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.TreeBuilder;
24 import jalview.analysis.TreeModel;
25 import jalview.bin.Cache;
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;
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;
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;
55 public class Tree extends DatastoreItem
61 uk.ac.vamsas.objects.core.Tree tree;
63 uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
66 private NewickFile ntree;
70 private AlignmentView inputData = null;
72 public static void updateFrom(VamsasAppDatastore datastore,
73 jalview.gui.AlignFrame alignFrame,
74 uk.ac.vamsas.objects.core.Tree vtree)
76 Tree toTree = new Tree(datastore, alignFrame, vtree);
79 public Tree(VamsasAppDatastore datastore,
80 jalview.gui.AlignFrame alignFrame,
81 uk.ac.vamsas.objects.core.Tree vtree)
83 super(datastore, vtree, TreePanel.class);
87 private NewickFile getNtree() throws IOException
89 return new jalview.io.NewickFile(tree.getNewick(0).getContent());
92 public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
93 uk.ac.vamsas.objects.core.Alignment alignment2)
95 super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
98 tp = (TreePanel) jvobj;
99 alignment = alignment2;
101 tree = (uk.ac.vamsas.objects.core.Tree) vobj;
108 * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
111 public void addFromDocument()
113 tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
114 TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
116 Object[] idata = recoverInputData(tree.getProvenance());
119 if (idata != null && idata[0] != null)
121 inputData = (AlignmentView) idata[0];
124 title = tree.getNewick(0).getTitle();
125 if (title == null || title.length() == 0)
127 title = tree.getTitle(); // hack!!!!
129 } catch (Exception e)
131 Cache.log.warn("Problems parsing treefile '"
132 + tree.getNewick(0).getContent() + "'", e);
139 * @see jalview.io.vamsas.DatastoreItem#conflict()
142 public void conflict()
145 .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
151 * @see jalview.io.vamsas.DatastoreItem#update()
154 public void updateToDoc()
156 if (isModifiable(tree.getModifiable()))
158 // synchronize(); // update();
159 // verify any changes.
160 log.info("TODO: Update tree in document from jalview.");
165 log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
172 * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
175 public void updateFromDoc()
177 // should probably just open a new tree panel in the same place as the old
179 // TODO: Tree.updateFromDoc
181 * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
183 * // make a new tree Object[] idata =
184 * recoverInputData(tree.getProvenance()); try { if (idata != null &&
185 * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
186 * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
187 * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
188 * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
189 * tree.getNewick(0).getContent() + "'", e); }
191 log.debug("Update the local tree in jalview from the document.");
193 if (isModifiable(tree.getModifiable()))
195 // synchronize(); // update();
196 // verify any changes.
197 log.debug("Update tree in document from jalview.");
202 log.debug("Add modified jalview tree as new tree in document.");
207 * correctly creates provenance for trees calculated on an alignment by
214 private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
216 Cache.log.debug("Making Tree provenance for " + tp.getTitle());
217 Provenance prov = new Provenance();
218 prov.addEntry(new Entry());
219 prov.getEntry(0).setAction("imported " + tp.getTitle());
220 prov.getEntry(0).setUser(provEntry.getUser());
221 prov.getEntry(0).setApp(provEntry.getApp());
222 prov.getEntry(0).setDate(provEntry.getDate());
223 if (tp.getTree().hasOriginalSequenceData())
225 Input vInput = new Input();
226 // LATER: check to see if tree input data is contained in this alignment -
227 // or just correctly resolve the tree's seqData to the correct alignment
230 Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
231 tp.getTree().seqData.getSequences()));
232 Object[] alsqs = new Object[alsqrefs.size()];
233 alsqrefs.copyInto(alsqs);
234 vInput.setObjRef(alsqs);
235 // now create main provenance data
236 prov.getEntry(0).setAction("created " + tp.getTitle());
237 prov.getEntry(0).addInput(vInput);
238 // jalview's special input parameter for distance matrix calculations
239 vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name.
240 prov.getEntry(0).addParam(new Param());
241 prov.getEntry(0).getParam(0).setName("treeType");
242 prov.getEntry(0).getParam(0).setType("utf8");
243 prov.getEntry(0).getParam(0)
244 .setContent(TreeBuilder.NEIGHBOUR_JOINING);
245 // TODO: type of tree is a general parameter
246 int ranges[] = tp.getTree().seqData.getVisibleContigs();
247 // VisibleContigs are with respect to alignment coordinates. Still need
249 int start = tp.getTree().seqData.getAlignmentOrigin();
250 for (int r = 0; r < ranges.length; r += 2)
252 Seg visSeg = new Seg();
253 visSeg.setStart(1 + start + ranges[r]);
254 visSeg.setEnd(start + ranges[r + 1]);
255 visSeg.setInclusive(true);
256 vInput.addSeg(visSeg);
259 Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
264 * look up SeqCigars in an existing alignment.
268 * @return vector of alignment sequences in order of SeqCigar array (but
269 * missing unfound seqcigars)
271 private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
273 SeqCigar[] tseqs = new SeqCigar[sequences.length];
274 System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
275 Vector alsq = new Vector();
276 List<SequenceI> jalsqs;
277 synchronized (jalsqs = jal.getSequences())
279 for (SequenceI asq : jalsqs)
281 for (int t = 0; t < sequences.length; t++)
284 && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
285 .getDatasetSequence()))
286 // && tseqs[t].getStart()>=asq.getStart() &&
287 // tseqs[t].getEnd()<=asq.getEnd())
295 if (alsq.size() < sequences.length)
298 .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
305 * Update jalview newick representation with TreeNode map
308 * the treepanel that this tree is bound to.
310 public void UpdateSequenceTreeMap(TreePanel tp)
312 if (tp == null || tree == null)
317 if (tp.getTree() == null)
319 Cache.log.warn("Not updating SequenceTreeMap for "
320 + tree.getVorbaId());
323 Vector<SequenceNode> leaves = tp.getTree().findLeaves(
324 tp.getTree().getTopNode());
325 Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
332 Treenode node = tn[i++];
333 BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
334 if (mappednode != null && mappednode instanceof SequenceNode)
336 SequenceNode leaf = (SequenceNode) mappednode;
337 // check if we can make the specified association
339 int vrf = 0, refv = 0;
340 while (jvseq == null && vrf < node.getVrefCount())
342 if (refv < node.getVref(vrf).getRefsCount())
344 Object noderef = node.getVref(vrf).getRefs(refv++);
345 if (noderef instanceof AlignmentSequence)
347 // we only make these kind of associations
348 jvseq = getvObj2jv((Vobject) noderef);
357 if (jvseq instanceof SequenceI)
359 leaf.setElement(jvseq);
360 leaf.setPlaceholder(false);
364 leaf.setPlaceholder(true);
365 leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
371 // / TODO: refactor to vamsas :start
373 * construct treenode mappings for mapped sequences
379 public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
381 Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
383 Vector tnv = new Vector();
384 Enumeration l = leaves.elements();
385 Hashtable nodespecs = new Hashtable();
386 while (l.hasMoreElements())
388 jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l
390 if (tnode instanceof jalview.datamodel.SequenceNode)
392 if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
394 Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
396 if (assocseq instanceof SequenceI)
398 Vobject vobj = this.getjv2vObj(assocseq);
401 Treenode node = new Treenode();
402 if (newick.isRegisterable())
404 this.cdoc.registerObject(newick);
405 node.addTreeId(newick);
407 node.setNodespec(makeNodeSpec(nodespecs, tnode));
408 node.setName(tnode.getName());
409 Vref vr = new Vref();
412 tnv.addElement(node);
416 System.err.println("WARNING: Unassociated treeNode "
417 + tnode.element().toString()
419 + ((tnode.getName() != null) ? " label "
420 + tnode.getName() : ""));
428 Treenode[] tn = new Treenode[tnv.size()];
432 return new Treenode[] {};
435 private String makeNodeSpec(Hashtable nodespecs,
436 jalview.datamodel.BinaryNode tnode)
438 String nname = new String(tnode.getName());
439 Integer nindx = (Integer) nodespecs.get(nname);
442 nindx = new Integer(1);
444 nname = nindx.toString() + " " + nname;
449 * call to match up Treenode specs to NJTree parsed from document object.
453 * as returned from NJTree.findLeaves( .., ..) ..
456 private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
460 String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
461 String oval = nodespec.substring(0, nodespec.indexOf(' '));
464 occurence = new Integer(oval).intValue();
465 } catch (Exception e)
467 System.err.println("Invalid nodespec '" + nodespec + "'");
470 jalview.datamodel.BinaryNode bn = null;
473 Enumeration en = leaves.elements();
474 while (en.hasMoreElements() && nocc < occurence)
476 bn = (jalview.datamodel.BinaryNode) en.nextElement();
477 if (bn instanceof jalview.datamodel.SequenceNode
478 && bn.getName().equals(nspec))
490 // todo: end refactor to vamsas library
492 * add jalview object to vamsas document
496 public void addToDocument()
498 tree = new uk.ac.vamsas.objects.core.Tree();
499 bindjvvobj(tp, tree);
500 tree.setTitle(tp.getTitle());
501 Newick newick = new Newick();
502 newick.setContent(tp.getTree().print());
503 newick.setTitle(tp.getTitle());
504 tree.addNewick(newick);
505 tree.setProvenance(makeTreeProvenance(jal, tp));
506 tree.setTreenode(makeTreeNodes(tp.getTree(), newick));
508 alignment.addTree(tree);
512 * note: this function assumes that all sequence and alignment objects
513 * referenced in input data has already been associated with jalview objects.
517 * @return Object[] { AlignmentView, AlignmentI - reference alignment for
520 public Object[] recoverInputData(Provenance tp)
522 AlignmentViewport javport = null;
523 jalview.datamodel.AlignmentI jal = null;
524 jalview.datamodel.CigarArray view = null;
525 for (int pe = 0; pe < tp.getEntryCount(); pe++)
527 if (tp.getEntry(pe).getInputCount() > 0)
529 if (tp.getEntry(pe).getInputCount() > 1)
532 .warn("Ignoring additional input spec in provenance entry "
533 + tp.getEntry(pe).toString());
535 // LATER: deal sensibly with multiple inputs
536 Input vInput = tp.getEntry(pe).getInput(0);
537 // is this the whole alignment or a specific set of sequences ?
538 if (vInput.getObjRefCount() == 0)
540 if (tree.getV_parent() != null
541 && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
543 javport = getViewport(tree.getV_parent());
544 jal = javport.getAlignment();
545 view = javport.getAlignment().getCompactAlignment();
550 // Explicit reference - to alignment, sequences or what.
551 if (vInput.getObjRefCount() == 1
552 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
554 // recover an AlignmentView for the input data
555 javport = getViewport((Vobject) vInput.getObjRef(0));
556 jal = javport.getAlignment();
557 view = javport.getAlignment().getCompactAlignment();
559 else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
561 // recover an AlignmentView for the input data
562 javport = getViewport(((Vobject) vInput.getObjRef(0))
564 jal = javport.getAlignment();
565 jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
567 for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
569 SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
573 view = new jalview.datamodel.Alignment(seqs)
574 .getCompactAlignment();
578 int from = 1, to = jal.getWidth();
579 int offset = 0; // deleteRange modifies its frame of reference
580 for (int r = 0, s = vInput.getSegCount(); r < s; r++)
582 Seg visSeg = vInput.getSeg(r);
583 int se[] = getSegRange(visSeg, true); // jalview doesn't do
584 // bidirection alignments yet.
587 Cache.log.warn("Ignoring invalid segment in InputData spec.");
593 view.deleteRange(offset + from - 1, offset + se[0] - 2);
594 offset -= se[0] - from;
601 view.deleteRange(offset + from - 1, offset + to - 1); // final
607 return new Object[] { new AlignmentView(view), jal };
611 .debug("Returning null for input data recovery from provenance.");
615 private AlignmentViewport getViewport(Vobject v_parent)
617 if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
620 .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent);
625 public NewickFile getNewickTree()
630 public String getTitle()
635 public AlignmentView getInputData()
640 public boolean isValidTree()
649 if (ntree.getTree() != null)
654 } catch (Exception e)
656 Cache.log.debug("Failed to parse newick tree string", e);