2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
28 import java.awt.event.KeyEvent;
29 import java.awt.event.KeyListener;
30 import java.math.BigDecimal;
32 import java.text.ParseException;
33 import java.util.ArrayList;
34 import java.util.HashMap;
35 import java.util.List;
38 import javax.swing.JEditorPane;
39 import javax.swing.JOptionPane;
40 import javax.swing.JPanel;
41 import javax.swing.JScrollPane;
42 import javax.swing.JSplitPane;
43 import javax.swing.JTree;
44 import javax.swing.event.TreeSelectionEvent;
45 import javax.swing.event.TreeSelectionListener;
46 import javax.swing.text.Position;
47 import javax.swing.tree.DefaultMutableTreeNode;
48 import javax.swing.tree.TreePath;
49 import javax.swing.tree.TreeSelectionModel;
51 import org.forester.archaeopteryx.tools.ImageLoader;
52 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
53 import org.forester.phylogeny.PhylogenyNode;
54 import org.forester.phylogeny.data.Accession;
55 import org.forester.phylogeny.data.BranchWidth;
56 import org.forester.phylogeny.data.Confidence;
57 import org.forester.phylogeny.data.Date;
58 import org.forester.phylogeny.data.Distribution;
59 import org.forester.phylogeny.data.Event;
60 import org.forester.phylogeny.data.Identifier;
61 import org.forester.phylogeny.data.MultipleUris;
62 import org.forester.phylogeny.data.PhylogenyData;
63 import org.forester.phylogeny.data.PhylogenyDataUtil;
64 import org.forester.phylogeny.data.Point;
65 import org.forester.phylogeny.data.Reference;
66 import org.forester.phylogeny.data.Sequence;
67 import org.forester.phylogeny.data.Taxonomy;
68 import org.forester.phylogeny.data.Uri;
69 import org.forester.util.FailedConditionCheckException;
70 import org.forester.util.ForesterUtil;
72 class NodeEditPanel extends JPanel {
74 private enum PHYLOXML_TAG {
79 TAXONOMY_SCIENTIFIC_NAME,
116 private class TagNumber {
118 final private PHYLOXML_TAG _tag;
119 final private int _number;
121 TagNumber( final PHYLOXML_TAG tag, final int number ) {
127 public String toString() {
128 return getTag() + "_" + getNumber();
135 PHYLOXML_TAG getTag() {
139 private static final long serialVersionUID = 5120159904388100771L;
140 private final JTree _tree;
141 private final JEditorPane _pane;
142 private final PhylogenyNode _my_node;
143 private final TreePanel _tree_panel;
144 private final Map<DefaultMutableTreeNode, TagNumber> _map;
146 public NodeEditPanel( final PhylogenyNode phylogeny_node, final TreePanel tree_panel ) {
147 _map = new HashMap<DefaultMutableTreeNode, TagNumber>();
148 _my_node = phylogeny_node;
149 _tree_panel = tree_panel;
150 String node_name = "";
151 if ( !ForesterUtil.isEmpty( phylogeny_node.getName() ) ) {
152 node_name = phylogeny_node.getName() + " ";
154 final DefaultMutableTreeNode top = new DefaultMutableTreeNode( "Node " + node_name );
155 createNodes( top, phylogeny_node );
156 _tree = new JTree( top );
157 getJTree().setEditable( true );
158 getJTree().setFocusable( true );
159 getJTree().setToggleClickCount( 1 );
160 getJTree().setInvokesStopCellEditing( true );
161 final JScrollPane tree_view = new JScrollPane( getJTree() );
162 _pane = new JEditorPane();
163 _pane.setEditable( true );
164 final JScrollPane data_view = new JScrollPane( _pane );
165 final JSplitPane split_pane = new JSplitPane( JSplitPane.VERTICAL_SPLIT );
166 split_pane.setTopComponent( tree_view );
167 // split_pane.setBottomComponent( data_view );
168 data_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
169 tree_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
170 // split_pane.setDividerLocation( 400 );
171 split_pane.setPreferredSize( Constants.NODE_PANEL_SIZE );
173 getJTree().getSelectionModel().setSelectionMode( TreeSelectionModel.SINGLE_TREE_SELECTION );
174 getJTree().addKeyListener( new KeyListener() {
177 public void keyPressed( final KeyEvent e ) {
182 public void keyReleased( final KeyEvent e ) {
187 public void keyTyped( final KeyEvent e ) {
191 for( int i = 0; i < getJTree().getRowCount(); i++ ) {
192 getJTree().expandRow( i );
194 collapsePath( NodePanel.BASIC );
195 collapsePath( NodePanel.TAXONOMY );
196 collapsePath( NodePanel.SEQUENCE );
197 collapsePath( NodePanel.EVENTS );
198 collapsePath( NodePanel.DATE );
199 collapsePath( NodePanel.DISTRIBUTION );
200 collapsePath( NodePanel.LIT_REFERENCE );
201 getJTree().addTreeSelectionListener( new TreeSelectionListener() {
204 public void valueChanged( final TreeSelectionEvent e ) {
205 final TreePath new_path = e.getNewLeadSelectionPath();
206 final TreePath old_path = e.getOldLeadSelectionPath();
207 if ( new_path != null ) {
208 writeBack( ( DefaultMutableTreeNode ) new_path.getLastPathComponent() );
210 if ( old_path != null ) {
211 writeBack( ( DefaultMutableTreeNode ) old_path.getLastPathComponent() );
217 private void addBasics( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node, final String name ) {
218 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
220 addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME );
222 if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
223 bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() );
225 addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH );
227 if ( phylogeny_node.getBranchData().isHasConfidences() ) {
228 for( int i = phylogeny_node.getBranchData().getConfidences().size() - 1; i >= 0; i-- ) {
229 if ( phylogeny_node.getBranchData().getConfidences().get( i ).getValue() == Confidence.CONFIDENCE_DEFAULT_VALUE ) {
230 phylogeny_node.getBranchData().getConfidences().remove( i );
233 for( final PhylogenyData conf : phylogeny_node.getBranchData().getConfidences() ) {
234 final Confidence my_conf = ( Confidence ) ( conf );
235 addSubelementEditable( category,
236 NodePanel.CONFIDENCE + " [" + counter + "]",
237 ForesterUtil.FORMATTER_6.format( my_conf.getValue() ),
238 PHYLOXML_TAG.CONFIDENCE_VALUE,
239 NodePanel.CONFIDENCE_TYPE,
241 PHYLOXML_TAG.CONFIDENCE_TYPE,
245 addSubelementEditable( category,
246 NodePanel.CONFIDENCE + " [" + counter + "]",
248 PHYLOXML_TAG.CONFIDENCE_VALUE,
249 NodePanel.CONFIDENCE_TYPE,
251 PHYLOXML_TAG.CONFIDENCE_TYPE,
254 if ( ( phylogeny_node.getBranchData().getBranchWidth() != null )
255 && ( phylogeny_node.getBranchData().getBranchWidth().getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) ) {
256 bw = ForesterUtil.FORMATTER_3.format( phylogeny_node.getBranchData().getBranchWidth().getValue() );
258 addSubelementEditable( category, NodePanel.NODE_BRANCH_WIDTH, bw, PHYLOXML_TAG.NODE_BRANCH_WIDTH );
261 // private void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) {
262 // DefaultMutableTreeNode category;
263 // category = new DefaultMutableTreeNode( name );
264 // top.add( category );
265 // addSubelementEditable( category, "Reference", ann.getRef() , PHYLOXML_TAG.);
266 // addSubelementEditable( category, "Description", ann.getDesc() , PHYLOXML_TAG.);
267 // addSubelementEditable( category, "Source", ann.getSource(), PHYLOXML_TAG. );
268 // addSubelementEditable( category, "Type", ann.getType(), PHYLOXML_TAG. );
269 // addSubelementEditable( category, "Evidence", ann.getEvidence() , PHYLOXML_TAG.);
270 // if ( ann.getConfidence() != null ) {
271 // addSubelementEditable( category, "Confidence", ann.getConfidence().asText().toString() , PHYLOXML_TAG.);
273 // if ( ann.getProperties() != null ) {
274 // addProperties( category, ann.getProperties(), "Properties", PHYLOXML_TAG. );
277 // private void addAnnotations( final DefaultMutableTreeNode top,
278 // final List<PhylogenyData> annotations,
279 // final DefaultMutableTreeNode category ) {
280 // if ( ( annotations != null ) && ( annotations.size() > 0 ) ) {
281 // category.add( new DefaultMutableTreeNode( "Annotations" ) );
282 // final DefaultMutableTreeNode last = top.getLastLeaf();
284 // for( final PhylogenyData ann : annotations ) {
285 // addAnnotation( last, ( Annotation ) ann, "Annotation " + ( i++ ) );
289 private void addDate( final DefaultMutableTreeNode top, Date date, final String name ) {
290 if ( date == null ) {
293 DefaultMutableTreeNode category;
294 category = new DefaultMutableTreeNode( name );
296 addSubelementEditable( category, NodePanel.DATE_DESCRIPTION, date.getDesc(), PHYLOXML_TAG.DATE_DESCRIPTION );
297 addSubelementEditable( category,
298 NodePanel.DATE_VALUE,
299 String.valueOf( date.getValue() != null ? date.getValue() : "" ),
300 PHYLOXML_TAG.DATE_VALUE );
301 addSubelementEditable( category,
303 String.valueOf( date.getMin() != null ? date.getMin() : "" ),
304 PHYLOXML_TAG.DATE_MIN );
305 addSubelementEditable( category,
307 String.valueOf( date.getMax() != null ? date.getMax() : "" ),
308 PHYLOXML_TAG.DATE_MAX );
309 addSubelementEditable( category, NodePanel.DATE_UNIT, date.getUnit(), PHYLOXML_TAG.DATE_UNIT );
312 private void addDistribution( final DefaultMutableTreeNode top, Distribution dist, final String name ) {
313 if ( dist == null ) {
314 dist = new Distribution( "" );
316 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
319 if ( ( dist.getPoints() != null ) && ( dist.getPoints().size() > 0 ) ) {
320 p0 = dist.getPoints().get( 0 );
325 addSubelementEditable( category, NodePanel.DIST_DESCRIPTION, dist.getDesc(), PHYLOXML_TAG.DIST_DESC );
326 addSubelementEditable( category,
327 NodePanel.DIST_GEODETIC_DATUM,
328 p0.getGeodeticDatum(),
329 PHYLOXML_TAG.DIST_GEODETIC );
330 addSubelementEditable( category,
331 NodePanel.DIST_LATITUDE,
332 String.valueOf( p0.getLatitude() != null ? p0.getLatitude() : "" ),
333 PHYLOXML_TAG.DIST_LAT );
334 addSubelementEditable( category,
335 NodePanel.DIST_LONGITUDE,
336 String.valueOf( p0.getLongitude() != null ? p0.getLongitude() : "" ),
337 PHYLOXML_TAG.DIST_LONG );
338 addSubelementEditable( category,
339 NodePanel.DIST_ALTITUDE,
340 String.valueOf( p0.getAltitude() != null ? p0.getAltitude() : "" ),
341 PHYLOXML_TAG.DIST_ALT );
342 addSubelementEditable( category,
343 NodePanel.DIST_ALT_UNIT,
344 String.valueOf( p0.getAltiudeUnit() != null ? p0.getAltiudeUnit() : "" ),
345 PHYLOXML_TAG.DIST_ALT_UNIT );
348 private void addEvents( final DefaultMutableTreeNode top, Event events, final String name ) {
349 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
350 if ( events == null ) {
351 events = new Event();
354 addSubelementEditable( category,
355 NodePanel.EVENTS_DUPLICATIONS,
356 String.valueOf( events.getNumberOfDuplications() >= 0 ? events.getNumberOfDuplications()
358 PHYLOXML_TAG.EVENTS_DUPLICATIONS );
359 addSubelementEditable( category,
360 NodePanel.EVENTS_SPECIATIONS,
361 String.valueOf( events.getNumberOfSpeciations() >= 0 ? events.getNumberOfSpeciations()
363 PHYLOXML_TAG.EVENTS_SPECIATIONS );
364 addSubelementEditable( category,
365 NodePanel.EVENTS_GENE_LOSSES,
366 String.valueOf( events.getNumberOfGeneLosses() >= 0 ? events.getNumberOfGeneLosses() : 0 ),
367 PHYLOXML_TAG.EVENTS_GENE_LOSSES );
370 private void addMapping( final DefaultMutableTreeNode mtn, final TagNumber tag ) {
371 if ( getMap().containsKey( mtn ) ) {
372 throw new IllegalArgumentException( "key " + mtn + " already present" );
374 if ( getMap().containsValue( tag ) ) {
375 throw new IllegalArgumentException( "value " + tag + " already present" );
377 getMap().put( mtn, tag );
380 private void addReference( final DefaultMutableTreeNode top, Reference ref, final String name ) {
382 ref = new Reference( "" );
384 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
386 addSubelementEditable( category,
387 NodePanel.LIT_REFERENCE_DESC,
388 ref.getDescription(),
389 PHYLOXML_TAG.LIT_REFERENCE_DESC );
390 addSubelementEditable( category, NodePanel.LIT_REFERENCE_DOI, ref.getDoi(), PHYLOXML_TAG.LIT_REFERENCE_DOI );
393 private void addSequence( final DefaultMutableTreeNode top, Sequence seq, final String name ) {
395 seq = new Sequence();
397 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
399 Accession acc = seq.getAccession();
401 acc = new Accession( "", "" );
403 addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME );
404 addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL );
405 addSubelementEditable( category, NodePanel.SEQ_GENE_NAME, seq.getGeneName(), PHYLOXML_TAG.SEQ_GENE_NAME );
406 addSubelementEditable( category,
407 NodePanel.SEQ_ACCESSION,
409 PHYLOXML_TAG.SEQ_ACC_VALUE,
412 PHYLOXML_TAG.SEQ_ACC_SOURCE );
413 addSubelementEditable( category, NodePanel.SEQ_LOCATION, seq.getLocation(), PHYLOXML_TAG.SEQ_LOCATION );
414 addSubelementEditable( category, NodePanel.SEQ_TYPE, seq.getType(), PHYLOXML_TAG.SEQ_TYPE );
415 addSubelementEditable( category, NodePanel.SEQ_MOL_SEQ, seq.getMolecularSequence(), PHYLOXML_TAG.SEQ_MOL_SEQ );
417 if ( seq.getUris() != null ) {
418 for( final Uri uri : seq.getUris() ) {
420 addSubelementEditable( category, NodePanel.SEQ_URI + " [" + uri_counter + "]", uri.getValue()
421 .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ );
425 addSubelementEditable( category,
426 NodePanel.SEQ_URI + " [" + uri_counter + "]",
428 PHYLOXML_TAG.SEQ_URI,
430 // addAnnotations( top, seq.getAnnotations(), category );
433 private void addSubelementEditable( final DefaultMutableTreeNode node,
436 final PHYLOXML_TAG phyloxml_tag ) {
437 addSubelementEditable( node, name, value, phyloxml_tag, 0 );
440 private void addSubelementEditable( final DefaultMutableTreeNode node,
443 final PHYLOXML_TAG phyloxml_tag,
445 String my_value = value;
446 if ( ForesterUtil.isEmpty( my_value ) ) {
449 final DefaultMutableTreeNode name_node = new DefaultMutableTreeNode( name );
450 final DefaultMutableTreeNode value_node = new DefaultMutableTreeNode( my_value );
451 name_node.add( value_node );
452 node.add( name_node );
453 addMapping( name_node, new TagNumber( phyloxml_tag, number ) );
456 private void addSubelementEditable( final DefaultMutableTreeNode node,
459 final PHYLOXML_TAG phyloxml_value_tag,
460 final String source_name,
461 final String source_value,
462 final PHYLOXML_TAG phyloxml_source_tag ) {
463 addSubelementEditable( node, name, value, phyloxml_value_tag, source_name, source_value, phyloxml_source_tag, 0 );
466 private void addSubelementEditable( final DefaultMutableTreeNode node,
469 final PHYLOXML_TAG phyloxml_value_tag,
470 final String source_name,
471 final String source_value,
472 final PHYLOXML_TAG phyloxml_source_tag,
474 String my_value = value;
475 if ( ForesterUtil.isEmpty( my_value ) ) {
478 String my_source_value = source_value;
479 if ( ForesterUtil.isEmpty( my_source_value ) ) {
480 my_source_value = "";
482 final DefaultMutableTreeNode name_node = new DefaultMutableTreeNode( name );
483 final DefaultMutableTreeNode source_name_node = new DefaultMutableTreeNode( source_name );
484 final DefaultMutableTreeNode source_value_node = new DefaultMutableTreeNode( my_source_value );
485 final DefaultMutableTreeNode value_node = new DefaultMutableTreeNode( my_value );
486 name_node.add( source_name_node );
487 source_name_node.add( source_value_node );
488 name_node.add( value_node );
489 node.add( name_node );
490 addMapping( name_node, new TagNumber( phyloxml_value_tag, number ) );
491 addMapping( source_name_node, new TagNumber( phyloxml_source_tag, number ) );
494 private void addTaxonomy( final DefaultMutableTreeNode top, Taxonomy tax, final String name ) {
496 tax = new Taxonomy();
498 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
500 Identifier id = tax.getIdentifier();
502 id = new Identifier();
504 addSubelementEditable( category,
505 NodePanel.TAXONOMY_IDENTIFIER,
507 PHYLOXML_TAG.TAXONOMY_ID_VALUE,
510 PHYLOXML_TAG.TAXONOMY_ID_PROVIDER );
511 addSubelementEditable( category, NodePanel.TAXONOMY_CODE, tax.getTaxonomyCode(), PHYLOXML_TAG.TAXONOMY_CODE );
512 addSubelementEditable( category,
513 NodePanel.TAXONOMY_SCIENTIFIC_NAME,
514 tax.getScientificName(),
515 PHYLOXML_TAG.TAXONOMY_SCIENTIFIC_NAME );
516 addSubelementEditable( category,
517 NodePanel.TAXONOMY_AUTHORITY,
519 PHYLOXML_TAG.TAXONOMY_AUTHORITY );
520 addSubelementEditable( category,
521 NodePanel.TAXONOMY_COMMON_NAME,
523 PHYLOXML_TAG.TAXONOMY_COMMON_NAME );
524 for( int i = tax.getSynonyms().size() - 1; i >= 0; i-- ) {
525 if ( ForesterUtil.isEmpty( tax.getSynonyms().get( i ) ) ) {
526 tax.getSynonyms().remove( i );
530 for( final String syn : tax.getSynonyms() ) {
531 addSubelementEditable( category,
532 NodePanel.TAXONOMY_SYNONYM + " [" + syn_counter + "]",
534 PHYLOXML_TAG.TAXONOMY_SYNONYM,
537 addSubelementEditable( category,
538 NodePanel.TAXONOMY_SYNONYM + " [" + syn_counter + "]",
540 PHYLOXML_TAG.TAXONOMY_SYNONYM,
542 addSubelementEditable( category, NodePanel.TAXONOMY_RANK, tax.getRank(), PHYLOXML_TAG.TAXONOMY_RANK );
544 if ( tax.getUris() != null ) {
545 for( final Uri uri : tax.getUris() ) {
547 addSubelementEditable( category, NodePanel.TAXONOMY_URI + " [" + uri_counter + "]", uri.getValue()
548 .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ );
552 addSubelementEditable( category,
553 NodePanel.TAXONOMY_URI + " [" + uri_counter + "]",
555 PHYLOXML_TAG.TAXONOMY_URI,
559 private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
561 if ( mu.getUris() == null ) {
562 mu.setUris( new ArrayList<Uri>() );
565 if ( ( uri != null ) && ( mu.getUris() == null ) ) {
566 mu.setUris( new ArrayList<Uri>() );
568 if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
569 mu.getUris().add( uri );
571 if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
572 mu.getUris().set( number, uri );
574 final ImageLoader il = new ImageLoader( getTreePanel() );
575 new Thread( il ).start();
578 private void collapsePath( final String name ) {
579 final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
581 getJTree().collapsePath( tp );
585 private void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {
586 if ( !phylogeny_node.getNodeData().isHasTaxonomy() ) {
587 phylogeny_node.getNodeData().addTaxonomy( new Taxonomy() );
589 if ( !phylogeny_node.getNodeData().isHasSequence() ) {
590 phylogeny_node.getNodeData().addSequence( new Sequence() );
592 if ( !phylogeny_node.getNodeData().isHasDistribution() ) {
593 phylogeny_node.getNodeData().addDistribution( new Distribution( "" ) );
595 if ( !phylogeny_node.getNodeData().isHasReference() ) {
596 phylogeny_node.getNodeData().addReference( new Reference( "" ) );
598 addBasics( top, phylogeny_node, NodePanel.BASIC );
599 addTaxonomy( top, phylogeny_node.getNodeData().getTaxonomy(), NodePanel.TAXONOMY );
600 addSequence( top, phylogeny_node.getNodeData().getSequence(), NodePanel.SEQUENCE );
601 if ( !phylogeny_node.isExternal() ) {
602 addEvents( top, phylogeny_node.getNodeData().getEvent(), NodePanel.EVENTS );
604 addDate( top, phylogeny_node.getNodeData().getDate(), NodePanel.DATE );
605 addDistribution( top, phylogeny_node.getNodeData().getDistribution(), NodePanel.DISTRIBUTION );
606 addReference( top, phylogeny_node.getNodeData().getReference(), NodePanel.LIT_REFERENCE );
607 // addProperties( top, phylogeny_node.getNodeData().getProperties(), "Properties" );
610 private void formatError( final DefaultMutableTreeNode mtn, final PhyloXmlDataFormatException e ) {
611 JOptionPane.showMessageDialog( this, e.getMessage(), "Format error", JOptionPane.ERROR_MESSAGE );
612 mtn.setUserObject( "" );
613 getJTree().repaint();
616 private JTree getJTree() {
620 private Map<DefaultMutableTreeNode, TagNumber> getMap() {
624 private TagNumber getMapping( final DefaultMutableTreeNode mtn ) {
625 return getMap().get( mtn );
628 private DefaultMutableTreeNode getSelectedTreeNode() {
629 final TreePath selectionPath = getJTree().getSelectionPath();
630 if ( selectionPath != null ) {
631 final Object[] path = selectionPath.getPath();
632 if ( path.length > 0 ) {
633 return ( DefaultMutableTreeNode ) path[ path.length - 1 ]; // Last node
639 private TreePanel getTreePanel() {
643 private void keyEvent( final KeyEvent e ) {
644 if ( e.getKeyCode() == KeyEvent.VK_ENTER ) {
645 writeBack( getSelectedTreeNode() );
649 private List<Point> obtainPoints() {
650 ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
651 Distribution d = getMyNode().getNodeData().getDistribution();
652 if ( d.getPoints() == null ) {
653 d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
654 getMyNode().getNodeData().setDistribution( d );
656 final List<Point> ps = d.getPoints();
657 if ( ps.isEmpty() ) {
658 ps.add( new Point() );
660 else if ( ps.get( 0 ) == null ) {
661 ps.set( 0, new Point() );
666 private BigDecimal parseBigDecimal( final DefaultMutableTreeNode mtn, final String value ) {
667 if ( ForesterUtil.isEmpty( value ) ) {
668 return new BigDecimal( 0 );
672 i = new BigDecimal( value );
674 catch ( final NumberFormatException e ) {
675 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
676 mtn.setUserObject( "" );
681 private int parsePositiveInt( final DefaultMutableTreeNode mtn, final String value ) {
682 if ( ForesterUtil.isEmpty( value ) ) {
687 i = ForesterUtil.parseInt( value );
689 catch ( final ParseException e ) {
690 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
691 mtn.setUserObject( "" );
694 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
695 mtn.setUserObject( "" );
700 private void writeBack( final DefaultMutableTreeNode mtn ) {
701 if ( !getMap().containsKey( mtn ) ) {
702 final DefaultMutableTreeNode parent = ( DefaultMutableTreeNode ) mtn.getParent();
703 if ( getMap().containsKey( parent ) ) {
704 writeBack( mtn, getMapping( parent ) );
709 private void writeBack( final DefaultMutableTreeNode mtn, final TagNumber tag_number ) {
710 if ( tag_number == null ) {
713 String value = mtn.toString();
714 if ( value == null ) {
717 value = value.replaceAll( "\\s+", " " );
718 value = value.trim();
719 mtn.setUserObject( value );
720 getJTree().repaint();
721 final PHYLOXML_TAG tag = tag_number.getTag();
722 final int number = tag_number.getNumber();
725 getMyNode().setName( value );
727 case NODE_BRANCH_LENGTH:
728 if ( ForesterUtil.isEmpty( value ) ) {
729 getMyNode().setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
733 getMyNode().setDistanceToParent( ForesterUtil.parseDouble( value ) );
735 catch ( final ParseException e ) {
736 JOptionPane.showMessageDialog( this,
737 "failed to parse branch length from: " + value,
739 JOptionPane.ERROR_MESSAGE );
740 mtn.setUserObject( "" );
744 case NODE_BRANCH_WIDTH:
745 if ( ForesterUtil.isEmpty( value ) || value.equals( "1" ) ) {
746 if ( getMyNode().getBranchData().getBranchWidth() != null ) {
747 getMyNode().getBranchData().setBranchWidth( new BranchWidth() );
752 final double bw = ForesterUtil.parseDouble( value );
754 getMyNode().getBranchData().setBranchWidth( new BranchWidth( bw ) );
757 catch ( final ParseException e ) {
758 JOptionPane.showMessageDialog( this,
759 "failed to parse branch width from: " + value,
761 JOptionPane.ERROR_MESSAGE );
762 mtn.setUserObject( "" );
766 case CONFIDENCE_VALUE:
767 double confidence = Confidence.CONFIDENCE_DEFAULT_VALUE;
768 if ( !ForesterUtil.isEmpty( value ) ) {
770 confidence = ForesterUtil.parseDouble( value );
772 catch ( final ParseException e ) {
773 JOptionPane.showMessageDialog( this,
774 "failed to parse confidence value from: " + value,
776 JOptionPane.ERROR_MESSAGE );
777 mtn.setUserObject( "" );
781 if ( getMyNode().getBranchData().getConfidences().size() < number ) {
782 throw new FailedConditionCheckException();
784 else if ( getMyNode().getBranchData().getConfidences().size() == number ) {
785 if ( confidence >= 0 ) {
786 getMyNode().getBranchData().getConfidences().add( new Confidence( confidence, "unknown" ) );
790 final String type = getMyNode().getBranchData().getConfidences().get( number ).getType();
791 final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation();
792 getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type, sd ) );
795 case CONFIDENCE_TYPE:
796 if ( getMyNode().getBranchData().getConfidences().size() < number ) {
797 throw new FailedConditionCheckException();
799 else if ( getMyNode().getBranchData().getConfidences().size() == number ) {
800 if ( !ForesterUtil.isEmpty( value ) ) {
801 getMyNode().getBranchData().getConfidences().add( new Confidence( 0, value ) );
805 final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue();
806 final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation();
807 getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value, sd ) );
811 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
813 getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
815 catch ( final PhyloXmlDataFormatException e ) {
816 formatError( mtn, e );
820 case TAXONOMY_SCIENTIFIC_NAME:
821 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
822 getMyNode().getNodeData().getTaxonomy().setScientificName( value );
824 case TAXONOMY_COMMON_NAME:
825 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
826 getMyNode().getNodeData().getTaxonomy().setCommonName( value );
829 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
831 getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
833 catch ( final PhyloXmlDataFormatException e ) {
834 formatError( mtn, e );
838 case TAXONOMY_AUTHORITY:
839 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
840 getMyNode().getNodeData().getTaxonomy().setAuthority( value );
844 if ( !ForesterUtil.isEmpty( value ) ) {
846 uri = new Uri( new URL( value ).toURI() );
848 catch ( final Exception e ) {
849 JOptionPane.showMessageDialog( this,
850 "failed to parse URL from: " + value,
852 JOptionPane.ERROR_MESSAGE );
853 mtn.setUserObject( "" );
857 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
859 addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
862 case TAXONOMY_SYNONYM:
863 if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() < number ) {
864 throw new FailedConditionCheckException();
866 else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
867 if ( !ForesterUtil.isEmpty( value ) ) {
868 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
869 getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
873 getMyNode().getNodeData().getTaxonomy().getSynonyms().set( number, value );
876 case TAXONOMY_ID_VALUE:
877 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
878 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
879 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
882 final String provider = getMyNode().getNodeData().getTaxonomy().getIdentifier().getProvider();
883 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value, provider ) );
886 case TAXONOMY_ID_PROVIDER:
887 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
888 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
889 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
892 final String v = getMyNode().getNodeData().getTaxonomy().getIdentifier().getValue();
893 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( v, value ) );
897 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
898 getMyNode().getNodeData().getSequence().setLocation( value );
901 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
902 getMyNode().getNodeData().getSequence().setMolecularSequence( value.replaceAll( "[^a-zA-Z-]", "" ) );
905 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
906 getMyNode().getNodeData().getSequence().setName( value );
909 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
911 getMyNode().getNodeData().getSequence().setSymbol( value );
913 catch ( final PhyloXmlDataFormatException e ) {
914 formatError( mtn, e );
919 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
920 getMyNode().getNodeData().getSequence().setGeneName( value );
923 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
925 getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
927 catch ( final PhyloXmlDataFormatException e ) {
928 formatError( mtn, e );
933 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
934 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
935 getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
938 final String v = getMyNode().getNodeData().getSequence().getAccession().getValue();
939 getMyNode().getNodeData().getSequence().setAccession( new Accession( v, value ) );
943 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
944 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
945 getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
948 final String source = getMyNode().getNodeData().getSequence().getAccession().getSource();
949 getMyNode().getNodeData().getSequence().setAccession( new Accession( value, source ) );
954 if ( !ForesterUtil.isEmpty( value ) ) {
956 uri = new Uri( new URL( value ).toURI() );
958 catch ( final Exception e ) {
959 JOptionPane.showMessageDialog( this,
960 "failed to parse URL from: " + value,
962 JOptionPane.ERROR_MESSAGE );
963 mtn.setUserObject( "" );
967 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
969 addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
972 case LIT_REFERENCE_DESC:
973 if ( !getMyNode().getNodeData().isHasReference() ) {
974 getMyNode().getNodeData().setReference( new Reference( "" ) );
976 getMyNode().getNodeData().getReference().setValue( value );
978 case LIT_REFERENCE_DOI:
979 if ( !getMyNode().getNodeData().isHasReference() ) {
980 getMyNode().getNodeData().setReference( new Reference( "" ) );
983 getMyNode().getNodeData().getReference().setDoi( value );
985 catch ( final PhyloXmlDataFormatException e ) {
986 formatError( mtn, e );
990 case EVENTS_DUPLICATIONS:
991 if ( !getMyNode().getNodeData().isHasEvent() ) {
992 getMyNode().getNodeData().setEvent( new Event() );
994 getMyNode().getNodeData().getEvent().setDuplications( parsePositiveInt( mtn, value ) );
996 case EVENTS_SPECIATIONS:
997 if ( !getMyNode().getNodeData().isHasEvent() ) {
998 getMyNode().getNodeData().setEvent( new Event() );
1000 getMyNode().getNodeData().getEvent().setSpeciations( parsePositiveInt( mtn, value ) );
1002 case EVENTS_GENE_LOSSES:
1003 if ( !getMyNode().getNodeData().isHasEvent() ) {
1004 getMyNode().getNodeData().setEvent( new Event() );
1006 getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
1008 case DATE_DESCRIPTION:
1009 ForesterUtil.ensurePresenceOfDate( getMyNode() );
1010 getMyNode().getNodeData().getDate().setDesc( value );
1013 ForesterUtil.ensurePresenceOfDate( getMyNode() );
1014 getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
1017 ForesterUtil.ensurePresenceOfDate( getMyNode() );
1018 getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
1021 ForesterUtil.ensurePresenceOfDate( getMyNode() );
1022 getMyNode().getNodeData().getDate().setUnit( value );
1025 ForesterUtil.ensurePresenceOfDate( getMyNode() );
1026 getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
1029 final BigDecimal new_value = parseBigDecimal( mtn, value );
1030 if ( new_value != null ) {
1031 final List<Point> ps = obtainPoints();
1032 final Point p = ps.get( 0 );
1033 final Point p_new = new Point( p.getGeodeticDatum(),
1037 ForesterUtil.isEmpty( p.getAltiudeUnit() ) ? "?"
1038 : p.getAltiudeUnit() );
1044 ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
1045 final Distribution d = getMyNode().getNodeData().getDistribution();
1046 getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
1049 case DIST_GEODETIC: {
1050 if ( !ForesterUtil.isEmpty( value ) ) {
1051 final List<Point> ps = obtainPoints();
1052 final Point p = ps.get( 0 );
1053 final Point p_new = new Point( value,
1057 p.getAltiudeUnit() );
1062 case DIST_ALT_UNIT: {
1063 if ( !ForesterUtil.isEmpty( value ) ) {
1064 final List<Point> ps = obtainPoints();
1065 final Point p = ps.get( 0 );
1066 final Point p_new = new Point( p.getGeodeticDatum(),
1076 final BigDecimal new_value = parseBigDecimal( mtn, value );
1077 if ( new_value != null ) {
1078 final List<Point> ps = obtainPoints();
1079 final Point p = ps.get( 0 );
1080 final Point p_new = new Point( p.getGeodeticDatum(),
1084 p.getAltiudeUnit() );
1090 final BigDecimal new_value = parseBigDecimal( mtn, value );
1091 if ( new_value != null ) {
1092 final List<Point> ps = obtainPoints();
1093 final Point p = ps.get( 0 );
1094 final Point p_new = new Point( p.getGeodeticDatum(),
1098 p.getAltiudeUnit() );
1104 throw new IllegalArgumentException( "unknown: " + tag );
1106 getJTree().repaint();
1107 getTreePanel().setEdited( true );
1108 getTreePanel().repaint();
1111 PhylogenyNode getMyNode() {
1116 for( int i = 0; i < getJTree().getRowCount(); i++ ) {
1117 final TreePath p = getJTree().getPathForRow( i );
1118 writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );