import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.util.Arrays;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
+import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
}
return str_array;
}
+
+ final static String[] getAllPossibleRanks(final Map<String, Integer> present_ranks) {
+ final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
+ int i = 0;
+ for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
+ if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
+ if ( present_ranks != null && present_ranks.containsKey( e ) ) {
+ str_array[ i++ ] = e + " (" + present_ranks.get(e) + ")";
+ }
+ else {
+ str_array[ i++ ] = e;
+ }
+ }
+ }
+ return str_array;
+ }
final static String[] getAllRanks( final Phylogeny tree ) {
final SortedSet<String> ranks = new TreeSet<String>();
final IIOImage iio_image = new IIOImage( image, null, null );
writer.write( null, iio_image, image_write_param );
}
+
+ final static Map<String, Integer> getRankCounts(final Phylogeny tree) {
+ final Map<String, Integer> present_ranks = new HashMap<String, Integer>();
+
+ if ( ( tree != null ) && !tree.isEmpty() ) {
+ for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) && !n.isRoot() ) {
+ final String rank = n.getNodeData().getTaxonomy().getRank().toLowerCase();
+ if (present_ranks.containsKey( rank ) ) {
+ present_ranks.put( rank, present_ranks.get( rank ) + 1 );
+ }
+ else {
+ present_ranks.put( rank, 1 );
+ }
+ }
+ }
+ }
+ return present_ranks;
+ }
}
}
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
- { "Go to Sub-/Super-Tree", "display" }, { "Swap Descendants", "display" },
+ { "Go to Sub/Supertree", "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" } };
+ { "List Node Data", "display" }, { "Select Node(s)", "display" } , { "Uncollapse All", "display" }, { "Order Subtree", "display" }, };
private final static String DEFAULT_SPECIES_COLORS[][] = {
{ "BRAFL", "0x00FFFF" }, { "SPHGR", "0x9620F0" }, { "STRPU", "0x9620F0" }, { "CIOIN", "0xFF1CAE" },
{ "CIOSA", "0xFF2CAE" }, { "BOVIN", "0x5C3317" }, { "CANFA", "0x8B2323" }, { "HUMAN", "0xFF2400" },
final static int sort_descendents = 18;
final static int get_ext_desc_data = 19;
final static int select_nodes = 20;
+ final static int uncollapse_all = 21;
+ final static int order_subtree = 22;
+
// ------------------
// Click-to options
// ------------------
{ "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" } };
+ { "Multiple Seq Alignment", "display", "no" }, { "Branch Length Values", "display", "no" }
+ , { "Taxonomy Rank", "display", "no" }};
final static int display_as_phylogram = 0;
final static int show_node_names = 1;
final static int show_tax_code = 2;
final static int show_gene_names = 26;
final static int show_mol_seqs = 27;
final static int write_branch_length_values = 28;
+ final static int show_tax_rank = 29;
+
static final String VALIDATE_AGAINST_PHYLOXML_XSD_SCHEMA = "validate_against_phyloxml_xsd_schema";
private static Hashtable<String, Color> _sequence_colors;
private static Hashtable<String, Color> _annotation_colors;
public void setDisplayTaxonomyCode( final boolean b ) {
display_options[ show_tax_code ][ 2 ] = b ? "yes" : "no";
}
+
+ public void setDisplayTaxonomyRank( final boolean b ) {
+ display_options[ show_tax_rank ][ 2 ] = b ? "yes" : "no";
+ }
public void setDisplayTaxonomyCommonNames( final boolean b ) {
display_options[ show_taxonomy_common_names ][ 2 ] = b ? "yes" : "no";
else if ( name.equals( "collapse_uncollapse" ) ) {
index = Configuration.collapse_uncollapse;
}
+ else if ( name.equals( "uncollapse_all" ) ) {
+ index = Configuration.uncollapse_all;
+ }
else if ( name.equals( "reroot" ) ) {
index = Configuration.reroot;
}
else if ( name.equals( "swap" ) ) {
index = Configuration.swap;
}
+ else if ( name.equals( "order_subtree" ) ) {
+ index = Configuration.order_subtree;
+ }
else if ( name.equals( "sort_descendants" ) ) {
index = Configuration.sort_descendents;
}
else if ( key.equals( "show_taxonomy_code" ) ) {
key_index = Configuration.show_tax_code;
}
+ else if ( key.equals( "show_taxonomy_rank" ) ) {
+ key_index = Configuration.show_tax_rank;
+ }
else if ( key.equals( "write_confidence_values" ) ) {
key_index = Configuration.write_confidence_values;
}
SUBTREE,
SWAP,
CHANGE_NODE_FONT,
- COLOR_NODE_FONT;
+ COLOR_NODE_FONT,
+ UNCOLLAPSE_ALL,
+ ORDER_SUBTREE;
}
final static Font jcb_bold_font = new Font( Configuration.getDefaultFontFamilyName(),
Font.BOLD,
private JLabel _click_to_label;
private List<String> _click_to_names;
private int _collapse_cb_item;
+ private int _uncollapse_all_cb_item;
+ private int _order_subtree_cb_item;
+
+
private JCheckBox _color_acc_species;
private JCheckBox _color_acc_sequence;
private JCheckBox _color_according_to_annotation;
private int _open_tax_web_item;
private int _color_node_font_item;
private JButton _order;
- private boolean _order_of_appearance;
private int _paste_subtree_item;
private int _reroot_cb_item;
private JButton _return_to_super_tree;
private JCheckBox _show_sequence_acc;
private JComboBox<String> _show_sequence_relations;
private JCheckBox _show_taxo_code;
+ private JCheckBox _show_taxo_rank;
private JCheckBox _show_taxo_common_names;
private JCheckBox _show_taxo_images_cb;
private JCheckBox _show_taxo_scientific_names;
setBorder( BorderFactory.createRaisedBevelBorder() );
}
setLayout( new GridLayout( 0, 1, 2, 2 ) );
- _order_of_appearance = true;
setupControls();
}
else if ( isShowSeqNames() || isShowSeqSymbols() || isShowGeneNames() ) {
pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
- PhylogenyMethods.orderAppearance( tp.getPhylogeny().getRoot(), _order_of_appearance, true, pri );
- _order_of_appearance = !_order_of_appearance;
+ PhylogenyMethods.orderAppearanceX( tp.getPhylogeny().getRoot(), true, pri );
+
tp.setNodeInPreorderToNull();
tp.getPhylogeny().externalNodesHaveChanged();
tp.getPhylogeny().clearHashIdToNodeMap();
}
cb_index++;
}
+if ( _configuration.doDisplayClickToOption( Configuration.uncollapse_all ) ) {
+ _uncollapse_all_cb_item = cb_index;
+ addClickToOption( Configuration.uncollapse_all,
+ _configuration.getClickToTitle( Configuration.uncollapse_all ) );
+ if ( default_option == Configuration.uncollapse_all ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+}
if ( _configuration.doDisplayClickToOption( Configuration.reroot ) ) {
_reroot_cb_item = cb_index;
addClickToOption( Configuration.reroot, _configuration.getClickToTitle( Configuration.reroot ) );
}
cb_index++;
}
+if ( _configuration.doDisplayClickToOption( Configuration.order_subtree ) ) {
+ _order_subtree_cb_item = cb_index;
+ addClickToOption( Configuration.order_subtree,
+ _configuration.getClickToTitle( Configuration.order_subtree ) );
+ if ( default_option == Configuration.order_subtree ) {
+ selected_index = cb_index;
+ }
+ cb_index++;
+}
+
if ( _configuration.doDisplayClickToOption( Configuration.sort_descendents ) ) {
_sort_descendents_item = cb_index;
addClickToOption( Configuration.sort_descendents,
setCheckbox( Configuration.show_taxonomy_common_names,
_configuration.doCheckOption( Configuration.show_taxonomy_common_names ) );
}
+ if ( _configuration.doDisplayOption( Configuration.show_tax_rank ) ) {
+ addCheckbox( Configuration.show_tax_rank, _configuration.getDisplayTitle( Configuration.show_tax_rank ) );
+ setCheckbox( Configuration.show_tax_rank, _configuration.doCheckOption( Configuration.show_tax_rank ) );
+ }
if ( _configuration.doDisplayOption( Configuration.show_seq_names ) ) {
addCheckbox( Configuration.show_seq_names, _configuration.getDisplayTitle( Configuration.show_seq_names ) );
setCheckbox( Configuration.show_seq_names, _configuration.doCheckOption( Configuration.show_seq_names ) );
_show_whole.setPreferredSize( new Dimension( 10, 10 ) );
_return_to_super_tree = new JButton( RETURN_TO_SUPER_TREE_TEXT );
_return_to_super_tree.setEnabled( false );
- _order = new JButton( "Order Subtrees" );
+ _order = new JButton( "Order Tree" );
_uncollapse_all = new JButton( "Uncollapse All" );
+
addJButton( _zoom_in_y, x_panel );
addJButton( _zoom_out_x, y_panel );
addJButton( _show_whole, y_panel );
addJCheckBox( _show_taxo_code, ch_panel );
add( ch_panel );
break;
+ case Configuration.show_tax_rank:
+ _show_taxo_rank = new JCheckBox( title );
+ addJCheckBox( _show_taxo_rank, ch_panel );
+ add( ch_panel );
+ break;
case Configuration.show_taxonomy_images:
_show_taxo_images_cb = new JCheckBox( title );
addJCheckBox( _show_taxo_images_cb, ch_panel );
boolean isShowTaxonomyCode() {
return ( ( _show_taxo_code != null ) && _show_taxo_code.isSelected() );
}
+
+ boolean isShowTaxonomyRank() {
+ return ( ( _show_taxo_rank != null ) && _show_taxo_rank.isSelected() );
+ }
boolean isShowTaxonomyCommonNames() {
return ( ( _show_taxo_common_names != null ) && _show_taxo_common_names.isSelected() );
_show_taxo_code.setSelected( state );
}
break;
+ case Configuration.show_tax_rank:
+ if ( _show_taxo_rank != null ) {
+ _show_taxo_rank.setSelected( state );
+ }
+ break;
case Configuration.show_taxonomy_images:
if ( _show_taxo_images_cb != null ) {
_show_taxo_images_cb.setSelected( state );
else if ( action == _change_node_font_item ) {
setActionWhenNodeClicked( NodeClickAction.CHANGE_NODE_FONT );
}
+ else if ( action == _uncollapse_all_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.UNCOLLAPSE_ALL );
+ }
+ else if ( action == _order_subtree_cb_item ) {
+ setActionWhenNodeClicked( NodeClickAction.ORDER_SUBTREE );
+ }
else {
throw new RuntimeException( "unknown action: " + action );
}
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
+import java.util.Map;
import java.util.NoSuchElementException;
import javax.swing.Box;
JMenuItem _confcolor_item;
JMenuItem _color_rank_jmi;
JMenuItem _collapse_species_specific_subtrees;
+
JMenuItem _obtain_detailed_taxonomic_information_jmi;
JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
JMenuItem _obtain_seq_information_jmi;
void colorRank() {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- final String[] ranks = AptxUtil.getAllPossibleRanks();
- final String rank = ( String ) JOptionPane
+ final Map<String, Integer> present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny());
+ final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks);
+ String rank = ( String ) JOptionPane
.showInputDialog( this,
"What rank should the colorization be based on",
"Rank Selection",
ranks,
null );
if ( !ForesterUtil.isEmpty( rank ) ) {
+ if ( rank.indexOf( '(' ) > 0 ) {
+ rank = rank.substring( 0, rank.indexOf( '(' ) ).trim();
+ }
_mainpanel.getCurrentTreePanel().colorRank( rank );
}
}
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import javax.swing.ButtonGroup;
// Application-only print menu items
private JMenuItem _collapse_below_threshold;
private JMenuItem _collapse_below_branch_length;
+ private JMenuItem _collapse_by_taxonomic_rank;
private ButtonGroup _radio_group_1;
private ButtonGroup _radio_group_2;
// Others:
}
}
else {
- final int r = JOptionPane.showConfirmDialog( null,
- "Exit Archaeopteryx?",
- "Exit?",
- JOptionPane.YES_NO_OPTION );
+ final int r = JOptionPane
+ .showConfirmDialog( null, "Exit Archaeopteryx?", "Exit?", JOptionPane.YES_NO_OPTION );
if ( r != JOptionPane.YES_OPTION ) {
return;
}
@Override
public void componentResized( final ComponentEvent e ) {
if ( _mainpanel.getCurrentTreePanel() != null ) {
- _mainpanel.getCurrentTreePanel().calcParametersForPainting( _mainpanel.getCurrentTreePanel()
- .getWidth(),
- _mainpanel.getCurrentTreePanel()
- .getHeight() );
+ _mainpanel.getCurrentTreePanel()
+ .calcParametersForPainting( _mainpanel.getCurrentTreePanel().getWidth(),
+ _mainpanel.getCurrentTreePanel().getHeight() );
}
}
} );
}
collapseBelowThreshold();
}
+ else if ( o == _collapse_by_taxonomic_rank ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ collapseByTaxonomicRank();
+ }
else if ( o == _collapse_below_branch_length ) {
if ( isSubtreeDisplayed() ) {
return;
JOptionPane.showMessageDialog( this,
"Table contains " + t.getNumberOfRows() + " rows, but tree contains "
+ phy.getNumberOfExternalNodes() + " external nodes",
- "Warning",
- JOptionPane.WARNING_MESSAGE );
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
}
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
int not_found = 0;
row = t.findRow( node_name );
}
catch ( final IllegalArgumentException e ) {
- JOptionPane
- .showMessageDialog( this,
- e.getMessage(),
- "Error Mapping Node Identifiers to Expression Value Identifiers",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ e.getMessage(),
+ "Error Mapping Node Identifiers to Expression Value Identifiers",
+ JOptionPane.ERROR_MESSAGE );
return;
}
if ( row < 0 ) {
catch ( final NumberFormatException e ) {
JOptionPane.showMessageDialog( this,
"Could not parse \"" + t.getValueAsString( col, row )
- + "\" into a decimal value",
+ + "\" into a decimal value",
"Issue with Expression Value Table",
JOptionPane.ERROR_MESSAGE );
return;
if ( !l.isEmpty() ) {
if ( node.getNodeData().getProperties() != null ) {
node.getNodeData().getProperties()
- .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
+ .removePropertiesWithGivenReferencePrefix( PhyloXmlUtil.VECTOR_PROPERTY_REF );
}
node.getNodeData().setVector( l );
}
}
}
if ( not_found > 0 ) {
- JOptionPane.showMessageDialog( this, "Could not fine expression values for " + not_found
- + " external node(s)", "Warning", JOptionPane.WARNING_MESSAGE );
+ JOptionPane
+ .showMessageDialog( this,
+ "Could not fine expression values for " + not_found + " external node(s)",
+ "Warning",
+ JOptionPane.WARNING_MESSAGE );
}
getCurrentTreePanel().setStatisticsForExpressionValues( stats );
}
seqs = FastaParser.parse( fis2 );
try {
fis2.close();
- }
- catch ( final Exception e ) {
- // Ignore.
- }
+ }
+ catch ( final Exception e ) {
+ // Ignore.
+ }
}
else {
JOptionPane.showMessageDialog( this,
fis1.close();
}
catch ( final Exception e ) {
- // Ignore.
+ // Ignore.
}
}
catch ( final MsaFormatException e ) {
nodes = phy.getNodes( seq_name_split );
}
if ( nodes.size() > 1 ) {
- JOptionPane.showMessageDialog( this, "Split sequence name \"" + seq_name_split
- + "\" is not unique", "Sequence name not unique", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "Split sequence name \"" + seq_name_split
+ + "\" is not unique",
+ "Sequence name not unique",
+ JOptionPane.ERROR_MESSAGE );
setArrowCursor();
return;
}
JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane.showMessageDialog( this, "Attached " + attached_counter
- + " sequences out of a total of " + total_counter + " sequences.\n" + s, attached_counter
- + " sequences attached", JOptionPane.WARNING_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "Attached " + attached_counter + " sequences out of a total of "
+ + total_counter + " sequences.\n" + s,
+ attached_counter + " sequences attached",
+ JOptionPane.WARNING_MESSAGE );
}
}
else {
- JOptionPane.showMessageDialog( this, "No maching tree node for any of the " + total_counter
- + " sequences", "Could not attach any sequences", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "No maching tree node for any of the " + total_counter + " sequences",
+ "Could not attach any sequences",
+ JOptionPane.ERROR_MESSAGE );
}
}
}
repaint();
}
if ( to_be_removed.size() > 0 ) {
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
- + " branches with\nconfidence values below " + getMinNotCollapseConfidenceValue(), "Collapsed "
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nconfidence values below "
+ + getMinNotCollapseConfidenceValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane.showMessageDialog( this, "No branch collapsed,\nminimum confidence value per branch is "
- + min_support, "No branch collapsed", JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "No branch collapsed,\nminimum confidence value per branch is "
+ + min_support,
+ "No branch collapsed",
+ JOptionPane.INFORMATION_MESSAGE );
}
}
else {
}
}
+ private void collapseByTaxonomicRank() {
+ if ( _mainpanel.getCurrentTreePanel() != null ) {
+ final Map<String, Integer> present_ranks = AptxUtil.getRankCounts( _mainpanel.getCurrentTreePanel().getPhylogeny());
+ final String[] ranks = AptxUtil.getAllPossibleRanks(present_ranks);
+ String rank = ( String ) JOptionPane
+ .showInputDialog( this,
+ "What rank should the collapsing be based on",
+ "Rank Selection",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ ranks,
+ null );
+ if ( !ForesterUtil.isEmpty( rank ) ) {
+ if ( rank.indexOf( '(' ) > 0 ) {
+ rank = rank.substring( 0, rank.indexOf( '(' ) ).trim();
+ }
+ _mainpanel.getCurrentTreePanel().collapseByTaxonomicRank( rank );
+ }
+ }
+ }
+
private void collapseBelowBranchLengthThreshold() {
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final String s = ( String ) JOptionPane
- .showInputDialog( this,
- "Please enter the minimum branch length value\n",
- "Minimal Branch Length Value",
- JOptionPane.QUESTION_MESSAGE,
- null,
- null,
- getMinNotCollapseBlValue() );
+ final String s = ( String ) JOptionPane.showInputDialog( this,
+ "Please enter the minimum branch length value\n",
+ "Minimal Branch Length Value",
+ JOptionPane.QUESTION_MESSAGE,
+ null,
+ null,
+ getMinNotCollapseBlValue() );
if ( !ForesterUtil.isEmpty( s ) ) {
boolean success = true;
double m = 0.0;
repaint();
}
if ( to_be_removed.size() > 0 ) {
- JOptionPane.showMessageDialog( this, "Collapsed " + to_be_removed.size()
- + " branches with\nbranch length values below " + getMinNotCollapseBlValue(), "Collapsed "
- + to_be_removed.size() + " branches", JOptionPane.INFORMATION_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "Collapsed " + to_be_removed.size()
+ + " branches with\nbranch length values below "
+ + getMinNotCollapseBlValue(),
+ "Collapsed " + to_be_removed.size() + " branches",
+ JOptionPane.INFORMATION_MESSAGE );
}
else {
JOptionPane.showMessageDialog( this,
if ( getMsa() != null ) {
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getMsa(),
getPhylogeneticInferenceOptions()
- .copy(), this );
+ .copy(),
+ this );
new Thread( inferrer ).start();
}
else {
if ( getSeqs() != null ) {
final PhylogeneticInferrer inferrer = new PhylogeneticInferrer( getSeqs(),
getPhylogeneticInferenceOptions()
- .copy(), this );
+ .copy(),
+ this );
new Thread( inferrer ).start();
}
else {
String all = "all ";
if ( counter_failed > 0 ) {
all = "";
- failed = "\nCould not extract taxonomic data for " + counter_failed
- + " named external nodes:\n" + sb_failed;
+ failed = "\nCould not extract taxonomic data for " + counter_failed + " named external nodes:\n"
+ + sb_failed;
}
JOptionPane.showMessageDialog( this,
"Extracted taxonomic data from " + all + counter
- + " named external nodes:\n" + sb.toString() + failed,
+ + " named external nodes:\n" + sb.toString() + failed,
"Taxonomic Data Extraction Completed",
counter_failed > 0 ? JOptionPane.WARNING_MESSAGE
: JOptionPane.INFORMATION_MESSAGE );
}
else {
- JOptionPane
- .showMessageDialog( this,
- "Could not extract any taxonomic data.\nMaybe node names are empty\n"
- + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
- + "or nodes already have taxonomic data?\n",
- "No Taxonomic Data Extracted",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "Could not extract any taxonomic data.\nMaybe node names are empty\n"
+ + "or not in the forms \"XYZ_CAEEL\", \"XYZ_6239\", or \"XYZ_Caenorhabditis_elegans\"\n"
+ + "or nodes already have taxonomic data?\n",
+ "No Taxonomic Data Extracted",
+ JOptionPane.ERROR_MESSAGE );
}
}
}
if ( getCurrentTreePanel() != null ) {
final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- PhylogenyMethods
- .transferNodeNameToField( phy, PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME, false );
+ PhylogenyMethods.transferNodeNameToField( phy,
+ PhylogenyMethods.PhylogenyNodeField.SEQUENCE_NAME,
+ false );
}
}
}
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() )
- .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+ .setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
}
else {
getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
else {
try {
final PhylogenyParser parser = ParserUtils
- .createParserDependingOnFileType( file, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
+ .createParserDependingOnFileType( file,
+ getConfiguration()
+ .isValidatePhyloXmlAgainstSchema() );
if ( parser instanceof NexusPhylogeniesParser ) {
final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
setSpecialOptionsForNexParser( nex );
getMainPanel() );
_mainpanel.getControlPanel().showWhole();
if ( nhx_or_nexus && one_desc ) {
- JOptionPane
- .showMessageDialog( this,
- "One or more trees contain (a) node(s) with one descendant, "
- + ForesterUtil.LINE_SEPARATOR
- + "possibly indicating illegal parentheses within node names.",
- "Warning: Possible Error in New Hampshire Formatted Data",
- JOptionPane.WARNING_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "One or more trees contain (a) node(s) with one descendant, "
+ + ForesterUtil.LINE_SEPARATOR
+ + "possibly indicating illegal parentheses within node names.",
+ "Warning: Possible Error in New Hampshire Formatted Data",
+ JOptionPane.WARNING_MESSAGE );
}
}
}
if ( ( file != null ) && ( result == JFileChooser.APPROVE_OPTION ) ) {
if ( _open_filechooser_for_species_tree.getFileFilter() == MainFrame.xmlfilter ) {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
- .createPhyloXmlParserXsdValidating(), file );
+ final Phylogeny[] trees = PhylogenyMethods
+ .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
// "*.*":
else {
try {
- final Phylogeny[] trees = PhylogenyMethods.readPhylogenies( PhyloXmlParser
- .createPhyloXmlParserXsdValidating(), file );
+ final Phylogeny[] trees = PhylogenyMethods
+ .readPhylogenies( PhyloXmlParser.createPhyloXmlParserXsdValidating(), file );
t = trees[ 0 ];
}
catch ( final Exception e ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
exception = true;
t = null;
- JOptionPane
- .showMessageDialog( this,
- "Species tree contains external node(s) without taxonomy information",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( this,
+ "Species tree contains external node(s) without taxonomy information",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
break;
}
else {
if ( tax_set.contains( node.getNodeData().getTaxonomy() ) ) {
exception = true;
t = null;
- JOptionPane.showMessageDialog( this,
- "Taxonomy ["
- + node.getNodeData().getTaxonomy().asSimpleText()
- + "] is not unique in species tree",
- "Species tree not loaded",
- JOptionPane.ERROR_MESSAGE );
+ JOptionPane
+ .showMessageDialog( this,
+ "Taxonomy [" + node.getNodeData().getTaxonomy().asSimpleText()
+ + "] is not unique in species tree",
+ "Species tree not loaded",
+ JOptionPane.ERROR_MESSAGE );
break;
}
else {
_file_jmenu.addSeparator();
final WebservicesManager webservices_manager = WebservicesManager.getInstance();
_load_phylogeny_from_webservice_menu_items = new JMenuItem[ webservices_manager
- .getAvailablePhylogeniesWebserviceClients().size() ];
+ .getAvailablePhylogeniesWebserviceClients().size() ];
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
final PhylogeniesWebserviceClient client = webservices_manager.getAvailablePhylogeniesWebserviceClient( i );
_load_phylogeny_from_webservice_menu_items[ i ] = new JMenuItem( client.getMenuName() );
_save_all_item.setEnabled( false );
_file_jmenu.addSeparator();
_file_jmenu.add( _write_to_pdf_item = new JMenuItem( "Export to PDF file ..." ) );
- if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" ) || AptxUtil.canWriteFormat( "TIF" ) ) {
+ if ( AptxUtil.canWriteFormat( "tif" ) || AptxUtil.canWriteFormat( "tiff" )
+ || AptxUtil.canWriteFormat( "TIF" ) ) {
_file_jmenu.add( _write_to_tif_item = new JMenuItem( "Export to TIFF file..." ) );
}
_file_jmenu.add( _write_to_png_item = new JMenuItem( "Export to PNG file..." ) );
_file_jmenu.addSeparator();
_file_jmenu.add( _exit_item = new JMenuItem( "Exit" ) );
customizeJMenuItem( _open_item );
- _open_item
- .setFont( new Font( _open_item.getFont().getFontName(), Font.BOLD, _open_item.getFont().getSize() + 4 ) );
+ _open_item.setFont( new Font( _open_item.getFont().getFontName(),
+ Font.BOLD,
+ _open_item.getFont().getSize() + 4 ) );
customizeJMenuItem( _open_url_item );
for( int i = 0; i < webservices_manager.getAvailablePhylogeniesWebserviceClients().size(); ++i ) {
customizeJMenuItem( _load_phylogeny_from_webservice_menu_items[ i ] );
public void stateChanged( final ChangeEvent e ) {
MainFrame.setOvPlacementColorChooseMenuItem( _overview_placment_mi, getOptions() );
MainFrame.setTextColorChooseMenuItem( _switch_colors_mi, getCurrentTreePanel() );
- MainFrame
- .setTextMinSupportMenuItem( _choose_minimal_confidence_mi, getOptions(), getCurrentTreePanel() );
- MainFrame.setTextForFontChooserMenuItem( _choose_font_mi, MainFrame
- .createCurrentFontDesc( getMainPanel().getTreeFontSet() ) );
- // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
+ MainFrame.setTextMinSupportMenuItem( _choose_minimal_confidence_mi,
+ getOptions(),
+ getCurrentTreePanel() );
+ MainFrame.setTextForFontChooserMenuItem( _choose_font_mi,
+ MainFrame.createCurrentFontDesc( getMainPanel()
+ .getTreeFontSet() ) );
+ // MainFrame.setTextForGraphicsSizeChooserMenuItem( _print_size_mi, getOptions() );
MainFrame.setTextForPdfLineWidthChooserMenuItem( _choose_pdf_width_mi, getOptions() );
MainFrame.setCycleNodeFillMenuItem( _cycle_node_fill_mi, getOptions() );
MainFrame.setCycleNodeShapeMenuItem( _cycle_node_shape_mi, getOptions() );
} );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( DISPLAY_SUBHEADER ), getConfiguration() ) );
_options_jmenu
- .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
+ .add( _ext_node_dependent_cladogram_rbmi = new JRadioButtonMenuItem( MainFrame.NONUNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _uniform_cladograms_rbmi = new JRadioButtonMenuItem( MainFrame.UNIFORM_CLADOGRAMS_LABEL ) );
_options_jmenu.add( _non_lined_up_cladograms_rbmi = new JRadioButtonMenuItem( NON_LINED_UP_CLADOGRAMS_LABEL ) );
_radio_group_1 = new ButtonGroup();
_options_jmenu.add( _show_overview_cbmi = new JCheckBoxMenuItem( SHOW_OVERVIEW_LABEL ) );
_options_jmenu.add( _show_scale_cbmi = new JCheckBoxMenuItem( DISPLAY_SCALE_LABEL ) );
_options_jmenu
- .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+ .add( _show_default_node_shapes_internal_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_INT ) );
+ _options_jmenu
+ .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
_options_jmenu
- .add( _show_default_node_shapes_external_cbmi = new JCheckBoxMenuItem( DISPLAY_NODE_BOXES_LABEL_EXT ) );
+ .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
_options_jmenu
- .add( _show_default_node_shapes_for_marked_cbmi = new JCheckBoxMenuItem( MainFrame.DISPLAY_NODE_BOXES_LABEL_MARKED ) );
- _options_jmenu.add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
+ .add( _line_up_renderable_data_cbmi = new JCheckBoxMenuItem( MainFrame.LINE_UP_RENDERABLE_DATA ) );
if ( getConfiguration().doDisplayOption( Configuration.show_domain_architectures ) ) {
- _options_jmenu.add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
+ _options_jmenu
+ .add( _right_line_up_domains_cbmi = new JCheckBoxMenuItem( MainFrame.RIGHT_LINE_UP_DOMAINS ) );
_options_jmenu.add( _show_domain_labels = new JCheckBoxMenuItem( MainFrame.SHOW_DOMAIN_LABELS_LABEL ) );
}
_options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) );
_options_jmenu.add( _search_with_regex_cbmi = new JCheckBoxMenuItem( MainFrame.SEARCH_REGEX_LABEL ) );
_search_with_regex_cbmi.setToolTipText( MainFrame.SEARCH_WITH_REGEX_TIP );
_options_jmenu.add( _inverse_search_result_cbmi = new JCheckBoxMenuItem( INVERSE_SEARCH_RESULT_LABEL ) );
- _options_jmenu.add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
+ _options_jmenu
+ .add( _color_all_found_nodes_when_coloring_subtree_cbmi = new JCheckBoxMenuItem( "Colorize All Found Nodes When Colorizing Subtree(s)" ) );
_options_jmenu.addSeparator();
- _options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ),
- getConfiguration() ) );
+ _options_jmenu
+ .add( customizeMenuItemAsLabel( new JMenuItem( "Graphics Export & Printing:" ), getConfiguration() ) );
_options_jmenu.add( _antialias_print_cbmi = new JCheckBoxMenuItem( "Antialias" ) );
_options_jmenu.add( _print_black_and_white_cbmi = new JCheckBoxMenuItem( "Export in Black and White" ) );
- _options_jmenu
- .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
+ _options_jmenu
+ .add( _graphics_export_visible_only_cbmi = new JCheckBoxMenuItem( "Limit to Visible ('Screenshot') for PNG, JPG, and GIF export" ) );
_options_jmenu.add( _choose_pdf_width_mi = new JMenuItem( "" ) );
_options_jmenu.addSeparator();
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/NHX/Nexus Read:" ), getConfiguration() ) );
_options_jmenu
- .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
+ .add( _internal_number_are_confidence_for_nh_parsing_cbmi = new JCheckBoxMenuItem( "Internal Node Names are Confidence Values" ) );
_options_jmenu.add( _replace_underscores_cbmi = new JCheckBoxMenuItem( "Replace Underscores with Spaces" ) );
- _options_jmenu.add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
-
- _parse_beast_style_extended_nexus_tags_cbmi.setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
-
-
_options_jmenu
- .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
+ .add( _parse_beast_style_extended_nexus_tags_cbmi = new JCheckBoxMenuItem( "Parse BEAST-style extended Newick/Nexus tags" ) );
+ _parse_beast_style_extended_nexus_tags_cbmi
+ .setToolTipText( "to parse elements in the form of \"[&!color=#800080]\" in Newick/Nexus formatted trees" );
+ _options_jmenu
+ .add( _allow_errors_in_distance_to_parent_cbmi = new JCheckBoxMenuItem( "Ignore Distance Values Format Errors" ) );
_options_jmenu.add( _extract_taxonomy_no_rbmi = new JRadioButtonMenuItem( "No Taxonomy Extraction" ) );
_options_jmenu
- .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
+ .add( _extract_taxonomy_pfam_strict_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style Node Names" ) );
_options_jmenu
- .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
+ .add( _extract_taxonomy_pfam_relaxed_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids from Pfam-style like Node Names" ) );
_options_jmenu
- .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
+ .add( _extract_taxonomy_agressive_rbmi = new JRadioButtonMenuItem( "Extract Taxonomy Codes/Ids/Scientific Names from Node Names" ) );
_extract_taxonomy_pfam_strict_rbmi
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"BCL2_MOUSE/123-304\" or \"BCL2_10090/123-304\"" );
_extract_taxonomy_pfam_relaxed_rbmi
- .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
+ .setToolTipText( "To extract taxonomy codes/ids from node names in the form of e.g. \"bax_MOUSE\" or \"bax_10090\"" );
_extract_taxonomy_agressive_rbmi
- .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
+ .setToolTipText( "To extract taxonomy codes/ids or scientific names from node names in the form of e.g. \"MOUSE\" or \"10090\" or \"xyz_Nematostella_vectensis\"" );
_radio_group_2 = new ButtonGroup();
_radio_group_2.add( _extract_taxonomy_no_rbmi );
_radio_group_2.add( _extract_taxonomy_pfam_strict_rbmi );
_radio_group_2.add( _extract_taxonomy_agressive_rbmi );
_options_jmenu.add( customizeMenuItemAsLabel( new JMenuItem( "Newick/Nexus Save:" ), getConfiguration() ) );
_options_jmenu
- .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
+ .add( _use_brackets_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_BRACKETS_FOR_CONF_IN_NH_LABEL ) );
_use_brackets_for_conf_in_nh_export_cbmi
- .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
+ .setToolTipText( "e.g. \"0.1[90]\" for a branch with support 90 and a length of 0.1" );
_options_jmenu
- .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
+ .add( _use_internal_names_for_conf_in_nh_export_cbmi = new JCheckBoxMenuItem( USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL ) );
customizeJMenuItem( _choose_font_mi );
customizeJMenuItem( _choose_minimal_confidence_mi );
customizeJMenuItem( _switch_colors_mi );
customizeJMenuItem( _choose_pdf_width_mi );
customizeJMenuItem( _overview_placment_mi );
- customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions()
- .isShowDefaultNodeShapesExternal() );
- customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions()
- .isShowDefaultNodeShapesInternal() );
- customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi, getOptions()
- .isShowDefaultNodeShapesForMarkedNodes() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi,
+ getOptions().isShowDefaultNodeShapesExternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi,
+ getOptions().isShowDefaultNodeShapesInternal() );
+ customizeCheckBoxMenuItem( _show_default_node_shapes_for_marked_cbmi,
+ getOptions().isShowDefaultNodeShapesForMarkedNodes() );
customizeJMenuItem( _cycle_node_shape_mi );
customizeJMenuItem( _cycle_node_fill_mi );
customizeJMenuItem( _choose_node_size_mi );
customizeJMenuItem( _cycle_data_return );
- customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch, getOptions().isColorLabelsSameAsParentBranch() );
+ customizeCheckBoxMenuItem( _color_labels_same_as_parent_branch,
+ getOptions().isColorLabelsSameAsParentBranch() );
customizeCheckBoxMenuItem( _color_by_taxonomic_group_cbmi, getOptions().isColorByTaxonomicGroup() );
customizeCheckBoxMenuItem( _screen_antialias_cbmi, getOptions().isAntialiasScreen() );
customizeCheckBoxMenuItem( _background_gradient_cbmi, getOptions().isBackgroundColorGradient() );
getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL );
customizeCheckBoxMenuItem( _antialias_print_cbmi, getOptions().isAntialiasPrint() );
customizeCheckBoxMenuItem( _print_black_and_white_cbmi, getOptions().isPrintBlackAndWhite() );
- customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi, getOptions()
- .isInternalNumberAreConfidenceForNhParsing() );
+ customizeCheckBoxMenuItem( _internal_number_are_confidence_for_nh_parsing_cbmi,
+ getOptions().isInternalNumberAreConfidenceForNhParsing() );
customizeRadioButtonMenuItem( _extract_taxonomy_no_rbmi,
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.NO );
customizeRadioButtonMenuItem( _extract_taxonomy_pfam_strict_rbmi,
customizeRadioButtonMenuItem( _extract_taxonomy_agressive_rbmi,
getOptions().getTaxonomyExtraction() == TAXONOMY_EXTRACTION.AGGRESSIVE );
customizeCheckBoxMenuItem( _replace_underscores_cbmi, getOptions().isReplaceUnderscoresInNhParsing() );
- customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi, getOptions()
- .isReplaceUnderscoresInNhParsing() );
+ customizeCheckBoxMenuItem( _allow_errors_in_distance_to_parent_cbmi,
+ getOptions().isReplaceUnderscoresInNhParsing() );
customizeCheckBoxMenuItem( _search_with_regex_cbmi, getOptions().isSearchWithRegex() );
customizeCheckBoxMenuItem( _search_whole_words_only_cbmi, getOptions().isMatchWholeTermsOnly() );
customizeCheckBoxMenuItem( _inverse_search_result_cbmi, getOptions().isInverseSearchResult() );
- customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi, getOptions().isColorAllFoundNodesWhenColoringSubtree() );
- customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi, getOptions().isParseBeastStyleExtendedNexusTags() );
-
+ customizeCheckBoxMenuItem( _color_all_found_nodes_when_coloring_subtree_cbmi,
+ getOptions().isColorAllFoundNodesWhenColoringSubtree() );
+ customizeCheckBoxMenuItem( _parse_beast_style_extended_nexus_tags_cbmi,
+ getOptions().isParseBeastStyleExtendedNexusTags() );
customizeCheckBoxMenuItem( _graphics_export_visible_only_cbmi, getOptions().isGraphicsExportVisibleOnly() );
customizeCheckBoxMenuItem( _show_confidence_stddev_cbmi, getOptions().isShowConfidenceStddev() );
- customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
- customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi, getOptions()
- .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
+ customizeCheckBoxMenuItem( _use_brackets_for_conf_in_nh_export_cbmi,
+ getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.IN_SQUARE_BRACKETS );
+ customizeCheckBoxMenuItem( _use_internal_names_for_conf_in_nh_export_cbmi,
+ getOptions()
+ .getNhConversionSupportValueStyle() == NH_CONVERSION_SUPPORT_VALUE_STYLE.AS_INTERNAL_NODE_NAMES );
customizeCheckBoxMenuItem( _line_up_renderable_data_cbmi, getOptions().isLineUpRendarableNodeData() );
customizeCheckBoxMenuItem( _right_line_up_domains_cbmi, getOptions().isRightLineUpDomains() );
_jmenubar.add( _options_jmenu );
_inference_menu.add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences..." ) );
customizeJMenuItem( _inference_from_seqs_item );
_inference_from_seqs_item
- .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
+ .setToolTipText( "Basic phylogenetic inference including multiple sequence alignment" );
}
else {
_inference_menu
- .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
+ .add( _inference_from_seqs_item = new JMenuItem( "From Unaligned Sequences (no program found)" ) );
customizeJMenuItem( _inference_from_seqs_item );
_inference_from_seqs_item.setEnabled( false );
}
_tools_menu.addSeparator();
_tools_menu.add( _remove_visual_styles_item = new JMenuItem( "Delete All Visual Styles From Nodes" ) );
_remove_visual_styles_item
- .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
+ .setToolTipText( "To remove all node visual styles (fonts, colors) from the current phylogeny" );
customizeJMenuItem( _remove_visual_styles_item );
_tools_menu.add( _remove_branch_color_item = new JMenuItem( "Delete All Colors From Branches" ) );
_remove_branch_color_item.setToolTipText( "To remove all branch color values from the current phylogeny" );
_tools_menu.add( _collapse_species_specific_subtrees = new JMenuItem( "Collapse Species-Specific Subtrees" ) );
customizeJMenuItem( _collapse_species_specific_subtrees );
_collapse_species_specific_subtrees.setToolTipText( "To (reversibly) collapse species-specific subtrees" );
+ _tools_menu.add( _collapse_by_taxonomic_rank = new JMenuItem( "Collapse By Taxonomic Rank" ) );
+ customizeJMenuItem( _collapse_by_taxonomic_rank );
+ _collapse_by_taxonomic_rank.setToolTipText( "To (reversibly) collapse subtrees by taxonomic rank" );
_tools_menu
- .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
+ .add( _collapse_below_threshold = new JMenuItem( "Collapse Branches with Confidence Below Threshold into Multifurcations" ) );
customizeJMenuItem( _collapse_below_threshold );
_collapse_below_threshold
- .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
+ .setToolTipText( "To (permanently) collapse branches with confidence values below a threshold into multifurcations (in the case of multiple confidences per branch: without at least one confidence value above a threshold)" );
//
_tools_menu
- .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
+ .add( _collapse_below_branch_length = new JMenuItem( "Collapse Branches with Branch Lengths Below Threshold into Multifurcations" ) );
customizeJMenuItem( _collapse_below_branch_length );
_collapse_below_branch_length
- .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
+ .setToolTipText( "To (permanently) collapse branches with branches with branch lengths below a threshold into multifurcations" );
//
_tools_menu.addSeparator();
_tools_menu
- .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
+ .add( _extract_tax_code_from_node_names_jmi = new JMenuItem( "Extract Taxonomic Data from Node Names" ) );
customizeJMenuItem( _extract_tax_code_from_node_names_jmi );
_extract_tax_code_from_node_names_jmi
- .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
+ .setToolTipText( "To extract SwissProt/Uniprot taxonomic codes (mnemonics) from nodes names in the form of 'xyz_CAEEL', Uniprot/NCBI identifiers form of 'xyz_6239', or scientific names form of 'xyz_Caenorhabditis_elegans'" );
_tools_menu
- .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
+ .add( _move_node_names_to_tax_sn_jmi = new JMenuItem( "Transfer Node Names to Taxonomic Scientific Names" ) );
customizeJMenuItem( _move_node_names_to_tax_sn_jmi );
_move_node_names_to_tax_sn_jmi.setToolTipText( "To interpret node names as taxonomic scientific names" );
_tools_menu.add( _move_node_names_to_seq_names_jmi = new JMenuItem( "Transfer Node Names to Sequence Names" ) );
customizeJMenuItem( _obtain_seq_information_jmi );
_obtain_seq_information_jmi.setToolTipText( "To add additional sequence information" );
_tools_menu
- .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
+ .add( _obtain_detailed_taxonomic_information_jmi = new JMenuItem( OBTAIN_DETAILED_TAXONOMIC_INFORMATION ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_jmi );
_obtain_detailed_taxonomic_information_jmi
- .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
+ .setToolTipText( "To add additional taxonomic information (from UniProt Taxonomy)" );
_tools_menu
- .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
+ .add( _obtain_detailed_taxonomic_information_deleting_jmi = new JMenuItem( "Obtain Detailed Taxonomic Information (deletes nodes!)" ) );
customizeJMenuItem( _obtain_detailed_taxonomic_information_deleting_jmi );
_obtain_detailed_taxonomic_information_deleting_jmi
- .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
+ .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
_tools_menu.addSeparator();
_tools_menu.add( _read_values_jmi = new JMenuItem( "Attach Vector/Expression Values" ) );
customizeJMenuItem( _read_values_jmi );
_tools_menu.add( _read_seqs_jmi = new JMenuItem( "Attach Molecular Sequences" ) );
customizeJMenuItem( _read_seqs_jmi );
_read_seqs_jmi
- .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
+ .setToolTipText( "To attach molecular sequences to tree nodes (from Fasta-formatted file) (beta)" );
_jmenubar.add( _tools_menu );
}
URL url = null;
Phylogeny[] phys = null;
final String message = "Please enter a complete URL, for example \"http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"";
- final String url_string = JOptionPane.showInputDialog( this,
- message,
- "Use URL/webservice to obtain a phylogeny",
- JOptionPane.QUESTION_MESSAGE );
+ final String url_string = JOptionPane
+ .showInputDialog( this,
+ message,
+ "Use URL/webservice to obtain a phylogeny",
+ JOptionPane.QUESTION_MESSAGE );
boolean nhx_or_nexus = false;
if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
try {
parser = new TolParser();
}
else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, getConfiguration()
- .isValidatePhyloXmlAgainstSchema() );
+ parser = ParserUtils
+ .createParserDependingOnUrlContents( url,
+ getConfiguration().isValidatePhyloXmlAgainstSchema() );
}
if ( parser instanceof NexusPhylogeniesParser ) {
nhx_or_nexus = true;
JOptionPane.showMessageDialog( this,
"Could not read from " + url + "\n"
+ ForesterUtil.wordWrap( e.getLocalizedMessage(), 80 ),
- "Failed to read URL",
- JOptionPane.ERROR_MESSAGE );
+ "Failed to read URL",
+ JOptionPane.ERROR_MESSAGE );
}
catch ( final Exception e ) {
JOptionPane.showMessageDialog( this,
static void warnIfNotPhyloXmlValidation( final Configuration c ) {
if ( !c.isValidatePhyloXmlAgainstSchema() ) {
- JOptionPane
- .showMessageDialog( null,
- ForesterUtil
- .wordWrap( "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
- 80 ),
+ JOptionPane.showMessageDialog( null,
+ ForesterUtil.wordWrap(
+ "phyloXML XSD-based validation is turned off [enable with line 'validate_against_phyloxml_xsd_schem: true' in configuration file]",
+ 80 ),
"Warning",
JOptionPane.WARNING_MESSAGE );
}
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.font.FontRenderContext;
+import java.awt.font.TextAttribute;
import java.awt.font.TextLayout;
import java.awt.geom.AffineTransform;
import java.awt.geom.Arc2D;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URLEncoder;
+import java.text.AttributedString;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
private float _y_distance = 0.0f;
private int _length_of_longest_text;
private int _longest_domain;
+ private Map<String, AttributedString> _attributed_string_map = null;
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
case GET_EXT_DESC_DATA:
showExtDescNodeData( node );
break;
+ case UNCOLLAPSE_ALL:
+ uncollapseAll( node );
+ break;
+ case ORDER_SUBTREE:
+ orderSubtree( node );
+ break;
default:
throw new IllegalArgumentException( "unknown action: " + action );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 );
}
+ else if ( title.equals( Configuration.clickto_options[ Configuration.uncollapse_all ][ 0 ] ) ) {
+ _node_popup_menu_items[ i ].setEnabled( isCanUncollapseAll( node ) );
+ }
_node_popup_menu_items[ i ].addActionListener( this );
_node_popup_menu.add( _node_popup_menu_items[ i ] );
}
}
private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
+ if ( _control_panel.isShowTaxonomyRank() && !ForesterUtil.isEmpty( taxonomy.getRank() ) ) {
+ sb.append( "[" );
+ sb.append( taxonomy.getRank() );
+ sb.append( "] " );
+ }
if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
sb.append( taxonomy.getTaxonomyCode() );
sb.append( " " );
x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
}
if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
- .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
+ .isShowTaxonomyCommonNames() || getControlPanel().isShowTaxonomyRank() ) && node.getNodeData().isHasTaxonomy() ) {
x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
}
setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
}
}
if ( sb_str.length() > 0 ) {
- TreePanel.drawString( sb_str, pos_x, pos_y, g );
+ if ( !isAllowAttributedStrings() ) {
+ TreePanel.drawString( sb_str, pos_x, pos_y, g );
+ }
+ else {
+ drawStringX( sb_str, pos_x, pos_y, g );
+ }
}
// GUILHEM_END _____________
if ( _sb.length() > 0 ) {
return x;
}
+ private final boolean isAllowAttributedStrings() {
+ return false;
+ }
+
final private void paintNodeDataUnrootedCirc( final Graphics2D g,
final PhylogenyNode node,
final boolean to_pdf,
repaint();
}
}
+
+ final void uncollapseAll( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot uncollapse in unrooted display type",
+ "Attempt to uncollapse in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ if ( !node.isExternal() ) {
+ TreePanelUtil.uncollapseSubtree( node);
+ updateSetOfCollapsedExternalNodes();
+ _phylogeny.recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ calculateLongestExtNodeInfo();
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
+ resetPreferredSize();
+ updateOvSizes();
+ _main_panel.adjustJScrollPane();
+ repaint();
+ }
+ }
final void collapseSpeciesSpecificSubtrees() {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
repaint();
}
+ final void collapseByTaxonomicRank( final String rank ) {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+
+ final int collapsed = TreePanelUtil.collapseByTaxonomicRank( _phylogeny, rank, this );
+
+ setArrowCursor();
+ repaint();
+ if ( collapsed > 0 ) {
+ String msg = "Collapsing via " + rank + " completed:\n";
+ if ( collapsed > 1 ) {
+ msg += "collapsed " + collapsed + " subtrees";
+ }
+ else {
+ msg += "collapsed one subtree";
+ }
+ setEdited( true );
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Rank-Collapsing Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ String msg = "Could not taxonomy rank-collapse any subtree via " + rank + ".\n";
+ msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+ msg += "select a different rank (e.g. phylum, genus, ...)\n";
+ msg += " and/or\n";
+ msg += "execute:\n";
+ msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy Rank-Collapsing Failed", JOptionPane.WARNING_MESSAGE );
+ }
+ }
+
+
+
final void colorRank( final String rank ) {
if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
return;
setEdited( true );
JOptionPane.showMessageDialog( this,
msg,
- "Taxonomy Colorization Completed (" + rank + ")",
+ "Taxonomy Rank-Colorization Completed (" + rank + ")",
JOptionPane.INFORMATION_MESSAGE );
}
else {
- String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
+ String msg = "Could not taxonomy rank-colorize any subtree via " + rank + ".\n";
msg += "Possible solutions (given that suitable taxonomic information is present):\n";
msg += "select a different rank (e.g. phylum, genus, ...)\n";
msg += " and/or\n";
msg += "execute:\n";
msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
- JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy Rank-Colorization Failed", JOptionPane.WARNING_MESSAGE );
}
}
final boolean isCanCollapse() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
-
+
+ final boolean isCanUncollapseAll( final PhylogenyNode node ) {
+ if ( node.isExternal() || getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ return false;
+ }
+ if ( node.isCollapse() ) {
+ return true;
+ }
+ final PhylogenyNodeIterator it = new PreorderTreeIterator( node );
+ while ( it.hasNext() ) {
+ if ( it.next().isCollapse() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
final boolean isCanColorSubtree() {
return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED );
}
updateSubSuperTreeButton();
}
+ final void orderSubtree( final PhylogenyNode node ) {
+ if ( node.isExternal() ) {
+ return;
+ }
+ DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME;
+ if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) {
+ pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
+ }
+ else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() || getControlPanel().isShowGeneNames() ) {
+ pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
+ }
+ PhylogenyMethods.orderAppearanceX( node, true, pri );
+
+ setNodeInPreorderToNull();
+ getPhylogeny().externalNodesHaveChanged();
+ getPhylogeny().clearHashIdToNodeMap();
+ getPhylogeny().recalculateNumberOfExternalDescendants( true );
+ resetNodeIdToDistToLeafMap();
+ setEdited( true );
+ getControlPanel().displayedPhylogenyMightHaveChanged( true );
+ repaint();
+ }
+
final void swap( final PhylogenyNode node ) {
if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) {
return;
final private static void drawString( final String str, final float x, final float y, final Graphics2D g ) {
g.drawString( str, x, y );
}
+
+
+ final private void drawStringX( final String str, final float x, final float y, final Graphics2D g ) {
+ //TODO
+ //FIXME
+ if ( getAttributedStringMap() == null /*&& getAttributedStringMap().containsKey(str) */ ) {
+ final AttributedString as = new AttributedString(str);
+ //Font plainFont = new Font("Times New Roman", Font.PLAIN, 24);
+
+ as.addAttribute(TextAttribute.FONT, g.getFont());
+ as.addAttribute(TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON, 1, 3);
+ as.addAttribute(TextAttribute.SUPERSCRIPT, TextAttribute.SUPERSCRIPT_SUPER, 3, 4);
+
+ as.addAttribute(TextAttribute.FOREGROUND, Color.BLUE, 1, 2);
+ as.addAttribute(TextAttribute.FOREGROUND, Color.PINK, 3, 5);
+ as.addAttribute(TextAttribute.STRIKETHROUGH,
+ TextAttribute.STRIKETHROUGH_ON, 2, 4);
+ g.drawString(as.getIterator(), x, y);
+ }
+ else {
+ g.drawString( str, x, y );
+ }
+ }
+
+
+ private final Map<String, AttributedString> getAttributedStringMap() {
+ return _attributed_string_map ;
+ }
+
+ private final void setAttributedStringMap( final Map<String, AttributedString> attributed_string_map ) {
+ _attributed_string_map = attributed_string_map;
+ }
final private static boolean plusPressed( final int key_code ) {
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
}
if ( cp.isShowSeqSymbols() && node.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
- TreePanelUtil
- .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(),
+ sb );
}
if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
}
if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
- TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
- .getTaxonomyCode(), sb );
+ TreePanelUtil
+ .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(),
+ sb );
}
if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
- TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy()
- .getScientificName(), sb );
+ TreePanelUtil
+ .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(),
+ sb );
}
if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
- TreePanelUtil
- .showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(),
+ sb );
}
// if ( ( cp.isShowSeqNames() || cp.isShowSeqSymbols() || cp.isShowSequenceAcc() )
// && node.getNodeData().isHasSequence()
}
}
+ final static void uncollapseSubtree( final PhylogenyNode node ) {
+ node.setCollapse( false );
+ if ( node.isExternal() ) {
+ return;
+ }
+ final PhylogenyNodeIterator it = new PreorderTreeIterator( node );
+ while ( it.hasNext() ) {
+ it.next().setCollapse( false );
+ }
+ }
+
static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
node.getBranchData().setBranchColor( c );
final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
if ( !n.getBranchData().isHasBranchColor() ) {
final Taxonomy tax = PhylogenyMethods.getExternalDescendantsTaxonomy( n );
if ( tax != null ) {
- n.getBranchData().setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
+ n.getBranchData()
+ .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
for( final PhylogenyNode desc : descs ) {
desc.getBranchData()
}
}
- final static int colorPhylogenyAccordingToRanks( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
+ final static int collapseByTaxonomicRank( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
+ final Set<String> true_lineage_set = new HashSet<String>();
+ for( final PhylogenyNodeIterator iter = tree.iteratorPreorder(); iter.hasNext(); ) {
+ iter.next().setCollapse( false );
+ }
+ int collapsed = 0;
+ for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.isExternal() && n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
+ && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) /*&& !n.isRoot()*/ ) {
+ TreePanelUtil.collapseSubtree( n, true );
+ ++collapsed;
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ true_lineage_set.add( n.getNodeData().getTaxonomy().getScientificName() );
+ System.out.println( "1 true_lineage_set added " + n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ }
+ }
+ for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode node = it.next();
+ if ( ( !node.isExternal() && !node.isCollapse() ) && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getLineage() ) /* && !node.isRoot()*/ ) {
+ boolean success = false;
+ if ( !true_lineage_set.isEmpty() ) {
+ for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
+ if ( true_lineage_set.contains( lin ) ) {
+ //TreePanelUtil
+ // .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
+ TreePanelUtil.collapseSubtree( node, true );
+ ++collapsed;
+ success = true;
+ break;
+ }
+ }
+ }
+ if ( !success ) {
+ final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap();
+ for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
+ final Taxonomy temp_tax = new Taxonomy();
+ temp_tax.setScientificName( lin );
+ if ( lineage_to_rank_map.containsKey( lin )
+ && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
+ && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) {
+ //final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
+ //TreePanelUtil.colorizeSubtree( node, c );
+ TreePanelUtil.collapseSubtree( node, true );
+ ++collapsed;
+ true_lineage_set.add( lin );
+ System.out.println( "2 true_lineage_set added " + lin );
+ break;
+ }
+ else {
+ UniProtTaxonomy up = null;
+ try {
+ up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
+ lineage_to_rank_map.put( lin, up.getRank() );
+ System.out.println( lin + "->" + up.getRank() );
+ if ( up.getRank().equalsIgnoreCase( rank ) ) {
+ // final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
+ // TreePanelUtil.colorizeSubtree( node, c );
+ TreePanelUtil.collapseSubtree( node, true );
+ ++collapsed;
+ true_lineage_set.add( lin );
+ System.out.println( "3 true_lineage_set added " + lin );
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return collapsed;
+ }
+
+ final static int colorPhylogenyAccordingToRanks( final Phylogeny tree,
+ final String rank,
+ final TreePanel tree_panel ) {
final Map<String, Color> true_lineage_to_color_map = new HashMap<String, Color>();
int colorizations = 0;
for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
if ( n.getNodeData().isHasTaxonomy()
&& ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
- || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
- .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() )
+ || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
&& n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
- final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
- .getTaxonomy() ) );
+ final BranchColor c = new BranchColor( tree_panel
+ .calculateTaxonomyBasedColor( n.getNodeData().getTaxonomy() ) );
TreePanelUtil.colorizeSubtree( n, c );
++colorizations;
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
- true_lineage_to_color_map.put( n.getNodeData().getTaxonomy().getScientificName(), c.getValue() );
+ true_lineage_to_color_map.put( n.getNodeData().getTaxonomy().getScientificName(),
+ c.getValue() );
}
}
}
if ( !true_lineage_to_color_map.isEmpty() ) {
for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
if ( true_lineage_to_color_map.containsKey( lin ) ) {
- TreePanelUtil
- .colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
+ TreePanelUtil.colorizeSubtree( node,
+ new BranchColor( true_lineage_to_color_map.get( lin ) ) );
++colorizations;
success = true;
break;
}
if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
lineage_to_rank_map.put( lin, up.getRank() );
+ System.out.println( lin + "->" + up.getRank() );
if ( up.getRank().equalsIgnoreCase( rank ) ) {
- final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
+ final BranchColor c = new BranchColor( tree_panel
+ .calculateTaxonomyBasedColor( temp_tax ) );
TreePanelUtil.colorizeSubtree( node, c );
++colorizations;
true_lineage_to_color_map.put( lin, c.getValue() );
return colorizations;
}
- final static String createAnnotationString( final SortedSet<Annotation> annotations, final boolean show_ref_sources ) {
+ final static String createAnnotationString( final SortedSet<Annotation> annotations,
+ final boolean show_ref_sources ) {
final SortedMap<String, List<Annotation>> m = new TreeMap<String, List<Annotation>>();
for( final Annotation an : annotations ) {
final String ref_source = ForesterUtil.isEmpty( an.getRefSource() ) ? "?" : an.getRefSource();
final static boolean isTaxonomyEmpty( final Taxonomy tax ) {
return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
- && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
- .getSynonyms().isEmpty() );
+ && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() )
+ && tax.getSynonyms().isEmpty() );
}
static final int nodeDataIntoStringBuffer( final List<String> data, final Options optz, final StringBuilder sb ) {
public static final String TAXONOMY_RANK = "rank";
public static final String TAXONOMY_SCIENTIFIC_NAME = "scientific_name";
public static final String TAXONOMY_SYNONYM = "synonym";
+ public static final String TAXONOMY_LINEAGE = "lineage";
public static final String TYPE_ATTR = "type";
public static final String URI = "uri";
public static final String URI_DESC_ATTR = "desc";
package org.forester.io.parsers.phyloxml.data;
+import java.util.Arrays;
+
import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
import org.forester.io.parsers.phyloxml.XmlElement;
else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.URI ) ) {
taxonomy.addUri( ( Uri ) UriParser.getInstance().parse( child_element ) );
}
+ else if ( child_element.getQualifiedName().equals( PhyloXmlMapping.TAXONOMY_LINEAGE ) ) {
+ final String[] lineage = child_element.getValueAsString().split( "," );
+ if ( lineage != null && lineage.length > 0 ) {
+ taxonomy.setLineage( Arrays.asList(lineage) );
+ }
+ }
}
}
return taxonomy;
public class PhylogenyMethods {
+ private static boolean _order_changed;
+
private PhylogenyMethods() {
// Hidden constructor.
}
return;
}
else {
- PhylogenyNode temp = null;
if ( ( n.getNumberOfDescendants() == 2 )
&& ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
&& ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
- temp = n.getChildNode1();
+ final PhylogenyNode temp = n.getChildNode1();
n.setChild1( n.getChildNode2() );
n.setChild2( temp );
+ _order_changed = true;
}
else if ( order_ext_alphabetically ) {
boolean all_ext = true;
}
}
}
+
+ public synchronized static void orderAppearanceX( final PhylogenyNode n,
+ final boolean order_ext_alphabetically,
+ final DESCENDANT_SORT_PRIORITY pri ) {
+ if ( n.isExternal() ) {
+ return;
+ }
+ else {
+ _order_changed = false;
+ orderAppearance( n,
+ true,
+ order_ext_alphabetically,
+ pri );
+ if (!_order_changed ) {
+ orderAppearance( n,
+ false,
+ order_ext_alphabetically,
+ pri );
+ }
+ }
+ }
public static void postorderBranchColorAveragingExternalNodeBased( final Phylogeny p ) {
for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
public boolean isEmpty() {
return ( ( getIdentifier() == null ) && ForesterUtil.isEmpty( getTaxonomyCode() )
- && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() ) && ForesterUtil
- .isEmpty( _lineage ) );
+ && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() )
+ && ForesterUtil.isEmpty( _lineage ) );
}
/**
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.TAXONOMY_AUTHORITY, getAuthority(), indentation );
}
if ( !ForesterUtil.isEmpty( getCommonName() ) ) {
- PhylogenyDataUtil
- .appendElement( writer, PhyloXmlMapping.TAXONOMY_COMMON_NAME, getCommonName(), indentation );
+ PhylogenyDataUtil.appendElement( writer,
+ PhyloXmlMapping.TAXONOMY_COMMON_NAME,
+ getCommonName(),
+ indentation );
}
if ( _synonyms != null ) {
for( final String syn : getSynonyms() ) {
}
}
}
+ if ( getLineage() != null ) {
+ final StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for( final String lin : getLineage() ) {
+ if ( !ForesterUtil.isEmpty( lin ) ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( "," );
+ }
+ sb.append( lin );
+ }
+ }
+ if ( sb.length() > 0 ) {
+ PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.TAXONOMY_LINEAGE, sb.toString(), indentation );
+ }
+ }
writer.write( ForesterUtil.LINE_SEPARATOR );
writer.write( indentation );
PhylogenyDataUtil.appendClose( writer, PhyloXmlMapping.TAXONOMY );
git://source.jalview.org / jalview.git / commitdiff