
+ || ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
+ .isDuplication()
+ || node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
+ .isSpeciationOrDuplication() ) ) ) {
NodeVisualData vis = null;
if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
&& ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
if ( getControlPanel().isWriteBranchLengthValues()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
+ && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation
.getRef1().isEqual( _query_sequence ) )
&& seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
- .getSelectedItem() );
+ .getSelectedItem() );
if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
final double linePosX = node.getXcoord() + 2 + half_box_size;
final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
- + ")";
+ + ")";
if ( sConfidence != null ) {
float confidenceX = pos_x;
if ( sb_str.length() > 0 ) {
}
if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code
final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc )
- .getBounds().getWidth();
+ .getBounds().getWidth();
TreePanel.drawString( sConfidence, confidenceX, pos_y, g );
x += CONFIDENCE_LEFT_MARGIN + confidenceWidth;
}
nodeTextBoundsWidth += 2;
}
g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x
- + nodeTextBoundsWidth, 3 + ( int ) pos_y );
+ + nodeTextBoundsWidth, 3 + ( int ) pos_y );
break;
}
}
}
final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
_sb.append( ann_str );
if ( _sb.length() > 0 ) {
}
if ( getControlPanel().isShowBinaryCharacters() ) {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
- .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
+ .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
- .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
- .getLostCharactersAsStringBuffer().toString() );
+ .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
+ .getLostCharactersAsStringBuffer().toString() );
}
else {
TreePanel
- .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + half_box_size,
- node.getYcoord()
- + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
- g );
+ .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
+ node.getXcoord() + x + 4 + half_box_size,
+ node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
+ g );
paintGainedAndLostCharacters( g, node, "+"
+ node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
- + node.getNodeData().getBinaryCharacters().getLostCount() );
+ + node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
g.setColor( getColorForFoundNode( node ) );
drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary()
- - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
+ - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g );
}
float new_x = 0;
if ( !node.isExternal() && !node.isCollapse() ) {
&& !node.isRoot()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && node.getBranchData().isHasConfidences() ) {
+ && node.getBranchData().isHasConfidences() ) {
paintConfidenceValues( g, node, to_pdf, to_graphics_file );
}
// Draw a line to root:
&& !is_in_found_nodes
&& ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
.isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
- .getHeight() ) ) ) ) ) {
+ .getHeight() ) ) ) ) ) {
return;
}
final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
if ( getOptions().isRightLineUpDomains() ) {
rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() )
+ _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds
- .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
+ .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf );
}
else {
rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ),
else {
if ( getOptions().isRightLineUpDomains() ) {
rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 )
- + ( ( _longest_domain - rds.getTotalLength() ) * rds
- .getRenderingFactorWidth() ),
- node.getYcoord() - ( h / 2.0f ),
- g,
- this,
- to_pdf );
+ + ( ( _longest_domain - rds.getTotalLength() ) * rds
+ .getRenderingFactorWidth() ),
+ node.getYcoord() - ( h / 2.0f ),
+ g,
+ this,
+ to_pdf );
}
else {
rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text,
&& ( node.getNodeData().getSequence().isMolecularSequenceAligned() )
&& ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) {
final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence()
- .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
+ .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() );
if ( rs != null ) {
final int default_height = 7;
float y = getYdistance();
final private void paintPhylogenyLite( final Graphics2D g ) {
_phylogeny
- .getRoot()
- .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
- .getWidth() ) ) ) );
+ .getRoot()
+ .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
+ .getWidth() ) ) ) );
_phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
final Stroke s = g.getStroke();
g.setStroke( STROKE_05 );
final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null,
false,
false ) )
- .getBounds();
+ .getBounds();
g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 );
g.setColor( getTreeColorSet().getBackgroundColor() );
}
ann_str = ann.toString();
}
sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
- .getMolecularSequence(), 60 ) );
+ .getMolecularSequence(), 60 ) );
data.add( sb.toString() );
}
break;
else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
if ( sb.length() < 1 ) {
TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
- + ")", "Descendants of selected node do not contain selected data" );
+ + ")", "Descendants of selected node do not contain selected data" );
clearCurrentExternalNodesDataBuffer();
}
else {
try {
if ( ( node.getName().length() > 0 )
|| ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
- .getTaxonomy() ) )
- || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
- .getSequence() ) ) || ( node.getNodeData().isHasDate() )
- || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
+ .getTaxonomy() ) )
+ || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
+ .getSequence() ) ) || ( node.getNodeData().isHasDate() )
+ || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
_popup_buffer.setLength( 0 );
short lines = 0;
if ( node.getName().length() > 0 ) {
_popup_buffer.append( "] " );
}
_popup_buffer
- .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
- getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
_popup_buffer.append( " (sd=" );
_popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
- .getStandardDeviation(), getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
_popup_buffer.append( ")" );
}
}
if ( _popup_buffer.length() > 0 ) {
if ( !getConfiguration().isUseNativeUI() ) {
_rollover_popup
- .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
+ .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
_rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
_rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
_rollover_popup,
e.getLocationOnScreen().x + 10,
e.getLocationOnScreen().y
- - ( lines * 20 ) );
+ - ( lines * 20 ) );
_node_desc_popup.show();
}
}
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
+ .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
}
else {
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() );
DOMAINS_ALL,\r
DOMAINS_COLLAPSED_PER_PROTEIN;\r
\r
- \r
+ @Override\r
public String toString() {\r
switch ( this ) {\r
case DOMAINS_ALL:\r
- return "Domain";\r
+ return "Domains";\r
case DOMAINS_COLLAPSED_PER_PROTEIN:\r
- return "Domain (collapsed per protein)";\r
+ return "Domains (collapsed per protein)";\r
case EVENT:\r
- return "Event";\r
+ return "Events";\r
case GENE_NAME:\r
- return "Gene Name";\r
+ return "Gene Names";\r
case GO_TERM_IDS:\r
- return "GO Term ID";\r
+ return "GO Term IDs";\r
case NODE_NAME:\r
- return "Node Name";\r
+ return "Node Names";\r
case SEQ_ANNOTATIONS:\r
- return "Sequence Annotation";\r
+ return "Sequence Annotations";\r
case SEQUENCE_ACC:\r
- return "Sequence Accessor";\r
+ return "Sequence Accessors";\r
case SEQUENCE_MOL_SEQ_FASTA:\r
- return "Molecular Sequence (Fasta)";\r
+ return "Molecular Sequences (Fasta)";\r
case SEQUENCE_NAME:\r
- return "Sequence Name";\r
+ return "Sequence Names";\r
case SEQUENCE_SYMBOL:\r
- return "Sequence Symbol";\r
+ return "Sequence Symbols";\r
case TAXONOMY_CODE:\r
- return "Taxonomy Code";\r
+ return "Taxonomy Codes";\r
case TAXONOMY_SCIENTIFIC_NAME:\r
- return "Scientific Name";\r
+ return "Scientific Names";\r
case UNKNOWN:\r
- return "User/UI Selected Data Field(s)";\r
+ return "User Selected Data Fields";\r
default:\r
throw new IllegalArgumentException();\r
}\r
git://source.jalview.org / jalview.git / commitdiff