X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=e56fa3fdb299189b2953cd7c7ae19b648369430c;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=af4e7b748e136d8a4c20c50ac1f54f824b9579e7;hpb=3ca49e9277c7939fa282b67d14ee49fa3352d9c7;p=jalview.git
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index af4e7b7..e56fa3f 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,568 +1,652 @@
-package jalview.io.vamsas;
-
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import jalview.analysis.NJTree;
-import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.BinaryNode;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.TreePanel;
-import jalview.io.NewickFile;
-import jalview.io.VamsasAppDatastore;
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.objects.core.AlignmentSequence;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Input;
-import uk.ac.vamsas.objects.core.Newick;
-import uk.ac.vamsas.objects.core.Param;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.Seg;
-import uk.ac.vamsas.objects.core.Treenode;
-import uk.ac.vamsas.objects.core.Vref;
-
-public class Tree extends DatastoreItem
-{
- AlignmentI jal;
-
- TreePanel tp;
-
- uk.ac.vamsas.objects.core.Tree tree;
-
- uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
-
- // other kind of tree
- private NewickFile ntree;
-
- private String title;
-
- private AlignmentView inputData = null;
-
- public static void updateFrom(VamsasAppDatastore datastore,
- jalview.gui.AlignFrame alignFrame,
- uk.ac.vamsas.objects.core.Tree vtree)
- {
- Tree toTree = new Tree(datastore, alignFrame, vtree);
-
- }
-
- public Tree(VamsasAppDatastore datastore,
- jalview.gui.AlignFrame alignFrame,
- uk.ac.vamsas.objects.core.Tree vtree)
- {
- super(datastore);
- tree = vtree;
- TreePanel tp = (TreePanel) getvObj2jv(tree);
- if (tp != null)
- {
- if (tree.isUpdated())
- {
- Cache.log
- .info("Update from vamsas document to alignment associated tree not implemented yet.");
- }
- }
- else
- {
- // make a new tree
- Object[] idata = recoverInputData(tree.getProvenance());
- try
- {
- if (idata != null && idata[0] != null)
- {
- inputData = (AlignmentView) idata[0];
- }
- ntree = getNtree();
- title = tree.getNewick(0).getTitle();
- if (title == null || title.length() == 0)
- {
- title = tree.getTitle(); // hack!!!!
- }
- } catch (Exception e)
- {
- Cache.log.warn("Problems parsing treefile '"
- + tree.getNewick(0).getContent() + "'", e);
- }
- }
- }
-
- private NewickFile getNtree() throws IOException
- {
- return new jalview.io.NewickFile(tree.getNewick(0).getContent());
- }
-
- public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
- uk.ac.vamsas.objects.core.Alignment alignment2)
- {
- super(datastore);
-
- jal = jal2;
- tp = tp2;
- alignment = alignment2;
-
- tree = (uk.ac.vamsas.objects.core.Tree) getjv2vObj(tp);
- if (tree == null)
- {
- add();
- }
- else
- {
- if (isModifiable(tree.getModifiable()))
- {
- // synchronize(); // update();
- // verify any changes.
- System.out.println("Update tree in document.");
- }
- else
- {
- // handle conflict
- System.out.println("Add modified tree as new tree in document.");
- }
- }
- }
-
- /**
- * correctly creates provenance for trees calculated on an alignment by
- * jalview.
- *
- * @param jal
- * @param tp
- * @return
- */
- private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
- {
- Cache.log.debug("Making Tree provenance for " + tp.getTitle());
- Provenance prov = new Provenance();
- prov.addEntry(new Entry());
- prov.getEntry(0).setAction("imported " + tp.getTitle());
- prov.getEntry(0).setUser(provEntry.getUser());
- prov.getEntry(0).setApp(provEntry.getApp());
- prov.getEntry(0).setDate(provEntry.getDate());
- if (tp.getTree().hasOriginalSequenceData())
- {
- Input vInput = new Input();
- // LATER: check to see if tree input data is contained in this alignment -
- // or just correctly resolve the tree's seqData to the correct alignment
- // in
- // the document.
- Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
- .getTree().seqData.getSequences()));
- Object[] alsqs = new Object[alsqrefs.size()];
- alsqrefs.copyInto(alsqs);
- vInput.setObjRef(alsqs);
- // now create main provenance data
- prov.getEntry(0).setAction("created " + tp.getTitle());
- prov.getEntry(0).addInput(vInput);
- // jalview's special input parameter for distance matrix calculations
- vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name.
- prov.getEntry(0).addParam(new Param());
- prov.getEntry(0).getParam(0).setName("treeType");
- prov.getEntry(0).getParam(0).setType("utf8");
- prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
- // general parameter
- int ranges[] = tp.getTree().seqData.getVisibleContigs();
- // VisibleContigs are with respect to alignment coordinates. Still need
- // offsets
- int start = tp.getTree().seqData.getAlignmentOrigin();
- for (int r = 0; r < ranges.length; r += 2)
- {
- Seg visSeg = new Seg();
- visSeg.setStart(1 + start + ranges[r]);
- visSeg.setEnd(start + ranges[r + 1]);
- visSeg.setInclusive(true);
- vInput.addSeg(visSeg);
- }
- }
- Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
- return prov;
- }
-
- /**
- * look up SeqCigars in an existing alignment.
- *
- * @param jal
- * @param sequences
- * @return vector of alignment sequences in order of SeqCigar array (but
- * missing unfound seqcigars)
- */
- private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
- {
- SeqCigar[] tseqs = new SeqCigar[sequences.length];
- System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
- Vector alsq = new Vector();
- Enumeration as = jal.getSequences().elements();
- while (as.hasMoreElements())
- {
- SequenceI asq = (SequenceI) as.nextElement();
- for (int t = 0; t < sequences.length; t++)
- {
- if (tseqs[t] != null
- && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
- .getDatasetSequence()))
- // && tseqs[t].getStart()>=asq.getStart() &&
- // tseqs[t].getEnd()<=asq.getEnd())
- {
- tseqs[t] = null;
- alsq.add(asq);
- }
- }
- }
- if (alsq.size() < sequences.length)
- Cache.log
- .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
- return alsq;
- }
-
- /**
- *
- * Update jalview newick representation with TreeNode map
- *
- * @param tp
- * the treepanel that this tree is bound to.
- */
- public void UpdateSequenceTreeMap(TreePanel tp)
- {
- if (tp == null || tree != null)
- return;
- Vector leaves = new Vector();
- tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
- Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
- // particular tree
- int sz = tn.length;
- int i = 0;
-
- while (i < sz)
- {
- Treenode node = tn[i++];
- BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
- if (mappednode != null && mappednode instanceof SequenceNode)
- {
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
- // check if we can make the specified association
- Object jvseq = null;
- int vrf = 0, refv = 0;
- while (jvseq == null && vrf < node.getVrefCount())
- {
- if (refv < node.getVref(vrf).getRefsCount())
- {
- Object noderef = node.getVref(vrf).getRefs(refv++);
- if (noderef instanceof AlignmentSequence)
- {
- // we only make these kind of associations
- jvseq = getvObj2jv((Vobject) noderef);
- }
- }
- else
- {
- refv = 0;
- vrf++;
- }
- }
- if (jvseq instanceof SequenceI)
- {
- leaf.setElement(jvseq);
- leaf.setPlaceholder(false);
- }
- else
- {
- leaf.setPlaceholder(true);
- leaf
- .setElement(new Sequence(leaf.getName(),
- "THISISAPLACEHLDER"));
- }
- }
- }
- }
-
- // / TODO: refactor to vamsas :start
- /**
- * construct treenode mappings for mapped sequences
- *
- * @param ntree
- * @param newick
- * @return
- */
- public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
- {
- Vector leaves = new Vector();
- ntree.findLeaves(ntree.getTopNode(), leaves);
- Vector tnv = new Vector();
- Enumeration l = leaves.elements();
- Hashtable nodespecs = new Hashtable();
- while (l.hasMoreElements())
- {
- jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l
- .nextElement();
- if (tnode instanceof jalview.datamodel.SequenceNode)
- {
- if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
- {
- Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
- .element();
- if (assocseq instanceof SequenceI)
- {
- Vobject vobj = this.getjv2vObj(assocseq);
- if (vobj != null)
- {
- Treenode node = new Treenode();
- if (newick.isRegisterable())
- {
- this.cdoc.registerObject(newick);
- node.addTreeId(newick);
- }
- node.setNodespec(makeNodeSpec(nodespecs, tnode));
- node.setName(tnode.getName());
- Vref vr = new Vref();
- vr.addRefs(vobj);
- node.addVref(vr);
- tnv.addElement(node);
- }
- else
- {
- System.err.println("WARNING: Unassociated treeNode "
- + tnode.element().toString()
- + " "
- + ((tnode.getName() != null) ? " label "
- + tnode.getName() : ""));
- }
- }
- }
- }
- }
- if (tnv.size() > 0)
- {
- Treenode[] tn = new Treenode[tnv.size()];
- tnv.copyInto(tn);
- return tn;
- }
- return new Treenode[]
- {};
- }
-
- private String makeNodeSpec(Hashtable nodespecs,
- jalview.datamodel.BinaryNode tnode)
- {
- String nname = new String(tnode.getName());
- Integer nindx = (Integer) nodespecs.get(nname);
- if (nindx == null)
- {
- nindx = new Integer(1);
- }
- nname = nindx.toString() + " " + nname;
- return nname;
- }
-
- /**
- * call to match up Treenode specs to NJTree parsed from document object.
- *
- * @param nodespec
- * @param leaves
- * as returned from NJTree.findLeaves( .., ..) ..
- * @return
- */
- private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
- Vector leaves)
- {
- int occurence = -1;
- String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
- String oval = nodespec.substring(0, nodespec.indexOf(' '));
- try
- {
- occurence = new Integer(oval).intValue();
- } catch (Exception e)
- {
- System.err.println("Invalid nodespec '" + nodespec + "'");
- return null;
- }
- jalview.datamodel.BinaryNode bn = null;
-
- int nocc = 0;
- Enumeration en = leaves.elements();
- while (en.hasMoreElements() && nocc < occurence)
- {
- bn = (jalview.datamodel.BinaryNode) en.nextElement();
- if (bn instanceof jalview.datamodel.SequenceNode
- && bn.getName().equals(nspec))
- {
- --occurence;
- }
- else
- bn = null;
- }
- return bn;
- }
-
- // todo: end refactor to vamsas library
- /**
- * add jalview object to vamsas document
- *
- */
- public void add()
- {
- tree = new uk.ac.vamsas.objects.core.Tree();
- bindjvvobj(tp, tree);
- tree.setTitle(tp.getTitle());
- Newick newick = new Newick();
- newick.setContent(tp.getTree().toString());
- newick.setTitle(tp.getTitle());
- tree.addNewick(newick);
- tree.setProvenance(makeTreeProvenance(jal, tp));
- tree.setTreenode(makeTreeNodes(tp.getTree(), newick));
-
- alignment.addTree(tree);
- }
-
- /**
- * note: this function assumes that all sequence and alignment objects
- * referenced in input data has already been associated with jalview objects.
- *
- * @param tp
- * @param alignFrame
- * @return Object[] { AlignmentView, AlignmentI - reference alignment for
- * input }
- */
- public Object[] recoverInputData(Provenance tp)
- {
- AlignViewport javport = null;
- jalview.datamodel.AlignmentI jal = null;
- jalview.datamodel.CigarArray view = null;
- for (int pe = 0; pe < tp.getEntryCount(); pe++)
- {
- if (tp.getEntry(pe).getInputCount() > 0)
- {
- if (tp.getEntry(pe).getInputCount() > 1)
- {
- Cache.log
- .warn("Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
- }
- // LATER: deal sensibly with multiple inputs
- Input vInput = tp.getEntry(pe).getInput(0);
- // is this the whole alignment or a specific set of sequences ?
- if (vInput.getObjRefCount() == 0)
- {
- if (tree.getV_parent()!=null && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
- {
- javport = getViewport(tree.getV_parent());
- jal = javport.getAlignment();
- view = javport.getAlignment().getCompactAlignment();
- }
- }
- else
- {
- // Explicit reference - to alignment, sequences or what.
- if (vInput.getObjRefCount() == 1
- && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
- {
- // recover an AlignmentView for the input data
- javport = getViewport((Vobject) vInput.getObjRef(0));
- jal = javport.getAlignment();
- view = javport.getAlignment().getCompactAlignment();
- }
- else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
- {
- // recover an AlignmentView for the input data
- javport = getViewport(((Vobject) vInput.getObjRef(0)).getV_parent());
- jal = javport.getAlignment();
- jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
- .getObjRefCount()];
- for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
- {
- SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
- .getObjRef(i));
- seqs[i] = seq;
- }
- view = new jalview.datamodel.Alignment(seqs)
- .getCompactAlignment();
-
- }
- }
- int from = 1, to = jal.getWidth();
- int offset = 0; // deleteRange modifies its frame of reference
- for (int r = 0, s = vInput.getSegCount(); r < s; r++)
- {
- Seg visSeg = vInput.getSeg(r);
- int se[] = getSegRange(visSeg, true); // jalview doesn't do
- // bidirection alignments yet.
- if (to < se[1])
- {
- Cache.log.warn("Ignoring invalid segment in InputData spec.");
- }
- else
- {
- if (se[0] > from)
- {
- view.deleteRange(offset + from - 1, offset + se[0] - 2);
- offset -= se[0] - from;
- }
- from = se[1] + 1;
- }
- }
- if (from < to)
- {
- view.deleteRange(offset + from - 1, offset + to - 1); // final
- // deletion -
- // TODO: check
- // off by
- // one for to
- }
- return new Object[]
- { new AlignmentView(view), jal };
- }
- }
- Cache.log
- .debug("Returning null for input data recovery from provenance.");
- return null;
- }
-
- private AlignViewport getViewport(Vobject v_parent)
- {
- if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
- {
- return datastore
- .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent);
- }
- return null;
- }
-
- public NewickFile getNewickTree()
- {
- return ntree;
- }
-
- public String getTitle()
- {
- return title;
- }
-
- public AlignmentView getInputData()
- {
- return inputData;
- }
-
- public boolean isValidTree()
- {
- try
- {
- ntree.parse();
- if (ntree.getTree() != null)
- {
- ntree = getNtree();
- }
- return true;
- } catch (Exception e)
- {
- Cache.log.debug("Failed to parse newick tree string", e);
- }
- return false;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io.vamsas;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.analysis.NJTree;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.gui.AlignViewport;
+import jalview.gui.TreePanel;
+import jalview.io.NewickFile;
+import jalview.io.VamsasAppDatastore;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Input;
+import uk.ac.vamsas.objects.core.Newick;
+import uk.ac.vamsas.objects.core.Param;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Treenode;
+import uk.ac.vamsas.objects.core.Vref;
+
+public class Tree extends DatastoreItem
+{
+ AlignmentI jal;
+
+ TreePanel tp;
+
+ uk.ac.vamsas.objects.core.Tree tree;
+
+ uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
+
+ // other kind of tree
+ private NewickFile ntree;
+
+ private String title;
+
+ private AlignmentView inputData = null;
+
+ public static void updateFrom(VamsasAppDatastore datastore,
+ jalview.gui.AlignFrame alignFrame,
+ uk.ac.vamsas.objects.core.Tree vtree)
+ {
+ Tree toTree = new Tree(datastore, alignFrame, vtree);
+ }
+
+ public Tree(VamsasAppDatastore datastore,
+ jalview.gui.AlignFrame alignFrame,
+ uk.ac.vamsas.objects.core.Tree vtree)
+ {
+ super(datastore, vtree, TreePanel.class);
+ doJvUpdate();
+ }
+
+ private NewickFile getNtree() throws IOException
+ {
+ return new jalview.io.NewickFile(tree.getNewick(0).getContent());
+ }
+
+ public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
+ uk.ac.vamsas.objects.core.Alignment alignment2)
+ {
+ super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
+
+ jal = jal2;
+ tp = (TreePanel) jvobj;
+ alignment = alignment2;
+
+ tree = (uk.ac.vamsas.objects.core.Tree) vobj;
+ doSync();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
+ */
+ @Override
+ public void addFromDocument()
+ {
+ tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
+ TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+ // make a new tree
+ Object[] idata = recoverInputData(tree.getProvenance());
+ try
+ {
+ if (idata != null && idata[0] != null)
+ {
+ inputData = (AlignmentView) idata[0];
+ }
+ ntree = getNtree();
+ title = tree.getNewick(0).getTitle();
+ if (title == null || title.length() == 0)
+ {
+ title = tree.getTitle(); // hack!!!!
+ }
+ } catch (Exception e)
+ {
+ Cache.log.warn("Problems parsing treefile '"
+ + tree.getNewick(0).getContent() + "'", e);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#conflict()
+ */
+ @Override
+ public void conflict()
+ {
+ Cache.log
+ .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#update()
+ */
+ @Override
+ public void updateToDoc()
+ {
+ if (isModifiable(tree.getModifiable()))
+ {
+ // synchronize(); // update();
+ // verify any changes.
+ log.info("TODO: Update tree in document from jalview.");
+ }
+ else
+ {
+ // handle conflict
+ log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
+ */
+ @Override
+ public void updateFromDoc()
+ {
+ // should probably just open a new tree panel in the same place as the old
+ // one
+ // TODO: Tree.updateFromDoc
+ /*
+ * TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+ *
+ * // make a new tree Object[] idata =
+ * recoverInputData(tree.getProvenance()); try { if (idata != null &&
+ * idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
+ * getNtree(); title = tree.getNewick(0).getTitle(); if (title == null ||
+ * title.length() == 0) { title = tree.getTitle(); // hack!!!! } } catch
+ * (Exception e) { Cache.log.warn("Problems parsing treefile '" +
+ * tree.getNewick(0).getContent() + "'", e); }
+ */
+ log.debug("Update the local tree in jalview from the document.");
+
+ if (isModifiable(tree.getModifiable()))
+ {
+ // synchronize(); // update();
+ // verify any changes.
+ log.debug("Update tree in document from jalview.");
+ }
+ else
+ {
+ // handle conflict
+ log.debug("Add modified jalview tree as new tree in document.");
+ }
+ }
+
+ /**
+ * correctly creates provenance for trees calculated on an alignment by
+ * jalview.
+ *
+ * @param jal
+ * @param tp
+ * @return
+ */
+ private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
+ {
+ Cache.log.debug("Making Tree provenance for " + tp.getTitle());
+ Provenance prov = new Provenance();
+ prov.addEntry(new Entry());
+ prov.getEntry(0).setAction("imported " + tp.getTitle());
+ prov.getEntry(0).setUser(provEntry.getUser());
+ prov.getEntry(0).setApp(provEntry.getApp());
+ prov.getEntry(0).setDate(provEntry.getDate());
+ if (tp.getTree().hasOriginalSequenceData())
+ {
+ Input vInput = new Input();
+ // LATER: check to see if tree input data is contained in this alignment -
+ // or just correctly resolve the tree's seqData to the correct alignment
+ // in
+ // the document.
+ Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
+ tp.getTree().seqData.getSequences()));
+ Object[] alsqs = new Object[alsqrefs.size()];
+ alsqrefs.copyInto(alsqs);
+ vInput.setObjRef(alsqs);
+ // now create main provenance data
+ prov.getEntry(0).setAction("created " + tp.getTitle());
+ prov.getEntry(0).addInput(vInput);
+ // jalview's special input parameter for distance matrix calculations
+ vInput.setName("jalview:seqdist"); // TODO: settle on appropriate name.
+ prov.getEntry(0).addParam(new Param());
+ prov.getEntry(0).getParam(0).setName("treeType");
+ prov.getEntry(0).getParam(0).setType("utf8");
+ prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
+ // general parameter
+ int ranges[] = tp.getTree().seqData.getVisibleContigs();
+ // VisibleContigs are with respect to alignment coordinates. Still need
+ // offsets
+ int start = tp.getTree().seqData.getAlignmentOrigin();
+ for (int r = 0; r < ranges.length; r += 2)
+ {
+ Seg visSeg = new Seg();
+ visSeg.setStart(1 + start + ranges[r]);
+ visSeg.setEnd(start + ranges[r + 1]);
+ visSeg.setInclusive(true);
+ vInput.addSeg(visSeg);
+ }
+ }
+ Cache.log.debug("Finished Tree provenance for " + tp.getTitle());
+ return prov;
+ }
+
+ /**
+ * look up SeqCigars in an existing alignment.
+ *
+ * @param jal
+ * @param sequences
+ * @return vector of alignment sequences in order of SeqCigar array (but
+ * missing unfound seqcigars)
+ */
+ private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
+ {
+ SeqCigar[] tseqs = new SeqCigar[sequences.length];
+ System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
+ Vector alsq = new Vector();
+ List jalsqs;
+ synchronized (jalsqs = jal.getSequences())
+ {
+ for (SequenceI asq : jalsqs)
+ {
+ for (int t = 0; t < sequences.length; t++)
+ {
+ if (tseqs[t] != null
+ && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
+ .getDatasetSequence()))
+ // && tseqs[t].getStart()>=asq.getStart() &&
+ // tseqs[t].getEnd()<=asq.getEnd())
+ {
+ tseqs[t] = null;
+ alsq.add(asq);
+ }
+ }
+ }
+ }
+ if (alsq.size() < sequences.length)
+ Cache.log
+ .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+ return alsq;
+ }
+
+ /**
+ *
+ * Update jalview newick representation with TreeNode map
+ *
+ * @param tp
+ * the treepanel that this tree is bound to.
+ */
+ public void UpdateSequenceTreeMap(TreePanel tp)
+ {
+ if (tp == null || tree == null)
+ return;
+ Vector leaves = new Vector();
+ if (tp.getTree() == null)
+ {
+ Cache.log.warn("Not updating SequenceTreeMap for "
+ + tree.getVorbaId());
+ return;
+ }
+ tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+ Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
+ // particular tree
+ int sz = tn.length;
+ int i = 0;
+
+ while (i < sz)
+ {
+ Treenode node = tn[i++];
+ BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
+ if (mappednode != null && mappednode instanceof SequenceNode)
+ {
+ SequenceNode leaf = (SequenceNode) mappednode;
+ // check if we can make the specified association
+ Object jvseq = null;
+ int vrf = 0, refv = 0;
+ while (jvseq == null && vrf < node.getVrefCount())
+ {
+ if (refv < node.getVref(vrf).getRefsCount())
+ {
+ Object noderef = node.getVref(vrf).getRefs(refv++);
+ if (noderef instanceof AlignmentSequence)
+ {
+ // we only make these kind of associations
+ jvseq = getvObj2jv((Vobject) noderef);
+ }
+ }
+ else
+ {
+ refv = 0;
+ vrf++;
+ }
+ }
+ if (jvseq instanceof SequenceI)
+ {
+ leaf.setElement(jvseq);
+ leaf.setPlaceholder(false);
+ }
+ else
+ {
+ leaf.setPlaceholder(true);
+ leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+ }
+ }
+ }
+ }
+
+ // / TODO: refactor to vamsas :start
+ /**
+ * construct treenode mappings for mapped sequences
+ *
+ * @param ntree
+ * @param newick
+ * @return
+ */
+ public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
+ {
+ Vector leaves = new Vector();
+ ntree.findLeaves(ntree.getTopNode(), leaves);
+ Vector tnv = new Vector();
+ Enumeration l = leaves.elements();
+ Hashtable nodespecs = new Hashtable();
+ while (l.hasMoreElements())
+ {
+ jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l
+ .nextElement();
+ if (tnode instanceof jalview.datamodel.SequenceNode)
+ {
+ if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
+ {
+ Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
+ .element();
+ if (assocseq instanceof SequenceI)
+ {
+ Vobject vobj = this.getjv2vObj(assocseq);
+ if (vobj != null)
+ {
+ Treenode node = new Treenode();
+ if (newick.isRegisterable())
+ {
+ this.cdoc.registerObject(newick);
+ node.addTreeId(newick);
+ }
+ node.setNodespec(makeNodeSpec(nodespecs, tnode));
+ node.setName(tnode.getName());
+ Vref vr = new Vref();
+ vr.addRefs(vobj);
+ node.addVref(vr);
+ tnv.addElement(node);
+ }
+ else
+ {
+ System.err.println("WARNING: Unassociated treeNode "
+ + tnode.element().toString()
+ + " "
+ + ((tnode.getName() != null) ? " label "
+ + tnode.getName() : ""));
+ }
+ }
+ }
+ }
+ }
+ if (tnv.size() > 0)
+ {
+ Treenode[] tn = new Treenode[tnv.size()];
+ tnv.copyInto(tn);
+ return tn;
+ }
+ return new Treenode[]
+ {};
+ }
+
+ private String makeNodeSpec(Hashtable nodespecs,
+ jalview.datamodel.BinaryNode tnode)
+ {
+ String nname = new String(tnode.getName());
+ Integer nindx = (Integer) nodespecs.get(nname);
+ if (nindx == null)
+ {
+ nindx = new Integer(1);
+ }
+ nname = nindx.toString() + " " + nname;
+ return nname;
+ }
+
+ /**
+ * call to match up Treenode specs to NJTree parsed from document object.
+ *
+ * @param nodespec
+ * @param leaves
+ * as returned from NJTree.findLeaves( .., ..) ..
+ * @return
+ */
+ private jalview.datamodel.BinaryNode findNodeSpec(String nodespec,
+ Vector leaves)
+ {
+ int occurence = -1;
+ String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
+ String oval = nodespec.substring(0, nodespec.indexOf(' '));
+ try
+ {
+ occurence = new Integer(oval).intValue();
+ } catch (Exception e)
+ {
+ System.err.println("Invalid nodespec '" + nodespec + "'");
+ return null;
+ }
+ jalview.datamodel.BinaryNode bn = null;
+
+ int nocc = 0;
+ Enumeration en = leaves.elements();
+ while (en.hasMoreElements() && nocc < occurence)
+ {
+ bn = (jalview.datamodel.BinaryNode) en.nextElement();
+ if (bn instanceof jalview.datamodel.SequenceNode
+ && bn.getName().equals(nspec))
+ {
+ --occurence;
+ }
+ else
+ bn = null;
+ }
+ return bn;
+ }
+
+ // todo: end refactor to vamsas library
+ /**
+ * add jalview object to vamsas document
+ *
+ */
+ @Override
+ public void addToDocument()
+ {
+ tree = new uk.ac.vamsas.objects.core.Tree();
+ bindjvvobj(tp, tree);
+ tree.setTitle(tp.getTitle());
+ Newick newick = new Newick();
+ newick.setContent(tp.getTree().toString());
+ newick.setTitle(tp.getTitle());
+ tree.addNewick(newick);
+ tree.setProvenance(makeTreeProvenance(jal, tp));
+ tree.setTreenode(makeTreeNodes(tp.getTree(), newick));
+
+ alignment.addTree(tree);
+ }
+
+ /**
+ * note: this function assumes that all sequence and alignment objects
+ * referenced in input data has already been associated with jalview objects.
+ *
+ * @param tp
+ * @param alignFrame
+ * @return Object[] { AlignmentView, AlignmentI - reference alignment for
+ * input }
+ */
+ public Object[] recoverInputData(Provenance tp)
+ {
+ AlignViewport javport = null;
+ jalview.datamodel.AlignmentI jal = null;
+ jalview.datamodel.CigarArray view = null;
+ for (int pe = 0; pe < tp.getEntryCount(); pe++)
+ {
+ if (tp.getEntry(pe).getInputCount() > 0)
+ {
+ if (tp.getEntry(pe).getInputCount() > 1)
+ {
+ Cache.log
+ .warn("Ignoring additional input spec in provenance entry "
+ + tp.getEntry(pe).toString());
+ }
+ // LATER: deal sensibly with multiple inputs
+ Input vInput = tp.getEntry(pe).getInput(0);
+ // is this the whole alignment or a specific set of sequences ?
+ if (vInput.getObjRefCount() == 0)
+ {
+ if (tree.getV_parent() != null
+ && tree.getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment)
+ {
+ javport = getViewport(tree.getV_parent());
+ jal = javport.getAlignment();
+ view = javport.getAlignment().getCompactAlignment();
+ }
+ }
+ else
+ {
+ // Explicit reference - to alignment, sequences or what.
+ if (vInput.getObjRefCount() == 1
+ && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
+ {
+ // recover an AlignmentView for the input data
+ javport = getViewport((Vobject) vInput.getObjRef(0));
+ jal = javport.getAlignment();
+ view = javport.getAlignment().getCompactAlignment();
+ }
+ else if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence)
+ {
+ // recover an AlignmentView for the input data
+ javport = getViewport(((Vobject) vInput.getObjRef(0))
+ .getV_parent());
+ jal = javport.getAlignment();
+ jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput
+ .getObjRefCount()];
+ for (int i = 0, iSize = vInput.getObjRefCount(); i < iSize; i++)
+ {
+ SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput
+ .getObjRef(i));
+ seqs[i] = seq;
+ }
+ view = new jalview.datamodel.Alignment(seqs)
+ .getCompactAlignment();
+
+ }
+ }
+ int from = 1, to = jal.getWidth();
+ int offset = 0; // deleteRange modifies its frame of reference
+ for (int r = 0, s = vInput.getSegCount(); r < s; r++)
+ {
+ Seg visSeg = vInput.getSeg(r);
+ int se[] = getSegRange(visSeg, true); // jalview doesn't do
+ // bidirection alignments yet.
+ if (to < se[1])
+ {
+ Cache.log.warn("Ignoring invalid segment in InputData spec.");
+ }
+ else
+ {
+ if (se[0] > from)
+ {
+ view.deleteRange(offset + from - 1, offset + se[0] - 2);
+ offset -= se[0] - from;
+ }
+ from = se[1] + 1;
+ }
+ }
+ if (from < to)
+ {
+ view.deleteRange(offset + from - 1, offset + to - 1); // final
+ // deletion -
+ // TODO: check
+ // off by
+ // one for to
+ }
+ return new Object[]
+ { new AlignmentView(view), jal };
+ }
+ }
+ Cache.log
+ .debug("Returning null for input data recovery from provenance.");
+ return null;
+ }
+
+ private AlignViewport getViewport(Vobject v_parent)
+ {
+ if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
+ {
+ return datastore
+ .findViewport((uk.ac.vamsas.objects.core.Alignment) v_parent);
+ }
+ return null;
+ }
+
+ public NewickFile getNewickTree()
+ {
+ return ntree;
+ }
+
+ public String getTitle()
+ {
+ return title;
+ }
+
+ public AlignmentView getInputData()
+ {
+ return inputData;
+ }
+
+ public boolean isValidTree()
+ {
+ try
+ {
+ if (ntree == null)
+ {
+ return false;
+ }
+ ntree.parse();
+ if (ntree.getTree() != null)
+ {
+ ntree = getNtree();
+ }
+ return true;
+ } catch (Exception e)
+ {
+ Cache.log.debug("Failed to parse newick tree string", e);
+ }
+ return false;
+ }
+}