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.io.parsers.phyloxml.PhyloXmlDataFormatException;
52 import org.forester.phylogeny.PhylogenyNode;
53 import org.forester.phylogeny.data.Accession;
54 import org.forester.phylogeny.data.Confidence;
55 import org.forester.phylogeny.data.Date;
56 import org.forester.phylogeny.data.Distribution;
57 import org.forester.phylogeny.data.Event;
58 import org.forester.phylogeny.data.Identifier;
59 import org.forester.phylogeny.data.MultipleUris;
60 import org.forester.phylogeny.data.PhylogenyData;
61 import org.forester.phylogeny.data.Point;
62 import org.forester.phylogeny.data.Reference;
63 import org.forester.phylogeny.data.Sequence;
64 import org.forester.phylogeny.data.Taxonomy;
65 import org.forester.phylogeny.data.Uri;
66 import org.forester.util.FailedConditionCheckException;
67 import org.forester.util.ForesterUtil;
69 class NodeEditPanel extends JPanel {
71 private static final long serialVersionUID = 5120159904388100771L;
72 private final JTree _tree;
73 private final JEditorPane _pane;
74 private final PhylogenyNode _my_node;
75 private final TreePanel _tree_panel;
76 private final Map<DefaultMutableTreeNode, TagNumber> _map;
78 public NodeEditPanel( final PhylogenyNode phylogeny_node, final TreePanel tree_panel ) {
79 _map = new HashMap<DefaultMutableTreeNode, TagNumber>();
80 _my_node = phylogeny_node;
81 _tree_panel = tree_panel;
82 String node_name = "";
83 if ( !ForesterUtil.isEmpty( phylogeny_node.getName() ) ) {
84 node_name = phylogeny_node.getName() + " ";
86 final DefaultMutableTreeNode top = new DefaultMutableTreeNode( "Node " + node_name );
87 createNodes( top, phylogeny_node );
88 _tree = new JTree( top );
89 getJTree().setEditable( true );
90 getJTree().setFocusable( true );
91 getJTree().setToggleClickCount( 1 );
92 getJTree().setInvokesStopCellEditing( true );
93 final JScrollPane tree_view = new JScrollPane( getJTree() );
94 _pane = new JEditorPane();
95 _pane.setEditable( true );
96 final JScrollPane data_view = new JScrollPane( _pane );
97 final JSplitPane split_pane = new JSplitPane( JSplitPane.VERTICAL_SPLIT );
98 split_pane.setTopComponent( tree_view );
99 // split_pane.setBottomComponent( data_view );
100 data_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
101 tree_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
102 // split_pane.setDividerLocation( 400 );
103 split_pane.setPreferredSize( Constants.NODE_PANEL_SIZE );
105 getJTree().getSelectionModel().setSelectionMode( TreeSelectionModel.SINGLE_TREE_SELECTION );
106 getJTree().addKeyListener( new KeyListener() {
109 public void keyPressed( final KeyEvent e ) {
114 public void keyReleased( final KeyEvent e ) {
119 public void keyTyped( final KeyEvent e ) {
123 for( int i = 0; i < getJTree().getRowCount(); i++ ) {
124 getJTree().expandRow( i );
126 collapsePath( NodePanel.BASIC );
127 collapsePath( NodePanel.TAXONOMY );
128 collapsePath( NodePanel.SEQUENCE );
129 collapsePath( NodePanel.EVENTS );
130 collapsePath( NodePanel.DATE );
131 collapsePath( NodePanel.DISTRIBUTION );
132 collapsePath( NodePanel.LIT_REFERENCE );
133 getJTree().addTreeSelectionListener( new TreeSelectionListener() {
136 public void valueChanged( final TreeSelectionEvent e ) {
137 final TreePath new_path = e.getNewLeadSelectionPath();
138 final TreePath old_path = e.getOldLeadSelectionPath();
139 if ( new_path != null ) {
140 writeBack( ( DefaultMutableTreeNode ) new_path.getLastPathComponent() );
142 if ( old_path != null ) {
143 writeBack( ( DefaultMutableTreeNode ) old_path.getLastPathComponent() );
149 private void addBasics( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node, final String name ) {
150 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
152 addSubelementEditable( category, NodePanel.NODE_NAME, phylogeny_node.getName(), PHYLOXML_TAG.NODE_NAME );
154 if ( phylogeny_node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) {
155 bl = ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() );
157 addSubelementEditable( category, NodePanel.NODE_BRANCH_LENGTH, bl, PHYLOXML_TAG.NODE_BRANCH_LENGTH );
159 if ( phylogeny_node.getBranchData().isHasConfidences() ) {
160 for( int i = phylogeny_node.getBranchData().getConfidences().size() - 1; i >= 0; i-- ) {
161 if ( phylogeny_node.getBranchData().getConfidences().get( i ).getValue() == Confidence.CONFIDENCE_DEFAULT_VALUE ) {
162 phylogeny_node.getBranchData().getConfidences().remove( i );
165 for( final PhylogenyData conf : phylogeny_node.getBranchData().getConfidences() ) {
166 final Confidence my_conf = ( Confidence ) ( conf );
167 addSubelementEditable( category,
168 NodePanel.CONFIDENCE + " [" + counter + "]",
169 ForesterUtil.FORMATTER_6.format( my_conf.getValue() ),
170 PHYLOXML_TAG.CONFIDENCE_VALUE,
171 NodePanel.CONFIDENCE_TYPE,
173 PHYLOXML_TAG.CONFIDENCE_TYPE,
177 addSubelementEditable( category,
178 NodePanel.CONFIDENCE + " [" + counter + "]",
180 PHYLOXML_TAG.CONFIDENCE_VALUE,
181 NodePanel.CONFIDENCE_TYPE,
183 PHYLOXML_TAG.CONFIDENCE_TYPE,
187 // private void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) {
188 // DefaultMutableTreeNode category;
189 // category = new DefaultMutableTreeNode( name );
190 // top.add( category );
191 // addSubelementEditable( category, "Reference", ann.getRef() , PHYLOXML_TAG.);
192 // addSubelementEditable( category, "Description", ann.getDesc() , PHYLOXML_TAG.);
193 // addSubelementEditable( category, "Source", ann.getSource(), PHYLOXML_TAG. );
194 // addSubelementEditable( category, "Type", ann.getType(), PHYLOXML_TAG. );
195 // addSubelementEditable( category, "Evidence", ann.getEvidence() , PHYLOXML_TAG.);
196 // if ( ann.getConfidence() != null ) {
197 // addSubelementEditable( category, "Confidence", ann.getConfidence().asText().toString() , PHYLOXML_TAG.);
199 // if ( ann.getProperties() != null ) {
200 // addProperties( category, ann.getProperties(), "Properties", PHYLOXML_TAG. );
203 // private void addAnnotations( final DefaultMutableTreeNode top,
204 // final List<PhylogenyData> annotations,
205 // final DefaultMutableTreeNode category ) {
206 // if ( ( annotations != null ) && ( annotations.size() > 0 ) ) {
207 // category.add( new DefaultMutableTreeNode( "Annotations" ) );
208 // final DefaultMutableTreeNode last = top.getLastLeaf();
210 // for( final PhylogenyData ann : annotations ) {
211 // addAnnotation( last, ( Annotation ) ann, "Annotation " + ( i++ ) );
215 private void addDate( final DefaultMutableTreeNode top, Date date, final String name ) {
216 if ( date == null ) {
219 DefaultMutableTreeNode category;
220 category = new DefaultMutableTreeNode( name );
222 addSubelementEditable( category, NodePanel.DATE_DESCRIPTION, date.getDesc(), PHYLOXML_TAG.DATE_DESCRIPTION );
223 addSubelementEditable( category, NodePanel.DATE_VALUE, String.valueOf( date.getValue() != null ? date
224 .getValue() : "" ), PHYLOXML_TAG.DATE_VALUE );
225 addSubelementEditable( category, NodePanel.DATE_MIN, String
226 .valueOf( date.getMin() != null ? date.getMin() : "" ), PHYLOXML_TAG.DATE_MIN );
227 addSubelementEditable( category, NodePanel.DATE_MAX, String
228 .valueOf( date.getMax() != null ? date.getMax() : "" ), PHYLOXML_TAG.DATE_MAX );
229 addSubelementEditable( category, NodePanel.DATE_UNIT, date.getUnit(), PHYLOXML_TAG.DATE_UNIT );
232 private void addDistribution( final DefaultMutableTreeNode top, Distribution dist, final String name ) {
233 if ( dist == null ) {
234 dist = new Distribution( "" );
236 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
239 if ( ( dist.getPoints() != null ) && ( dist.getPoints().size() > 0 ) ) {
240 p0 = dist.getPoints().get( 0 );
245 addSubelementEditable( category, NodePanel.DIST_DESCRIPTION, dist.getDesc(), PHYLOXML_TAG.DIST_DESC );
246 addSubelementEditable( category,
247 NodePanel.DIST_GEODETIC_DATUM,
248 p0.getGeodeticDatum(),
249 PHYLOXML_TAG.DIST_GEODETIC );
250 addSubelementEditable( category, NodePanel.DIST_LATITUDE, String.valueOf( p0.getLatitude() != null ? p0
251 .getLatitude() : "" ), PHYLOXML_TAG.DIST_LAT );
252 addSubelementEditable( category, NodePanel.DIST_LONGITUDE, String.valueOf( p0.getLongitude() != null ? p0
253 .getLongitude() : "" ), PHYLOXML_TAG.DIST_LONG );
254 addSubelementEditable( category, NodePanel.DIST_ALTITUDE, String.valueOf( p0.getAltitude() != null ? p0
255 .getAltitude() : "" ), PHYLOXML_TAG.DIST_ALT );
256 addSubelementEditable( category, NodePanel.DIST_ALT_UNIT, String.valueOf( p0.getAltiudeUnit() != null ? p0
257 .getAltiudeUnit() : "" ), PHYLOXML_TAG.DIST_ALT_UNIT );
260 private void addEvents( final DefaultMutableTreeNode top, Event events, final String name ) {
261 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
262 if ( events == null ) {
263 events = new Event();
266 addSubelementEditable( category,
267 NodePanel.EVENTS_DUPLICATIONS,
268 String.valueOf( events.getNumberOfDuplications() >= 0 ? events.getNumberOfDuplications()
270 PHYLOXML_TAG.EVENTS_DUPLICATIONS );
271 addSubelementEditable( category,
272 NodePanel.EVENTS_SPECIATIONS,
273 String.valueOf( events.getNumberOfSpeciations() >= 0 ? events.getNumberOfSpeciations()
275 PHYLOXML_TAG.EVENTS_SPECIATIONS );
276 addSubelementEditable( category,
277 NodePanel.EVENTS_GENE_LOSSES,
279 .valueOf( events.getNumberOfGeneLosses() >= 0 ? events.getNumberOfGeneLosses()
281 PHYLOXML_TAG.EVENTS_GENE_LOSSES );
284 private void addMapping( final DefaultMutableTreeNode mtn, final TagNumber tag ) {
285 if ( getMap().containsKey( mtn ) ) {
286 throw new IllegalArgumentException( "key " + mtn + " already present" );
288 if ( getMap().containsValue( tag ) ) {
289 throw new IllegalArgumentException( "value " + tag + " already present" );
291 getMap().put( mtn, tag );
294 private void addReference( final DefaultMutableTreeNode top, Reference ref, final String name ) {
296 ref = new Reference( "" );
298 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
300 addSubelementEditable( category,
301 NodePanel.LIT_REFERENCE_DESC,
302 ref.getDescription(),
303 PHYLOXML_TAG.LIT_REFERENCE_DESC );
304 addSubelementEditable( category, NodePanel.LIT_REFERENCE_DOI, ref.getDoi(), PHYLOXML_TAG.LIT_REFERENCE_DOI );
307 private void addSequence( final DefaultMutableTreeNode top, Sequence seq, final String name ) {
309 seq = new Sequence();
311 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
313 Accession acc = seq.getAccession();
315 acc = new Accession( "", "" );
317 addSubelementEditable( category, NodePanel.SEQ_NAME, seq.getName(), PHYLOXML_TAG.SEQ_NAME );
318 addSubelementEditable( category, NodePanel.SEQ_SYMBOL, seq.getSymbol(), PHYLOXML_TAG.SEQ_SYMBOL );
319 addSubelementEditable( category,
320 NodePanel.SEQ_ACCESSION,
322 PHYLOXML_TAG.SEQ_ACC_VALUE,
325 PHYLOXML_TAG.SEQ_ACC_SOURCE );
326 addSubelementEditable( category, NodePanel.SEQ_LOCATION, seq.getLocation(), PHYLOXML_TAG.SEQ_LOCATION );
327 addSubelementEditable( category, NodePanel.SEQ_TYPE, seq.getType(), PHYLOXML_TAG.SEQ_TYPE );
328 addSubelementEditable( category, NodePanel.SEQ_MOL_SEQ, seq.getMolecularSequence(), PHYLOXML_TAG.SEQ_MOL_SEQ );
330 if ( seq.getUris() != null ) {
331 for( final Uri uri : seq.getUris() ) {
333 addSubelementEditable( category, NodePanel.SEQ_URI + " [" + uri_counter + "]", uri.getValue()
334 .toString(), PHYLOXML_TAG.SEQ_URI, uri_counter++ );
338 addSubelementEditable( category,
339 NodePanel.SEQ_URI + " [" + uri_counter + "]",
341 PHYLOXML_TAG.SEQ_URI,
343 // addAnnotations( top, seq.getAnnotations(), category );
346 private void addSubelementEditable( final DefaultMutableTreeNode node,
349 final PHYLOXML_TAG phyloxml_tag ) {
350 addSubelementEditable( node, name, value, phyloxml_tag, 0 );
353 private void addSubelementEditable( final DefaultMutableTreeNode node,
356 final PHYLOXML_TAG phyloxml_tag,
358 String my_value = value;
359 if ( ForesterUtil.isEmpty( my_value ) ) {
362 final DefaultMutableTreeNode name_node = new DefaultMutableTreeNode( name );
363 final DefaultMutableTreeNode value_node = new DefaultMutableTreeNode( my_value );
364 name_node.add( value_node );
365 node.add( name_node );
366 addMapping( name_node, new TagNumber( phyloxml_tag, number ) );
369 private void addSubelementEditable( final DefaultMutableTreeNode node,
372 final PHYLOXML_TAG phyloxml_value_tag,
373 final String source_name,
374 final String source_value,
375 final PHYLOXML_TAG phyloxml_source_tag ) {
376 addSubelementEditable( node, name, value, phyloxml_value_tag, source_name, source_value, phyloxml_source_tag, 0 );
379 private void addSubelementEditable( final DefaultMutableTreeNode node,
382 final PHYLOXML_TAG phyloxml_value_tag,
383 final String source_name,
384 final String source_value,
385 final PHYLOXML_TAG phyloxml_source_tag,
387 String my_value = value;
388 if ( ForesterUtil.isEmpty( my_value ) ) {
391 String my_source_value = source_value;
392 if ( ForesterUtil.isEmpty( my_source_value ) ) {
393 my_source_value = "";
395 final DefaultMutableTreeNode name_node = new DefaultMutableTreeNode( name );
396 final DefaultMutableTreeNode source_name_node = new DefaultMutableTreeNode( source_name );
397 final DefaultMutableTreeNode source_value_node = new DefaultMutableTreeNode( my_source_value );
398 final DefaultMutableTreeNode value_node = new DefaultMutableTreeNode( my_value );
399 name_node.add( source_name_node );
400 source_name_node.add( source_value_node );
401 name_node.add( value_node );
402 node.add( name_node );
403 addMapping( name_node, new TagNumber( phyloxml_value_tag, number ) );
404 addMapping( source_name_node, new TagNumber( phyloxml_source_tag, number ) );
407 private void addTaxonomy( final DefaultMutableTreeNode top, Taxonomy tax, final String name ) {
409 tax = new Taxonomy();
411 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
413 Identifier id = tax.getIdentifier();
415 id = new Identifier();
417 addSubelementEditable( category,
418 NodePanel.TAXONOMY_IDENTIFIER,
420 PHYLOXML_TAG.TAXONOMY_ID_VALUE,
423 PHYLOXML_TAG.TAXONOMY_ID_PROVIDER );
424 addSubelementEditable( category, NodePanel.TAXONOMY_CODE, tax.getTaxonomyCode(), PHYLOXML_TAG.TAXONOMY_CODE );
425 addSubelementEditable( category,
426 NodePanel.TAXONOMY_SCIENTIFIC_NAME,
427 tax.getScientificName(),
428 PHYLOXML_TAG.TAXONOMY_SCIENTIFIC_NAME );
429 addSubelementEditable( category,
430 NodePanel.TAXONOMY_AUTHORITY,
432 PHYLOXML_TAG.TAXONOMY_AUTHORITY );
433 addSubelementEditable( category,
434 NodePanel.TAXONOMY_COMMON_NAME,
436 PHYLOXML_TAG.TAXONOMY_COMMON_NAME );
437 for( int i = tax.getSynonyms().size() - 1; i >= 0; i-- ) {
438 if ( ForesterUtil.isEmpty( tax.getSynonyms().get( i ) ) ) {
439 tax.getSynonyms().remove( i );
443 for( final String syn : tax.getSynonyms() ) {
444 addSubelementEditable( category,
445 NodePanel.TAXONOMY_SYNONYM + " [" + syn_counter + "]",
447 PHYLOXML_TAG.TAXONOMY_SYNONYM,
450 addSubelementEditable( category,
451 NodePanel.TAXONOMY_SYNONYM + " [" + syn_counter + "]",
453 PHYLOXML_TAG.TAXONOMY_SYNONYM,
455 addSubelementEditable( category, NodePanel.TAXONOMY_RANK, tax.getRank(), PHYLOXML_TAG.TAXONOMY_RANK );
457 if ( tax.getUris() != null ) {
458 for( final Uri uri : tax.getUris() ) {
460 addSubelementEditable( category, NodePanel.TAXONOMY_URI + " [" + uri_counter + "]", uri.getValue()
461 .toString(), PHYLOXML_TAG.TAXONOMY_URI, uri_counter++ );
465 addSubelementEditable( category,
466 NodePanel.TAXONOMY_URI + " [" + uri_counter + "]",
468 PHYLOXML_TAG.TAXONOMY_URI,
472 private void collapsePath( final String name ) {
473 final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
475 getJTree().collapsePath( tp );
479 private void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {
480 if ( !phylogeny_node.getNodeData().isHasTaxonomy() ) {
481 phylogeny_node.getNodeData().addTaxonomy( new Taxonomy() );
483 if ( !phylogeny_node.getNodeData().isHasSequence() ) {
484 phylogeny_node.getNodeData().addSequence( new Sequence() );
486 if ( !phylogeny_node.getNodeData().isHasDistribution() ) {
487 phylogeny_node.getNodeData().addDistribution( new Distribution( "" ) );
489 if ( !phylogeny_node.getNodeData().isHasReference() ) {
490 phylogeny_node.getNodeData().addReference( new Reference( "" ) );
492 addBasics( top, phylogeny_node, NodePanel.BASIC );
493 addTaxonomy( top, phylogeny_node.getNodeData().getTaxonomy(), NodePanel.TAXONOMY );
494 addSequence( top, phylogeny_node.getNodeData().getSequence(), NodePanel.SEQUENCE );
495 if ( !phylogeny_node.isExternal() ) {
496 addEvents( top, phylogeny_node.getNodeData().getEvent(), NodePanel.EVENTS );
498 addDate( top, phylogeny_node.getNodeData().getDate(), NodePanel.DATE );
499 addDistribution( top, phylogeny_node.getNodeData().getDistribution(), NodePanel.DISTRIBUTION );
500 addReference( top, phylogeny_node.getNodeData().getReference(), NodePanel.LIT_REFERENCE );
501 // addProperties( top, phylogeny_node.getNodeData().getProperties(), "Properties" );
504 private void formatError( final DefaultMutableTreeNode mtn, final PhyloXmlDataFormatException e ) {
505 JOptionPane.showMessageDialog( this, e.getMessage(), "Format error", JOptionPane.ERROR_MESSAGE );
506 mtn.setUserObject( "" );
507 getJTree().repaint();
510 private JTree getJTree() {
514 private Map<DefaultMutableTreeNode, TagNumber> getMap() {
518 private TagNumber getMapping( final DefaultMutableTreeNode mtn ) {
519 return getMap().get( mtn );
522 PhylogenyNode getMyNode() {
526 private DefaultMutableTreeNode getSelectedTreeNode() {
527 final TreePath selectionPath = getJTree().getSelectionPath();
528 if ( selectionPath != null ) {
529 final Object[] path = selectionPath.getPath();
530 if ( path.length > 0 ) {
531 return ( DefaultMutableTreeNode ) path[ path.length - 1 ]; // Last node
537 private TreePanel getTreePanel() {
541 private void keyEvent( final KeyEvent e ) {
542 if ( e.getKeyCode() == KeyEvent.VK_ENTER ) {
543 writeBack( getSelectedTreeNode() );
547 private List<Point> obtainPoints() {
548 ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
549 Distribution d = getMyNode().getNodeData().getDistribution();
550 if ( d.getPoints() == null ) {
551 d = new Distribution( d.getDesc(), new ArrayList<Point>(), d.getPolygons() );
552 getMyNode().getNodeData().setDistribution( d );
554 final List<Point> ps = d.getPoints();
555 if ( ps.isEmpty() ) {
556 ps.add( new Point() );
558 else if ( ps.get( 0 ) == null ) {
559 ps.set( 0, new Point() );
564 private BigDecimal parseBigDecimal( final DefaultMutableTreeNode mtn, final String value ) {
565 if ( ForesterUtil.isEmpty( value ) ) {
566 return new BigDecimal( 0 );
570 i = new BigDecimal( value );
572 catch ( final NumberFormatException e ) {
573 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
574 mtn.setUserObject( "" );
579 private int parsePositiveInt( final DefaultMutableTreeNode mtn, final String value ) {
580 if ( ForesterUtil.isEmpty( value ) ) {
585 i = ForesterUtil.parseInt( value );
587 catch ( final ParseException e ) {
588 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
589 mtn.setUserObject( "" );
592 JOptionPane.showMessageDialog( this, "illegal value: " + value, "Error", JOptionPane.ERROR_MESSAGE );
593 mtn.setUserObject( "" );
599 for( int i = 0; i < getJTree().getRowCount(); i++ ) {
600 final TreePath p = getJTree().getPathForRow( i );
601 writeBack( ( DefaultMutableTreeNode ) p.getLastPathComponent() );
605 private void writeBack( final DefaultMutableTreeNode mtn ) {
606 if ( !getMap().containsKey( mtn ) ) {
607 final DefaultMutableTreeNode parent = ( DefaultMutableTreeNode ) mtn.getParent();
608 if ( getMap().containsKey( parent ) ) {
609 writeBack( mtn, getMapping( parent ) );
614 private void writeBack( final DefaultMutableTreeNode mtn, final TagNumber tag_number ) {
615 if ( tag_number == null ) {
618 String value = mtn.toString();
619 if ( value == null ) {
622 value = value.replaceAll( "\\s+", " " );
623 value = value.trim();
624 mtn.setUserObject( value );
625 getJTree().repaint();
626 final PHYLOXML_TAG tag = tag_number.getTag();
627 final int number = tag_number.getNumber();
630 getMyNode().setName( value );
632 case NODE_BRANCH_LENGTH:
633 if ( ForesterUtil.isEmpty( value ) ) {
634 getMyNode().setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
638 getMyNode().setDistanceToParent( ForesterUtil.parseDouble( value ) );
640 catch ( final ParseException e ) {
641 JOptionPane.showMessageDialog( this,
642 "failed to parse branch length from: " + value,
644 JOptionPane.ERROR_MESSAGE );
645 mtn.setUserObject( "" );
649 case CONFIDENCE_VALUE:
650 double confidence = Confidence.CONFIDENCE_DEFAULT_VALUE;
651 if ( !ForesterUtil.isEmpty( value ) ) {
653 confidence = ForesterUtil.parseDouble( value );
655 catch ( final ParseException e ) {
656 JOptionPane.showMessageDialog( this,
657 "failed to parse confidence value from: " + value,
659 JOptionPane.ERROR_MESSAGE );
660 mtn.setUserObject( "" );
664 if ( getMyNode().getBranchData().getConfidences().size() < number ) {
665 throw new FailedConditionCheckException();
667 else if ( getMyNode().getBranchData().getConfidences().size() == number ) {
668 if ( confidence >= 0 ) {
669 getMyNode().getBranchData().getConfidences().add( new Confidence( confidence, "unknown" ) );
673 final String type = getMyNode().getBranchData().getConfidences().get( number ).getType();
674 getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type ) );
677 case CONFIDENCE_TYPE:
678 if ( getMyNode().getBranchData().getConfidences().size() < number ) {
679 throw new FailedConditionCheckException();
681 else if ( getMyNode().getBranchData().getConfidences().size() == number ) {
682 if ( !ForesterUtil.isEmpty( value ) ) {
683 getMyNode().getBranchData().getConfidences().add( new Confidence( 0, value ) );
687 final double v = getMyNode().getBranchData().getConfidences().get( number ).getValue();
688 getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value ) );
692 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
694 getMyNode().getNodeData().getTaxonomy().setTaxonomyCode( value );
696 catch ( final PhyloXmlDataFormatException e ) {
697 formatError( mtn, e );
701 case TAXONOMY_SCIENTIFIC_NAME:
702 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
703 getMyNode().getNodeData().getTaxonomy().setScientificName( value );
705 case TAXONOMY_COMMON_NAME:
706 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
707 getMyNode().getNodeData().getTaxonomy().setCommonName( value );
710 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
712 getMyNode().getNodeData().getTaxonomy().setRank( value.toLowerCase() );
714 catch ( final PhyloXmlDataFormatException e ) {
715 formatError( mtn, e );
719 case TAXONOMY_AUTHORITY:
720 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
721 getMyNode().getNodeData().getTaxonomy().setAuthority( value );
725 if ( !ForesterUtil.isEmpty( value ) ) {
727 uri = new Uri( new URL( value ).toURI() );
729 catch ( final Exception e ) {
730 JOptionPane.showMessageDialog( this,
731 "failed to parse URL from: " + value,
733 JOptionPane.ERROR_MESSAGE );
734 mtn.setUserObject( "" );
738 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
740 addUri( mtn, uri, number, getMyNode().getNodeData().getTaxonomy() );
743 case TAXONOMY_SYNONYM:
744 if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() < number ) {
745 throw new FailedConditionCheckException();
747 else if ( getMyNode().getNodeData().getTaxonomy().getSynonyms().size() == number ) {
748 if ( !ForesterUtil.isEmpty( value ) ) {
749 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
750 getMyNode().getNodeData().getTaxonomy().getSynonyms().add( value );
754 getMyNode().getNodeData().getTaxonomy().getSynonyms().set( number, value );
757 case TAXONOMY_ID_VALUE:
758 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
759 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
760 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value ) );
763 final String provider = getMyNode().getNodeData().getTaxonomy().getIdentifier().getProvider();
764 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( value, provider ) );
767 case TAXONOMY_ID_PROVIDER:
768 ForesterUtil.ensurePresenceOfTaxonomy( getMyNode() );
769 if ( getMyNode().getNodeData().getTaxonomy().getIdentifier() == null ) {
770 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( "", value ) );
773 final String v = getMyNode().getNodeData().getTaxonomy().getIdentifier().getValue();
774 getMyNode().getNodeData().getTaxonomy().setIdentifier( new Identifier( v, value ) );
778 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
779 getMyNode().getNodeData().getSequence().setLocation( value );
782 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
783 getMyNode().getNodeData().getSequence().setMolecularSequence( value );
786 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
787 getMyNode().getNodeData().getSequence().setName( value );
790 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
792 getMyNode().getNodeData().getSequence().setSymbol( value );
794 catch ( final PhyloXmlDataFormatException e ) {
795 formatError( mtn, e );
800 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
802 getMyNode().getNodeData().getSequence().setType( value.toLowerCase() );
804 catch ( final PhyloXmlDataFormatException e ) {
805 formatError( mtn, e );
810 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
811 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
812 getMyNode().getNodeData().getSequence().setAccession( new Accession( "", value ) );
815 final String v = getMyNode().getNodeData().getSequence().getAccession().getValue();
816 getMyNode().getNodeData().getSequence().setAccession( new Accession( v, value ) );
820 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
821 if ( getMyNode().getNodeData().getSequence().getAccession() == null ) {
822 getMyNode().getNodeData().getSequence().setAccession( new Accession( value, "" ) );
825 final String source = getMyNode().getNodeData().getSequence().getAccession().getSource();
826 getMyNode().getNodeData().getSequence().setAccession( new Accession( value, source ) );
831 if ( !ForesterUtil.isEmpty( value ) ) {
833 uri = new Uri( new URL( value ).toURI() );
835 catch ( final Exception e ) {
836 JOptionPane.showMessageDialog( this,
837 "failed to parse URL from: " + value,
839 JOptionPane.ERROR_MESSAGE );
840 mtn.setUserObject( "" );
844 ForesterUtil.ensurePresenceOfSequence( getMyNode() );
846 addUri( mtn, uri, number, getMyNode().getNodeData().getSequence() );
849 case LIT_REFERENCE_DESC:
850 if ( !getMyNode().getNodeData().isHasReference() ) {
851 getMyNode().getNodeData().setReference( new Reference( "" ) );
853 getMyNode().getNodeData().getReference().setValue( value );
855 case LIT_REFERENCE_DOI:
856 if ( !getMyNode().getNodeData().isHasReference() ) {
857 getMyNode().getNodeData().setReference( new Reference( "" ) );
860 getMyNode().getNodeData().getReference().setDoi( value );
862 catch ( final PhyloXmlDataFormatException e ) {
863 formatError( mtn, e );
867 case EVENTS_DUPLICATIONS:
868 if ( !getMyNode().getNodeData().isHasEvent() ) {
869 getMyNode().getNodeData().setEvent( new Event() );
871 getMyNode().getNodeData().getEvent().setDuplications( parsePositiveInt( mtn, value ) );
873 case EVENTS_SPECIATIONS:
874 if ( !getMyNode().getNodeData().isHasEvent() ) {
875 getMyNode().getNodeData().setEvent( new Event() );
877 getMyNode().getNodeData().getEvent().setSpeciations( parsePositiveInt( mtn, value ) );
879 case EVENTS_GENE_LOSSES:
880 if ( !getMyNode().getNodeData().isHasEvent() ) {
881 getMyNode().getNodeData().setEvent( new Event() );
883 getMyNode().getNodeData().getEvent().setGeneLosses( parsePositiveInt( mtn, value ) );
885 case DATE_DESCRIPTION:
886 ForesterUtil.ensurePresenceOfDate( getMyNode() );
887 getMyNode().getNodeData().getDate().setDesc( value );
890 ForesterUtil.ensurePresenceOfDate( getMyNode() );
891 getMyNode().getNodeData().getDate().setMax( parseBigDecimal( mtn, value ) );
894 ForesterUtil.ensurePresenceOfDate( getMyNode() );
895 getMyNode().getNodeData().getDate().setMin( parseBigDecimal( mtn, value ) );
898 ForesterUtil.ensurePresenceOfDate( getMyNode() );
899 getMyNode().getNodeData().getDate().setUnit( value );
902 ForesterUtil.ensurePresenceOfDate( getMyNode() );
903 getMyNode().getNodeData().getDate().setValue( parseBigDecimal( mtn, value ) );
906 final BigDecimal new_value = parseBigDecimal( mtn, value );
907 if ( new_value != null ) {
908 final List<Point> ps = obtainPoints();
909 final Point p = ps.get( 0 );
910 final Point p_new = new Point( p.getGeodeticDatum(),
914 ForesterUtil.isEmpty( p.getAltiudeUnit() ) ? "?" : p
921 ForesterUtil.ensurePresenceOfDistribution( getMyNode() );
922 final Distribution d = getMyNode().getNodeData().getDistribution();
923 getMyNode().getNodeData().setDistribution( new Distribution( value, d.getPoints(), d.getPolygons() ) );
926 case DIST_GEODETIC: {
927 if ( !ForesterUtil.isEmpty( value ) ) {
928 final List<Point> ps = obtainPoints();
929 final Point p = ps.get( 0 );
930 final Point p_new = new Point( value, p.getLatitude(), p.getLongitude(), p.getAltitude(), p
936 case DIST_ALT_UNIT: {
937 if ( !ForesterUtil.isEmpty( value ) ) {
938 final List<Point> ps = obtainPoints();
939 final Point p = ps.get( 0 );
940 final Point p_new = new Point( p.getGeodeticDatum(), p.getLatitude(), p.getLongitude(), p
941 .getAltitude(), value );
947 final BigDecimal new_value = parseBigDecimal( mtn, value );
948 if ( new_value != null ) {
949 final List<Point> ps = obtainPoints();
950 final Point p = ps.get( 0 );
951 final Point p_new = new Point( p.getGeodeticDatum(),
955 p.getAltiudeUnit() );
961 final BigDecimal new_value = parseBigDecimal( mtn, value );
962 if ( new_value != null ) {
963 final List<Point> ps = obtainPoints();
964 final Point p = ps.get( 0 );
965 final Point p_new = new Point( p.getGeodeticDatum(), p.getLatitude(), new_value, p.getAltitude(), p
972 throw new IllegalArgumentException( "unknown: " + tag );
974 getJTree().repaint();
975 getTreePanel().setEdited( true );
976 getTreePanel().repaint();
979 private void addUri( final DefaultMutableTreeNode mtn, final Uri uri, final int number, final MultipleUris mu ) {
981 if ( mu.getUris() == null ) {
982 mu.setUris( new ArrayList<Uri>() );
985 if ( ( uri != null ) && ( mu.getUris() == null ) ) {
986 mu.setUris( new ArrayList<Uri>() );
988 if ( ( uri != null ) && ( mu.getUris().size() == number ) ) {
989 mu.getUris().add( uri );
991 if ( ( mu.getUris() != null ) && ( mu.getUris().size() != number ) ) {
992 mu.getUris().set( number, uri );
994 final ImageLoader il = new ImageLoader( getTreePanel() );
995 new Thread( il ).start();
998 private enum PHYLOXML_TAG {
1002 TAXONOMY_SCIENTIFIC_NAME,
1004 TAXONOMY_COMMON_NAME,
1020 TAXONOMY_ID_PROVIDER,
1027 EVENTS_DUPLICATIONS,
1038 private class TagNumber {
1040 final private PHYLOXML_TAG _tag;
1041 final private int _number;
1043 TagNumber( final PHYLOXML_TAG tag, final int number ) {
1052 PHYLOXML_TAG getTag() {
1057 public String toString() {
1058 return getTag() + "_" + getNumber();