X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=1b7a8bf1d8d8765ebafbd8f50886259effcfe466;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=a3781a7d09e8b2809ed8fdf7dd81fc40044a6ed8;hpb=9b9b058f82be7403a76d41fe17016b8b44b12db7;p=jalview.git diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index a3781a7..1b7a8bf 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -20,8 +20,9 @@ */ package jalview.io.vamsas; -import jalview.analysis.NJTree; -import jalview.bin.Cache; +import jalview.analysis.TreeBuilder; +import jalview.analysis.TreeModel; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.BinaryNode; @@ -127,7 +128,7 @@ public class Tree extends DatastoreItem } } catch (Exception e) { - Cache.log.warn("Problems parsing treefile '" + Console.warn("Problems parsing treefile '" + tree.getNewick(0).getContent() + "'", e); } } @@ -140,8 +141,8 @@ public class Tree extends DatastoreItem @Override public void conflict() { - Cache.log - .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet."); + Console.info( + "Update (with conflict) from vamsas document to alignment associated tree not implemented yet."); } /* @@ -161,7 +162,8 @@ public class Tree extends DatastoreItem else { // handle conflict - log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged."); + log.info( + "TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged."); } } @@ -184,7 +186,7 @@ public class Tree extends DatastoreItem * 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 '" + + * (Exception e) { Cache.warn("Problems parsing treefile '" + * tree.getNewick(0).getContent() + "'", e); } */ log.debug("Update the local tree in jalview from the document."); @@ -212,14 +214,16 @@ public class Tree extends DatastoreItem */ private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp) { - Cache.log.debug("Making Tree provenance for " + tp.getTitle()); + Console.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()) + + AlignmentView originalData = tp.getTree().getOriginalData(); + if (originalData != null) { Input vInput = new Input(); // LATER: check to see if tree input data is contained in this alignment - @@ -227,7 +231,7 @@ public class Tree extends DatastoreItem // in // the document. Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, - tp.getTree().seqData.getSequences())); + tp.getTree().getOriginalData().getSequences())); Object[] alsqs = new Object[alsqrefs.size()]; alsqrefs.copyInto(alsqs); vInput.setObjRef(alsqs); @@ -239,12 +243,13 @@ public class Tree extends DatastoreItem 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(); + prov.getEntry(0).getParam(0) + .setContent(TreeBuilder.NEIGHBOUR_JOINING); + // TODO: type of tree is a general parameter + int ranges[] = originalData.getVisibleContigs(); // VisibleContigs are with respect to alignment coordinates. Still need // offsets - int start = tp.getTree().seqData.getAlignmentOrigin(); + int start = tp.getTree().getOriginalData().getAlignmentOrigin(); for (int r = 0; r < ranges.length; r += 2) { Seg visSeg = new Seg(); @@ -254,7 +259,7 @@ public class Tree extends DatastoreItem vInput.addSeg(visSeg); } } - Cache.log.debug("Finished Tree provenance for " + tp.getTitle()); + Console.debug("Finished Tree provenance for " + tp.getTitle()); return prov; } @@ -266,21 +271,21 @@ public class Tree extends DatastoreItem * @return vector of alignment sequences in order of SeqCigar array (but * missing unfound seqcigars) */ - private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences) + 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()) + Vector alsq = new Vector<>(); + List jalsqs = jal.getSequences(); + synchronized (jalsqs) { 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())) + if (tseqs[t] != null && (tseqs[t].getRefSeq() == asq + || tseqs[t].getRefSeq() == asq.getDatasetSequence())) // && tseqs[t].getStart()>=asq.getStart() && // tseqs[t].getEnd()<=asq.getEnd()) { @@ -292,8 +297,8 @@ public class Tree extends DatastoreItem } if (alsq.size() < sequences.length) { - Cache.log - .warn("Not recovered all alignment sequences for given set of input sequence CIGARS"); + Console.warn( + "Not recovered all alignment sequences for given set of input sequence CIGARS"); } return alsq; } @@ -314,12 +319,12 @@ public class Tree extends DatastoreItem if (tp.getTree() == null) { - Cache.log.warn("Not updating SequenceTreeMap for " - + tree.getVorbaId()); + Console.warn( + "Not updating SequenceTreeMap for " + tree.getVorbaId()); return; } - Vector leaves = tp.getTree().findLeaves( - tp.getTree().getTopNode()); + Vector leaves = tp.getTree() + .findLeaves(tp.getTree().getTopNode()); Treenode[] tn = tree.getTreenode(); // todo: select nodes for this // particular tree int sz = tn.length; @@ -360,7 +365,8 @@ public class Tree extends DatastoreItem else { leaf.setPlaceholder(true); - leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER")); + leaf.setElement( + new Sequence(leaf.getName(), "THISISAPLACEHLDER")); } } } @@ -370,13 +376,14 @@ public class Tree extends DatastoreItem /** * construct treenode mappings for mapped sequences * - * @param ntree + * @param treeModel * @param newick * @return */ - public Treenode[] makeTreeNodes(NJTree ntree, Newick newick) + public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick) { - Vector leaves = ntree.findLeaves(ntree.getTopNode()); + Vector leaves = treeModel + .findLeaves(treeModel.getTopNode()); Vector tnv = new Vector(); Enumeration l = leaves.elements(); Hashtable nodespecs = new Hashtable(); @@ -411,10 +418,10 @@ public class Tree extends DatastoreItem else { System.err.println("WARNING: Unassociated treeNode " - + tnode.element().toString() - + " " - + ((tnode.getName() != null) ? " label " - + tnode.getName() : "")); + + tnode.element().toString() + " " + + ((tnode.getName() != null) + ? " label " + tnode.getName() + : "")); } } } @@ -436,7 +443,7 @@ public class Tree extends DatastoreItem Integer nindx = (Integer) nodespecs.get(nname); if (nindx == null) { - nindx = new Integer(1); + nindx = Integer.valueOf(1); } nname = nindx.toString() + " " + nname; return nname; @@ -458,7 +465,7 @@ public class Tree extends DatastoreItem String oval = nodespec.substring(0, nodespec.indexOf(' ')); try { - occurence = new Integer(oval).intValue(); + occurence = Integer.valueOf(oval).intValue(); } catch (Exception e) { System.err.println("Invalid nodespec '" + nodespec + "'"); @@ -496,7 +503,7 @@ public class Tree extends DatastoreItem bindjvvobj(tp, tree); tree.setTitle(tp.getTitle()); Newick newick = new Newick(); - newick.setContent(tp.getTree().toString()); + newick.setContent(tp.getTree().print()); newick.setTitle(tp.getTitle()); tree.addNewick(newick); tree.setProvenance(makeTreeProvenance(jal, tp)); @@ -525,8 +532,8 @@ public class Tree extends DatastoreItem { if (tp.getEntry(pe).getInputCount() > 1) { - Cache.log - .warn("Ignoring additional input spec in provenance entry " + Console.warn( + "Ignoring additional input spec in provenance entry " + tp.getEntry(pe).toString()); } // LATER: deal sensibly with multiple inputs @@ -534,8 +541,8 @@ public class Tree extends DatastoreItem // 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) + if (tree.getV_parent() != null && tree + .getV_parent() instanceof uk.ac.vamsas.objects.core.Alignment) { javport = getViewport(tree.getV_parent()); jal = javport.getAlignment(); @@ -545,26 +552,27 @@ public class Tree extends DatastoreItem else { // Explicit reference - to alignment, sequences or what. - if (vInput.getObjRefCount() == 1 - && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment) + 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) + 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()); + 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)); + SequenceI seq = (SequenceI) getvObj2jv( + (Vobject) vInput.getObjRef(i)); seqs[i] = seq; } view = new jalview.datamodel.Alignment(seqs) @@ -581,7 +589,7 @@ public class Tree extends DatastoreItem // bidirection alignments yet. if (to < se[1]) { - Cache.log.warn("Ignoring invalid segment in InputData spec."); + Console.warn("Ignoring invalid segment in InputData spec."); } else { @@ -604,8 +612,8 @@ public class Tree extends DatastoreItem return new Object[] { new AlignmentView(view), jal }; } } - Cache.log - .debug("Returning null for input data recovery from provenance."); + Console.debug( + "Returning null for input data recovery from provenance."); return null; } @@ -650,7 +658,7 @@ public class Tree extends DatastoreItem return true; } catch (Exception e) { - Cache.log.debug("Failed to parse newick tree string", e); + Console.debug("Failed to parse newick tree string", e); } return false; }