2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.io.vamsas;
21 import java.io.IOException;
22 import java.util.Enumeration;
23 import java.util.Hashtable;
24 import java.util.List;
25 import java.util.Vector;
27 import jalview.analysis.NJTree;
28 import jalview.bin.Cache;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.BinaryNode;
32 import jalview.datamodel.SeqCigar;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceI;
35 import jalview.datamodel.SequenceNode;
36 import jalview.gui.AlignViewport;
37 import jalview.gui.TreePanel;
38 import jalview.io.NewickFile;
39 import jalview.io.VamsasAppDatastore;
40 import uk.ac.vamsas.client.Vobject;
41 import uk.ac.vamsas.objects.core.AlignmentSequence;
42 import uk.ac.vamsas.objects.core.Entry;
43 import uk.ac.vamsas.objects.core.Input;
44 import uk.ac.vamsas.objects.core.Newick;
45 import uk.ac.vamsas.objects.core.Param;
46 import uk.ac.vamsas.objects.core.Provenance;
47 import uk.ac.vamsas.objects.core.Seg;
48 import uk.ac.vamsas.objects.core.Treenode;
49 import uk.ac.vamsas.objects.core.Vref;
51 public class Tree extends DatastoreItem
57 uk.ac.vamsas.objects.core.Tree tree;
59 uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
62 private NewickFile ntree;
66 private AlignmentView inputData = null;
68 public static void updateFrom(VamsasAppDatastore datastore,
69 jalview.gui.AlignFrame alignFrame,
70 uk.ac.vamsas.objects.core.Tree vtree)
72 Tree toTree = new Tree(datastore, alignFrame, vtree);
75 public Tree(VamsasAppDatastore datastore,
76 jalview.gui.AlignFrame alignFrame,
77 uk.ac.vamsas.objects.core.Tree vtree)
79 super(datastore, vtree, TreePanel.class);
83 private NewickFile getNtree() throws IOException
85 return new jalview.io.NewickFile(tree.getNewick(0).getContent());
88 public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
89 uk.ac.vamsas.objects.core.Alignment alignment2)
91 super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
94 tp = (TreePanel) jvobj;
95 alignment = alignment2;
97 tree = (uk.ac.vamsas.objects.core.Tree) vobj;
104 * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
107 public void addFromDocument()
109 tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
110 TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
112 Object[] idata = recoverInputData(tree.getProvenance());
115 if (idata != null && idata[0] != null)
117 inputData = (AlignmentView) idata[0];
120 title = tree.getNewick(0).getTitle();
121 if (title == null || title.length() == 0)
123 title = tree.getTitle(); // hack!!!!
125 } catch (Exception e)
127 Cache.log.warn("Problems parsing treefile '"
128 + tree.getNewick(0).getContent() + "'", e);
135 * @see jalview.io.vamsas.DatastoreItem#conflict()
138 public void conflict()
141 .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
147 * @see jalview.io.vamsas.DatastoreItem#update()
150 public void updateToDoc()
152 if (isModifiable(tree.getModifiable()))
154 // synchronize(); // update();
155 // verify any changes.
156 log.info("TODO: Update tree in document from jalview.");
161 log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
168 * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
171 public void updateFromDoc()
173 // should probably just open a new tree panel in the same place as the old
175 // TODO: Tree.updateFromDoc
177 * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
179 * // make a new tree Object[] idata =
180 * recoverInputData(tree.getProvenance()); try { if (idata != null &&
181 * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
182 * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
183 * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
184 * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
185 * tree.getNewick(0).getContent() + "'", e); }
187 log.debug("Update the local tree in jalview from the document.");
189 if (isModifiable(tree.getModifiable()))
191 // synchronize(); // update();
192 // verify any changes.
193 log.debug("Update tree in document from jalview.");
198 log.debug("Add modified jalview tree as new tree in document.");
203 * correctly creates provenance for trees calculated on an alignment by
210 private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
212 Cache.log.debug("Making Tree provenance for " + tp.getTitle());
213 Provenance prov = new Provenance();
214 prov.addEntry(new Entry());
215 prov.getEntry(0).setAction("imported " + tp.getTitle());
216 prov.getEntry(0).setUser(provEntry.getUser());
217 prov.getEntry(0).setApp(provEntry.getApp());
218 prov.getEntry(0).setDate(provEntry.getDate());
219 if (tp.getTree().hasOriginalSequenceData())
221 Input vInput = new Input();
222 // LATER: check to see if tree input data is contained in this alignment -
223 // or just correctly resolve the tree's seqData to the correct alignment
226 Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
227 tp.getTree().seqData.getSequences()));
228 Object[] alsqs = new Object[alsqrefs.size()];
229 alsqrefs.copyInto(alsqs);
230 vInput.setObjRef(alsqs);
231 // now create main provenance data
232 prov.getEntry(0).setAction("created " + tp.getTitle());
233 prov.getEntry(0).addInput(vInput);
234 // jalview's special input parameter for distance matrix calculations
235 vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name.
236 prov.getEntry(0).addParam(new Param());
237 prov.getEntry(0).getParam(0).setName("treeType");
238 prov.getEntry(0).getParam(0).setType("utf8");
239 prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
241 int ranges[] = tp.getTree().seqData.getVisibleContigs();
242 // VisibleContigs are with respect to alignment coordinates. Still need
244 int start = tp.getTree().seqData.getAlignmentOrigin();
245 for (int r = 0; r < ranges.length; r += 2)
247 Seg visSeg = new Seg();
248 visSeg.setStart(1 + start + ranges[r]);
249 visSeg.setEnd(start + ranges[r + 1]);
250 visSeg.setInclusive(true);
251 vInput.addSeg(visSeg);
254 Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
259 * look up SeqCigars in an existing alignment.
263 * @return vector of alignment sequences in order of SeqCigar array (but
264 * missing unfound seqcigars)
266 private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
268 SeqCigar[] tseqs = new SeqCigar[sequences.length];
269 System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
270 Vector alsq = new Vector();
271 List<SequenceI> jalsqs;
272 synchronized (jalsqs = jal.getSequences())
274 for (SequenceI asq : jalsqs)
276 for (int t = 0; t < sequences.length; t++)
279 && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
280 .getDatasetSequence()))
281 // && tseqs[t].getStart()>=asq.getStart() &&
282 // tseqs[t].getEnd()<=asq.getEnd())
290 if (alsq.size() < sequences.length)
292 .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
298 * Update jalview newick representation with TreeNode map
301 * the treepanel that this tree is bound to.
303 public void UpdateSequenceTreeMap(TreePanel tp)
305 if (tp == null || tree == null)
307 Vector leaves = new Vector();
308 if (tp.getTree() == null)
310 Cache.log.warn("Not updating SequenceTreeMap for "
311 + tree.getVorbaId());
314 tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
315 Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
322 Treenode node = tn[i++];
323 BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
324 if (mappednode != null && mappednode instanceof SequenceNode)
326 SequenceNode leaf = (SequenceNode) mappednode;
327 // check if we can make the specified association
329 int vrf = 0, refv = 0;
330 while (jvseq == null && vrf < node.getVrefCount())
332 if (refv < node.getVref(vrf).getRefsCount())
334 Object noderef = node.getVref(vrf).getRefs(refv++);
335 if (noderef instanceof AlignmentSequence)
337 // we only make these kind of associations
338 jvseq = getvObj2jv((Vobject) noderef);
347 if (jvseq instanceof SequenceI)
349 leaf.setElement(jvseq);
350 leaf.setPlaceholder(false);
354 leaf.setPlaceholder(true);
355 leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
361 // / TODO: refactor to vamsas :start
363 * construct treenode mappings for mapped sequences
369 public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
371 Vector leaves = new Vector();
372 ntree.findLeaves(ntree.getTopNode(), leaves);
373 Vector tnv = new Vector();
374 Enumeration l = leaves.elements();
375 Hashtable nodespecs = new Hashtable();
376 while (l.hasMoreElements())
378 jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l
380 if (tnode instanceof jalview.datamodel.SequenceNode)
382 if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
384 Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
386 if (assocseq instanceof SequenceI)
388 Vobject vobj = this.getjv2vObj(assocseq);
391 Treenode node = new Treenode();
392 if (newick.isRegisterable())
394 this.cdoc.registerObject(newick);
395 node.addTreeId(newick);
397 node.setNodespec(makeNodeSpec(nodespecs, tnode));
398 node.setName(tnode.getName());
399 Vref vr = new Vref();
402 tnv.addElement(node);
406 System.err.println("WARNING: Unassociated treeNode "
407 + tnode.element().toString()
409 + ((tnode.getName() != null) ? " label "
410 + tnode.getName() : ""));
418 Treenode[] tn = new Treenode[tnv.size()];
422 return new Treenode[]
426 private String makeNodeSpec(Hashtable nodespecs,
427 jalview.datamodel.BinaryNode tnode)
429 String nname = new String(tnode.getName());
430 Integer nindx = (Integer) nodespecs.get(nname);
433 nindx = new Integer(1);
435 nname = nindx.toString() + " " + nname;
440 * call to match up Treenode specs to NJTree parsed from document object.
444 * as returned from NJTree.findLeaves( .., ..) ..
447 private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
451 String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
452 String oval = nodespec.substring(0, nodespec.indexOf(' '));
455 occurence = new Integer(oval).intValue();
456 } catch (Exception e)
458 System.err.println("Invalid nodespec '" + nodespec + "'");
461 jalview.datamodel.BinaryNode bn = null;
464 Enumeration en = leaves.elements();
465 while (en.hasMoreElements() && nocc < occurence)
467 bn = (jalview.datamodel.BinaryNode) en.nextElement();
468 if (bn instanceof jalview.datamodel.SequenceNode
469 && bn.getName().equals(nspec))
479 // todo: end refactor to vamsas library
481 * add jalview object to vamsas document
485 public void addToDocument()
487 tree = new uk.ac.vamsas.objects.core.Tree();
488 bindjvvobj(tp, tree);
489 tree.setTitle(tp.getTitle());
490 Newick newick = new Newick();
491 newick.setContent(tp.getTree().toString());
492 newick.setTitle(tp.getTitle());
493 tree.addNewick(newick);
494 tree.setProvenance(makeTreeProvenance(jal, tp));
495 tree.setTreenode(makeTreeNodes(tp.getTree(), newick));
497 alignment.addTree(tree);
501 * note: this function assumes that all sequence and alignment objects
502 * referenced in input data has already been associated with jalview objects.
506 * @return Object[] { AlignmentView, AlignmentI - reference alignment for
509 public Object[] recoverInputData(Provenance tp)
511 AlignViewport javport = null;
512 jalview.datamodel.AlignmentI jal = null;
513 jalview.datamodel.CigarArray view = null;
514 for (int pe = 0; pe < tp.getEntryCount(); pe++)
516 if (tp.getEntry(pe).getInputCount() > 0)
518 if (tp.getEntry(pe).getInputCount() > 1)
521 .warn("Ignoring additional input spec in provenance entry "
522 + tp.getEntry(pe).toString());
524 // LATER: deal sensibly with multiple inputs
525 Input vInput = tp.getEntry(pe).getInput(0);
526 // is this the whole alignment or a specific set of sequences ?
527 if (vInput.getObjRefCount() == 0)
529 if (tree.getV_parent() != null
530 && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
532 javport = getViewport(tree.getV_parent());
533 jal = javport.getAlignment();
534 view = javport.getAlignment().getCompactAlignment();
539 // Explicit reference - to alignment, sequences or what.
540 if (vInput.getObjRefCount() == 1
541 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
543 // recover an AlignmentView for the input data
544 javport = getViewport((Vobject) vInput.getObjRef(0));
545 jal = javport.getAlignment();
546 view = javport.getAlignment().getCompactAlignment();
548 else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
550 // recover an AlignmentView for the input data
551 javport = getViewport(((Vobject) vInput.getObjRef(0))
553 jal = javport.getAlignment();
554 jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
556 for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
558 SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
562 view = new jalview.datamodel.Alignment(seqs)
563 .getCompactAlignment();
567 int from = 1, to = jal.getWidth();
568 int offset = 0; // deleteRange modifies its frame of reference
569 for (int r = 0, s = vInput.getSegCount(); r < s; r++)
571 Seg visSeg = vInput.getSeg(r);
572 int se[] = getSegRange(visSeg, true); // jalview doesn't do
573 // bidirection alignments yet.
576 Cache.log.warn("Ignoring invalid segment in InputData spec.");
582 view.deleteRange(offset + from - 1, offset + se[0] - 2);
583 offset -= se[0] - from;
590 view.deleteRange(offset + from - 1, offset + to - 1); // final
597 { new AlignmentView(view), jal };
601 .debug("Returning null for input data recovery from provenance.");
605 private AlignViewport getViewport(Vobject v_parent)
607 if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
610 .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent);
615 public NewickFile getNewickTree()
620 public String getTitle()
625 public AlignmentView getInputData()
630 public boolean isValidTree()
639 if (ntree.getTree() != null)
644 } catch (Exception e)
646 Cache.log.debug("Failed to parse newick tree string", e);