1 package jalview.io.vamsas;
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3 import java.io.IOException;
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4 import java.util.Enumeration;
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5 import java.util.Hashtable;
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6 import java.util.Vector;
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8 import jalview.analysis.NJTree;
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9 import jalview.bin.Cache;
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10 import jalview.datamodel.AlignmentI;
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11 import jalview.datamodel.AlignmentView;
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12 import jalview.datamodel.SeqCigar;
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13 import jalview.datamodel.SequenceI;
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14 import jalview.gui.AlignViewport;
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15 import jalview.gui.TreePanel;
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16 import jalview.io.NewickFile;
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17 import jalview.io.VamsasAppDatastore;
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18 import uk.ac.vamsas.client.Vobject;
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19 import uk.ac.vamsas.objects.core.Entry;
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20 import uk.ac.vamsas.objects.core.Input;
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21 import uk.ac.vamsas.objects.core.Newick;
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22 import uk.ac.vamsas.objects.core.Param;
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23 import uk.ac.vamsas.objects.core.Provenance;
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24 import uk.ac.vamsas.objects.core.Seg;
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25 import uk.ac.vamsas.objects.core.Treenode;
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26 import uk.ac.vamsas.objects.core.Vref;
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28 public class Tree extends DatastoreItem
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32 uk.ac.vamsas.objects.core.Tree tree;
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33 uk.ac.vamsas.objects.core.Alignment alignment; // may be null => dataset or
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34 // other kind of tree
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35 private NewickFile ntree;
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36 private String title;
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37 private AlignmentView inputData = null;
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38 public static void updateFrom(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree) {
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39 Tree toTree = new Tree(datastore, alignFrame, vtree);
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42 public Tree(VamsasAppDatastore datastore, jalview.gui.AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree)
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46 TreePanel tp = (TreePanel) getvObj2jv(tree);
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48 if (tree.isUpdated())
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51 "Update from vamsas document to alignment associated tree not implemented yet.");
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57 Object[] idata = this.recoverInputData(tree.getProvenance());
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60 if (idata != null && idata[0] != null)
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62 inputData = (AlignmentView) idata[0];
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65 title = tree.getNewick(0).getTitle();
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66 if (title==null || title.length()==0)
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68 title = tree.getTitle(); // hack!!!!
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73 Cache.log.warn("Problems parsing treefile '" +
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74 tree.getNewick(0).getContent() + "'", e);
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78 private NewickFile getNtree() throws IOException
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80 return new jalview.io.NewickFile(tree.getNewick(0).getContent());
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82 public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2)
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88 alignment = alignment2;
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90 tree = (uk.ac.vamsas.objects.core.Tree) getjv2vObj(tp);
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97 if (isModifiable(tree.getModifiable()))
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99 // synchronize(); // update();
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100 // verify any changes.
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101 System.out.println("Update tree in document.");
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107 .println("Add modified tree as new tree in document.");
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112 * correctly creates provenance for trees calculated on an alignment by
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119 private Provenance makeTreeProvenance(AlignmentI jal, TreePanel tp)
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121 Cache.log.debug("Making Tree provenance for "+tp.getTitle());
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122 Provenance prov = new Provenance();
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123 prov.addEntry(new Entry());
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124 prov.getEntry(0).setAction("imported " + tp.getTitle());
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125 prov.getEntry(0).setUser(provEntry.getUser());
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126 prov.getEntry(0).setApp(provEntry.getApp());
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127 prov.getEntry(0).setDate(provEntry.getDate());
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128 if (tp.getTree().hasOriginalSequenceData())
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130 Input vInput = new Input();
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131 // LATER: check to see if tree input data is contained in this alignment -
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132 // or just correctly resolve the tree's seqData to the correct alignment
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135 Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp.getTree().seqData.getSequences()));
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136 Object[] alsqs = new Object[alsqrefs.size()];
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137 alsqrefs.copyInto(alsqs);
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138 vInput.setObjRef(alsqs);
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139 // now create main provenance data
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140 prov.getEntry(0).setAction("created " + tp.getTitle());
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141 prov.getEntry(0).addInput(vInput);
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142 // jalview's special input parameter for distance matrix calculations
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143 vInput.setName("jalview:seqdist");
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144 prov.getEntry(0).addParam(new Param());
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145 prov.getEntry(0).getParam(0).setName("treeType");
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146 prov.getEntry(0).getParam(0).setType("utf8");
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147 prov.getEntry(0).getParam(0).setContent("NJ");
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148 int ranges[] = tp.getTree().seqData.getVisibleContigs();
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149 // VisibleContigs are with respect to alignment coordinates. Still need
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151 int start = tp.getTree().seqData.getAlignmentOrigin();
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152 for (int r = 0; r < ranges.length; r += 2)
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154 Seg visSeg = new Seg();
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155 visSeg.setStart(1 + start + ranges[r]);
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156 visSeg.setEnd(start + ranges[r + 1]);
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157 visSeg.setInclusive(true);
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158 vInput.addSeg(visSeg);
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161 Cache.log.debug("Finished Tree provenance for "+tp.getTitle());
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165 * look up SeqCigars in an existing alignment.
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169 * @return vector of alignment sequences in order of SeqCigar array (but
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170 * missing unfound seqcigars)
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172 private Vector findAlignmentSequences(AlignmentI jal, SeqCigar[] sequences)
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174 SeqCigar[] tseqs = new SeqCigar[sequences.length];
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175 System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
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176 Vector alsq = new Vector();
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177 Enumeration as = jal.getSequences().elements();
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178 while (as.hasMoreElements())
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180 SequenceI asq = (SequenceI) as.nextElement();
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181 for (int t = 0; t<sequences.length; t++)
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183 if (tseqs[t]!=null
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184 && (tseqs[t].getRefSeq()==asq || tseqs[t].getRefSeq() == asq.getDatasetSequence()))
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185 // && tseqs[t].getStart()>=asq.getStart() && tseqs[t].getEnd()<=asq.getEnd())
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192 if (alsq.size()<sequences.length)
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193 Cache.log.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
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197 * construct treenode mappings for mapped sequences
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202 public Treenode[] makeTreeNodes(NJTree ntree) {
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203 Vector leaves = new Vector();
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204 ntree.findLeaves(ntree.getTopNode(), leaves);
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205 Vector tnv = new Vector();
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206 Enumeration l = leaves.elements();
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208 Hashtable nodespecs = new Hashtable();
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209 while (l.hasMoreElements())
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211 jalview.datamodel.BinaryNode tnode = (jalview.datamodel.BinaryNode) l.nextElement();
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212 if (tnode instanceof jalview.datamodel.SequenceNode)
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214 if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
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216 Object assocseq = ((jalview.datamodel.SequenceNode) tnode).element();
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217 if (assocseq instanceof SequenceI)
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219 Vobject vobj = this.getjv2vObj(assocseq);
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222 Treenode node = new Treenode();
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223 node.setNodespec(makeNodeSpec(nodespecs, tnode));
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224 node.setName(tnode.getName());
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225 Vref vr = new Vref();
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228 tnv.addElement(node);
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232 System.err.println("WARNING: Unassociated treeNode "+tnode.element().toString()+" "
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233 +((tnode.getName()!=null) ? " label "+tnode.getName() : ""));
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241 Treenode[] tn = new Treenode[tnv.size()];
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245 return new Treenode[] {};
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247 private String makeNodeSpec(Hashtable nodespecs, jalview.datamodel.BinaryNode tnode)
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249 String nname = new String(tnode.getName());
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250 Integer nindx = (Integer) nodespecs.get(nname);
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253 nindx = new Integer(1);
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255 nname = nindx.toString()+" "+nname;
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259 * call to match up Treenode specs to NJTree parsed from document object.
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263 * as returned from NJTree.findLeaves( .., ..) ..
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266 private jalview.datamodel.BinaryNode findNodeSpec(String nodespec, Vector leaves)
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269 String nspec = nodespec.substring(nodespec.indexOf(' ')+1);
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270 String oval = nodespec.substring(0, nodespec.indexOf(' '));
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272 occurence = new Integer(oval).intValue();
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274 catch (Exception e)
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276 System.err.println("Invalid nodespec '"+nodespec+"'");
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279 jalview.datamodel.BinaryNode bn = null;
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282 Enumeration en = leaves.elements();
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283 while (en.hasMoreElements() && nocc<occurence)
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285 bn = (jalview.datamodel.BinaryNode) en.nextElement();
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286 if (bn instanceof jalview.datamodel.SequenceNode && bn.getName().equals(nspec))
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295 * add jalview object to vamsas document
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298 public void add() {
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299 tree = new uk.ac.vamsas.objects.core.Tree();
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300 bindjvvobj(tp, tree);
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301 tree.setTitle(tp.getTitle());
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302 Newick newick = new Newick();
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303 newick.setContent(tp.getTree().toString());
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304 newick.setTitle(tp.getTitle());
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305 tree.addNewick(newick);
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306 tree.setProvenance(makeTreeProvenance(jal, tp));
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307 tree.setTreenode(makeTreeNodes(tp.getTree()));
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309 alignment.addTree(tree);
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313 * note: this function assumes that all sequence and alignment objects
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314 * referenced in input data has already been associated with jalview objects.
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317 * @return Object[] { AlignmentView, AlignmentI - reference alignment for
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320 public Object[] recoverInputData(Provenance tp)
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322 AlignViewport javport=null;
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323 jalview.datamodel.AlignmentI jal=null;
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324 jalview.datamodel.CigarArray view=null;
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325 for (int pe = 0; pe < tp.getEntryCount(); pe++)
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327 if (tp.getEntry(pe).getInputCount() > 0)
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329 if (tp.getEntry(pe).getInputCount() > 1)
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331 Cache.log.warn("Ignoring additional input spec in provenance entry "
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332 + tp.getEntry(pe).toString());
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334 // LATER: deal sensibly with multiple inputs
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335 Input vInput = tp.getEntry(pe).getInput(0);
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336 // is this the whole alignment or a specific set of sequences ?
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337 if (vInput.getObjRefCount()==0)
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339 if (vInput.getObjRefCount()==1 && vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.Alignment)
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341 // recover an AlignmentView for the input data
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342 javport = (AlignViewport) getvObj2jv( (uk.ac.vamsas.
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343 client.Vobject) vInput
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345 jal = javport.getAlignment();
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346 view = javport.getAlignment().
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347 getCompactAlignment();
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349 if (vInput.getObjRef(0) instanceof uk.ac.vamsas.objects.core.AlignmentSequence) {
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350 // recover an AlignmentView for the input data
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351 javport = (AlignViewport) getvObj2jv(((Vobject)vInput.getObjRef(0)).getV_parent());
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352 jal = javport.getAlignment();
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353 jalview.datamodel.SequenceI[] seqs = new jalview.datamodel.SequenceI[vInput.getObjRefCount()];
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354 for (int i=0,iSize=vInput.getObjRefCount(); i<iSize; i++)
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356 SequenceI seq = (SequenceI) getvObj2jv((Vobject) vInput.getObjRef(i));
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359 view = new jalview.datamodel.Alignment(seqs).getCompactAlignment();
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363 int from = 1, to = jal.getWidth();
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364 int offset = 0; // deleteRange modifies its frame of reference
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365 for (int r = 0, s = vInput.getSegCount(); r < s; r++)
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367 Seg visSeg = vInput.getSeg(r);
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368 int se[] = getSegRange(visSeg, true); // jalview doesn't do
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369 // bidirection alignments yet.
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372 Cache.log.warn("Ignoring invalid segment in InputData spec.");
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378 view.deleteRange(offset + from - 1, offset + se[0] - 2);
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379 offset -= se[0] - from;
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386 view.deleteRange(offset + from - 1, offset + to - 1); // final
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392 return new Object[]{new AlignmentView(view), jal};
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395 Cache.log.debug("Returning null for input data recovery from provenance.");
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398 public NewickFile getNewickTree()
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402 public String getTitle()
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406 public AlignmentView getInputData()
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410 public boolean isValidTree()
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414 if (ntree.getTree()!=null)
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416 ntree = getNtree();
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420 catch (Exception e)
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422 Cache.log.debug("Failed to parse newick tree string",e);
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