2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.io.vamsas;
23 import jalview.analysis.NJTree;
24 import jalview.bin.Cache;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.AlignmentView;
27 import jalview.datamodel.BinaryNode;
28 import jalview.datamodel.SeqCigar;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
31 import jalview.datamodel.SequenceNode;
32 import jalview.gui.TreePanel;
33 import jalview.io.NewickFile;
34 import jalview.io.VamsasAppDatastore;
35 import jalview.viewmodel.AlignmentViewport;
37 import java.io.IOException;
38 import java.util.Enumeration;
39 import java.util.Hashtable;
40 import java.util.List;
41 import java.util.Vector;
43 import uk.ac.vamsas.client.Vobject;
44 import uk.ac.vamsas.objects.core.AlignmentSequence;
45 import uk.ac.vamsas.objects.core.Entry;
46 import uk.ac.vamsas.objects.core.Input;
47 import uk.ac.vamsas.objects.core.Newick;
48 import uk.ac.vamsas.objects.core.Param;
49 import uk.ac.vamsas.objects.core.Provenance;
50 import uk.ac.vamsas.objects.core.Seg;
51 import uk.ac.vamsas.objects.core.Treenode;
52 import uk.ac.vamsas.objects.core.Vref;
54 public class Tree extends DatastoreItem
60 uk.ac.vamsas.objects.core.Tree tree;
62 uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
65 private NewickFile ntree;
69 private AlignmentView inputData = null;
71 public static void updateFrom(VamsasAppDatastore datastore,
72 jalview.gui.AlignFrame alignFrame,
73 uk.ac.vamsas.objects.core.Tree vtree)
75 Tree toTree = new Tree(datastore, alignFrame, vtree);
78 public Tree(VamsasAppDatastore datastore,
79 jalview.gui.AlignFrame alignFrame,
80 uk.ac.vamsas.objects.core.Tree vtree)
82 super(datastore, vtree, TreePanel.class);
86 private NewickFile getNtree() throws IOException
88 return new jalview.io.NewickFile(tree.getNewick(0).getContent());
91 public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
92 uk.ac.vamsas.objects.core.Alignment alignment2)
94 super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
97 tp = (TreePanel) jvobj;
98 alignment = alignment2;
100 tree = (uk.ac.vamsas.objects.core.Tree) vobj;
107 * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
110 public void addFromDocument()
112 tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
113 TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
115 Object[] idata = recoverInputData(tree.getProvenance());
118 if (idata != null && idata[0] != null)
120 inputData = (AlignmentView) idata[0];
123 title = tree.getNewick(0).getTitle();
124 if (title == null || title.length() == 0)
126 title = tree.getTitle(); // hack!!!!
128 } catch (Exception e)
130 Cache.log.warn("Problems parsing treefile '"
131 + tree.getNewick(0).getContent() + "'", e);
138 * @see jalview.io.vamsas.DatastoreItem#conflict()
141 public void conflict()
144 .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
150 * @see jalview.io.vamsas.DatastoreItem#update()
153 public void updateToDoc()
155 if (isModifiable(tree.getModifiable()))
157 // synchronize(); // update();
158 // verify any changes.
159 log.info("TODO: Update tree in document from jalview.");
164 log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
171 * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
174 public void updateFromDoc()
176 // should probably just open a new tree panel in the same place as the old
178 // TODO: Tree.updateFromDoc
180 * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
182 * // make a new tree Object[] idata =
183 * recoverInputData(tree.getProvenance()); try { if (idata != null &&
184 * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
185 * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
186 * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
187 * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
188 * tree.getNewick(0).getContent() + "'", e); }
190 log.debug("Update the local tree in jalview from the document.");
192 if (isModifiable(tree.getModifiable()))
194 // synchronize(); // update();
195 // verify any changes.
196 log.debug("Update tree in document from jalview.");
201 log.debug("Add modified jalview tree as new tree in document.");
206 * correctly creates provenance for trees calculated on an alignment by
213 private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
215 Cache.log.debug("Making Tree provenance for " + tp.getTitle());
216 Provenance prov = new Provenance();
217 prov.addEntry(new Entry());
218 prov.getEntry(0).setAction("imported " + tp.getTitle());
219 prov.getEntry(0).setUser(provEntry.getUser());
220 prov.getEntry(0).setApp(provEntry.getApp());
221 prov.getEntry(0).setDate(provEntry.getDate());
222 if (tp.getTree().hasOriginalSequenceData())
224 Input vInput = new Input();
225 // LATER: check to see if tree input data is contained in this alignment -
226 // or just correctly resolve the tree's seqData to the correct alignment
229 Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
230 tp.getTree().seqData.getSequences()));
231 Object[] alsqs = new Object[alsqrefs.size()];
232 alsqrefs.copyInto(alsqs);
233 vInput.setObjRef(alsqs);
234 // now create main provenance data
235 prov.getEntry(0).setAction("created " + tp.getTitle());
236 prov.getEntry(0).addInput(vInput);
237 // jalview's special input parameter for distance matrix calculations
238 vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name.
239 prov.getEntry(0).addParam(new Param());
240 prov.getEntry(0).getParam(0).setName("treeType");
241 prov.getEntry(0).getParam(0).setType("utf8");
242 prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
244 int ranges[] = tp.getTree().seqData.getVisibleContigs();
245 // VisibleContigs are with respect to alignment coordinates. Still need
247 int start = tp.getTree().seqData.getAlignmentOrigin();
248 for (int r = 0; r < ranges.length; r += 2)
250 Seg visSeg = new Seg();
251 visSeg.setStart(1 + start + ranges[r]);
252 visSeg.setEnd(start + ranges[r + 1]);
253 visSeg.setInclusive(true);
254 vInput.addSeg(visSeg);
257 Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
262 * look up SeqCigars in an existing alignment.
266 * @return vector of alignment sequences in order of SeqCigar array (but
267 * missing unfound seqcigars)
269 private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
271 SeqCigar[] tseqs = new SeqCigar[sequences.length];
272 System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
273 Vector alsq = new Vector();
274 List<SequenceI> jalsqs;
275 synchronized (jalsqs = jal.getSequences())
277 for (SequenceI asq : jalsqs)
279 for (int t = 0; t < sequences.length; t++)
282 && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
283 .getDatasetSequence()))
284 // && tseqs[t].getStart()>=asq.getStart() &&
285 // tseqs[t].getEnd()<=asq.getEnd())
293 if (alsq.size() < sequences.length)
295 .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
301 * Update jalview newick representation with TreeNode map
304 * the treepanel that this tree is bound to.
306 public void UpdateSequenceTreeMap(TreePanel tp)
308 if (tp == null || tree == null)
310 Vector leaves = new Vector();
311 if (tp.getTree() == null)
313 Cache.log.warn("Not updating SequenceTreeMap for "
314 + tree.getVorbaId());
317 tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
318 Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
325 Treenode node = tn[i++];
326 BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
327 if (mappednode != null && mappednode instanceof SequenceNode)
329 SequenceNode leaf = (SequenceNode) mappednode;
330 // check if we can make the specified association
332 int vrf = 0, refv = 0;
333 while (jvseq == null && vrf < node.getVrefCount())
335 if (refv < node.getVref(vrf).getRefsCount())
337 Object noderef = node.getVref(vrf).getRefs(refv++);
338 if (noderef instanceof AlignmentSequence)
340 // we only make these kind of associations
341 jvseq = getvObj2jv((Vobject) noderef);
350 if (jvseq instanceof SequenceI)
352 leaf.setElement(jvseq);
353 leaf.setPlaceholder(false);
357 leaf.setPlaceholder(true);
358 leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
364 // / TODO: refactor to vamsas :start
366 * construct treenode mappings for mapped sequences
372 public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
374 Vector leaves = new Vector();
375 ntree.findLeaves(ntree.getTopNode(), leaves);
376 Vector tnv = new Vector();
377 Enumeration l = leaves.elements();
378 Hashtable nodespecs = new Hashtable();
379 while (l.hasMoreElements())
381 jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l
383 if (tnode instanceof jalview.datamodel.SequenceNode)
385 if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
387 Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
389 if (assocseq instanceof SequenceI)
391 Vobject vobj = this.getjv2vObj(assocseq);
394 Treenode node = new Treenode();
395 if (newick.isRegisterable())
397 this.cdoc.registerObject(newick);
398 node.addTreeId(newick);
400 node.setNodespec(makeNodeSpec(nodespecs, tnode));
401 node.setName(tnode.getName());
402 Vref vr = new Vref();
405 tnv.addElement(node);
409 System.err.println("WARNING: Unassociated treeNode "
410 + tnode.element().toString()
412 + ((tnode.getName() != null) ? " label "
413 + tnode.getName() : ""));
421 Treenode[] tn = new Treenode[tnv.size()];
425 return new Treenode[] {};
428 private String makeNodeSpec(Hashtable nodespecs,
429 jalview.datamodel.BinaryNode tnode)
431 String nname = new String(tnode.getName());
432 Integer nindx = (Integer) nodespecs.get(nname);
435 nindx = new Integer(1);
437 nname = nindx.toString() + " " + nname;
442 * call to match up Treenode specs to NJTree parsed from document object.
446 * as returned from NJTree.findLeaves( .., ..) ..
449 private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
453 String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
454 String oval = nodespec.substring(0, nodespec.indexOf(' '));
457 occurence = new Integer(oval).intValue();
458 } catch (Exception e)
460 System.err.println("Invalid nodespec '" + nodespec + "'");
463 jalview.datamodel.BinaryNode bn = null;
466 Enumeration en = leaves.elements();
467 while (en.hasMoreElements() && nocc < occurence)
469 bn = (jalview.datamodel.BinaryNode) en.nextElement();
470 if (bn instanceof jalview.datamodel.SequenceNode
471 && bn.getName().equals(nspec))
481 // todo: end refactor to vamsas library
483 * add jalview object to vamsas document
487 public void addToDocument()
489 tree = new uk.ac.vamsas.objects.core.Tree();
490 bindjvvobj(tp, tree);
491 tree.setTitle(tp.getTitle());
492 Newick newick = new Newick();
493 newick.setContent(tp.getTree().toString());
494 newick.setTitle(tp.getTitle());
495 tree.addNewick(newick);
496 tree.setProvenance(makeTreeProvenance(jal, tp));
497 tree.setTreenode(makeTreeNodes(tp.getTree(), newick));
499 alignment.addTree(tree);
503 * note: this function assumes that all sequence and alignment objects
504 * referenced in input data has already been associated with jalview objects.
508 * @return Object[] { AlignmentView, AlignmentI - reference alignment for
511 public Object[] recoverInputData(Provenance tp)
513 AlignmentViewport javport = null;
514 jalview.datamodel.AlignmentI jal = null;
515 jalview.datamodel.CigarArray view = null;
516 for (int pe = 0; pe < tp.getEntryCount(); pe++)
518 if (tp.getEntry(pe).getInputCount() > 0)
520 if (tp.getEntry(pe).getInputCount() > 1)
523 .warn("Ignoring additional input spec in provenance entry "
524 + tp.getEntry(pe).toString());
526 // LATER: deal sensibly with multiple inputs
527 Input vInput = tp.getEntry(pe).getInput(0);
528 // is this the whole alignment or a specific set of sequences ?
529 if (vInput.getObjRefCount() == 0)
531 if (tree.getV_parent() != null
532 && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
534 javport = getViewport(tree.getV_parent());
535 jal = javport.getAlignment();
536 view = javport.getAlignment().getCompactAlignment();
541 // Explicit reference - to alignment, sequences or what.
542 if (vInput.getObjRefCount() == 1
543 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
545 // recover an AlignmentView for the input data
546 javport = getViewport((Vobject) vInput.getObjRef(0));
547 jal = javport.getAlignment();
548 view = javport.getAlignment().getCompactAlignment();
550 else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
552 // recover an AlignmentView for the input data
553 javport = getViewport(((Vobject) vInput.getObjRef(0))
555 jal = javport.getAlignment();
556 jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
558 for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
560 SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
564 view = new jalview.datamodel.Alignment(seqs)
565 .getCompactAlignment();
569 int from = 1, to = jal.getWidth();
570 int offset = 0; // deleteRange modifies its frame of reference
571 for (int r = 0, s = vInput.getSegCount(); r < s; r++)
573 Seg visSeg = vInput.getSeg(r);
574 int se[] = getSegRange(visSeg, true); // jalview doesn't do
575 // bidirection alignments yet.
578 Cache.log.warn("Ignoring invalid segment in InputData spec.");
584 view.deleteRange(offset + from - 1, offset + se[0] - 2);
585 offset -= se[0] - from;
592 view.deleteRange(offset + from - 1, offset + to - 1); // final
598 return new Object[] { new AlignmentView(view), jal };
602 .debug("Returning null for input data recovery from provenance.");
606 private AlignmentViewport getViewport(Vobject v_parent)
608 if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
611 .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent);
616 public NewickFile getNewickTree()
621 public String getTitle()
626 public AlignmentView getInputData()
631 public boolean isValidTree()
640 if (ntree.getTree() != null)
645 } catch (Exception e)
647 Cache.log.debug("Failed to parse newick tree string", e);