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1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.io.vamsas; | |
22 | ||
23 | import jalview.analysis.TreeBuilder; | |
24 | import jalview.analysis.TreeModel; | |
25 | import jalview.bin.Console; | |
26 | import jalview.datamodel.AlignmentI; | |
27 | import jalview.datamodel.AlignmentView; | |
28 | import jalview.datamodel.BinaryNode; | |
29 | import jalview.datamodel.SeqCigar; | |
30 | import jalview.datamodel.Sequence; | |
31 | import jalview.datamodel.SequenceI; | |
32 | import jalview.datamodel.SequenceNode; | |
33 | import jalview.gui.TreePanel; | |
34 | import jalview.io.NewickFile; | |
35 | import jalview.io.VamsasAppDatastore; | |
36 | import jalview.viewmodel.AlignmentViewport; | |
37 | ||
38 | import java.io.IOException; | |
39 | import java.util.Enumeration; | |
40 | import java.util.Hashtable; | |
41 | import java.util.List; | |
42 | import java.util.Vector; | |
43 | ||
44 | import uk.ac.vamsas.client.Vobject; | |
45 | import uk.ac.vamsas.objects.core.AlignmentSequence; | |
46 | import uk.ac.vamsas.objects.core.Entry; | |
47 | import uk.ac.vamsas.objects.core.Input; | |
48 | import uk.ac.vamsas.objects.core.Newick; | |
49 | import uk.ac.vamsas.objects.core.Param; | |
50 | import uk.ac.vamsas.objects.core.Provenance; | |
51 | import uk.ac.vamsas.objects.core.Seg; | |
52 | import uk.ac.vamsas.objects.core.Treenode; | |
53 | import uk.ac.vamsas.objects.core.Vref; | |
54 | ||
55 | public class Tree extends DatastoreItem | |
56 | { | |
57 | AlignmentI jal; | |
58 | ||
59 | TreePanel tp; | |
60 | ||
61 | uk.ac.vamsas.objects.core.Tree tree; | |
62 | ||
63 | uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or | |
64 | ||
65 | // other kind of tree | |
66 | private NewickFile ntree; | |
67 | ||
68 | private String title; | |
69 | ||
70 | private AlignmentView inputData = null; | |
71 | ||
72 | 0 | public static void updateFrom(VamsasAppDatastore datastore, |
73 | jalview.gui.AlignFrame alignFrame, | |
74 | uk.ac.vamsas.objects.core.Tree vtree) | |
75 | { | |
76 | 0 | Tree toTree = new Tree(datastore, alignFrame, vtree); |
77 | } | |
78 | ||
79 | 0 | public Tree(VamsasAppDatastore datastore, |
80 | jalview.gui.AlignFrame alignFrame, | |
81 | uk.ac.vamsas.objects.core.Tree vtree) | |
82 | { | |
83 | 0 | super(datastore, vtree, TreePanel.class); |
84 | 0 | doJvUpdate(); |
85 | } | |
86 | ||
87 | 0 | private NewickFile getNtree() throws IOException |
88 | { | |
89 | 0 | return new jalview.io.NewickFile(tree.getNewick(0).getContent()); |
90 | } | |
91 | ||
92 | 0 | public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, |
93 | uk.ac.vamsas.objects.core.Alignment alignment2) | |
94 | { | |
95 | 0 | super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class); |
96 | ||
97 | 0 | jal = jal2; |
98 | 0 | tp = (TreePanel) jvobj; |
99 | 0 | alignment = alignment2; |
100 | ||
101 | 0 | tree = (uk.ac.vamsas.objects.core.Tree) vobj; |
102 | 0 | doSync(); |
103 | } | |
104 | ||
105 | /* | |
106 | * (non-Javadoc) | |
107 | * | |
108 | * @see jalview.io.vamsas.DatastoreItem#addFromDocument() | |
109 | */ | |
110 | 0 | @Override |
111 | public void addFromDocument() | |
112 | { | |
113 | 0 | tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree; |
114 | 0 | TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree); |
115 | // make a new tree | |
116 | 0 | Object[] idata = recoverInputData(tree.getProvenance()); |
117 | 0 | try |
118 | { | |
119 | 0 | if (idata != null && idata[0] != null) |
120 | { | |
121 | 0 | inputData = (AlignmentView) idata[0]; |
122 | } | |
123 | 0 | ntree = getNtree(); |
124 | 0 | title = tree.getNewick(0).getTitle(); |
125 | 0 | if (title == null || title.length() == 0) |
126 | { | |
127 | 0 | title = tree.getTitle(); // hack!!!! |
128 | } | |
129 | } catch (Exception e) | |
130 | { | |
131 | 0 | Console.warn("Problems parsing treefile '" |
132 | + tree.getNewick(0).getContent() + "'", e); | |
133 | } | |
134 | } | |
135 | ||
136 | /* | |
137 | * (non-Javadoc) | |
138 | * | |
139 | * @see jalview.io.vamsas.DatastoreItem#conflict() | |
140 | */ | |
141 | 0 | @Override |
142 | public void conflict() | |
143 | { | |
144 | 0 | Console.info( |
145 | "Update (with conflict) from vamsas document to alignment associated tree not implemented yet."); | |
146 | } | |
147 | ||
148 | /* | |
149 | * (non-Javadoc) | |
150 | * | |
151 | * @see jalview.io.vamsas.DatastoreItem#update() | |
152 | */ | |
153 | 0 | @Override |
154 | public void updateToDoc() | |
155 | { | |
156 | 0 | if (isModifiable(tree.getModifiable())) |
157 | { | |
158 | // synchronize(); // update(); | |
159 | // verify any changes. | |
160 | 0 | log.info("TODO: Update tree in document from jalview."); |
161 | } | |
162 | else | |
163 | { | |
164 | // handle conflict | |
165 | 0 | log.info( |
166 | "TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged."); | |
167 | } | |
168 | } | |
169 | ||
170 | /* | |
171 | * (non-Javadoc) | |
172 | * | |
173 | * @see jalview.io.vamsas.DatastoreItem#updateFromDoc() | |
174 | */ | |
175 | 0 | @Override |
176 | public void updateFromDoc() | |
177 | { | |
178 | // should probably just open a new tree panel in the same place as the old | |
179 | // one | |
180 | // TODO: Tree.updateFromDoc | |
181 | /* | |
182 | * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree); | |
183 | * | |
184 | * // make a new tree Object[] idata = | |
185 | * recoverInputData(tree.getProvenance()); try { if (idata != null && | |
186 | * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree = | |
187 | * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null || | |
188 | * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch | |
189 | * (Exception e) { Cache.warn("Problems parsing treefile '" + | |
190 | * tree.getNewick(0).getContent() + "'", e); } | |
191 | */ | |
192 | 0 | log.debug("Update the local tree in jalview from the document."); |
193 | ||
194 | 0 | if (isModifiable(tree.getModifiable())) |
195 | { | |
196 | // synchronize(); // update(); | |
197 | // verify any changes. | |
198 | 0 | log.debug("Update tree in document from jalview."); |
199 | } | |
200 | else | |
201 | { | |
202 | // handle conflict | |
203 | 0 | log.debug("Add modified jalview tree as new tree in document."); |
204 | } | |
205 | } | |
206 | ||
207 | /** | |
208 | * correctly creates provenance for trees calculated on an alignment by | |
209 | * jalview. | |
210 | * | |
211 | * @param jal | |
212 | * @param tp | |
213 | * @return | |
214 | */ | |
215 | 0 | private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) |
216 | { | |
217 | 0 | Console.debug("Making Tree provenance for " + tp.getTitle()); |
218 | 0 | Provenance prov = new Provenance(); |
219 | 0 | prov.addEntry(new Entry()); |
220 | 0 | prov.getEntry(0).setAction("imported " + tp.getTitle()); |
221 | 0 | prov.getEntry(0).setUser(provEntry.getUser()); |
222 | 0 | prov.getEntry(0).setApp(provEntry.getApp()); |
223 | 0 | prov.getEntry(0).setDate(provEntry.getDate()); |
224 | ||
225 | 0 | AlignmentView originalData = tp.getTree().getOriginalData(); |
226 | 0 | if (originalData != null) |
227 | { | |
228 | 0 | Input vInput = new Input(); |
229 | // LATER: check to see if tree input data is contained in this alignment - | |
230 | // or just correctly resolve the tree's seqData to the correct alignment | |
231 | // in | |
232 | // the document. | |
233 | 0 | Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, |
234 | tp.getTree().getOriginalData().getSequences())); | |
235 | 0 | Object[] alsqs = new Object[alsqrefs.size()]; |
236 | 0 | alsqrefs.copyInto(alsqs); |
237 | 0 | vInput.setObjRef(alsqs); |
238 | // now create main provenance data | |
239 | 0 | prov.getEntry(0).setAction("created " + tp.getTitle()); |
240 | 0 | prov.getEntry(0).addInput(vInput); |
241 | // jalview's special input parameter for distance matrix calculations | |
242 | 0 | vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name. |
243 | 0 | prov.getEntry(0).addParam(new Param()); |
244 | 0 | prov.getEntry(0).getParam(0).setName("treeType"); |
245 | 0 | prov.getEntry(0).getParam(0).setType("utf8"); |
246 | 0 | prov.getEntry(0).getParam(0) |
247 | .setContent(TreeBuilder.NEIGHBOUR_JOINING); | |
248 | // TODO: type of tree is a general parameter | |
249 | 0 | int ranges[] = originalData.getVisibleContigs(); |
250 | // VisibleContigs are with respect to alignment coordinates. Still need | |
251 | // offsets | |
252 | 0 | int start = tp.getTree().getOriginalData().getAlignmentOrigin(); |
253 | 0 | for (int r = 0; r < ranges.length; r += 2) |
254 | { | |
255 | 0 | Seg visSeg = new Seg(); |
256 | 0 | visSeg.setStart(1 + start + ranges[r]); |
257 | 0 | visSeg.setEnd(start + ranges[r + 1]); |
258 | 0 | visSeg.setInclusive(true); |
259 | 0 | vInput.addSeg(visSeg); |
260 | } | |
261 | } | |
262 | 0 | Console.debug("Finished Tree provenance for " + tp.getTitle()); |
263 | 0 | return prov; |
264 | } | |
265 | ||
266 | /** | |
267 | * look up SeqCigars in an existing alignment. | |
268 | * | |
269 | * @param jal | |
270 | * @param sequences | |
271 | * @return vector of alignment sequences in order of SeqCigar array (but | |
272 | * missing unfound seqcigars) | |
273 | */ | |
274 | 0 | private Vector<SequenceI> findAlignmentSequences(AlignmentI jal, |
275 | SeqCigar[] sequences) | |
276 | { | |
277 | 0 | SeqCigar[] tseqs = new SeqCigar[sequences.length]; |
278 | 0 | System.arraycopy(sequences, 0, tseqs, 0, sequences.length); |
279 | 0 | Vector<SequenceI> alsq = new Vector<>(); |
280 | 0 | List<SequenceI> jalsqs = jal.getSequences(); |
281 | 0 | synchronized (jalsqs) |
282 | { | |
283 | 0 | for (SequenceI asq : jalsqs) |
284 | { | |
285 | 0 | for (int t = 0; t < sequences.length; t++) |
286 | { | |
287 | 0 | if (tseqs[t] != null && (tseqs[t].getRefSeq() == asq |
288 | || tseqs[t].getRefSeq() == asq.getDatasetSequence())) | |
289 | // && tseqs[t].getStart()>=asq.getStart() && | |
290 | // tseqs[t].getEnd()<=asq.getEnd()) | |
291 | { | |
292 | 0 | tseqs[t] = null; |
293 | 0 | alsq.add(asq); |
294 | } | |
295 | } | |
296 | } | |
297 | } | |
298 | 0 | if (alsq.size() < sequences.length) |
299 | { | |
300 | 0 | Console.warn( |
301 | "Not recovered all alignment sequences for given set of input sequence CIGARS"); | |
302 | } | |
303 | 0 | return alsq; |
304 | } | |
305 | ||
306 | /** | |
307 | * | |
308 | * Update jalview newick representation with TreeNode map | |
309 | * | |
310 | * @param tp | |
311 | * the treepanel that this tree is bound to. | |
312 | */ | |
313 | 0 | public void UpdateSequenceTreeMap(TreePanel tp) |
314 | { | |
315 | 0 | if (tp == null || tree == null) |
316 | { | |
317 | 0 | return; |
318 | } | |
319 | ||
320 | 0 | if (tp.getTree() == null) |
321 | { | |
322 | 0 | Console.warn("Not updating SequenceTreeMap for " + tree.getVorbaId()); |
323 | 0 | return; |
324 | } | |
325 | 0 | Vector<BinaryNode> leaves = tp.getTree() |
326 | .findLeaves(tp.getTree().getTopNode()); | |
327 | 0 | Treenode[] tn = tree.getTreenode(); // todo: select nodes for this |
328 | // particular tree | |
329 | 0 | int sz = tn.length; |
330 | 0 | int i = 0; |
331 | ||
332 | 0 | while (i < sz) |
333 | { | |
334 | 0 | Treenode node = tn[i++]; |
335 | 0 | BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves); |
336 | 0 | if (mappednode != null && mappednode instanceof SequenceNode) |
337 | { | |
338 | 0 | SequenceNode leaf = (SequenceNode) mappednode; |
339 | // check if we can make the specified association | |
340 | 0 | Object jvseq = null; |
341 | 0 | int vrf = 0, refv = 0; |
342 | 0 | while (jvseq == null && vrf < node.getVrefCount()) |
343 | { | |
344 | 0 | if (refv < node.getVref(vrf).getRefsCount()) |
345 | { | |
346 | 0 | Object noderef = node.getVref(vrf).getRefs(refv++); |
347 | 0 | if (noderef instanceof AlignmentSequence) |
348 | { | |
349 | // we only make these kind of associations | |
350 | 0 | jvseq = getvObj2jv((Vobject) noderef); |
351 | } | |
352 | } | |
353 | else | |
354 | { | |
355 | 0 | refv = 0; |
356 | 0 | vrf++; |
357 | } | |
358 | } | |
359 | 0 | if (jvseq instanceof SequenceI) |
360 | { | |
361 | 0 | leaf.setElement((SequenceI) jvseq); |
362 | 0 | leaf.setPlaceholder(false); |
363 | } | |
364 | else | |
365 | { | |
366 | 0 | leaf.setPlaceholder(true); |
367 | 0 | leaf.setElement( |
368 | new Sequence(leaf.getName(), "THISISAPLACEHLDER")); | |
369 | } | |
370 | } | |
371 | } | |
372 | } | |
373 | ||
374 | // / TODO: refactor to vamsas :start | |
375 | /** | |
376 | * construct treenode mappings for mapped sequences | |
377 | * | |
378 | * @param treeModel | |
379 | * @param newick | |
380 | * @return | |
381 | */ | |
382 | 0 | public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick) |
383 | { | |
384 | 0 | Vector<BinaryNode> leaves = treeModel |
385 | .findLeaves(treeModel.getTopNode()); | |
386 | 0 | Vector tnv = new Vector(); |
387 | 0 | Enumeration l = leaves.elements(); |
388 | 0 | Hashtable nodespecs = new Hashtable(); |
389 | 0 | while (l.hasMoreElements()) |
390 | { | |
391 | 0 | jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l |
392 | .nextElement(); | |
393 | 0 | if (tnode instanceof jalview.datamodel.SequenceNode) |
394 | { | |
395 | 0 | if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder()) |
396 | { | |
397 | 0 | Object assocseq = ((BinaryNode) tnode).element(); |
398 | 0 | if (assocseq instanceof SequenceI) |
399 | { | |
400 | 0 | Vobject vobj = this.getjv2vObj(assocseq); |
401 | 0 | if (vobj != null) |
402 | { | |
403 | 0 | Treenode node = new Treenode(); |
404 | 0 | if (newick.isRegisterable()) |
405 | { | |
406 | 0 | this.cdoc.registerObject(newick); |
407 | 0 | node.addTreeId(newick); |
408 | } | |
409 | 0 | node.setNodespec(makeNodeSpec(nodespecs, tnode)); |
410 | 0 | node.setName(tnode.getName()); |
411 | 0 | Vref vr = new Vref(); |
412 | 0 | vr.addRefs(vobj); |
413 | 0 | node.addVref(vr); |
414 | 0 | tnv.addElement(node); |
415 | } | |
416 | else | |
417 | { | |
418 | 0 | jalview.bin.Console |
419 | .errPrintln("WARNING: Unassociated treeNode " | |
420 | + tnode.element().toString() + " " | |
421 | 0 | + ((tnode.getName() != null) |
422 | ? " label " + tnode.getName() | |
423 | : "")); | |
424 | } | |
425 | } | |
426 | } | |
427 | } | |
428 | } | |
429 | 0 | if (tnv.size() > 0) |
430 | { | |
431 | 0 | Treenode[] tn = new Treenode[tnv.size()]; |
432 | 0 | tnv.copyInto(tn); |
433 | 0 | return tn; |
434 | } | |
435 | 0 | return new Treenode[] {}; |
436 | } | |
437 | ||
438 | 0 | private String makeNodeSpec(Hashtable nodespecs, |
439 | jalview.datamodel.BinaryNode tnode) | |
440 | { | |
441 | 0 | String nname = new String(tnode.getName()); |
442 | 0 | Integer nindx = (Integer) nodespecs.get(nname); |
443 | 0 | if (nindx == null) |
444 | { | |
445 | 0 | nindx = Integer.valueOf(1); |
446 | } | |
447 | 0 | nname = nindx.toString() + " " + nname; |
448 | 0 | return nname; |
449 | } | |
450 | ||
451 | /** | |
452 | * call to match up Treenode specs to NJTree parsed from document object. | |
453 | * | |
454 | * @param nodespec | |
455 | * @param leaves | |
456 | * as returned from NJTree.findLeaves( .., ..) .. | |
457 | * @return | |
458 | */ | |
459 | 0 | private jalview.datamodel.BinaryNode findNodeSpec(String nodespec, |
460 | Vector leaves) | |
461 | { | |
462 | 0 | int occurence = -1; |
463 | 0 | String nspec = nodespec.substring(nodespec.indexOf(' ') + 1); |
464 | 0 | String oval = nodespec.substring(0, nodespec.indexOf(' ')); |
465 | 0 | try |
466 | { | |
467 | 0 | occurence = Integer.valueOf(oval).intValue(); |
468 | } catch (Exception e) | |
469 | { | |
470 | 0 | jalview.bin.Console.errPrintln("Invalid nodespec '" + nodespec + "'"); |
471 | 0 | return null; |
472 | } | |
473 | 0 | jalview.datamodel.BinaryNode bn = null; |
474 | ||
475 | 0 | int nocc = 0; |
476 | 0 | Enumeration en = leaves.elements(); |
477 | 0 | while (en.hasMoreElements() && nocc < occurence) |
478 | { | |
479 | 0 | bn = (jalview.datamodel.BinaryNode) en.nextElement(); |
480 | 0 | if (bn instanceof jalview.datamodel.SequenceNode |
481 | && bn.getName().equals(nspec)) | |
482 | { | |
483 | 0 | --occurence; |
484 | } | |
485 | else | |
486 | { | |
487 | 0 | bn = null; |
488 | } | |
489 | } | |
490 | 0 | return bn; |
491 | } | |
492 | ||
493 | // todo: end refactor to vamsas library | |
494 | /** | |
495 | * add jalview object to vamsas document | |
496 | * | |
497 | */ | |
498 | 0 | @Override |
499 | public void addToDocument() | |
500 | { | |
501 | 0 | tree = new uk.ac.vamsas.objects.core.Tree(); |
502 | 0 | bindjvvobj(tp, tree); |
503 | 0 | tree.setTitle(tp.getTitle()); |
504 | 0 | Newick newick = new Newick(); |
505 | 0 | newick.setContent(tp.getTree().print()); |
506 | 0 | newick.setTitle(tp.getTitle()); |
507 | 0 | tree.addNewick(newick); |
508 | 0 | tree.setProvenance(makeTreeProvenance(jal, tp)); |
509 | 0 | tree.setTreenode(makeTreeNodes(tp.getTree(), newick)); |
510 | ||
511 | 0 | alignment.addTree(tree); |
512 | } | |
513 | ||
514 | /** | |
515 | * note: this function assumes that all sequence and alignment objects | |
516 | * referenced in input data has already been associated with jalview objects. | |
517 | * | |
518 | * @param tp | |
519 | * @param alignFrame | |
520 | * @return Object[] { AlignmentView, AlignmentI - reference alignment for | |
521 | * input } | |
522 | */ | |
523 | 0 | public Object[] recoverInputData(Provenance tp) |
524 | { | |
525 | 0 | AlignmentViewport javport = null; |
526 | 0 | jalview.datamodel.AlignmentI jal = null; |
527 | 0 | jalview.datamodel.CigarArray view = null; |
528 | 0 | for (int pe = 0; pe < tp.getEntryCount(); pe++) |
529 | { | |
530 | 0 | if (tp.getEntry(pe).getInputCount() > 0) |
531 | { | |
532 | 0 | if (tp.getEntry(pe).getInputCount() > 1) |
533 | { | |
534 | 0 | Console.warn("Ignoring additional input spec in provenance entry " |
535 | + tp.getEntry(pe).toString()); | |
536 | } | |
537 | // LATER: deal sensibly with multiple inputs | |
538 | 0 | Input vInput = tp.getEntry(pe).getInput(0); |
539 | // is this the whole alignment or a specific set of sequences ? | |
540 | 0 | if (vInput.getObjRefCount() == 0) |
541 | { | |
542 | 0 | if (tree.getV_parent() != null && tree |
543 | .getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment) | |
544 | { | |
545 | 0 | javport = getViewport(tree.getV_parent()); |
546 | 0 | jal = javport.getAlignment(); |
547 | 0 | view = javport.getAlignment().getCompactAlignment(); |
548 | } | |
549 | } | |
550 | else | |
551 | { | |
552 | // Explicit reference - to alignment, sequences or what. | |
553 | 0 | if (vInput.getObjRefCount() == 1 && vInput.getObjRef( |
554 | 0) instanceof uk.ac.vamsas.objects.core.Alignment) | |
555 | { | |
556 | // recover an AlignmentView for the input data | |
557 | 0 | javport = getViewport((Vobject) vInput.getObjRef(0)); |
558 | 0 | jal = javport.getAlignment(); |
559 | 0 | view = javport.getAlignment().getCompactAlignment(); |
560 | } | |
561 | 0 | else if (vInput.getObjRef( |
562 | 0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence) | |
563 | { | |
564 | // recover an AlignmentView for the input data | |
565 | 0 | javport = getViewport( |
566 | ((Vobject) vInput.getObjRef(0)).getV_parent()); | |
567 | 0 | jal = javport.getAlignment(); |
568 | 0 | jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput |
569 | .getObjRefCount()]; | |
570 | 0 | for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++) |
571 | { | |
572 | 0 | SequenceI seq = (SequenceI) getvObj2jv( |
573 | (Vobject) vInput.getObjRef(i)); | |
574 | 0 | seqs[i] = seq; |
575 | } | |
576 | 0 | view = new jalview.datamodel.Alignment(seqs) |
577 | .getCompactAlignment(); | |
578 | ||
579 | } | |
580 | } | |
581 | 0 | int from = 1, to = jal.getWidth(); |
582 | 0 | int offset = 0; // deleteRange modifies its frame of reference |
583 | 0 | for (int r = 0, s = vInput.getSegCount(); r < s; r++) |
584 | { | |
585 | 0 | Seg visSeg = vInput.getSeg(r); |
586 | 0 | int se[] = getSegRange(visSeg, true); // jalview doesn't do |
587 | // bidirection alignments yet. | |
588 | 0 | if (to < se[1]) |
589 | { | |
590 | 0 | Console.warn("Ignoring invalid segment in InputData spec."); |
591 | } | |
592 | else | |
593 | { | |
594 | 0 | if (se[0] > from) |
595 | { | |
596 | 0 | view.deleteRange(offset + from - 1, offset + se[0] - 2); |
597 | 0 | offset -= se[0] - from; |
598 | } | |
599 | 0 | from = se[1] + 1; |
600 | } | |
601 | } | |
602 | 0 | if (from < to) |
603 | { | |
604 | 0 | view.deleteRange(offset + from - 1, offset + to - 1); // final |
605 | // deletion - | |
606 | // TODO: check | |
607 | // off by | |
608 | // one for to | |
609 | } | |
610 | 0 | return new Object[] { new AlignmentView(view), jal }; |
611 | } | |
612 | } | |
613 | 0 | Console.debug( |
614 | "Returning null for input data recovery from provenance."); | |
615 | 0 | return null; |
616 | } | |
617 | ||
618 | 0 | private AlignmentViewport getViewport(Vobject v_parent) |
619 | { | |
620 | 0 | if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment) |
621 | { | |
622 | 0 | return datastore |
623 | .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent); | |
624 | } | |
625 | 0 | return null; |
626 | } | |
627 | ||
628 | 0 | public NewickFile getNewickTree() |
629 | { | |
630 | 0 | return ntree; |
631 | } | |
632 | ||
633 | 0 | public String getTitle() |
634 | { | |
635 | 0 | return title; |
636 | } | |
637 | ||
638 | 0 | public AlignmentView getInputData() |
639 | { | |
640 | 0 | return inputData; |
641 | } | |
642 | ||
643 | 0 | public boolean isValidTree() |
644 | { | |
645 | 0 | try |
646 | { | |
647 | 0 | if (ntree == null) |
648 | { | |
649 | 0 | return false; |
650 | } | |
651 | 0 | ntree.parse(); |
652 | 0 | if (ntree.getTree() != null) |
653 | { | |
654 | 0 | ntree = getNtree(); |
655 | } | |
656 | 0 | return true; |
657 | } catch (Exception e) | |
658 | { | |
659 | 0 | Console.debug("Failed to parse newick tree string", e); |
660 | } | |
661 | 0 | return false; |
662 | } | |
663 | } |