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: www.phylosoft.org/
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.Point;
64 import org.forester.phylogeny.data.Reference;
65 import org.forester.phylogeny.data.Sequence;
66 import org.forester.phylogeny.data.Taxonomy;
67 import org.forester.phylogeny.data.Uri;
68 import org.forester.util.FailedConditionCheckException;
69 import org.forester.util.ForesterUtil;
71 class NodeEditPanel extends JPanel {
73 private static final long serialVersionUID = 5120159904388100771L;
74 private final JTree _tree;
75 private final JEditorPane _pane;
76 private final PhylogenyNode _my_node;
77 private final TreePanel _tree_panel;
78 private final Map<DefaultMutableTreeNode, TagNumber> _map;
80 public NodeEditPanel( final PhylogenyNode phylogeny_node, final TreePanel tree_panel ) {
81 _map = new HashMap<DefaultMutableTreeNode, TagNumber>();
82 _my_node = phylogeny_node;
83 _tree_panel = tree_panel;
84 String node_name = "";
85 if ( !ForesterUtil.isEmpty( phylogeny_node.getName() ) ) {
86 node_name = phylogeny_node.getName() + " ";
88 final DefaultMutableTreeNode top = new DefaultMutableTreeNode( "Node " + node_name );
89 createNodes( top, phylogeny_node );
90 _tree = new JTree( top );
91 getJTree().setEditable( true );
92 getJTree().setFocusable( true );
93 getJTree().setToggleClickCount( 1 );
94 getJTree().setInvokesStopCellEditing( true );
95 final JScrollPane tree_view = new JScrollPane( getJTree() );
96 _pane = new JEditorPane();
97 _pane.setEditable( true );
98 final JScrollPane data_view = new JScrollPane( _pane );
99 final JSplitPane split_pane = new JSplitPane( JSplitPane.VERTICAL_SPLIT );
100 split_pane.setTopComponent( tree_view );
101 // split_pane.setBottomComponent( data_view );
102 data_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
103 tree_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
104 // split_pane.setDividerLocation( 400 );
105 split_pane.setPreferredSize( Constants.NODE_PANEL_SIZE );
107 getJTree().getSelectionModel().setSelectionMode( TreeSelectionModel.SINGLE_TREE_SELECTION );
108 getJTree().addKeyListener( new KeyListener() {
111 public void keyPressed( final KeyEvent e ) {
116 public void keyReleased( final KeyEvent e ) {
121 public void keyTyped( final KeyEvent e ) {
125 for( int i = 0; i < getJTree().getRowCount(); i++ ) {
126 getJTree().expandRow( i );
128 collapsePath( NodePanel.BASIC );
129 collapsePath( NodePanel.TAXONOMY );
130 collapsePath( NodePanel.SEQUENCE );
131 collapsePath( NodePanel.EVENTS );
132 collapsePath( NodePanel.DATE );
133 collapsePath( NodePanel.DISTRIBUTION );
134 collapsePath( NodePanel.LIT_REFERENCE );
135 getJTree().addTreeSelectionListener( new TreeSelectionListener() {
138 public void valueChanged( final TreeSelectionEvent e ) {
139 final TreePath new_path = e.getNewLeadSelectionPath();
140 final TreePath old_path = e.getOldLeadSelectionPath();
141 if ( new_path != null ) {
142 writeBack( ( DefaultMutableTreeNode ) new_path.getLastPathComponent() );
144 if ( old_path != null ) {
145 writeBack( ( DefaultMutableTreeNode ) old_path.getLastPathComponent() );
151 private void addBasics( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node, final String name ) {
152 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
154 addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME );
156 if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
157 bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() );
159 addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH );
161 if ( phylogeny_node.getBranchData().isHasConfidences() ) {
162 for( int i = phylogeny_node.getBranchData().getConfidences().size() - 1; i >= 0; i-- ) {
163 if ( phylogeny_node.getBranchData().getConfidences().get( i ).getValue() == Confidence.CONFIDENCE_DEFAULT_VALUE ) {
164 phylogeny_node.getBranchData().getConfidences().remove( i );
167 for( final PhylogenyData conf : phylogeny_node.getBranchData().getConfidences() ) {
168 final Confidence my_conf = ( Confidence ) ( conf );
169 addSubelementEditable( category,
170 NodePanel.CONFIDENCE + " [" + counter + "]",
171 ForesterUtil.FORMATTER_6.format( my_conf.getValue() ),
172 PHYLOXML_TAG.CONFIDENCE_VALUE,
173 NodePanel.CONFIDENCE_TYPE,
175 PHYLOXML_TAG.CONFIDENCE_TYPE,
179 addSubelementEditable( category,
180 NodePanel.CONFIDENCE + " [" + counter + "]",
182 PHYLOXML_TAG.CONFIDENCE_VALUE,
183 NodePanel.CONFIDENCE_TYPE,
185 PHYLOXML_TAG.CONFIDENCE_TYPE,
188 if ( ( phylogeny_node.getBranchData().getBranchWidth() != null )
189 && ( phylogeny_node.getBranchData().getBranchWidth().getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) ) {
190 bw = ForesterUtil.FORMATTER_3.format( phylogeny_node.getBranchData().getBranchWidth().getValue() );
192 addSubelementEditable( category, NodePanel.NODE_BRANCH_WIDTH, bw, PHYLOXML_TAG.NODE_BRANCH_WIDTH );
195 // private void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) {
196 // DefaultMutableTreeNode category;
197 // category = new DefaultMutableTreeNode( name );
198 // top.add( category );
199 // addSubelementEditable( category, "Reference", ann.getRef() , PHYLOXML_TAG.);
200 // addSubelementEditable( category, "Description", ann.getDesc() , PHYLOXML_TAG.);
201 // addSubelementEditable( category, "Source", ann.getSource(), PHYLOXML_TAG. );
202 // addSubelementEditable( category, "Type", ann.getType(), PHYLOXML_TAG. );
203 // addSubelementEditable( category, "Evidence", ann.getEvidence() , PHYLOXML_TAG.);
204 // if ( ann.getConfidence() != null ) {
205 // addSubelementEditable( category, "Confidence", ann.getConfidence().asText().toString() , PHYLOXML_TAG.);
207 // if ( ann.getProperties() != null ) {
208 // addProperties( category, ann.getProperties(), "Properties", PHYLOXML_TAG. );
211 // private void addAnnotations( final DefaultMutableTreeNode top,
212 // final List<PhylogenyData> annotations,
213 // final DefaultMutableTreeNode category ) {
214 // if ( ( annotations != null ) && ( annotations.size() > 0 ) ) {
215 // category.add( new DefaultMutableTreeNode( "Annotations" ) );
216 // final DefaultMutableTreeNode last = top.getLastLeaf();
218 // for( final PhylogenyData ann : annotations ) {
219 // addAnnotation( last, ( Annotation ) ann, "Annotation " + ( i++ ) );
223 private void addDate( final DefaultMutableTreeNode top, Date date, final String name ) {
224 if ( date == null ) {
227 DefaultMutableTreeNode category;
228 category = new DefaultMutableTreeNode( name );
230 addSubelementEditable( category, NodePanel.DATE_DESCRIPTION, date.getDesc(), PHYLOXML_TAG.DATE_DESCRIPTION );
231 addSubelementEditable( category,
232 NodePanel.DATE_VALUE,
233 String.valueOf( date.getValue() != null ? date.getValue() : "" ),
234 PHYLOXML_TAG.DATE_VALUE );
235 addSubelementEditable( category,
237 String.valueOf( date.getMin() != null ? date.getMin() : "" ),
238 PHYLOXML_TAG.DATE_MIN );
239 addSubelementEditable( category,
241 String.valueOf( date.getMax() != null ? date.getMax() : "" ),
242 PHYLOXML_TAG.DATE_MAX );
243 addSubelementEditable( category, NodePanel.DATE_UNIT, date.getUnit(), PHYLOXML_TAG.DATE_UNIT );
246 private void addDistribution( final DefaultMutableTreeNode top, Distribution dist, final String name ) {
247 if ( dist == null ) {
248 dist = new Distribution( "" );
250 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
253 if ( ( dist.getPoints() != null ) && ( dist.getPoints().size() > 0 ) ) {
254 p0 = dist.getPoints().get( 0 );
259 addSubelementEditable( category, NodePanel.DIST_DESCRIPTION, dist.getDesc(), PHYLOXML_TAG.DIST_DESC );
260 addSubelementEditable( category,
261 NodePanel.DIST_GEODETIC_DATUM,
262 p0.getGeodeticDatum(),
263 PHYLOXML_TAG.DIST_GEODETIC );
264 addSubelementEditable( category,
265 NodePanel.DIST_LATITUDE,
266 String.valueOf( p0.getLatitude() != null ? p0.getLatitude() : "" ),
267 PHYLOXML_TAG.DIST_LAT );
268 addSubelementEditable( category,
269 NodePanel.DIST_LONGITUDE,
270 String.valueOf( p0.getLongitude() != null ? p0.getLongitude() : "" ),
271 PHYLOXML_TAG.DIST_LONG );
272 addSubelementEditable( category,
273 NodePanel.DIST_ALTITUDE,
274 String.valueOf( p0.getAltitude() != null ? p0.getAltitude() : "" ),
275 PHYLOXML_TAG.DIST_ALT );
276 addSubelementEditable( category,
277 NodePanel.DIST_ALT_UNIT,
278 String.valueOf( p0.getAltiudeUnit() != null ? p0.getAltiudeUnit() : "" ),
279 PHYLOXML_TAG.DIST_ALT_UNIT );
282 private void addEvents( final DefaultMutableTreeNode top, Event events, final String name ) {
283 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
284 if ( events == null ) {
285 events = new Event();
288 addSubelementEditable( category,
289 NodePanel.EVENTS_DUPLICATIONS,
290 String.valueOf( events.getNumberOfDuplications() >= 0 ? events.getNumberOfDuplications()
292 PHYLOXML_TAG.EVENTS_DUPLICATIONS );
293 addSubelementEditable( category,
294 NodePanel.EVENTS_SPECIATIONS,
295 String.valueOf( events.getNumberOfSpeciations() >= 0 ? events.getNumberOfSpeciations()
297 PHYLOXML_TAG.EVENTS_SPECIATIONS );
298 addSubelementEditable( category,
299 NodePanel.EVENTS_GENE_LOSSES,
300 String.valueOf( events.getNumberOfGeneLosses() >= 0 ? events.getNumberOfGeneLosses() : 0 ),
301 PHYLOXML_TAG.EVENTS_GENE_LOSSES );
304 private void addMapping( final DefaultMutableTreeNode mtn, final TagNumber tag ) {
305 if ( getMap().containsKey( mtn ) ) {
306 throw new IllegalArgumentException( "key " + mtn + " already present" );
308 if ( getMap().containsValue( tag ) ) {
309 throw new IllegalArgumentException( "value " + tag + " already present" );
311 getMap().put( mtn, tag );
314 private void addReference( final DefaultMutableTreeNode top, Reference ref, final String name ) {
316 ref = new Reference( "" );
318 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
320 addSubelementEditable( category,
321 NodePanel.LIT_REFERENCE_DESC,
322 ref.getDescription(),
323 PHYLOXML_TAG.LIT_REFERENCE_DESC );
324 addSubelementEditable( category, NodePanel.LIT_REFERENCE_DOI, ref.getDoi(), PHYLOXML_TAG.LIT_REFERENCE_DOI );
327 private void addSequence( final DefaultMutableTreeNode top, Sequence seq, final String name ) {
329 seq = new Sequence();
331 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
333 Accession acc = seq.getAccession();
335 acc = new Accession( "", "" );
337 addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME );
338 addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL );
339 addSubelementEditable( category,
340 NodePanel.SEQ_ACCESSION,
342 PHYLOXML_TAG.SEQ_ACC_VALUE,
345 PHYLOXML_TAG.SEQ_ACC_SOURCE );
346 addSubelementEditable( category, NodePanel.SEQ_LOCATION, seq.getLocation(), PHYLOXML_TAG.SEQ_LOCATION );
347 addSubelementEditable( category, NodePanel.SEQ_TYPE, seq.getType(), PHYLOXML_TAG.SEQ_TYPE );
348 addSubelementEditable( category, NodePanel.SEQ_MOL_SEQ, seq.getMolecularSequence(), PHYLOXML_TAG.SEQ_MOL_SEQ );
350 if ( seq.getUris() != null ) {
351 for( final Uri uri : seq.getUris() ) {
353 addSubelementEditable( category, NodePanel.SEQ_URI + " [" + uri_counter + "]", uri.getValue()
354 .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ );
358 addSubelementEditable( category,
359 NodePanel.SEQ_URI + " [" + uri_counter + "]",
361 PHYLOXML_TAG.SEQ_URI,
363 // addAnnotations( top, seq.getAnnotations(), category );
366 private void addSubelementEditable( final DefaultMutableTreeNode node,
369 final PHYLOXML_TAG phyloxml_tag ) {
370 addSubelementEditable( node, name, value, phyloxml_tag, 0 );
373 private void addSubelementEditable( final DefaultMutableTreeNode node,
376 final PHYLOXML_TAG phyloxml_tag,
378 String my_value = value;
379 if ( ForesterUtil.isEmpty( my_value ) ) {
382 final DefaultMutableTreeNode name_node = new DefaultMutableTreeNode( name );
383 final DefaultMutableTreeNode value_node = new DefaultMutableTreeNode( my_value );
384 name_node.add( value_node );
385 node.add( name_node );
386 addMapping( name_node, new TagNumber( phyloxml_tag, number ) );
389 private void addSubelementEditable( final DefaultMutableTreeNode node,
392 final PHYLOXML_TAG phyloxml_value_tag,
393 final String source_name,
394 final String source_value,
395 final PHYLOXML_TAG phyloxml_source_tag ) {
396 addSubelementEditable( node, name, value, phyloxml_value_tag, source_name, source_value, phyloxml_source_tag, 0 );
399 private void addSubelementEditable( final DefaultMutableTreeNode node,
402 final PHYLOXML_TAG phyloxml_value_tag,
403 final String source_name,
404 final String source_value,
405 final PHYLOXML_TAG phyloxml_source_tag,
407 String my_value = value;
408 if ( ForesterUtil.isEmpty( my_value ) ) {
411 String my_source_value = source_value;
412 if ( ForesterUtil.isEmpty( my_source_value ) ) {
413 my_source_value = "";
415 final DefaultMutableTreeNode name_node = new DefaultMutableTreeNode( name );
416 final DefaultMutableTreeNode source_name_node = new DefaultMutableTreeNode( source_name );
417 final DefaultMutableTreeNode source_value_node = new DefaultMutableTreeNode( my_source_value );
418 final DefaultMutableTreeNode value_node = new DefaultMutableTreeNode( my_value );
419 name_node.add( source_name_node );
420 source_name_node.add( source_value_node );
421 name_node.add( value_node );
422 node.add( name_node );
423 addMapping( name_node, new TagNumber( phyloxml_value_tag, number ) );
424 addMapping( source_name_node, new TagNumber( phyloxml_source_tag, number ) );
427 private void addTaxonomy( final DefaultMutableTreeNode top, Taxonomy tax, final String name ) {
429 tax = new Taxonomy();
431 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
433 Identifier id = tax.getIdentifier();
435 id = new Identifier();
437 addSubelementEditable( category,
438 NodePanel.TAXONOMY_IDENTIFIER,
440 PHYLOXML_TAG.TAXONOMY_ID_VALUE,
443 PHYLOXML_TAG.TAXONOMY_ID_PROVIDER );
444 addSubelementEditable( category, NodePanel.TAXONOMY_CODE, tax.getTaxonomyCode(), PHYLOXML_TAG.TAXONOMY_CODE );
445 addSubelementEditable( category,
446 NodePanel.TAXONOMY_SCIENTIFIC_NAME,
447 tax.getScientificName(),
448 PHYLOXML_TAG.TAXONOMY_SCIENTIFIC_NAME );
449 addSubelementEditable( category,
450 NodePanel.TAXONOMY_AUTHORITY,
452 PHYLOXML_TAG.TAXONOMY_AUTHORITY );
453 addSubelementEditable( category,
454 NodePanel.TAXONOMY_COMMON_NAME,
456 PHYLOXML_TAG.TAXONOMY_COMMON_NAME );
457 for( int i = tax.getSynonyms().size() - 1; i >= 0; i-- ) {
458 if ( ForesterUtil.isEmpty( tax.getSynonyms().get( i ) ) ) {
459 tax.getSynonyms().remove( i );
463 for( final String syn : tax.getSynonyms() ) {
464 addSubelementEditable( category,
465 NodePanel.TAXONOMY_SYNONYM + " [" + syn_counter + "]",
467 PHYLOXML_TAG.TAXONOMY_SYNONYM,
470 addSubelementEditable( category,
471 NodePanel.TAXONOMY_SYNONYM + " [" + syn_counter + "]",
473 PHYLOXML_TAG.TAXONOMY_SYNONYM,
475 addSubelementEditable( category, NodePanel.TAXONOMY_RANK, tax.getRank(), PHYLOXML_TAG.TAXONOMY_RANK );
477 if ( tax.getUris() != null ) {
478 for( final Uri uri : tax.getUris() ) {
480 addSubelementEditable( category, NodePanel.TAXONOMY_URI + " [" + uri_counter + "]", uri.getValue()
481 .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ );
485 addSubelementEditable( category,
486 NodePanel.TAXONOMY_URI + " [" + uri_counter + "]",
488 PHYLOXML_TAG.TAXONOMY_URI,
492 private void collapsePath( final String name ) {
493 final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
495 getJTree().collapsePath( tp );
499 private void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {
500 if ( !phylogeny_node.getNodeData().isHasTaxonomy() ) {
501 phylogeny_node.getNodeData().addTaxonomy( new Taxonomy() );
503 if ( !phylogeny_node.getNodeData().isHasSequence() ) {
504 phylogeny_node.getNodeData().addSequence( new Sequence() );
506 if ( !phylogeny_node.getNodeData().isHasDistribution() ) {
507 phylogeny_node.getNodeData().addDistribution( new Distribution( "" ) );
509 if ( !phylogeny_node.getNodeData().isHasReference() ) {
510 phylogeny_node.getNodeData().addReference( new Reference( "" ) );
512 addBasics( top, phylogeny_node, NodePanel.BASIC );
513 addTaxonomy( top, phylogeny_node.getNodeData().getTaxonomy(), NodePanel.TAXONOMY );
514 addSequence( top, phylogeny_node.getNodeData().getSequence(), NodePanel.SEQUENCE );
515 if ( !phylogeny_node.isExternal() ) {
516 addEvents( top, phylogeny_node.getNodeData().getEvent(), NodePanel.EVENTS );
518 addDate( top, phylogeny_node.getNodeData().getDate(), NodePanel.DATE );
519 addDistribution( top, phylogeny_node.getNodeData().getDistribution(), NodePanel.DISTRIBUTION );
520 addReference( top, phylogeny_node.getNodeData().getReference(), NodePanel.LIT_REFERENCE );
521 // addProperties( top, phylogeny_node.getNodeData().getProperties(), "Properties" );
524 private void formatError( final DefaultMutableTreeNode mtn, final PhyloXmlDataFormatException e ) {
525 JOptionPane.showMessageDialog( this, e.getMessage(), "Format error", JOptionPane.ERROR_MESSAGE );
526 mtn.setUserObject( "" );
527 getJTree().repaint();
530 private JTree getJTree() {
534 private Map<DefaultMutableTreeNode, TagNumber> getMap() {
538 private TagNumber getMapping( final DefaultMutableTreeNode mtn ) {
539 return getMap().get( mtn );
542 PhylogenyNode getMyNode() {
546 private DefaultMutableTreeNode getSelectedTreeNode() {
547 final TreePath selectionPath = getJTree().getSelectionPath();
548 if ( selectionPath != null ) {
549 final Object[] path = selectionPath.getPath();
550 if ( path.length > 0 ) {
551 return ( DefaultMutableTreeNode ) path[ path.length - 1 ]; // Last node
557 private TreePanel getTreePanel() {
561 private void keyEvent( final KeyEvent e ) {
562 if ( e.getKeyCode() == KeyEvent.VK_ENTER ) {
563 writeBack( getSelectedTreeNode() );
567 private List<Point> obtainPoints() {
568 ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
569 Distribution d = getMyNode().getNodeData().getDistribution();
570 if ( d.getPoints() == null ) {
571 d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
572 getMyNode().getNodeData().setDistribution( d );
574 final List<Point> ps = d.getPoints();
575 if ( ps.isEmpty() ) {
576 ps.add( new Point() );
578 else if ( ps.get( 0 ) == null ) {
579 ps.set( 0, new Point() );
584 private BigDecimal parseBigDecimal( final DefaultMutableTreeNode mtn, final String value ) {
585 if ( ForesterUtil.isEmpty( value ) ) {
586 return new BigDecimal( 0 );
590 i = new BigDecimal( value );
592 catch ( final NumberFormatException e ) {
593 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
594 mtn.setUserObject( "" );
599 private int parsePositiveInt( final DefaultMutableTreeNode mtn, final String value ) {
600 if ( ForesterUtil.isEmpty( value ) ) {
605 i = ForesterUtil.parseInt( value );
607 catch ( final ParseException e ) {
608 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
609 mtn.setUserObject( "" );
612 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
613 mtn.setUserObject( "" );
619 for( int i = 0; i < getJTree().getRowCount(); i++ ) {
620 final TreePath p = getJTree().getPathForRow( i );
621 writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );
625 private void writeBack( final DefaultMutableTreeNode mtn ) {
626 if ( !getMap().containsKey( mtn ) ) {
627 final DefaultMutableTreeNode parent = ( DefaultMutableTreeNode ) mtn.getParent();
628 if ( getMap().containsKey( parent ) ) {
629 writeBack( mtn, getMapping( parent ) );
634 private void writeBack( final DefaultMutableTreeNode mtn, final TagNumber tag_number ) {
635 if ( tag_number == null ) {
638 String value = mtn.toString();
639 if ( value == null ) {
642 value = value.replaceAll( "\\s+", " " );
643 value = value.trim();
644 mtn.setUserObject( value );
645 getJTree().repaint();
646 final PHYLOXML_TAG tag = tag_number.getTag();
647 final int number = tag_number.getNumber();
650 getMyNode().setName( value );
652 case NODE_BRANCH_LENGTH:
653 if ( ForesterUtil.isEmpty( value ) ) {
654 getMyNode().setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
658 getMyNode().setDistanceToParent( ForesterUtil.parseDouble( value ) );
660 catch ( final ParseException e ) {
661 JOptionPane.showMessageDialog( this,
662 "failed to parse branch length from: " + value,
664 JOptionPane.ERROR_MESSAGE );
665 mtn.setUserObject( "" );
669 case NODE_BRANCH_WIDTH:
670 if ( ForesterUtil.isEmpty( value ) || value.equals( "1" ) ) {
671 if ( getMyNode().getBranchData().getBranchWidth() != null ) {
672 getMyNode().getBranchData().setBranchWidth( new BranchWidth() );
677 final double bw = ForesterUtil.parseDouble( value );
679 getMyNode().getBranchData().setBranchWidth( new BranchWidth( bw ) );
682 catch ( final ParseException e ) {
683 JOptionPane.showMessageDialog( this,
684 "failed to parse branch width from: " + value,
686 JOptionPane.ERROR_MESSAGE );
687 mtn.setUserObject( "" );
691 case CONFIDENCE_VALUE:
692 double confidence = Confidence.CONFIDENCE_DEFAULT_VALUE;
693 if ( !ForesterUtil.isEmpty( value ) ) {
695 confidence = ForesterUtil.parseDouble( value );
697 catch ( final ParseException e ) {
698 JOptionPane.showMessageDialog( this,
699 "failed to parse confidence value from: " + value,
701 JOptionPane.ERROR_MESSAGE );
702 mtn.setUserObject( "" );
706 if ( getMyNode().getBranchData().getConfidences().size() < number ) {
707 throw new FailedConditionCheckException();
709 else if ( getMyNode().getBranchData().getConfidences().size() == number ) {
710 if ( confidence >= 0 ) {
711 getMyNode().getBranchData().getConfidences().add( new Confidence( confidence, "unknown" ) );
715 final String type = getMyNode().getBranchData().getConfidences().get( number ).getType();
716 getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type ) );
719 case CONFIDENCE_TYPE:
720 if ( getMyNode().getBranchData().getConfidences().size() < number ) {
721 throw new FailedConditionCheckException();
723 else if ( getMyNode().getBranchData().getConfidences().size() == number ) {
724 if ( !ForesterUtil.isEmpty( value ) ) {
725 getMyNode().getBranchData().getConfidences().add( new Confidence( 0, value ) );
729 final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue();
730 getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value ) );
734 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
736 getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
738 catch ( final PhyloXmlDataFormatException e ) {
739 formatError( mtn, e );
743 case TAXONOMY_SCIENTIFIC_NAME:
744 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
745 getMyNode().getNodeData().getTaxonomy().setScientificName( value );
747 case TAXONOMY_COMMON_NAME:
748 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
749 getMyNode().getNodeData().getTaxonomy().setCommonName( value );
752 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
754 getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
756 catch ( final PhyloXmlDataFormatException e ) {
757 formatError( mtn, e );
761 case TAXONOMY_AUTHORITY:
762 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
763 getMyNode().getNodeData().getTaxonomy().setAuthority( value );
767 if ( !ForesterUtil.isEmpty( value ) ) {
769 uri = new Uri( new URL( value ).toURI() );
771 catch ( final Exception e ) {
772 JOptionPane.showMessageDialog( this,
773 "failed to parse URL from: " + value,
775 JOptionPane.ERROR_MESSAGE );
776 mtn.setUserObject( "" );
780 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
782 addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
785 case TAXONOMY_SYNONYM:
786 if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() < number ) {
787 throw new FailedConditionCheckException();
789 else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
790 if ( !ForesterUtil.isEmpty( value ) ) {
791 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
792 getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
796 getMyNode().getNodeData().getTaxonomy().getSynonyms().set( number, value );
799 case TAXONOMY_ID_VALUE:
800 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
801 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
802 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
805 final String provider = getMyNode().getNodeData().getTaxonomy().getIdentifier().getProvider();
806 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value, provider ) );
809 case TAXONOMY_ID_PROVIDER:
810 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
811 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
812 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
815 final String v = getMyNode().getNodeData().getTaxonomy().getIdentifier().getValue();
816 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( v, value ) );
820 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
821 getMyNode().getNodeData().getSequence().setLocation( value );
824 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
825 getMyNode().getNodeData().getSequence().setMolecularSequence( value );
828 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
829 getMyNode().getNodeData().getSequence().setName( value );
832 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
834 getMyNode().getNodeData().getSequence().setSymbol( value );
836 catch ( final PhyloXmlDataFormatException e ) {
837 formatError( mtn, e );
842 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
844 getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
846 catch ( final PhyloXmlDataFormatException e ) {
847 formatError( mtn, e );
852 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
853 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
854 getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
857 final String v = getMyNode().getNodeData().getSequence().getAccession().getValue();
858 getMyNode().getNodeData().getSequence().setAccession( new Accession( v, value ) );
862 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
863 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
864 getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
867 final String source = getMyNode().getNodeData().getSequence().getAccession().getSource();
868 getMyNode().getNodeData().getSequence().setAccession( new Accession( value, source ) );
873 if ( !ForesterUtil.isEmpty( value ) ) {
875 uri = new Uri( new URL( value ).toURI() );
877 catch ( final Exception e ) {
878 JOptionPane.showMessageDialog( this,
879 "failed to parse URL from: " + value,
881 JOptionPane.ERROR_MESSAGE );
882 mtn.setUserObject( "" );
886 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
888 addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
891 case LIT_REFERENCE_DESC:
892 if ( !getMyNode().getNodeData().isHasReference() ) {
893 getMyNode().getNodeData().setReference( new Reference( "" ) );
895 getMyNode().getNodeData().getReference().setValue( value );
897 case LIT_REFERENCE_DOI:
898 if ( !getMyNode().getNodeData().isHasReference() ) {
899 getMyNode().getNodeData().setReference( new Reference( "" ) );
902 getMyNode().getNodeData().getReference().setDoi( value );
904 catch ( final PhyloXmlDataFormatException e ) {
905 formatError( mtn, e );
909 case EVENTS_DUPLICATIONS:
910 if ( !getMyNode().getNodeData().isHasEvent() ) {
911 getMyNode().getNodeData().setEvent( new Event() );
913 getMyNode().getNodeData().getEvent().setDuplications( parsePositiveInt( mtn, value ) );
915 case EVENTS_SPECIATIONS:
916 if ( !getMyNode().getNodeData().isHasEvent() ) {
917 getMyNode().getNodeData().setEvent( new Event() );
919 getMyNode().getNodeData().getEvent().setSpeciations( parsePositiveInt( mtn, value ) );
921 case EVENTS_GENE_LOSSES:
922 if ( !getMyNode().getNodeData().isHasEvent() ) {
923 getMyNode().getNodeData().setEvent( new Event() );
925 getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
927 case DATE_DESCRIPTION:
928 ForesterUtil.ensurePresenceOfDate( getMyNode() );
929 getMyNode().getNodeData().getDate().setDesc( value );
932 ForesterUtil.ensurePresenceOfDate( getMyNode() );
933 getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
936 ForesterUtil.ensurePresenceOfDate( getMyNode() );
937 getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
940 ForesterUtil.ensurePresenceOfDate( getMyNode() );
941 getMyNode().getNodeData().getDate().setUnit( value );
944 ForesterUtil.ensurePresenceOfDate( getMyNode() );
945 getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
948 final BigDecimal new_value = parseBigDecimal( mtn, value );
949 if ( new_value != null ) {
950 final List<Point> ps = obtainPoints();
951 final Point p = ps.get( 0 );
952 final Point p_new = new Point( p.getGeodeticDatum(),
956 ForesterUtil.isEmpty( p.getAltiudeUnit() ) ? "?"
957 : p.getAltiudeUnit() );
963 ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
964 final Distribution d = getMyNode().getNodeData().getDistribution();
965 getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
968 case DIST_GEODETIC: {
969 if ( !ForesterUtil.isEmpty( value ) ) {
970 final List<Point> ps = obtainPoints();
971 final Point p = ps.get( 0 );
972 final Point p_new = new Point( value,
976 p.getAltiudeUnit() );
981 case DIST_ALT_UNIT: {
982 if ( !ForesterUtil.isEmpty( value ) ) {
983 final List<Point> ps = obtainPoints();
984 final Point p = ps.get( 0 );
985 final Point p_new = new Point( p.getGeodeticDatum(),
995 final BigDecimal new_value = parseBigDecimal( mtn, value );
996 if ( new_value != null ) {
997 final List<Point> ps = obtainPoints();
998 final Point p = ps.get( 0 );
999 final Point p_new = new Point( p.getGeodeticDatum(),
1003 p.getAltiudeUnit() );
1009 final BigDecimal new_value = parseBigDecimal( mtn, value );
1010 if ( new_value != null ) {
1011 final List<Point> ps = obtainPoints();
1012 final Point p = ps.get( 0 );
1013 final Point p_new = new Point( p.getGeodeticDatum(),
1017 p.getAltiudeUnit() );
1023 throw new IllegalArgumentException( "unknown: " + tag );
1025 getJTree().repaint();
1026 getTreePanel().setEdited( true );
1027 getTreePanel().repaint();
1030 private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
1031 if ( uri != null ) {
1032 if ( mu.getUris() == null ) {
1033 mu.setUris( new ArrayList<Uri>() );
1036 if ( ( uri != null ) && ( mu.getUris() == null ) ) {
1037 mu.setUris( new ArrayList<Uri>() );
1039 if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
1040 mu.getUris().add( uri );
1042 if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
1043 mu.getUris().set( number, uri );
1045 final ImageLoader il = new ImageLoader( getTreePanel() );
1046 new Thread( il ).start();
1049 private enum PHYLOXML_TAG {
1054 TAXONOMY_SCIENTIFIC_NAME,
1056 TAXONOMY_COMMON_NAME,
1072 TAXONOMY_ID_PROVIDER,
1079 EVENTS_DUPLICATIONS,
1090 private class TagNumber {
1092 final private PHYLOXML_TAG _tag;
1093 final private int _number;
1095 TagNumber( final PHYLOXML_TAG tag, final int number ) {
1104 PHYLOXML_TAG getTag() {
1109 public String toString() {
1110 return getTag() + "_" + getNumber();