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.Color;
29 import java.util.List;
31 import java.util.SortedMap;
32 import java.util.SortedSet;
34 import javax.swing.JEditorPane;
35 import javax.swing.JPanel;
36 import javax.swing.JScrollPane;
37 import javax.swing.JSplitPane;
38 import javax.swing.JTree;
39 import javax.swing.event.TreeSelectionEvent;
40 import javax.swing.event.TreeSelectionListener;
41 import javax.swing.text.Position;
42 import javax.swing.tree.DefaultMutableTreeNode;
43 import javax.swing.tree.TreePath;
45 import org.forester.phylogeny.PhylogenyMethods;
46 import org.forester.phylogeny.PhylogenyNode;
47 import org.forester.phylogeny.data.Accession;
48 import org.forester.phylogeny.data.Annotation;
49 import org.forester.phylogeny.data.BinaryCharacters;
50 import org.forester.phylogeny.data.BranchWidth;
51 import org.forester.phylogeny.data.Date;
52 import org.forester.phylogeny.data.Distribution;
53 import org.forester.phylogeny.data.Event;
54 import org.forester.phylogeny.data.PhylogenyData;
55 import org.forester.phylogeny.data.PhylogenyDataUtil;
56 import org.forester.phylogeny.data.Point;
57 import org.forester.phylogeny.data.PropertiesMap;
58 import org.forester.phylogeny.data.Property;
59 import org.forester.phylogeny.data.Reference;
60 import org.forester.phylogeny.data.Sequence;
61 import org.forester.phylogeny.data.Taxonomy;
62 import org.forester.phylogeny.data.Uri;
63 import org.forester.util.ForesterUtil;
65 class NodePanel extends JPanel implements TreeSelectionListener {
67 static final String BASIC = "Basic";
68 static final String BINARY_CHARACTERS = "Binary characters";
69 static final String CONFIDENCE = "Confidence";
70 static final String CONFIDENCE_TYPE = "type";
71 static final String DATE = "Date";
72 static final String DATE_DESCRIPTION = "Description";
73 static final String DATE_MAX = "Max";
74 static final String DATE_MIN = "Min";
75 static final String DATE_UNIT = "Unit";
76 static final String DATE_VALUE = "Value";
77 static final String DIST_ALT_UNIT = "Altitude unit";
78 static final String DIST_ALTITUDE = "Altitude";
79 static final String DIST_DESCRIPTION = "Description";
80 static final String DIST_GEODETIC_DATUM = "Geodetic datum";
81 static final String DIST_LATITUDE = "Latitude";
82 static final String DIST_LONGITUDE = "Longitude";
83 static final String DISTRIBUTION = "Distribution";
84 static final String EVENTS = "Events";
85 static final String EVENTS_DUPLICATIONS = "Duplications";
86 static final String EVENTS_GENE_LOSSES = "Gene losses";
87 static final String EVENTS_SPECIATIONS = "Speciations";
88 static final String LIT_REFERENCE = "Reference";
89 static final String LIT_REFERENCE_DESC = "Description";
90 static final String LIT_REFERENCE_DOI = "DOI";
91 static final String NODE_BRANCH_COLOR = "Branch color";
92 static final String NODE_BRANCH_LENGTH = "Branch length";
93 static final String NODE_BRANCH_WIDTH = "Branch width";
94 static final String NODE_NAME = "Name";
95 static final String PROP = "Properties";
96 static final String REFERENCE = "Reference";
97 static final String SEQ_ACCESSION = "Accession";
98 static final String SEQ_LOCATION = "Location";
99 static final String SEQ_MOL_SEQ = "Mol seq";
100 static final String SEQ_NAME = "Name";
101 static final String SEQ_SYMBOL = "Symbol";
102 static final String SEQ_GENE_NAME = "Gene name";
103 static final String SEQ_TYPE = "Type";
104 static final String SEQ_URI = "URI";
105 static final String SEQUENCE = "Sequence";
106 static final String TAXONOMY = "Taxonomy";
107 static final String TAXONOMY_AUTHORITY = "Authority";
108 static final String TAXONOMY_CODE = "Code";
109 static final String TAXONOMY_COMMON_NAME = "Common name";
110 static final String TAXONOMY_IDENTIFIER = "Identifier";
111 static final String TAXONOMY_RANK = "Rank";
112 static final String TAXONOMY_SCIENTIFIC_NAME = "Scientific name";
113 static final String TAXONOMY_SYNONYM = "Synonym";
114 static final String TAXONOMY_URI = "URI";
115 private static final long serialVersionUID = 5120159904388100771L;
116 private final JEditorPane _pane;
117 private final JTree _tree;
119 public NodePanel( final PhylogenyNode phylogeny_node ) {
120 String node_name = "";
121 if ( !ForesterUtil.isEmpty( phylogeny_node.getName() ) ) {
122 node_name = phylogeny_node.getName() + " ";
124 final DefaultMutableTreeNode top = new DefaultMutableTreeNode( "Node " + node_name );
125 createNodes( top, phylogeny_node );
126 _tree = new JTree( top );
127 _tree.setEditable( false );
128 getJTree().setToggleClickCount( 1 );
130 expandPath( TAXONOMY );
131 expandPath( SEQUENCE );
132 expandPath( EVENTS );
133 final JScrollPane tree_view = new JScrollPane( getJTree() );
134 _pane = new JEditorPane();
135 _pane.setEditable( false );
136 final JScrollPane data_view = new JScrollPane( _pane );
137 final JSplitPane split_pane = new JSplitPane( JSplitPane.VERTICAL_SPLIT );
138 split_pane.setTopComponent( tree_view );
139 split_pane.setBottomComponent( data_view );
140 data_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
141 tree_view.setMinimumSize( Constants.NODE_PANEL_SPLIT_MINIMUM_SIZE );
142 split_pane.setDividerLocation( 400 );
143 split_pane.setPreferredSize( Constants.NODE_PANEL_SIZE );
148 public void valueChanged( final TreeSelectionEvent e ) {
152 private void expandPath( final String name ) {
153 final TreePath tp = getJTree().getNextMatch( name, 0, Position.Bias.Forward );
155 getJTree().expandPath( tp );
159 private JTree getJTree() {
163 private static void addAnnotation( final DefaultMutableTreeNode top, final Annotation ann, final String name ) {
164 DefaultMutableTreeNode category;
165 category = new DefaultMutableTreeNode( name );
167 addSubelement( category, "Source", ann.getSource() );
168 addSubelement( category, "Type", ann.getType() );
169 addSubelement( category, "Evidence", ann.getEvidence() );
170 if ( ann.getConfidence() != null ) {
171 addSubelement( category, CONFIDENCE, ann.getConfidence().asText().toString() );
173 if ( ann.getProperties() != null ) {
174 addProperties( category, ann.getProperties(), PROP );
178 private static void addAnnotations( final DefaultMutableTreeNode top,
179 final SortedSet<Annotation> annotations,
180 final DefaultMutableTreeNode category ) {
181 if ( ( annotations != null ) && ( annotations.size() > 0 ) ) {
182 category.add( new DefaultMutableTreeNode( "Annotations" ) );
183 final DefaultMutableTreeNode last = top.getLastLeaf();
184 for( final Annotation ann : annotations ) {
185 addAnnotation( last, ann, ann.asText().toString() );
190 private static void addBasics( final DefaultMutableTreeNode top,
191 final PhylogenyNode phylogeny_node,
192 final String name ) {
193 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
195 addSubelement( category, NODE_NAME, phylogeny_node.getName() );
196 if ( phylogeny_node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) {
197 addSubelement( category,
199 ForesterUtil.FORMATTER_6.format( phylogeny_node.getDistanceToParent() ) );
201 if ( phylogeny_node.getBranchData().isHasConfidences() ) {
202 for( final PhylogenyData conf : phylogeny_node.getBranchData().getConfidences() ) {
203 addSubelement( category, CONFIDENCE, conf.asText().toString() );
206 if ( !phylogeny_node.isExternal() ) {
207 addSubelement( category, "Children", String.valueOf( phylogeny_node.getNumberOfDescendants() ) );
208 addSubelement( category,
210 String.valueOf( phylogeny_node.getAllExternalDescendants().size() ) );
211 final Map<Taxonomy, Integer> distinct_tax = PhylogenyMethods.obtainDistinctTaxonomyCounts( phylogeny_node );
212 if ( distinct_tax != null ) {
213 final int no_tax = PhylogenyMethods.calculateNumberOfExternalNodesWithoutTaxonomy( phylogeny_node );
214 final int tax_count = distinct_tax.size();
215 addSubelement( category, "Distinct external taxonomies", String.valueOf( tax_count ) );
217 addSubelement( category, "External nodes without taxonomy", String.valueOf( no_tax ) );
221 if ( !phylogeny_node.isRoot() ) {
222 addSubelement( category, "Depth", String.valueOf( phylogeny_node.calculateDepth() ) );
223 final double d = phylogeny_node.calculateDistanceToRoot();
225 addSubelement( category, "Distance to root", String.valueOf( ForesterUtil.FORMATTER_6.format( d ) ) );
228 if ( ( phylogeny_node.getBranchData().getBranchWidth() != null )
229 && ( phylogeny_node.getBranchData().getBranchWidth().getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE ) ) {
230 addSubelement( category,
232 ForesterUtil.FORMATTER_3.format( phylogeny_node.getBranchData().getBranchWidth().getValue() ) );
234 if ( ( phylogeny_node.getBranchData().getBranchColor() != null ) ) {
235 final Color c = phylogeny_node.getBranchData().getBranchColor().getValue();
236 addSubelement( category, NODE_BRANCH_COLOR, c.getRed() + ", " + c.getGreen() + ", " + c.getBlue() );
240 private static void addBinaryCharacters( final DefaultMutableTreeNode top,
241 final BinaryCharacters bc,
242 final String name ) {
243 DefaultMutableTreeNode category;
244 category = new DefaultMutableTreeNode( name );
246 addSubelement( category, "Gained", String.valueOf( bc.getGainedCount() ) );
247 addSubelement( category, "Lost", String.valueOf( bc.getLostCount() ) );
248 addSubelement( category, "Present", String.valueOf( bc.getPresentCount() ) );
249 final DefaultMutableTreeNode chars = new DefaultMutableTreeNode( "Lists" );
250 category.add( chars );
251 addSubelement( chars, "Gained", bc.getGainedCharactersAsStringBuffer().toString() );
252 addSubelement( chars, "Lost", bc.getLostCharactersAsStringBuffer().toString() );
253 addSubelement( chars, "Present", bc.getPresentCharactersAsStringBuffer().toString() );
256 private static void addCrossReference( final DefaultMutableTreeNode top, final Accession x, final String name ) {
257 DefaultMutableTreeNode category;
258 category = new DefaultMutableTreeNode( name );
262 private static void addCrossReferences( final DefaultMutableTreeNode top,
263 final SortedSet<Accession> xs,
264 final DefaultMutableTreeNode category ) {
265 if ( ( xs != null ) && ( xs.size() > 0 ) ) {
266 category.add( new DefaultMutableTreeNode( "Cross references" ) );
267 final DefaultMutableTreeNode last = top.getLastLeaf();
268 for( final Accession x : xs ) {
269 addCrossReference( last, x, x.asText().toString() );
274 private static void addDate( final DefaultMutableTreeNode top, final Date date, final String name ) {
275 DefaultMutableTreeNode category;
276 category = new DefaultMutableTreeNode( name );
278 addSubelement( category, DATE_DESCRIPTION, date.getDesc() );
279 addSubelement( category, DATE_VALUE, String.valueOf( date.getValue() ) );
280 addSubelement( category, DATE_MIN, String.valueOf( date.getMin() ) );
281 addSubelement( category, DATE_MAX, String.valueOf( date.getMax() ) );
282 addSubelement( category, DATE_UNIT, date.getUnit() );
285 private static void addDistribution( final DefaultMutableTreeNode top, final Distribution dist, final String name ) {
286 DefaultMutableTreeNode category;
287 category = new DefaultMutableTreeNode( name );
289 addSubelement( category, DIST_DESCRIPTION, dist.getDesc() );
290 if ( ( dist.getPoints() != null ) && ( dist.getPoints().size() > 0 ) ) {
291 final Point p0 = dist.getPoints().get( 0 );
292 if ( ( p0 != null ) && !Point.isSeemsEmpty( p0 ) ) {
293 addSubelement( category, DIST_GEODETIC_DATUM, p0.getGeodeticDatum() );
294 addSubelement( category, DIST_LATITUDE, String.valueOf( p0.getLatitude() ) );
295 addSubelement( category, DIST_LONGITUDE, String.valueOf( p0.getLongitude() ) );
296 String alt_unit = p0.getAltiudeUnit();
297 if ( ForesterUtil.isEmpty( alt_unit ) ) {
300 addSubelement( category, DIST_ALTITUDE, String.valueOf( p0.getAltitude() ) + alt_unit );
305 private static void addEvents( final DefaultMutableTreeNode top, final Event events, final String name ) {
306 DefaultMutableTreeNode category;
307 category = new DefaultMutableTreeNode( name );
309 if ( events.getNumberOfDuplications() > 0 ) {
310 addSubelement( category, EVENTS_DUPLICATIONS, String.valueOf( events.getNumberOfDuplications() ) );
312 if ( events.getNumberOfSpeciations() > 0 ) {
313 addSubelement( category, EVENTS_SPECIATIONS, String.valueOf( events.getNumberOfSpeciations() ) );
315 if ( events.getNumberOfGeneLosses() > 0 ) {
316 addSubelement( category, EVENTS_GENE_LOSSES, String.valueOf( events.getNumberOfGeneLosses() ) );
318 addSubelement( category, "Type", events.getEventType().toString() );
319 if ( events.getConfidence() != null ) {
320 addSubelement( category, CONFIDENCE, events.getConfidence().asText().toString() );
324 private static void addLineage( final DefaultMutableTreeNode top,
325 final List<String> lineage,
326 final DefaultMutableTreeNode category ) {
327 if ( ( lineage != null ) && ( lineage.size() > 0 ) ) {
328 final StringBuilder sb = new StringBuilder();
329 for( final String lin : lineage ) {
330 if ( !ForesterUtil.isEmpty( lin ) ) {
336 if ( sb.length() > 1 ) {
337 str = sb.substring( 0, sb.length() - 3 );
339 if ( !ForesterUtil.isEmpty( str ) ) {
340 addSubelement( category, "Lineage", str );
345 private static void addProperties( final DefaultMutableTreeNode top,
346 final PropertiesMap properties,
347 final String string ) {
348 final SortedMap<String, Property> properties_map = properties.getProperties();
349 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( "Properties " );
351 for( final String key : properties_map.keySet() ) {
352 final Property prop = properties_map.get( key );
353 category.add( new DefaultMutableTreeNode( prop.getRef() + "=" + prop.getValue() + " " + prop.getUnit()
354 + " [" + prop.getAppliesTo().toString() + "]" ) );
358 private static void addReference( final DefaultMutableTreeNode top, final Reference ref, final String name ) {
359 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
361 addSubelement( category, LIT_REFERENCE_DOI, ref.getDoi() );
362 addSubelement( category, LIT_REFERENCE_DESC, ref.getDescription() );
365 private static void addSequence( final DefaultMutableTreeNode top, final Sequence seq, final String name ) {
366 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
368 addSubelement( category, SEQ_NAME, seq.getName() );
369 addSubelement( category, SEQ_SYMBOL, seq.getSymbol() );
370 addSubelement( category, SEQ_GENE_NAME, seq.getGeneName() );
371 if ( seq.getAccession() != null ) {
372 addSubelement( category, SEQ_ACCESSION, seq.getAccession().asText().toString() );
374 addSubelement( category, SEQ_LOCATION, seq.getLocation() );
375 addSubelement( category, SEQ_TYPE, seq.getType() );
376 addSubelement( category, SEQ_MOL_SEQ, seq.getMolecularSequence() );
377 if ( ( seq.getAnnotations() != null ) && !seq.getAnnotations().isEmpty() ) {
378 addAnnotations( top, seq.getAnnotations(), category );
380 if ( ( seq.getCrossReferences() != null ) && !seq.getCrossReferences().isEmpty() ) {
381 addCrossReferences( top, seq.getCrossReferences(), category );
383 if ( ( seq.getUris() != null ) && !seq.getUris().isEmpty() ) {
384 addUris( top, seq.getUris(), category );
388 private static void addSubelement( final DefaultMutableTreeNode node, final String name, final String value ) {
389 if ( !ForesterUtil.isEmpty( value ) ) {
390 node.add( new DefaultMutableTreeNode( name + ": " + value ) );
394 private static void addTaxonomy( final DefaultMutableTreeNode top, final Taxonomy tax, final String name ) {
395 final DefaultMutableTreeNode category = new DefaultMutableTreeNode( name );
397 if ( tax.getIdentifier() != null ) {
398 addSubelement( category, TAXONOMY_IDENTIFIER, tax.getIdentifier().asText().toString() );
400 addSubelement( category, TAXONOMY_CODE, tax.getTaxonomyCode() );
401 addSubelement( category, TAXONOMY_SCIENTIFIC_NAME, tax.getScientificName() );
402 addSubelement( category, TAXONOMY_AUTHORITY, tax.getAuthority() );
403 addSubelement( category, TAXONOMY_COMMON_NAME, tax.getCommonName() );
404 for( final String syn : tax.getSynonyms() ) {
405 addSubelement( category, TAXONOMY_SYNONYM, syn );
407 addSubelement( category, TAXONOMY_RANK, tax.getRank() );
408 if ( ( tax.getUris() != null ) && !tax.getUris().isEmpty() ) {
409 addUris( top, tax.getUris(), category );
411 if ( ( tax.getLineage() != null ) && !tax.getLineage().isEmpty() ) {
412 addLineage( top, tax.getLineage(), category );
416 private static void addUri( final DefaultMutableTreeNode top, final Uri uri, final String name ) {
417 DefaultMutableTreeNode category;
418 category = new DefaultMutableTreeNode( name );
420 addSubelement( category, "Description", uri.getDescription() );
421 addSubelement( category, "Type", uri.getType() );
422 addSubelement( category, "URI", uri.getValue().toString() );
425 private static void addUris( final DefaultMutableTreeNode top,
426 final List<Uri> uris,
427 final DefaultMutableTreeNode category ) {
428 if ( ( uris != null ) && ( uris.size() > 0 ) ) {
429 category.add( new DefaultMutableTreeNode( "URIs" ) );
430 final DefaultMutableTreeNode last = top.getLastLeaf();
432 for( final Uri uri : uris ) {
434 addUri( last, uri, "URI " + ( i++ ) );
440 private static void createNodes( final DefaultMutableTreeNode top, final PhylogenyNode phylogeny_node ) {
441 addBasics( top, phylogeny_node, BASIC );
443 if ( phylogeny_node.getNodeData().isHasTaxonomy() ) {
444 addTaxonomy( top, phylogeny_node.getNodeData().getTaxonomy(), TAXONOMY );
447 if ( phylogeny_node.getNodeData().isHasSequence() ) {
448 addSequence( top, phylogeny_node.getNodeData().getSequence(), SEQUENCE );
451 if ( phylogeny_node.getNodeData().isHasEvent() ) {
452 addEvents( top, phylogeny_node.getNodeData().getEvent(), EVENTS );
455 if ( phylogeny_node.getNodeData().isHasDate() ) {
456 addDate( top, phylogeny_node.getNodeData().getDate(), DATE );
459 if ( phylogeny_node.getNodeData().isHasDistribution() ) {
460 addDistribution( top, phylogeny_node.getNodeData().getDistribution(), DISTRIBUTION );
463 if ( phylogeny_node.getNodeData().isHasReference() ) {
464 addReference( top, phylogeny_node.getNodeData().getReference(), LIT_REFERENCE );
467 if ( phylogeny_node.getNodeData().isHasBinaryCharacters() ) {
468 addBinaryCharacters( top, phylogeny_node.getNodeData().getBinaryCharacters(), BINARY_CHARACTERS );
471 if ( phylogeny_node.getNodeData().isHasProperties() ) {
472 addProperties( top, phylogeny_node.getNodeData().getProperties(), PROP );