// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
-import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Set;
import org.forester.archaeopteryx.tools.InferenceManager;
import org.forester.archaeopteryx.tools.ProcessPool;
import org.forester.archaeopteryx.tools.ProcessRunning;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.NodeVisualization.NodeFill;
import org.forester.phylogeny.data.NodeVisualization.NodeShape;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDIException;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
static final String SCREEN_ANTIALIAS_LABEL = "Antialias";
static final String COLOR_LABELS_LABEL = "Colorize Labels Same as Parent Branch";
static final String BG_GRAD_LABEL = "Background Color Gradient";
- static final String DISPLAY_NODE_BOXES_LABEL = "Show Node Shapes";
+ static final String DISPLAY_NODE_BOXES_LABEL_EXT = "Show External Node Shapes";
+ static final String DISPLAY_NODE_BOXES_LABEL_INT = "Show Internal Node Shapes";
static final String SHOW_OVERVIEW_LABEL = "Show Overview";
static final String FONT_SIZE_MENU_LABEL = "Font Size";
static final String NONUNIFORM_CLADOGRAMS_LABEL = "External Node Sum Dependent Cladograms";
static final String SHOW_CONF_STDDEV_LABEL = "Show Confidence Standard Deviations";
static final String USE_BRACKETS_FOR_CONF_IN_NH_LABEL = "Use Brackets for Confidence Values";
static final String USE_INTERNAL_NAMES_FOR_CONF_IN_NH_LABEL = "Use Internal Node Names for Confidence Values";
+ static final String SHOW_BASIC_TREE_INFORMATION_LABEL = "Show Basic Tree Information";
JMenuBar _jmenubar;
JMenu _file_jmenu;
JMenu _tools_menu;
JMenu _font_size_menu;
JMenu _help_jmenu;
JMenuItem[] _load_phylogeny_from_webservice_menu_items;
+ // Analysis menu
+ JMenu _analysis_menu;
+ JMenuItem _load_species_tree_item;
+ JMenuItem _gsdi_item;
+ JMenuItem _gsdir_item;
+ JMenuItem _lineage_inference;
+ JMenuItem _function_analysis;
// file menu:
JMenuItem _open_item;
JMenuItem _open_url_item;
JMenuItem _taxcolor_item;
JMenuItem _confcolor_item;
JMenuItem _color_rank_jmi;
- JMenuItem _infer_common_sn_names_item;
JMenuItem _collapse_species_specific_subtrees;
JMenuItem _collapse_below_threshold; //TODO implememt me
JMenuItem _obtain_detailed_taxonomic_information_jmi;
JMenuItem _obtain_detailed_taxonomic_information_deleting_jmi;
- JMenuItem _obtain_uniprot_seq_information_jmi;
+ JMenuItem _obtain_seq_information_jmi;
JMenuItem _move_node_names_to_tax_sn_jmi;
JMenuItem _move_node_names_to_seq_names_jmi;
JMenuItem _extract_tax_code_from_node_names_jmi;
JCheckBoxMenuItem _color_labels_same_as_parent_branch;
JMenuItem _overview_placment_mi;
JMenuItem _choose_minimal_confidence_mi;
- JCheckBoxMenuItem _show_default_node_shapes_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_internal_cbmi;
+ JCheckBoxMenuItem _show_default_node_shapes_external_cbmi;
JMenuItem _cycle_node_shape_mi;
JMenuItem _cycle_node_fill_mi;
JMenuItem _choose_node_size_mi;
JMenuItem _choose_pdf_width_mi;
// _ parsing
JCheckBoxMenuItem _internal_number_are_confidence_for_nh_parsing_cbmi;
- JCheckBoxMenuItem _extract_pfam_style_tax_codes_cbmi;
+ JRadioButtonMenuItem _extract_taxonomy_no_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_agressive_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_strict_rbmi;
+ JRadioButtonMenuItem _extract_taxonomy_pfam_relaxed_rbmi;
JCheckBoxMenuItem _replace_underscores_cbmi;
JCheckBoxMenuItem _use_brackets_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _use_internal_names_for_conf_in_nh_export_cbmi;
JCheckBoxMenuItem _circular_type_cbmi;
// view as text menu:
JMenuItem _view_as_NH_item;
- JMenuItem _view_as_NHX_item;
JMenuItem _view_as_XML_item;
JMenuItem _view_as_nexus_item;
JMenuItem _display_basic_information_item;
Configuration _configuration;
JMenuItem _remove_branch_color_item;
Options _options;
+ private Phylogeny _species_tree;
InferenceManager _inference_manager;
final ProcessPool _process_pool;
private String _previous_node_annotation_ref;
else if ( o == _exit_item ) {
close();
}
+ else if ( o == _gsdi_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDI();
+ }
+ else if ( o == _gsdir_item ) {
+ if ( isSubtreeDisplayed() ) {
+ return;
+ }
+ executeGSDIR();
+ }
else if ( o == _taxcolor_item ) {
taxColor();
}
else if ( o == _color_rank_jmi ) {
colorRank();
}
- else if ( o == _infer_common_sn_names_item ) {
- if ( isSubtreeDisplayed() ) {
- return;
- }
- if ( getCurrentTreePanel() != null ) {
- getCurrentTreePanel().inferCommonPartOfScientificNames();
- }
- }
else if ( o == _collapse_species_specific_subtrees ) {
if ( isSubtreeDisplayed() ) {
return;
else if ( o == _view_as_NH_item ) {
viewAsNH();
}
- else if ( o == _view_as_NHX_item ) {
- viewAsNHX();
- }
else if ( o == _view_as_XML_item ) {
viewAsXML();
}
else if ( o == _color_labels_same_as_parent_branch ) {
updateOptions( getOptions() );
}
- else if ( o == _show_default_node_shapes_cbmi ) {
+ else if ( o == _show_default_node_shapes_internal_cbmi ) {
+ updateOptions( getOptions() );
+ }
+ else if ( o == _show_default_node_shapes_external_cbmi ) {
updateOptions( getOptions() );
}
else if ( o == _taxonomy_colorize_node_shapes_cbmi ) {
about();
}
else if ( o == _help_item ) {
- help( getConfiguration().getWebLinks() );
+ help();
}
else if ( o == _website_item ) {
try {
return _configuration;
}
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
+ }
+
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
+ }
+
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
public InferenceManager getInferenceManager() {
return _inference_manager;
}
void buildViewMenu() {
_view_jmenu = createMenu( "View", getConfiguration() );
- _view_jmenu.add( _display_basic_information_item = new JMenuItem( "Display Basic Information" ) );
+ _view_jmenu.add( _display_basic_information_item = new JMenuItem( SHOW_BASIC_TREE_INFORMATION_LABEL ) );
_view_jmenu.addSeparator();
_view_jmenu.add( _view_as_XML_item = new JMenuItem( "View as phyloXML" ) );
_view_jmenu.add( _view_as_NH_item = new JMenuItem( "View as Newick" ) );
- _view_jmenu.add( _view_as_NHX_item = new JMenuItem( "View as NHX" ) );
_view_jmenu.add( _view_as_nexus_item = new JMenuItem( "View as Nexus" ) );
customizeJMenuItem( _display_basic_information_item );
customizeJMenuItem( _view_as_NH_item );
- customizeJMenuItem( _view_as_NHX_item );
customizeJMenuItem( _view_as_XML_item );
customizeJMenuItem( _view_as_nexus_item );
_jmenubar.add( _view_jmenu );
JOptionPane.showMessageDialog( this, "Exception" + e, "Error during File|SaveAs", JOptionPane.ERROR_MESSAGE );
}
+ void executeGSDI() {
+ if ( !isOKforSDI( false, true ) ) {
+ return;
+ }
+ if ( !_mainpanel.getCurrentPhylogeny().isRooted() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not rooted.",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDI gsdi = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdi = new GSDI( gene_tree, species_tree, false, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ gene_tree.setRerootable( false );
+ gene_tree.clearHashIdToNodeMap();
+ gene_tree.recalculateNumberOfExternalDescendants( true );
+ _mainpanel.addPhylogenyInNewTab( gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdi.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Duplications: " + gsdi.getDuplicationsSum() + "\n"
+ + "Potential duplications: "
+ + gsdi.getSpeciationOrDuplicationEventsSum() + "\n"
+ + "Speciations: " + gsdi.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdi.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdi.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDI successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
+ void executeGSDIR() {
+ if ( !isOKforSDI( false, false ) ) {
+ return;
+ }
+ final int p = PhylogenyMethods.countNumberOfPolytomies( _mainpanel.getCurrentPhylogeny() );
+ if ( ( p > 0 )
+ && !( ( p == 1 ) && ( _mainpanel.getCurrentPhylogeny().getRoot().getNumberOfDescendants() == 3 ) ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ final Phylogeny gene_tree = _mainpanel.getCurrentPhylogeny().copy();
+ gene_tree.setAllNodesToNotCollapse();
+ gene_tree.recalculateNumberOfExternalDescendants( false );
+ GSDIR gsdir = null;
+ final Phylogeny species_tree = getSpeciesTree().copy();
+ try {
+ gsdir = new GSDIR( gene_tree, species_tree, true, true, true );
+ }
+ catch ( final SDIException e ) {
+ JOptionPane.showMessageDialog( this,
+ e.getLocalizedMessage(),
+ "Error during GSDIR",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ catch ( final Exception e ) {
+ AptxUtil.unexpectedException( e );
+ return;
+ }
+ final Phylogeny result_gene_tree = gsdir.getMinDuplicationsSumGeneTree();
+ result_gene_tree.setRerootable( false );
+ result_gene_tree.clearHashIdToNodeMap();
+ result_gene_tree.recalculateNumberOfExternalDescendants( true );
+ PhylogenyMethods.orderAppearance( result_gene_tree.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ _mainpanel.addPhylogenyInNewTab( result_gene_tree, getConfiguration(), "gene tree", null );
+ getMainPanel().getControlPanel().setShowEvents( true );
+ showWhole();
+ final int selected = _mainpanel.getTabbedPane().getSelectedIndex();
+ _mainpanel.addPhylogenyInNewTab( species_tree, getConfiguration(), "species tree", null );
+ showWhole();
+ _mainpanel.getTabbedPane().setSelectedIndex( selected );
+ showWhole();
+ _mainpanel.getCurrentTreePanel().setEdited( true );
+ final int poly = PhylogenyMethods.countNumberOfPolytomies( species_tree );
+ if ( gsdir.getStrippedExternalGeneTreeNodes().size() > 0 ) {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.WARNING_MESSAGE );
+ }
+ else {
+ JOptionPane.showMessageDialog( this,
+ "Minimal duplications: " + gsdir.getMinDuplicationsSum() + "\n"
+ + "Speciations: " + gsdir.getSpeciationsSum() + "\n"
+ + "Stripped gene tree nodes: "
+ + gsdir.getStrippedExternalGeneTreeNodes().size() + "\n"
+ + "Taxonomy linkage based on: " + gsdir.getTaxCompBase() + "\n"
+ + "Number of polytomies in species tree used: " + poly + "\n",
+ "GSDIR successfully completed",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ }
+
boolean GAndSDoHaveMoreThanOneSpeciesInComman( final Phylogeny gene_tree ) {
if ( ( gene_tree == null ) || gene_tree.isEmpty() ) {
JOptionPane.showMessageDialog( this,
return _jmenubar;
}
- void help( final Map<String, WebLink> weblinks ) {
+ final Phylogeny getSpeciesTree() {
+ return _species_tree;
+ }
+
+ void help() {
final StringBuilder sb = new StringBuilder();
sb.append( "Display options\n" );
sb.append( "-------------------\n" );
sb.append( "Since the Java default memory allocation is quite small, it might by necessary (for trees\n" );
sb.append( "with more than approximately 5000 external nodes) to increase the memory which Java can use, with\n" );
sb.append( "the '-Xmx' Java command line option. For example:\n" );
- sb.append( "java -Xms32m -Xmx256m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
- if ( ( weblinks != null ) && ( weblinks.size() > 0 ) ) {
- sb.append( "Active web links\n" );
- sb.append( "--------------------\n" );
- for( final String key : weblinks.keySet() ) {
- sb.append( " " + weblinks.get( key ).toString() + "\n" );
- }
- }
+ sb.append( "java -Xmx1024m -cp path\\to\\forester.jar org.forester.archaeopteryx.Archaeopteryx\n\n" );
// + "General remarks\n"
// + "---------------\n"
// +
// + " incorrect and need to be inferred again\n"
// +
// " with: \"SDI\"|\"SDI (Speciation Duplication Inference)\n\n"
- sb.append( "\n" );
sb.append( "phyloXML\n" );
sb.append( "-------------------\n" );
sb.append( "Reference: " + Constants.PHYLOXML_REFERENCE + "\n" );
sb.append( "Website: " + Constants.PHYLOXML_WEB_SITE + "\n" );
sb.append( "Version: " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
sb.append( "\n" );
- sb.append( "For more information: http://www.phylosoft.org/archaeopteryx/\n" );
+ sb.append( "For more information: https://sites.google.com/site/cmzmasek/home/software/archaeopteryx\n" );
sb.append( "Email: " + Constants.AUTHOR_EMAIL + "\n\n" );
TextFrame.instantiate( sb.toString(), "Help", _textframes );
}
}
}
+ boolean isOKforSDI( final boolean species_tree_has_to_binary, final boolean gene_tree_has_to_binary ) {
+ if ( ( _mainpanel.getCurrentPhylogeny() == null ) || _mainpanel.getCurrentPhylogeny().isEmpty() ) {
+ return false;
+ }
+ else if ( ( getSpeciesTree() == null ) || getSpeciesTree().isEmpty() ) {
+ JOptionPane.showMessageDialog( this,
+ "No species tree loaded",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( species_tree_has_to_binary && !getSpeciesTree().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Species tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else if ( gene_tree_has_to_binary && !_mainpanel.getCurrentPhylogeny().isCompletelyBinary() ) {
+ JOptionPane.showMessageDialog( this,
+ "Gene tree is not completely binary",
+ "Cannot execute GSDI",
+ JOptionPane.ERROR_MESSAGE );
+ return false;
+ }
+ else {
+ return true;
+ }
+ }
+
boolean isSubtreeDisplayed() {
if ( getCurrentTreePanel() != null ) {
if ( getCurrentTreePanel().isCurrentTreeIsSubtree() ) {
}
}
+ final void setSpeciesTree( final Phylogeny species_tree ) {
+ _species_tree = species_tree;
+ }
+
void setTypeMenuToAllUnselected() {
_convex_type_cbmi.setSelected( false );
_curved_type_cbmi.setSelected( false );
&& _abbreviate_scientific_names.isSelected() );
options.setColorLabelsSameAsParentBranch( ( _color_labels_same_as_parent_branch != null )
&& _color_labels_same_as_parent_branch.isSelected() );
- options.setShowDefaultNodeShapes( ( _show_default_node_shapes_cbmi != null )
- && _show_default_node_shapes_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesInternal( ( _show_default_node_shapes_internal_cbmi != null )
+ && _show_default_node_shapes_internal_cbmi.isSelected() );
+ options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null )
+ && _show_default_node_shapes_external_cbmi.isSelected() );
options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null )
&& _taxonomy_colorize_node_shapes_cbmi.isSelected() );
if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) {
&& _print_black_and_white_cbmi.isSelected() );
options.setInternalNumberAreConfidenceForNhParsing( ( _internal_number_are_confidence_for_nh_parsing_cbmi != null )
&& _internal_number_are_confidence_for_nh_parsing_cbmi.isSelected() );
- options.setExtractPfamTaxonomyCodesInNhParsing( ( _extract_pfam_style_tax_codes_cbmi != null )
- && _extract_pfam_style_tax_codes_cbmi.isSelected() );
+ if ( ( _extract_taxonomy_pfam_strict_rbmi != null ) && _extract_taxonomy_pfam_strict_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
+ }
+ else if ( ( _extract_taxonomy_pfam_relaxed_rbmi != null ) && _extract_taxonomy_pfam_relaxed_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+ }
+ else if ( ( _extract_taxonomy_agressive_rbmi != null ) && _extract_taxonomy_agressive_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
+ }
+ else if ( ( _extract_taxonomy_no_rbmi != null ) && _extract_taxonomy_no_rbmi.isSelected() ) {
+ options.setTaxonomyExtraction( TAXONOMY_EXTRACTION.NO );
+ }
options.setReplaceUnderscoresInNhParsing( ( _replace_underscores_cbmi != null )
&& _replace_underscores_cbmi.isSelected() );
options.setMatchWholeTermsOnly( ( _search_whole_words_only_cbmi != null )
}
}
- void viewAsNHX() {
- if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
- String title = "NHX";
- if ( !ForesterUtil.isEmpty( _mainpanel.getCurrentPhylogeny().getName() ) ) {
- title = _mainpanel.getCurrentPhylogeny().getName() + " " + title;
- }
- showTextFrame( _mainpanel.getCurrentPhylogeny().toNewHampshireX(), title );
- }
- }
-
void viewAsXML() {
if ( ( _mainpanel.getCurrentPhylogeny() != null ) && !_mainpanel.getCurrentPhylogeny().isEmpty() ) {
String title = "phyloXML";
private void annotateSequences() {
if ( getCurrentTreePanel() != null ) {
- final Set<Integer> nodes = getCurrentTreePanel().getFoundNodes();
+ final Set<Long> nodes = getCurrentTreePanel().getFoundNodes();
if ( ( nodes == null ) || nodes.isEmpty() ) {
JOptionPane
.showMessageDialog( this,
}
final Phylogeny phy = getMainPanel().getCurrentPhylogeny();
if ( ( phy != null ) && !phy.isEmpty() ) {
- final JTextField xField = new JTextField( 10 );
- final JTextField yField = new JTextField( 20 );
- xField.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
+ final JTextField ref_field = new JTextField( 10 );
+ final JTextField desc_filed = new JTextField( 20 );
+ ref_field.setText( ForesterUtil.isEmpty( getPreviousNodeAnnotationReference() ) ? ""
: getPreviousNodeAnnotationReference() );
- final JPanel myPanel = new JPanel();
- myPanel.add( new JLabel( "Reference " ) );
- myPanel.add( xField );
- myPanel.add( Box.createHorizontalStrut( 15 ) );
- myPanel.add( new JLabel( "Description " ) );
- myPanel.add( yField );
+ final JPanel my_panel = new JPanel();
+ my_panel.add( new JLabel( "Reference " ) );
+ my_panel.add( ref_field );
+ my_panel.add( Box.createHorizontalStrut( 15 ) );
+ my_panel.add( new JLabel( "Description " ) );
+ my_panel.add( desc_filed );
final int result = JOptionPane.showConfirmDialog( null,
- myPanel,
+ my_panel,
"Enter the sequence annotation(s) for the "
+ nodes.size() + " selected nodes",
JOptionPane.OK_CANCEL_OPTION );
if ( result == JOptionPane.OK_OPTION ) {
- String ref = xField.getText();
- String desc = yField.getText();
- if ( ref != null ) {
+ String ref = ref_field.getText();
+ String desc = desc_filed.getText();
+ if ( !ForesterUtil.isEmpty( ref ) ) {
ref = ref.trim();
ref = ref.replaceAll( "\\s+", " " );
+ if ( ( ref.indexOf( ':' ) < 1 ) || ( ref.indexOf( ':' ) > ref.length() - 2 )
+ || ( ref.length() < 3 ) ) {
+ JOptionPane.showMessageDialog( this,
+ "Reference needs to be in the form of \"GO:1234567\"",
+ "Illegal Format for Annotation Reference",
+ JOptionPane.ERROR_MESSAGE );
+ return;
+ }
+ }
+ if ( ref != null ) {
+ setPreviousNodeAnnotationReference( ref );
}
if ( desc != null ) {
desc = desc.trim();
desc = desc.replaceAll( "\\s+", " " );
}
- if ( ref != null ) {
- setPreviousNodeAnnotationReference( ref );
- }
if ( !ForesterUtil.isEmpty( ref ) || !ForesterUtil.isEmpty( desc ) ) {
- for( final Integer id : nodes ) {
+ for( final Long id : nodes ) {
final PhylogenyNode n = phy.getNode( id );
ForesterUtil.ensurePresenceOfSequence( n );
final Annotation ann = ForesterUtil.isEmpty( ref ) ? new Annotation()
n.getNodeData().getSequence().addAnnotation( ann );
}
}
+ getMainPanel().getControlPanel().showAnnotations();
}
}
}
}
- private String getPreviousNodeAnnotationReference() {
- return _previous_node_annotation_ref;
- }
-
- private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
- _previous_node_annotation_ref = previous_node_annotation_ref;
- }
-
private void chooseFont() {
final FontChooser fc = new FontChooser();
fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
repaint();
}
+ private String getPreviousNodeAnnotationReference() {
+ return _previous_node_annotation_ref;
+ }
+
private void removeBranchColors() {
if ( getMainPanel().getCurrentPhylogeny() != null ) {
AptxUtil.removeBranchColors( getMainPanel().getCurrentPhylogeny() );
}
}
+ private void setPreviousNodeAnnotationReference( final String previous_node_annotation_ref ) {
+ _previous_node_annotation_ref = previous_node_annotation_ref;
+ }
+
/**
* Display the about box.
*/
static void about() {
final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + Constants.VERSION + "\n" );
- about.append( "Copyright (C) 2007-2012 Christian M. Zmasek\n" );
+ about.append( "Copyright (C) 2013 Christian M. Zmasek\n" );
about.append( "All Rights Reserved\n" );
about.append( "License: GNU Lesser General Public License (LGPL)\n" );
about.append( "Last modified: " + Constants.PRG_DATE + "\n" );
git://source.jalview.org / jalview.git / blobdiff