import java.util.Vector;\r
\r
import jalview.analysis.NJTree;\r
+import jalview.bin.Cache;\r
import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentView;\r
import jalview.datamodel.SeqCigar;\r
import jalview.datamodel.SequenceI;\r
+import jalview.gui.AlignViewport;\r
import jalview.gui.TreePanel;\r
+import jalview.io.NewickFile;\r
import jalview.io.VamsasAppDatastore;\r
import uk.ac.vamsas.client.Vobject;\r
import uk.ac.vamsas.objects.core.Entry;\r
AlignmentI jal;\r
TreePanel tp;\r
uk.ac.vamsas.objects.core.Tree tree;\r
- uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or other kind of tree\r
+ uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or\r
+ // other kind of tree\r
+ private NewickFile ntree;\r
+ private String title;\r
+ private AlignmentView inputData = null;\r
+ public static void updateFrom(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree) {\r
+ Tree toTree = new Tree(datastore, alignFrame, vtree);\r
+ \r
+ }\r
+ public Tree(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree)\r
+ {\r
+ super(datastore);\r
+ tree = vtree;\r
+ TreePanel tp = (TreePanel) getvObj2jv(tree);\r
+ if (tp != null) {\r
+ if (tree.isUpdated())\r
+ {\r
+ Cache.log.info(\r
+ "Update from vamsas document to alignment associated tree not implemented yet.");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // make a new tree\r
+ Object[] idata = this.recoverInputData(tree.getProvenance());\r
+ try\r
+ {\r
+ if (idata != null && idata[0] != null)\r
+ {\r
+ inputData = (AlignmentView) idata[0];\r
+ }\r
+ ntree = new jalview.io.NewickFile(tree.getNewick(0).getContent());\r
+ title = tree.getNewick(0).getTitle();\r
+ if (title==null || title.length()==0)\r
+ {\r
+ title = tree.getTitle(); // hack!!!!\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ Cache.log.warn("Problems parsing treefile '" +\r
+ tree.getNewick(0).getContent() + "'", e);\r
+ }\r
+ }\r
+ }\r
public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2)\r
{\r
super(datastore);\r
/**\r
* correctly creates provenance for trees calculated on an alignment by\r
* jalview.\r
- *\r
+ * \r
* @param jal\r
* @param tp\r
* @return\r
*/\r
private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)\r
{\r
+ Cache.log.debug("Making Tree provenance for "+tp.getTitle());\r
Provenance prov = new Provenance();\r
prov.addEntry(new Entry());\r
prov.getEntry(0).setAction("imported " + tp.getTitle());\r
{\r
Input vInput = new Input();\r
// LATER: check to see if tree input data is contained in this alignment -\r
- // or just correctly resolve the tree's seqData to the correct alignment in\r
+ // or just correctly resolve the tree's seqData to the correct alignment\r
+ // in\r
// the document.\r
Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp.getTree().seqData.getSequences()));\r
Object[] alsqs = new Object[alsqrefs.size()];\r
prov.getEntry(0).getParam(0).setType("utf8");\r
prov.getEntry(0).getParam(0).setContent("NJ");\r
int ranges[] = tp.getTree().seqData.getVisibleContigs();\r
- // VisibleContigs are with respect to alignment coordinates. Still need offsets\r
+ // VisibleContigs are with respect to alignment coordinates. Still need\r
+ // offsets\r
int start = tp.getTree().seqData.getAlignmentOrigin();\r
for (int r = 0; r < ranges.length; r += 2)\r
{\r
vInput.addSeg(visSeg);\r
}\r
}\r
+ Cache.log.debug("Finished Tree provenance for "+tp.getTitle());\r
return prov;\r
}\r
/**\r
* look up SeqCigars in an existing alignment.\r
+ * \r
* @param jal\r
* @param sequences\r
- * @return vector of alignment sequences in order of SeqCigar array (but missing unfound seqcigars)\r
+ * @return vector of alignment sequences in order of SeqCigar array (but\r
+ * missing unfound seqcigars)\r
*/\r
private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)\r
{\r
for (int t = 0; t<sequences.length; t++)\r
{\r
if (tseqs[t]!=null \r
- && (tseqs[t].getRefSeq()==asq || tseqs[t].getRefSeq() == asq.getDatasetSequence())\r
- && tseqs[t].getStart()>=asq.getStart() && tseqs[t].getEnd()<=asq.getEnd())\r
+ && (tseqs[t].getRefSeq()==asq || tseqs[t].getRefSeq() == asq.getDatasetSequence()))\r
+ // && tseqs[t].getStart()>=asq.getStart() && tseqs[t].getEnd()<=asq.getEnd())\r
{\r
tseqs[t] = null;\r
alsq.add(asq);\r
}\r
}\r
}\r
+ if (alsq.size()<sequences.length)\r
+ Cache.log.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");\r
return alsq;\r
}\r
+ /**\r
+ * construct treenode mappings for mapped sequences\r
+ * \r
+ * @param ntree\r
+ * @return\r
+ */\r
public Treenode[] makeTreeNodes(NJTree ntree) {\r
Vector leaves = new Vector();\r
ntree.findLeaves(ntree.getTopNode(), leaves);\r
}\r
/**\r
* call to match up Treenode specs to NJTree parsed from document object.\r
+ * \r
* @param nodespec\r
- * @param leaves as returned from NJTree.findLeaves( .., ..) .. \r
+ * @param leaves\r
+ * as returned from NJTree.findLeaves( .., ..) ..\r
* @return\r
*/\r
private jalview.datamodel.BinaryNode findNodeSpec(String nodespec, Vector leaves)\r
}\r
return bn;\r
}\r
- \r
+ /**\r
+ * add jalview object to vamsas document\r
+ * \r
+ */\r
public void add() {\r
tree = new uk.ac.vamsas.objects.core.Tree();\r
bindjvvobj(tp, tree);\r
\r
alignment.addTree(tree);\r
}\r
+\r
+ /**\r
+ * note: this function assumes that all sequence and alignment objects\r
+ * referenced in input data has already been associated with jalview objects.\r
+ * \r
+ * @param tp\r
+ * @return Object[] { AlignmentView, AlignmentI - reference alignment for\r
+ * input }\r
+ */\r
+ public Object[] recoverInputData(Provenance tp)\r
+ {\r
+ AlignViewport javport=null;\r
+ jalview.datamodel.AlignmentI jal=null;\r
+ jalview.datamodel.CigarArray view=null;\r
+ for (int pe = 0; pe < tp.getEntryCount(); pe++)\r
+ {\r
+ if (tp.getEntry(pe).getInputCount() > 0)\r
+ {\r
+ if (tp.getEntry(pe).getInputCount() > 1)\r
+ {\r
+ Cache.log.warn("Ignoring additional input spec in provenance entry "\r
+ + tp.getEntry(pe).toString());\r
+ }\r
+ // LATER: deal sensibly with multiple inputs\r
+ Input vInput = tp.getEntry(pe).getInput(0);\r
+ // is this the whole alignment or a specific set of sequences ?\r
+ if (vInput.getObjRefCount()==0)\r
+ continue;\r
+ if (vInput.getObjRefCount()==1 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)\r
+ {\r
+ // recover an AlignmentView for the input data\r
+ javport = (AlignViewport) getvObj2jv( (uk.ac.vamsas.\r
+ client.Vobject) vInput\r
+ .getObjRef(0));\r
+ jal = javport.getAlignment();\r
+ view = javport.getAlignment().\r
+ getCompactAlignment();\r
+ } else \r
+ if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence) {\r
+ // recover an AlignmentView for the input data\r
+ javport = (AlignViewport) getvObj2jv(((Vobject)vInput.getObjRef(0)).getV_parent());\r
+ jal = javport.getAlignment();\r
+ jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput.getObjRefCount()];\r
+ for (int i=0,iSize=vInput.getObjRefCount(); i<iSize; i++)\r
+ {\r
+ SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput.getObjRef(i));\r
+ seqs[i] = seq;\r
+ }\r
+ view = new jalview.datamodel.Alignment(seqs).getCompactAlignment();\r
+ \r
+ \r
+ }\r
+ int from = 1, to = jal.getWidth();\r
+ int offset = 0; // deleteRange modifies its frame of reference\r
+ for (int r = 0, s = vInput.getSegCount(); r < s; r++)\r
+ {\r
+ Seg visSeg = vInput.getSeg(r);\r
+ int se[] = getSegRange(visSeg, true); // jalview doesn't do\r
+ // bidirection alignments yet.\r
+ if (to < se[1])\r
+ {\r
+ Cache.log.warn("Ignoring invalid segment in InputData spec.");\r
+ }\r
+ else\r
+ {\r
+ if (se[0] > from)\r
+ {\r
+ view.deleteRange(offset + from - 1, offset + se[0] - 2);\r
+ offset -= se[0] - from;\r
+ }\r
+ from = se[1] + 1;\r
+ }\r
+ }\r
+ if (from < to)\r
+ {\r
+ view.deleteRange(offset + from - 1, offset + to - 1); // final\r
+ // deletion -\r
+ // TODO: check\r
+ // off by\r
+ // one for to\r
+ }\r
+ return new Object[]{new AlignmentView(view), jal};\r
+ }\r
+ }\r
+ Cache.log.debug("Returning null for input data recovery from provenance.");\r
+ return null;\r
+ }\r
+ public NewickFile getNewickTree()\r
+ {\r
+ return ntree;\r
+ }\r
+ public String getTitle()\r
+ {\r
+ return title;\r
+ }\r
+ public AlignmentView getInputData()\r
+ {\r
+ return inputData;\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff