2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.io.vamsas;
21 import java.io.IOException;
22 import java.util.Enumeration;
23 import java.util.Hashtable;
24 import java.util.Vector;
26 import jalview.analysis.NJTree;
27 import jalview.analysis.SequenceIdMatcher;
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.AlignFrame;
37 import jalview.gui.AlignViewport;
38 import jalview.gui.TreePanel;
39 import jalview.io.NewickFile;
40 import jalview.io.VamsasAppDatastore;
41 import uk.ac.vamsas.client.Vobject;
42 import uk.ac.vamsas.objects.core.AlignmentSequence;
43 import uk.ac.vamsas.objects.core.Entry;
44 import uk.ac.vamsas.objects.core.Input;
45 import uk.ac.vamsas.objects.core.Newick;
46 import uk.ac.vamsas.objects.core.Param;
47 import uk.ac.vamsas.objects.core.Provenance;
48 import uk.ac.vamsas.objects.core.Seg;
49 import uk.ac.vamsas.objects.core.Treenode;
50 import uk.ac.vamsas.objects.core.Vref;
52 public class Tree extends DatastoreItem
58 uk.ac.vamsas.objects.core.Tree tree;
60 uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
63 private NewickFile ntree;
67 private AlignmentView inputData = null;
69 public static void updateFrom(VamsasAppDatastore datastore,
70 jalview.gui.AlignFrame alignFrame,
71 uk.ac.vamsas.objects.core.Tree vtree)
73 Tree toTree = new Tree(datastore, alignFrame, vtree);
76 public Tree(VamsasAppDatastore datastore,
77 jalview.gui.AlignFrame alignFrame,
78 uk.ac.vamsas.objects.core.Tree vtree)
80 super(datastore, vtree, TreePanel.class);
84 private NewickFile getNtree() throws IOException
86 return new jalview.io.NewickFile(tree.getNewick(0).getContent());
89 public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
90 uk.ac.vamsas.objects.core.Alignment alignment2)
92 super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
95 tp = (TreePanel) jvobj;
96 alignment = alignment2;
98 tree = (uk.ac.vamsas.objects.core.Tree) vobj;
103 * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
105 public void addFromDocument()
107 tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
108 TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
110 Object[] idata = recoverInputData(tree.getProvenance());
113 if (idata != null && idata[0] != null)
115 inputData = (AlignmentView) idata[0];
118 title = tree.getNewick(0).getTitle();
119 if (title == null || title.length() == 0)
121 title = tree.getTitle(); // hack!!!!
123 } catch (Exception e)
125 Cache.log.warn("Problems parsing treefile '"
126 + tree.getNewick(0).getContent() + "'", e);
131 * @see jalview.io.vamsas.DatastoreItem#conflict()
133 public void conflict()
136 .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
140 * @see jalview.io.vamsas.DatastoreItem#update()
142 public void updateToDoc()
144 if (isModifiable(tree.getModifiable()))
146 // synchronize(); // update();
147 // verify any changes.
148 log.info("TODO: Update tree in document from jalview.");
153 log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
157 * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
159 public void updateFromDoc()
161 // should probably just open a new tree panel in the same place as the old one
162 // TODO: Tree.updateFromDoc
164 TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
167 Object[] idata = recoverInputData(tree.getProvenance());
170 if (idata != null && idata[0] != null)
172 inputData = (AlignmentView) idata[0];
175 title = tree.getNewick(0).getTitle();
176 if (title == null || title.length() == 0)
178 title = tree.getTitle(); // hack!!!!
180 } catch (Exception e)
182 Cache.log.warn("Problems parsing treefile '"
183 + tree.getNewick(0).getContent() + "'", e);
185 log.debug("Update the local tree in jalview from the document.");
187 if (isModifiable(tree.getModifiable()))
189 // synchronize(); // update();
190 // verify any changes.
191 log.debug("Update tree in document from jalview.");
196 log.debug("Add modified jalview tree as new tree in document.");
201 * correctly creates provenance for trees calculated on an alignment by
208 private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
210 Cache.log.debug("Making Tree provenance for " + tp.getTitle());
211 Provenance prov = new Provenance();
212 prov.addEntry(new Entry());
213 prov.getEntry(0).setAction("imported " + tp.getTitle());
214 prov.getEntry(0).setUser(provEntry.getUser());
215 prov.getEntry(0).setApp(provEntry.getApp());
216 prov.getEntry(0).setDate(provEntry.getDate());
217 if (tp.getTree().hasOriginalSequenceData())
219 Input vInput = new Input();
220 // LATER: check to see if tree input data is contained in this alignment -
221 // or just correctly resolve the tree's seqData to the correct alignment
224 Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
225 .getTree().seqData.getSequences()));
226 Object[] alsqs = new Object[alsqrefs.size()];
227 alsqrefs.copyInto(alsqs);
228 vInput.setObjRef(alsqs);
229 // now create main provenance data
230 prov.getEntry(0).setAction("created " + tp.getTitle());
231 prov.getEntry(0).addInput(vInput);
232 // jalview's special input parameter for distance matrix calculations
233 vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name.
234 prov.getEntry(0).addParam(new Param());
235 prov.getEntry(0).getParam(0).setName("treeType");
236 prov.getEntry(0).getParam(0).setType("utf8");
237 prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
239 int ranges[] = tp.getTree().seqData.getVisibleContigs();
240 // VisibleContigs are with respect to alignment coordinates. Still need
242 int start = tp.getTree().seqData.getAlignmentOrigin();
243 for (int r = 0; r < ranges.length; r += 2)
245 Seg visSeg = new Seg();
246 visSeg.setStart(1 + start + ranges[r]);
247 visSeg.setEnd(start + ranges[r + 1]);
248 visSeg.setInclusive(true);
249 vInput.addSeg(visSeg);
252 Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
257 * look up SeqCigars in an existing alignment.
261 * @return vector of alignment sequences in order of SeqCigar array (but
262 * missing unfound seqcigars)
264 private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
266 SeqCigar[] tseqs = new SeqCigar[sequences.length];
267 System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
268 Vector alsq = new Vector();
269 Enumeration as = jal.getSequences().elements();
270 while (as.hasMoreElements())
272 SequenceI asq = (SequenceI) as.nextElement();
273 for (int t = 0; t < sequences.length; t++)
276 && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
277 .getDatasetSequence()))
278 // && tseqs[t].getStart()>=asq.getStart() &&
279 // tseqs[t].getEnd()<=asq.getEnd())
286 if (alsq.size() < sequences.length)
288 .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
294 * Update jalview newick representation with TreeNode map
297 * the treepanel that this tree is bound to.
299 public void UpdateSequenceTreeMap(TreePanel tp)
301 if (tp == null || tree == null)
303 Vector leaves = new Vector();
304 if (tp.getTree() == null)
306 Cache.log.warn("Not updating SequenceTreeMap for "
307 + tree.getVorbaId());
310 tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
311 Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
318 Treenode node = tn[i++];
319 BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
320 if (mappednode != null && mappednode instanceof SequenceNode)
322 SequenceNode leaf = (SequenceNode) mappednode;
323 // check if we can make the specified association
325 int vrf = 0, refv = 0;
326 while (jvseq == null && vrf < node.getVrefCount())
328 if (refv < node.getVref(vrf).getRefsCount())
330 Object noderef = node.getVref(vrf).getRefs(refv++);
331 if (noderef instanceof AlignmentSequence)
333 // we only make these kind of associations
334 jvseq = getvObj2jv((Vobject) noderef);
343 if (jvseq instanceof SequenceI)
345 leaf.setElement(jvseq);
346 leaf.setPlaceholder(false);
350 leaf.setPlaceholder(true);
352 .setElement(new Sequence(leaf.getName(),
353 "THISISAPLACEHLDER"));
359 // / TODO: refactor to vamsas :start
361 * construct treenode mappings for mapped sequences
367 public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
369 Vector leaves = new Vector();
370 ntree.findLeaves(ntree.getTopNode(), leaves);
371 Vector tnv = new Vector();
372 Enumeration l = leaves.elements();
373 Hashtable nodespecs = new Hashtable();
374 while (l.hasMoreElements())
376 jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l
378 if (tnode instanceof jalview.datamodel.SequenceNode)
380 if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
382 Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
384 if (assocseq instanceof SequenceI)
386 Vobject vobj = this.getjv2vObj(assocseq);
389 Treenode node = new Treenode();
390 if (newick.isRegisterable())
392 this.cdoc.registerObject(newick);
393 node.addTreeId(newick);
395 node.setNodespec(makeNodeSpec(nodespecs, tnode));
396 node.setName(tnode.getName());
397 Vref vr = new Vref();
400 tnv.addElement(node);
404 System.err.println("WARNING: Unassociated treeNode "
405 + tnode.element().toString()
407 + ((tnode.getName() != null) ? " label "
408 + tnode.getName() : ""));
416 Treenode[] tn = new Treenode[tnv.size()];
420 return new Treenode[]
424 private String makeNodeSpec(Hashtable nodespecs,
425 jalview.datamodel.BinaryNode tnode)
427 String nname = new String(tnode.getName());
428 Integer nindx = (Integer) nodespecs.get(nname);
431 nindx = new Integer(1);
433 nname = nindx.toString() + " " + nname;
438 * call to match up Treenode specs to NJTree parsed from document object.
442 * as returned from NJTree.findLeaves( .., ..) ..
445 private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
449 String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
450 String oval = nodespec.substring(0, nodespec.indexOf(' '));
453 occurence = new Integer(oval).intValue();
454 } catch (Exception e)
456 System.err.println("Invalid nodespec '" + nodespec + "'");
459 jalview.datamodel.BinaryNode bn = null;
462 Enumeration en = leaves.elements();
463 while (en.hasMoreElements() && nocc < occurence)
465 bn = (jalview.datamodel.BinaryNode) en.nextElement();
466 if (bn instanceof jalview.datamodel.SequenceNode
467 && bn.getName().equals(nspec))
477 // todo: end refactor to vamsas library
479 * add jalview object to vamsas document
482 public void addToDocument()
484 tree = new uk.ac.vamsas.objects.core.Tree();
485 bindjvvobj(tp, tree);
486 tree.setTitle(tp.getTitle());
487 Newick newick = new Newick();
488 newick.setContent(tp.getTree().toString());
489 newick.setTitle(tp.getTitle());
490 tree.addNewick(newick);
491 tree.setProvenance(makeTreeProvenance(jal, tp));
492 tree.setTreenode(makeTreeNodes(tp.getTree(), newick));
494 alignment.addTree(tree);
498 * note: this function assumes that all sequence and alignment objects
499 * referenced in input data has already been associated with jalview objects.
503 * @return Object[] { AlignmentView, AlignmentI - reference alignment for
506 public Object[] recoverInputData(Provenance tp)
508 AlignViewport javport = null;
509 jalview.datamodel.AlignmentI jal = null;
510 jalview.datamodel.CigarArray view = null;
511 for (int pe = 0; pe < tp.getEntryCount(); pe++)
513 if (tp.getEntry(pe).getInputCount() > 0)
515 if (tp.getEntry(pe).getInputCount() > 1)
518 .warn("Ignoring additional input spec in provenance entry "
519 + tp.getEntry(pe).toString());
521 // LATER: deal sensibly with multiple inputs
522 Input vInput = tp.getEntry(pe).getInput(0);
523 // is this the whole alignment or a specific set of sequences ?
524 if (vInput.getObjRefCount() == 0)
526 if (tree.getV_parent() != null
527 && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
529 javport = getViewport(tree.getV_parent());
530 jal = javport.getAlignment();
531 view = javport.getAlignment().getCompactAlignment();
536 // Explicit reference - to alignment, sequences or what.
537 if (vInput.getObjRefCount() == 1
538 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
540 // recover an AlignmentView for the input data
541 javport = getViewport((Vobject) vInput.getObjRef(0));
542 jal = javport.getAlignment();
543 view = javport.getAlignment().getCompactAlignment();
545 else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
547 // recover an AlignmentView for the input data
548 javport = getViewport(((Vobject) vInput.getObjRef(0))
550 jal = javport.getAlignment();
551 jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
553 for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
555 SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
559 view = new jalview.datamodel.Alignment(seqs)
560 .getCompactAlignment();
564 int from = 1, to = jal.getWidth();
565 int offset = 0; // deleteRange modifies its frame of reference
566 for (int r = 0, s = vInput.getSegCount(); r < s; r++)
568 Seg visSeg = vInput.getSeg(r);
569 int se[] = getSegRange(visSeg, true); // jalview doesn't do
570 // bidirection alignments yet.
573 Cache.log.warn("Ignoring invalid segment in InputData spec.");
579 view.deleteRange(offset + from - 1, offset + se[0] - 2);
580 offset -= se[0] - from;
587 view.deleteRange(offset + from - 1, offset + to - 1); // final
594 { new AlignmentView(view), jal };
598 .debug("Returning null for input data recovery from provenance.");
602 private AlignViewport getViewport(Vobject v_parent)
604 if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
607 .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent);
612 public NewickFile getNewickTree()
617 public String getTitle()
622 public AlignmentView getInputData()
627 public boolean isValidTree()
636 if (ntree.getTree() != null)
641 } catch (Exception e)
643 Cache.log.debug("Failed to parse newick tree string", e);