static boolean sortOrderAscending = true;
- static NJTree lastTree = null;
+ static TreeModel lastTree = null;
static boolean sortTreeAscending = true;
* @return DOCUMENT ME!
*/
private static List<SequenceI> getOrderByTree(AlignmentI align,
- NJTree tree)
+ TreeModel tree)
{
int nSeq = align.getHeight();
* @param tree
* tree which has
*/
- public static void sortByTree(AlignmentI align, NJTree tree)
+ public static void sortByTree(AlignmentI align, TreeModel tree)
{
List<SequenceI> tmp = getOrderByTree(align, tree);
--- /dev/null
+package jalview.analysis;
+
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.SequenceNode;
+import jalview.viewmodel.AlignmentViewport;
+
+public class AverageDistanceTree extends TreeBuilder
+{
+ /**
+ * Constructor
+ *
+ * @param av
+ * @param sm
+ * @param scoreParameters
+ */
+ public AverageDistanceTree(AlignmentViewport av, ScoreModelI sm,
+ SimilarityParamsI scoreParameters)
+ {
+ super(av, sm, scoreParameters);
+ }
+
+ /**
+ * Calculates and saves the distance between the combination of cluster(i) and
+ * cluster(j) and all other clusters. An average of the distances from
+ * cluster(i) and cluster(j) is calculated, weighted by the sizes of each
+ * cluster.
+ *
+ * @param i
+ * @param j
+ */
+ @Override
+ protected void findClusterDistance(int i, int j)
+ {
+ int noi = clusters.elementAt(i).cardinality();
+ int noj = clusters.elementAt(j).cardinality();
+
+ // New distances from cluster i to others
+ double[] newdist = new double[noseqs];
+
+ for (int l = 0; l < noseqs; l++)
+ {
+ if ((l != i) && (l != j))
+ {
+ newdist[l] = ((distances.getValue(i, l) * noi) + (distances
+ .getValue(j, l) * noj)) / (noi + noj);
+ }
+ else
+ {
+ newdist[l] = 0;
+ }
+ }
+
+ for (int ii = 0; ii < noseqs; ii++)
+ {
+ distances.setValue(i, ii, newdist[ii]);
+ distances.setValue(ii, i, newdist[ii]);
+ System.out.println(String.format(
+ "findClusterDistance(%d, %d) newdist to %d is %f", i, j, ii,
+ newdist[ii]));
+ }
+ }
+
+ /**
+ * Returns the minimum distance between two clusters, and also sets the
+ * indices of the clusters in fields mini and minj
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ protected double findMinDistance()
+ {
+ double min = Double.MAX_VALUE;
+
+ for (int i = 0; i < (noseqs - 1); i++)
+ {
+ for (int j = i + 1; j < noseqs; j++)
+ {
+ if (!done.get(i) && !done.get(j))
+ {
+ if (distances.getValue(i, j) < min)
+ {
+ mini = i;
+ minj = j;
+
+ min = distances.getValue(i, j);
+ }
+ }
+ }
+ }
+ System.out.println("findMinDistance found " + min + " at " + mini + ","
+ + minj);
+ return min;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tmpi
+ * DOCUMENT ME!
+ * @param tmpj
+ * DOCUMENT ME!
+ * @param dist
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+ double dist)
+ {
+ double ih = 0;
+ double jh = 0;
+
+ SequenceNode sni = tmpi;
+ SequenceNode snj = tmpj;
+
+ while (sni != null)
+ {
+ ih = ih + sni.dist;
+ sni = (SequenceNode) sni.left();
+ }
+
+ while (snj != null)
+ {
+ jh = jh + snj.dist;
+ snj = (SequenceNode) snj.left();
+ }
+
+ tmpi.dist = ((dist / 2) - ih);
+ tmpj.dist = ((dist / 2) - jh);
+ System.out.println("findNewDistances set tmpi to " + tmpi.dist
+ + ", tmpj to " + tmpj.dist);
+ }
+
+}
*/
package jalview.analysis;
-import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.BinaryNode;
-import jalview.datamodel.CigarArray;
-import jalview.datamodel.NodeTransformI;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.io.NewickFile;
-import jalview.math.MatrixI;
import jalview.viewmodel.AlignmentViewport;
-import java.util.BitSet;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public class NJTree
+public class NJTree extends TreeBuilder
{
- public static final String AVERAGE_DISTANCE = "AV";
-
- public static final String NEIGHBOUR_JOINING = "NJ";
-
- public static final String FROM_FILE = "FromFile";
-
- /*
- * Bit j in each BitSet is set if the cluster includes the j'th sequence.
- * Clusters are grouped as the tree is built, from an initial state
- * where each cluster is a single sequence, until only two clusters are left.
- * These are the children of the root of the tree.
- */
- Vector<BitSet> clusters;
-
- SequenceI[] sequences;
-
- /*
- * SequenceData is a string representation of what the user
- * sees. The display may contain hidden columns.
- */
- public AlignmentView seqData = null;
-
- /*
- * Bit j is set when cluster j has been combined to another cluster.
- * The last two bits left unset are the indices of the clusters which
- * are the children of the root node.
- */
- BitSet done;
-
- int noseqs;
-
- int noClus;
-
- /*
- * Value [i, j] is the distance between cluster[i] and cluster[j].
- * Initially these are the pairwise distances of all sequences.
- * As the tree is built, these are updated to be the distances
- * between the clusters as they are assembled.
- */
- MatrixI distances;
-
- int mini;
-
- int minj;
-
- double ri;
-
- double rj;
-
- Vector<SequenceNode> groups = new Vector<SequenceNode>();
-
- SequenceNode maxdist;
-
- SequenceNode top;
-
- double maxDistValue;
-
- double maxheight;
-
- int ycount;
-
- Vector<SequenceNode> node;
-
- String type;
-
- String pwtype;
-
- boolean hasDistances = true; // normal case for jalview trees
-
- boolean hasBootstrap = false; // normal case for jalview trees
-
- private boolean hasRootDistance = true;
-
- /**
- * Create a new NJTree object with leaves associated with sequences in seqs,
- * and original alignment data represented by Cigar strings.
- *
- * @param seqs
- * SequenceI[]
- * @param odata
- * Cigar[]
- * @param treefile
- * NewickFile
- */
- public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
- {
- this(seqs, treefile);
- if (odata != null)
- {
- seqData = odata;
- }
- /*
- * sequenceString = new String[odata.length]; char gapChar =
- * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
- * odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
- * sequenceString[i] = oseq_aligned.getSequence(); }
- */
- }
-
- /**
- * Creates a new NJTree object from a tree from an external source
- *
- * @param seqs
- * SequenceI which should be associated with leafs of treefile
- * @param treefile
- * A parsed tree
- */
- public NJTree(SequenceI[] seqs, NewickFile treefile)
- {
- this.sequences = seqs;
- top = treefile.getTree();
-
- /**
- * There is no dependent alignment to be recovered from an imported tree.
- *
- * if (sequenceString == null) { sequenceString = new String[seqs.length];
- * for (int i = 0; i < seqs.length; i++) { sequenceString[i] =
- * seqs[i].getSequence(); } }
- */
-
- hasDistances = treefile.HasDistances();
- hasBootstrap = treefile.HasBootstrap();
- hasRootDistance = treefile.HasRootDistance();
-
- maxheight = findHeight(top);
-
- SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
-
- Vector<SequenceNode> leaves = findLeaves(top);
-
- int i = 0;
- int namesleft = seqs.length;
-
- SequenceNode j;
- SequenceI nam;
- String realnam;
- Vector<SequenceI> one2many = new Vector<SequenceI>();
- int countOne2Many = 0;
- while (i < leaves.size())
- {
- j = leaves.elementAt(i++);
- realnam = j.getName();
- nam = null;
-
- if (namesleft > -1)
- {
- nam = algnIds.findIdMatch(realnam);
- }
-
- if (nam != null)
- {
- j.setElement(nam);
- if (one2many.contains(nam))
- {
- countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
- // "+nam.getName());
- }
- else
- {
- one2many.addElement(nam);
- namesleft--;
- }
- }
- else
- {
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
- j.setPlaceholder(true);
- }
- }
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
- // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
- // more leaves.");
- // }
- // one2many.clear();
- }
-
/**
* Constructor given a viewport, tree type and score model
*
* @param av
* the current alignment viewport
- * @param treeType
- * NJ or AV
* @param sm
* a distance or similarity score model to use to compute the tree
- * @param scoreParameters TODO
- */
- public NJTree(AlignmentViewport av, String treeType, ScoreModelI sm, SimilarityParamsI scoreParameters)
- {
- // TODO handle type "FromFile" more elegantly
- if (!(treeType.equals(NEIGHBOUR_JOINING)))
- {
- treeType = AVERAGE_DISTANCE;
- }
- this.type = treeType;
- int start, end;
- boolean selview = av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() > 1;
- AlignmentView seqStrings = av.getAlignmentView(selview);
- if (!selview)
- {
- start = 0;
- end = av.getAlignment().getWidth();
- this.sequences = av.getAlignment().getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- this.sequences = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
- }
-
- init(seqStrings, start, end);
-
- computeTree(sm, scoreParameters);
- }
-
- void init(AlignmentView seqView, int start, int end)
- {
- this.node = new Vector<SequenceNode>();
- if (seqView != null)
- {
- this.seqData = seqView;
- }
- else
- {
- SeqCigar[] seqs = new SeqCigar[sequences.length];
- for (int i = 0; i < sequences.length; i++)
- {
- seqs[i] = new SeqCigar(sequences[i], start, end);
- }
- CigarArray sdata = new CigarArray(seqs);
- sdata.addOperation(CigarArray.M, end - start + 1);
- this.seqData = new AlignmentView(sdata, start);
- }
-
- /*
- * count the non-null sequences
- */
- noseqs = 0;
-
- done = new BitSet();
-
- for (SequenceI seq : sequences)
- {
- if (seq != null)
- {
- noseqs++;
- }
- }
- }
-
- /**
- * Calculates the tree using the given score model and parameters, and the
- * configured tree type
- * <p>
- * If the score model computes pairwise distance scores, then these are used
- * directly to derive the tree
- * <p>
- * If the score model computes similarity scores, then the range of the scores
- * is reversed to give a distance measure, and this is used to derive the tree
- *
- * @param sm
- * @param scoreOptions
+ * @param scoreParameters
*/
- protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
+ public NJTree(AlignmentViewport av, ScoreModelI sm,
+ SimilarityParamsI scoreParameters)
{
- if (sm instanceof DistanceScoreModelI)
- {
- distances = ((DistanceScoreModelI) sm).findDistances(seqData,
- scoreOptions);
- }
- else if (sm instanceof SimilarityScoreModelI)
- {
- /*
- * compute similarity and invert it to give a distance measure
- */
- MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
- seqData, scoreOptions);
- result.reverseRange(true);
- distances = result;
- }
-
- makeLeaves();
-
- noClus = clusters.size();
-
- cluster();
+ super(av, sm, scoreParameters);
}
+ // private long _lycount = 0, _lylimit = 0;
/**
- * Generate a string representation of the Tree
+ * DOCUMENT ME!
*
- * @return Newick File with all tree data available
+ * @return DOCUMENT ME!
*/
@Override
- public String toString()
- {
- jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
-
- return fout.print(hasBootstrap(), hasDistances(),
- hasRootDistance()); // output all data available for tree
- }
-
- /**
- *
- * used when the alignment associated to a tree has changed.
- *
- * @param list
- * Sequence set to be associated with tree nodes
- */
- public void updatePlaceHolders(List<SequenceI> list)
+ protected
+ double findMinDistance()
{
- Vector<SequenceNode> leaves = findLeaves(top);
-
- int sz = leaves.size();
- SequenceIdMatcher seqmatcher = null;
- int i = 0;
+ double min = Double.MAX_VALUE;
- while (i < sz)
+ for (int i = 0; i < (noseqs - 1); i++)
{
- SequenceNode leaf = leaves.elementAt(i++);
-
- if (list.contains(leaf.element()))
- {
- leaf.setPlaceholder(false);
- }
- else
+ for (int j = i + 1; j < noseqs; j++)
{
- if (seqmatcher == null)
+ if (!done.get(i) && !done.get(j))
{
- // Only create this the first time we need it
- SequenceI[] seqs = new SequenceI[list.size()];
+ double tmp = distances.getValue(i, j)
+ - (findr(i, j) + findr(j, i));
- for (int j = 0; j < seqs.length; j++)
+ if (tmp < min)
{
- seqs[j] = list.get(j);
- }
-
- seqmatcher = new SequenceIdMatcher(seqs);
- }
-
- SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
+ mini = i;
+ minj = j;
- if (nam != null)
- {
- if (!leaf.isPlaceholder())
- {
- // remapping the node to a new sequenceI - should remove any refs to
- // old one.
- // TODO - make many sequenceI to one leaf mappings possible!
- // (JBPNote)
- }
- leaf.setPlaceholder(false);
- leaf.setElement(nam);
- }
- else
- {
- if (!leaf.isPlaceholder())
- {
- // Construct a new placeholder sequence object for this leaf
- leaf.setElement(new Sequence(leaf.getName(),
- "THISISAPLACEHLDER"));
+ min = tmp;
}
- leaf.setPlaceholder(true);
-
- }
- }
- }
- }
-
- /**
- * rename any nodes according to their associated sequence. This will modify
- * the tree's metadata! (ie the original NewickFile or newly generated
- * BinaryTree's label data)
- */
- public void renameAssociatedNodes()
- {
- applyToNodes(new NodeTransformI()
- {
-
- @Override
- public void transform(BinaryNode nd)
- {
- Object el = nd.element();
- if (el != null && el instanceof SequenceI)
- {
- nd.setName(((SequenceI) el).getName());
}
}
- });
- }
-
- /**
- * Form clusters by grouping sub-clusters, starting from one sequence per
- * cluster, and finishing when only two clusters remain
- */
- void cluster()
- {
- while (noClus > 2)
- {
- if (type.equals(NEIGHBOUR_JOINING))
- {
- findMinNJDistance();
- }
- else
- {
- findMinDistance();
- }
-
- BitSet combined = joinClusters(mini, minj);
-
- done.set(minj);
-
- clusters.setElementAt(null, minj);
- clusters.setElementAt(combined, mini);
-
- noClus--;
- }
-
- int rightChild = done.nextClearBit(0);
- int leftChild = done.nextClearBit(rightChild + 1);
-
- joinClusters(leftChild, rightChild);
- top = (node.elementAt(leftChild));
-
- reCount(top);
- findHeight(top);
- findMaxDist(top);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- BitSet joinClusters(int i, int j)
- {
- double dist = distances.getValue(i, j);
-
- BitSet combined = new BitSet();
- combined.or(clusters.get(i));
- combined.or(clusters.get(j));
-
- ri = findr(i, j);
- rj = findr(j, i);
-
- if (type.equals(NEIGHBOUR_JOINING))
- {
- findClusterNJDistance(i, j);
- }
- else
- {
- findClusterDistance(i, j);
- }
-
- SequenceNode sn = new SequenceNode();
-
- sn.setLeft((node.elementAt(i)));
- sn.setRight((node.elementAt(j)));
-
- SequenceNode tmpi = (node.elementAt(i));
- SequenceNode tmpj = (node.elementAt(j));
-
- if (type.equals(NEIGHBOUR_JOINING))
- {
- findNewNJDistances(tmpi, tmpj, dist);
- }
- else
- {
- findNewDistances(tmpi, tmpj, dist);
}
- tmpi.setParent(sn);
- tmpj.setParent(sn);
-
- node.setElementAt(sn, i);
-
- return combined;
+ return min;
}
/**
* @param dist
* DOCUMENT ME!
*/
- void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
- double dist)
+ @Override
+ protected
+ void findNewDistances(SequenceNode tmpi, SequenceNode tmpj, double dist)
{
tmpi.dist = ((dist + ri) - rj) / 2;
}
}
- /**
- * DOCUMENT ME!
- *
- * @param tmpi
- * DOCUMENT ME!
- * @param tmpj
- * DOCUMENT ME!
- * @param dist
- * DOCUMENT ME!
- */
- void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- double dist)
- {
- double ih = 0;
- double jh = 0;
-
- SequenceNode sni = tmpi;
- SequenceNode snj = tmpj;
-
- while (sni != null)
- {
- ih = ih + sni.dist;
- sni = (SequenceNode) sni.left();
- }
-
- while (snj != null)
- {
- jh = jh + snj.dist;
- snj = (SequenceNode) snj.left();
- }
- tmpi.dist = ((dist / 2) - ih);
- tmpj.dist = ((dist / 2) - jh);
- }
/**
- * DOCUMENT ME!
+ * Calculates and saves the distance between the combination of cluster(i) and
+ * cluster(j) and all other clusters. The new distance to cluster k is
+ * calculated as the average of the distances from i to k and from j to k,
+ * less half the distance from i to j.
*
* @param i
- * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
*/
+ @Override
+ protected
void findClusterDistance(int i, int j)
{
- int noi = clusters.elementAt(i).cardinality();
- int noj = clusters.elementAt(j).cardinality();
-
- // New distances from cluster to others
+ // New distances from cluster i to others
double[] newdist = new double[noseqs];
-
+
+ double ijDistance = distances.getValue(i, j);
for (int l = 0; l < noseqs; l++)
{
if ((l != i) && (l != j))
{
- newdist[l] = ((distances.getValue(i, l) * noi) + (distances.getValue(
- j, l) * noj))
- / (noi + noj);
+ newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l) - ijDistance) / 2;
}
else
{
newdist[l] = 0;
}
}
-
+
for (int ii = 0; ii < noseqs; ii++)
{
distances.setValue(i, ii, newdist[ii]);
distances.setValue(ii, i, newdist[ii]);
}
}
-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- */
- void findClusterNJDistance(int i, int j)
- {
-
- // New distances from cluster to others
- double[] newdist = new double[noseqs];
-
- for (int l = 0; l < noseqs; l++)
- {
- if ((l != i) && (l != j))
- {
- newdist[l] = (distances.getValue(i, l) + distances.getValue(j, l) - distances
- .getValue(i, j)) / 2;
- }
- else
- {
- newdist[l] = 0;
- }
- }
-
- for (int ii = 0; ii < noseqs; ii++)
- {
- distances.setValue(i, ii, newdist[ii]);
- distances.setValue(ii, i, newdist[ii]);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findr(int i, int j)
- {
- double tmp = 1;
-
- for (int k = 0; k < noseqs; k++)
- {
- if ((k != i) && (k != j) && (!done.get(k)))
- {
- tmp = tmp + distances.getValue(i, k);
- }
- }
-
- if (noClus > 2)
- {
- tmp = tmp / (noClus - 2);
- }
-
- return tmp;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findMinNJDistance()
- {
- double min = Double.MAX_VALUE;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i + 1; j < noseqs; j++)
- {
- if (!done.get(i) && !done.get(j))
- {
- double tmp = distances.getValue(i, j)
- - (findr(i, j) + findr(j, i));
-
- if (tmp < min)
- {
- mini = i;
- minj = j;
-
- min = tmp;
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- double findMinDistance()
- {
- double min = Double.MAX_VALUE;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i + 1; j < noseqs; j++)
- {
- if (!done.get(i) && !done.get(j))
- {
- if (distances.getValue(i, j) < min)
- {
- mini = i;
- minj = j;
-
- min = distances.getValue(i, j);
- }
- }
- }
- }
-
- return min;
- }
-
- /**
- * Start by making a cluster for each individual sequence
- */
- void makeLeaves()
- {
- clusters = new Vector<BitSet>();
-
- for (int i = 0; i < noseqs; i++)
- {
- SequenceNode sn = new SequenceNode();
-
- sn.setElement(sequences[i]);
- sn.setName(sequences[i].getName());
- node.addElement(sn);
- BitSet bs = new BitSet();
- bs.set(i);
- clusters.addElement(bs);
- }
- }
-
- /**
- * Search for leaf nodes below (or at) the given node
- *
- * @param nd
- * root node to search from
- *
- * @return
- */
- public Vector<SequenceNode> findLeaves(SequenceNode nd)
- {
- Vector<SequenceNode> leaves = new Vector<SequenceNode>();
- findLeaves(nd, leaves);
- return leaves;
- }
-
- /**
- * Search for leaf nodes.
- *
- * @param nd
- * root node to search from
- * @param leaves
- * Vector of leaves to add leaf node objects too.
- *
- * @return Vector of leaf nodes on binary tree
- */
- Vector<SequenceNode> findLeaves(SequenceNode nd,
- Vector<SequenceNode> leaves)
- {
- if (nd == null)
- {
- return leaves;
- }
-
- if ((nd.left() == null) && (nd.right() == null)) // Interior node
- // detection
- {
- leaves.addElement(nd);
-
- return leaves;
- }
- else
- {
- /*
- * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
- * leaves.addElement(node); }
- */
- findLeaves((SequenceNode) nd.left(), leaves);
- findLeaves((SequenceNode) nd.right(), leaves);
- }
-
- return leaves;
- }
-
- /**
- * printNode is mainly for debugging purposes.
- *
- * @param nd
- * SequenceNode
- */
- void printNode(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
- System.out.println("Dist " + nd.dist);
- System.out.println("Boot " + nd.getBootstrap());
- }
- else
- {
- System.out.println("Dist " + nd.dist);
- printNode((SequenceNode) nd.left());
- printNode((SequenceNode) nd.right());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void findMaxDist(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- double dist = nd.dist;
-
- if (dist > maxDistValue)
- {
- maxdist = nd;
- maxDistValue = dist;
- }
- }
- else
- {
- findMaxDist((SequenceNode) nd.left());
- findMaxDist((SequenceNode) nd.right());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector<SequenceNode> getGroups()
- {
- return groups;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public double getMaxHeight()
- {
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- * @param threshold
- * DOCUMENT ME!
- */
- public void groupNodes(SequenceNode nd, float threshold)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.height / maxheight) > threshold)
- {
- groups.addElement(nd);
- }
- else
- {
- groupNodes((SequenceNode) nd.left(), threshold);
- groupNodes((SequenceNode) nd.right(), threshold);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public double findHeight(SequenceNode nd)
- {
- if (nd == null)
- {
- return maxheight;
- }
-
- if ((nd.left() == null) && (nd.right() == null))
- {
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
-
- if (nd.height > maxheight)
- {
- return nd.height;
- }
- else
- {
- return maxheight;
- }
- }
- else
- {
- if (nd.parent() != null)
- {
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
- }
- else
- {
- maxheight = 0;
- nd.height = (float) 0.0;
- }
-
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
- }
-
- return maxheight;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- SequenceNode reRoot()
- {
- // TODO not used - remove?
- if (maxdist != null)
- {
- ycount = 0;
-
- double tmpdist = maxdist.dist;
-
- // New top
- SequenceNode sn = new SequenceNode();
- sn.setParent(null);
-
- // New right hand of top
- SequenceNode snr = (SequenceNode) maxdist.parent();
- changeDirection(snr, maxdist);
- System.out.println("Printing reversed tree");
- printN(snr);
- snr.dist = tmpdist / 2;
- maxdist.dist = tmpdist / 2;
-
- snr.setParent(sn);
- maxdist.setParent(sn);
-
- sn.setRight(snr);
- sn.setLeft(maxdist);
-
- top = sn;
-
- ycount = 0;
- reCount(top);
- findHeight(top);
- }
-
- return top;
- }
-
- /**
- *
- * @return true if original sequence data can be recovered
- */
- public boolean hasOriginalSequenceData()
- {
- return seqData != null;
- }
-
- /**
- * Returns original alignment data used for calculation - or null where not
- * available.
- *
- * @return null or cut'n'pasteable alignment
- */
- public String printOriginalSequenceData(char gapChar)
- {
- if (seqData == null)
- {
- return null;
- }
-
- StringBuffer sb = new StringBuffer();
- String[] seqdatas = seqData.getSequenceStrings(gapChar);
- for (int i = 0; i < seqdatas.length; i++)
- {
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequences[i]
- .getName()));
- sb.append(" " + seqdatas[i] + "\n");
- }
- return sb.toString();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void printN(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- if ((nd.left() != null) && (nd.right() != null))
- {
- printN((SequenceNode) nd.left());
- printN((SequenceNode) nd.right());
- }
- else
- {
- System.out.println(" name = " + ((SequenceI) nd.element()).getName());
- }
-
- System.out.println(" dist = " + nd.dist + " " + nd.count + " "
- + nd.height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- public void reCount(SequenceNode nd)
- {
- ycount = 0;
- // _lycount = 0;
- // _lylimit = this.node.size();
- _reCount(nd);
- }
-
- // private long _lycount = 0, _lylimit = 0;
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- void _reCount(SequenceNode nd)
- {
- // if (_lycount<_lylimit)
- // {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
- // }
- if (nd == null)
- {
- return;
- }
- // _lycount++;
-
- if ((nd.left() != null) && (nd.right() != null))
- {
-
- _reCount((SequenceNode) nd.left());
- _reCount((SequenceNode) nd.right());
-
- SequenceNode l = (SequenceNode) nd.left();
- SequenceNode r = (SequenceNode) nd.right();
-
- nd.count = l.count + r.count;
- nd.ycount = (l.ycount + r.ycount) / 2;
- }
- else
- {
- nd.count = 1;
- nd.ycount = ycount++;
- }
- // _lycount--;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- */
- public void swapNodes(SequenceNode nd)
- {
- if (nd == null)
- {
- return;
- }
-
- SequenceNode tmp = (SequenceNode) nd.left();
-
- nd.setLeft(nd.right());
- nd.setRight(tmp);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param nd
- * DOCUMENT ME!
- * @param dir
- * DOCUMENT ME!
- */
- void changeDirection(SequenceNode nd, SequenceNode dir)
- {
- if (nd == null)
- {
- return;
- }
-
- if (nd.parent() != top)
- {
- changeDirection((SequenceNode) nd.parent(), nd);
-
- SequenceNode tmp = (SequenceNode) nd.parent();
-
- if (dir == nd.left())
- {
- nd.setParent(dir);
- nd.setLeft(tmp);
- }
- else if (dir == nd.right())
- {
- nd.setParent(dir);
- nd.setRight(tmp);
- }
- }
- else
- {
- if (dir == nd.left())
- {
- nd.setParent(nd.left());
-
- if (top.left() == nd)
- {
- nd.setRight(top.right());
- }
- else
- {
- nd.setRight(top.left());
- }
- }
- else
- {
- nd.setParent(nd.right());
-
- if (top.left() == nd)
- {
- nd.setLeft(top.right());
- }
- else
- {
- nd.setLeft(top.left());
- }
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getMaxDist()
- {
- return maxdist;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getTopNode()
- {
- return top;
- }
-
- /**
- *
- * @return true if tree has real distances
- */
- public boolean hasDistances()
- {
- return hasDistances;
- }
-
- /**
- *
- * @return true if tree has real bootstrap values
- */
- public boolean hasBootstrap()
- {
- return hasBootstrap;
- }
-
- public boolean hasRootDistance()
- {
- return hasRootDistance;
- }
-
- /**
- * apply the given transform to all the nodes in the tree.
- *
- * @param nodeTransformI
- */
- public void applyToNodes(NodeTransformI nodeTransformI)
- {
- for (Enumeration<SequenceNode> nodes = node.elements(); nodes
- .hasMoreElements(); nodeTransformI.transform(nodes
- .nextElement()))
- {
- ;
- }
- }
}
--- /dev/null
+package jalview.analysis;
+
+import jalview.api.analysis.DistanceScoreModelI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.api.analysis.SimilarityScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.math.MatrixI;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.util.BitSet;
+import java.util.Vector;
+
+public abstract class TreeBuilder
+{
+ public static final String AVERAGE_DISTANCE = "AV";
+
+ public static final String NEIGHBOUR_JOINING = "NJ";
+
+ protected Vector<BitSet> clusters;
+
+ protected SequenceI[] sequences;
+
+ public AlignmentView seqData;
+
+ protected BitSet done;
+
+ protected int noseqs;
+
+ int noClus;
+
+ protected MatrixI distances;
+
+ protected int mini;
+
+ protected int minj;
+
+ protected double ri;
+
+ protected double rj;
+
+ SequenceNode maxdist;
+
+ SequenceNode top;
+
+ double maxDistValue;
+
+ double maxheight;
+
+ int ycount;
+
+ Vector<SequenceNode> node;
+
+ /**
+ * Constructor
+ *
+ * @param av
+ * @param sm
+ * @param scoreParameters
+ */
+ public TreeBuilder(AlignmentViewport av, ScoreModelI sm,
+ SimilarityParamsI scoreParameters)
+ {
+ int start, end;
+ boolean selview = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 1;
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
+ {
+ start = 0;
+ end = av.getAlignment().getWidth();
+ this.sequences = av.getAlignment().getSequencesArray();
+ }
+ else
+ {
+ start = av.getSelectionGroup().getStartRes();
+ end = av.getSelectionGroup().getEndRes() + 1;
+ this.sequences = av.getSelectionGroup().getSequencesInOrder(
+ av.getAlignment());
+ }
+
+ init(seqStrings, start, end);
+
+ computeTree(sm, scoreParameters);
+ }
+
+ public SequenceI[] getSequences()
+ {
+ return sequences;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ double findHeight(SequenceNode nd)
+ {
+ if (nd == null)
+ {
+ return maxheight;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null))
+ {
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+
+ if (nd.height > maxheight)
+ {
+ return nd.height;
+ }
+ else
+ {
+ return maxheight;
+ }
+ }
+ else
+ {
+ if (nd.parent() != null)
+ {
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+ }
+ else
+ {
+ maxheight = 0;
+ nd.height = (float) 0.0;
+ }
+
+ maxheight = findHeight((SequenceNode) (nd.left()));
+ maxheight = findHeight((SequenceNode) (nd.right()));
+ }
+
+ return maxheight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ void reCount(SequenceNode nd)
+ {
+ ycount = 0;
+ // _lycount = 0;
+ // _lylimit = this.node.size();
+ _reCount(nd);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ void _reCount(SequenceNode nd)
+ {
+ // if (_lycount<_lylimit)
+ // {
+ // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // }
+ if (nd == null)
+ {
+ return;
+ }
+ // _lycount++;
+
+ if ((nd.left() != null) && (nd.right() != null))
+ {
+
+ _reCount((SequenceNode) nd.left());
+ _reCount((SequenceNode) nd.right());
+
+ SequenceNode l = (SequenceNode) nd.left();
+ SequenceNode r = (SequenceNode) nd.right();
+
+ nd.count = l.count + r.count;
+ nd.ycount = (l.ycount + r.ycount) / 2;
+ }
+ else
+ {
+ nd.count = 1;
+ nd.ycount = ycount++;
+ }
+ // _lycount--;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getTopNode()
+ {
+ return top;
+ }
+
+ /**
+ *
+ * @return true if tree has real distances
+ */
+ public boolean hasDistances()
+ {
+ return true;
+ }
+
+ /**
+ *
+ * @return true if tree has real bootstrap values
+ */
+ public boolean hasBootstrap()
+ {
+ return false;
+ }
+
+ public boolean hasRootDistance()
+ {
+ return true;
+ }
+
+ /**
+ * Form clusters by grouping sub-clusters, starting from one sequence per
+ * cluster, and finishing when only two clusters remain
+ */
+ void cluster()
+ {
+ while (noClus > 2)
+ {
+ findMinDistance();
+
+ joinClusters(mini, minj);
+
+ noClus--;
+ }
+
+ int rightChild = done.nextClearBit(0);
+ int leftChild = done.nextClearBit(rightChild + 1);
+
+ joinClusters(leftChild, rightChild);
+ top = (node.elementAt(leftChild));
+
+ reCount(top);
+ findHeight(top);
+ findMaxDist(top);
+ }
+
+ protected abstract double findMinDistance();
+
+ /**
+ * Calculates the tree using the given score model and parameters, and the
+ * configured tree type
+ * <p>
+ * If the score model computes pairwise distance scores, then these are used
+ * directly to derive the tree
+ * <p>
+ * If the score model computes similarity scores, then the range of the scores
+ * is reversed to give a distance measure, and this is used to derive the tree
+ *
+ * @param sm
+ * @param scoreOptions
+ */
+ protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
+ {
+ if (sm instanceof DistanceScoreModelI)
+ {
+ distances = ((DistanceScoreModelI) sm).findDistances(seqData,
+ scoreOptions);
+ }
+ else if (sm instanceof SimilarityScoreModelI)
+ {
+ /*
+ * compute similarity and invert it to give a distance measure
+ */
+ MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
+ seqData, scoreOptions);
+ result.reverseRange(true);
+ distances = result;
+ }
+
+ makeLeaves();
+
+ noClus = clusters.size();
+
+ cluster();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ void findMaxDist(SequenceNode nd)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null))
+ {
+ double dist = nd.dist;
+
+ if (dist > maxDistValue)
+ {
+ maxdist = nd;
+ maxDistValue = dist;
+ }
+ }
+ else
+ {
+ findMaxDist((SequenceNode) nd.left());
+ findMaxDist((SequenceNode) nd.right());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ protected double findr(int i, int j)
+ {
+ double tmp = 1;
+
+ for (int k = 0; k < noseqs; k++)
+ {
+ if ((k != i) && (k != j) && (!done.get(k)))
+ {
+ tmp = tmp + distances.getValue(i, k);
+ }
+ }
+
+ if (noClus > 2)
+ {
+ tmp = tmp / (noClus - 2);
+ }
+
+ return tmp;
+ }
+
+ protected void init(AlignmentView seqView, int start, int end)
+ {
+ this.node = new Vector<SequenceNode>();
+ if (seqView != null)
+ {
+ this.seqData = seqView;
+ }
+ else
+ {
+ SeqCigar[] seqs = new SeqCigar[sequences.length];
+ for (int i = 0; i < sequences.length; i++)
+ {
+ seqs[i] = new SeqCigar(sequences[i], start, end);
+ }
+ CigarArray sdata = new CigarArray(seqs);
+ sdata.addOperation(CigarArray.M, end - start + 1);
+ this.seqData = new AlignmentView(sdata, start);
+ }
+
+ /*
+ * count the non-null sequences
+ */
+ noseqs = 0;
+
+ done = new BitSet();
+
+ for (SequenceI seq : sequences)
+ {
+ if (seq != null)
+ {
+ noseqs++;
+ }
+ }
+ }
+
+ /**
+ * Merges cluster(j) to cluster(i) and recalculates cluster and node distances
+ *
+ * @param i
+ * @param j
+ */
+ void joinClusters(final int i, final int j)
+ {
+ double dist = distances.getValue(i, j);
+
+ /*
+ * add the members of cluster(j) to cluster(i)
+ */
+ clusters.get(i).or(clusters.get(j));
+
+ ri = findr(i, j);
+ rj = findr(j, i);
+
+ findClusterDistance(i, j);
+
+ SequenceNode sn = new SequenceNode();
+
+ sn.setLeft((node.elementAt(i)));
+ sn.setRight((node.elementAt(j)));
+
+ SequenceNode tmpi = (node.elementAt(i));
+ SequenceNode tmpj = (node.elementAt(j));
+
+ findNewDistances(tmpi, tmpj, dist);
+
+ tmpi.setParent(sn);
+ tmpj.setParent(sn);
+
+ node.setElementAt(sn, i);
+
+ /*
+ * mark cluster j as disposed of
+ */
+ done.set(j);
+ clusters.setElementAt(null, j);
+ }
+
+ protected abstract void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+ double dist);
+
+ /**
+ * Calculates and saves the distance between the combination of cluster(i) and
+ * cluster(j) and all other clusters. The form of the calculation depends on
+ * the tree clustering method being used.
+ *
+ * @param i
+ * @param j
+ */
+ protected abstract void findClusterDistance(int i, int j);
+
+ /**
+ * Start by making a cluster for each individual sequence
+ */
+ void makeLeaves()
+ {
+ clusters = new Vector<BitSet>();
+
+ for (int i = 0; i < noseqs; i++)
+ {
+ SequenceNode sn = new SequenceNode();
+
+ sn.setElement(sequences[i]);
+ sn.setName(sequences[i].getName());
+ node.addElement(sn);
+ BitSet bs = new BitSet();
+ bs.set(i);
+ clusters.addElement(bs);
+ }
+ }
+
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
+/**
+ * A model of a tree, either computed by Jalview or loaded from a file or other
+ * resource or service
+ */
+public class TreeModel
+{
+
+ SequenceI[] sequences;
+
+ /*
+ * SequenceData is a string representation of what the user
+ * sees. The display may contain hidden columns.
+ */
+ public AlignmentView seqData;
+
+ int noseqs;
+
+ SequenceNode top;
+
+ double maxDistValue;
+
+ double maxheight;
+
+ int ycount;
+
+ Vector<SequenceNode> node;
+
+ boolean hasDistances = true; // normal case for jalview trees
+
+ boolean hasBootstrap = false; // normal case for jalview trees
+
+ private boolean hasRootDistance = true;
+
+ /**
+ * Create a new TreeModel object with leaves associated with sequences in
+ * seqs, and original alignment data represented by Cigar strings
+ *
+ * @param seqs
+ * SequenceI[]
+ * @param odata
+ * Cigar[]
+ * @param treefile
+ * NewickFile
+ */
+ public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
+ {
+ this(seqs, treefile);
+ seqData = odata;
+ }
+
+ /**
+ * Creates a new TreeModel object from a tree from an external source
+ *
+ * @param seqs
+ * SequenceI which should be associated with leafs of treefile
+ * @param treefile
+ * A parsed tree
+ */
+ public TreeModel(SequenceI[] seqs, NewickFile treefile)
+ {
+ this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
+ .HasBootstrap(), treefile.HasRootDistance());
+
+ associateLeavesToSequences(seqs);
+ }
+
+ /**
+ * Constructor given a calculated tree
+ *
+ * @param tree
+ */
+ public TreeModel(TreeBuilder tree)
+ {
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(), tree
+ .hasBootstrap(), tree.hasRootDistance());
+ }
+
+ /**
+ * Constructor given sequences, root node and tree property flags
+ *
+ * @param seqs
+ * @param root
+ * @param hasDist
+ * @param hasBoot
+ * @param hasRootDist
+ */
+ public TreeModel(SequenceI[] seqs, SequenceNode root, boolean hasDist,
+ boolean hasBoot, boolean hasRootDist)
+ {
+ this.sequences = seqs;
+ top = root;
+
+ hasDistances = hasDist;
+ hasBootstrap = hasBoot;
+ hasRootDistance = hasRootDist;
+
+ maxheight = findHeight(top);
+ }
+
+ /**
+ * @param seqs
+ */
+ public void associateLeavesToSequences(SequenceI[] seqs)
+ {
+ SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
+
+ Vector<SequenceNode> leaves = findLeaves(top);
+
+ int i = 0;
+ int namesleft = seqs.length;
+
+ SequenceNode j;
+ SequenceI nam;
+ String realnam;
+ Vector<SequenceI> one2many = new Vector<SequenceI>();
+ // int countOne2Many = 0;
+ while (i < leaves.size())
+ {
+ j = leaves.elementAt(i++);
+ realnam = j.getName();
+ nam = null;
+
+ if (namesleft > -1)
+ {
+ nam = algnIds.findIdMatch(realnam);
+ }
+
+ if (nam != null)
+ {
+ j.setElement(nam);
+ if (one2many.contains(nam))
+ {
+ // countOne2Many++;
+ // if (jalview.bin.Cache.log.isDebugEnabled())
+ // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // "+nam.getName());
+ }
+ else
+ {
+ one2many.addElement(nam);
+ namesleft--;
+ }
+ }
+ else
+ {
+ j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
+ j.setPlaceholder(true);
+ }
+ }
+ // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
+ // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
+ // more leaves.");
+ // }
+ // one2many.clear();
+ }
+
+ /**
+ * Generate a string representation of the Tree
+ *
+ * @return Newick File with all tree data available
+ */
+ public String print()
+ {
+ NewickFile fout = new NewickFile(getTopNode());
+
+ return fout.print(hasBootstrap(), hasDistances(),
+ hasRootDistance()); // output all data available for tree
+ }
+
+ /**
+ *
+ * used when the alignment associated to a tree has changed.
+ *
+ * @param list
+ * Sequence set to be associated with tree nodes
+ */
+ public void updatePlaceHolders(List<SequenceI> list)
+ {
+ Vector<SequenceNode> leaves = findLeaves(top);
+
+ int sz = leaves.size();
+ SequenceIdMatcher seqmatcher = null;
+ int i = 0;
+
+ while (i < sz)
+ {
+ SequenceNode leaf = leaves.elementAt(i++);
+
+ if (list.contains(leaf.element()))
+ {
+ leaf.setPlaceholder(false);
+ }
+ else
+ {
+ if (seqmatcher == null)
+ {
+ // Only create this the first time we need it
+ SequenceI[] seqs = new SequenceI[list.size()];
+
+ for (int j = 0; j < seqs.length; j++)
+ {
+ seqs[j] = list.get(j);
+ }
+
+ seqmatcher = new SequenceIdMatcher(seqs);
+ }
+
+ SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
+
+ if (nam != null)
+ {
+ if (!leaf.isPlaceholder())
+ {
+ // remapping the node to a new sequenceI - should remove any refs to
+ // old one.
+ // TODO - make many sequenceI to one leaf mappings possible!
+ // (JBPNote)
+ }
+ leaf.setPlaceholder(false);
+ leaf.setElement(nam);
+ }
+ else
+ {
+ if (!leaf.isPlaceholder())
+ {
+ // Construct a new placeholder sequence object for this leaf
+ leaf.setElement(new Sequence(leaf.getName(),
+ "THISISAPLACEHLDER"));
+ }
+ leaf.setPlaceholder(true);
+
+ }
+ }
+ }
+ }
+
+ /**
+ * rename any nodes according to their associated sequence. This will modify
+ * the tree's metadata! (ie the original NewickFile or newly generated
+ * BinaryTree's label data)
+ */
+ public void renameAssociatedNodes()
+ {
+ applyToNodes(new NodeTransformI()
+ {
+
+ @Override
+ public void transform(BinaryNode nd)
+ {
+ Object el = nd.element();
+ if (el != null && el instanceof SequenceI)
+ {
+ nd.setName(((SequenceI) el).getName());
+ }
+ }
+ });
+ }
+
+ /**
+ * Search for leaf nodes below (or at) the given node
+ *
+ * @param nd
+ * root node to search from
+ *
+ * @return
+ */
+ public Vector<SequenceNode> findLeaves(SequenceNode nd)
+ {
+ Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+ findLeaves(nd, leaves);
+ return leaves;
+ }
+
+ /**
+ * Search for leaf nodes.
+ *
+ * @param nd
+ * root node to search from
+ * @param leaves
+ * Vector of leaves to add leaf node objects too.
+ *
+ * @return Vector of leaf nodes on binary tree
+ */
+ Vector<SequenceNode> findLeaves(SequenceNode nd,
+ Vector<SequenceNode> leaves)
+ {
+ if (nd == null)
+ {
+ return leaves;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null)) // Interior node
+ // detection
+ {
+ leaves.addElement(nd);
+
+ return leaves;
+ }
+ else
+ {
+ /*
+ * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
+ * leaves.addElement(node); }
+ */
+ findLeaves((SequenceNode) nd.left(), leaves);
+ findLeaves((SequenceNode) nd.right(), leaves);
+ }
+
+ return leaves;
+ }
+
+ /**
+ * printNode is mainly for debugging purposes.
+ *
+ * @param nd
+ * SequenceNode
+ */
+ void printNode(SequenceNode nd)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null))
+ {
+ System.out.println("Leaf = " + ((SequenceI) nd.element()).getName());
+ System.out.println("Dist " + nd.dist);
+ System.out.println("Boot " + nd.getBootstrap());
+ }
+ else
+ {
+ System.out.println("Dist " + nd.dist);
+ printNode((SequenceNode) nd.left());
+ printNode((SequenceNode) nd.right());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double getMaxHeight()
+ {
+ return maxheight;
+ }
+
+ /**
+ * Makes a list of groups, where each group is represented by a node whose
+ * height (distance from the root node), as a fraction of the height of the
+ * whole tree, is greater than the given threshold. This corresponds to
+ * selecting the nodes immediately to the right of a vertical line
+ * partitioning the tree (if the tree is drawn with root to the left). Each
+ * such node represents a group that contains all of the sequences linked to
+ * the child leaf nodes.
+ *
+ * @param threshold
+ * @see #getGroups()
+ */
+ public List<SequenceNode> groupNodes(float threshold)
+ {
+ List<SequenceNode> groups = new ArrayList<SequenceNode>();
+ _groupNodes(groups, getTopNode(), threshold);
+ return groups;
+ }
+
+ protected void _groupNodes(List<SequenceNode> groups, SequenceNode nd,
+ float threshold)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ if ((nd.height / maxheight) > threshold)
+ {
+ groups.add(nd);
+ }
+ else
+ {
+ _groupNodes(groups, (SequenceNode) nd.left(), threshold);
+ _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double findHeight(SequenceNode nd)
+ {
+ if (nd == null)
+ {
+ return maxheight;
+ }
+
+ if ((nd.left() == null) && (nd.right() == null))
+ {
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+
+ if (nd.height > maxheight)
+ {
+ return nd.height;
+ }
+ else
+ {
+ return maxheight;
+ }
+ }
+ else
+ {
+ if (nd.parent() != null)
+ {
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+ }
+ else
+ {
+ maxheight = 0;
+ nd.height = (float) 0.0;
+ }
+
+ maxheight = findHeight((SequenceNode) (nd.left()));
+ maxheight = findHeight((SequenceNode) (nd.right()));
+ }
+
+ return maxheight;
+ }
+
+ /**
+ *
+ * @return true if original sequence data can be recovered
+ */
+ public boolean hasOriginalSequenceData()
+ {
+ return seqData != null;
+ }
+
+ /**
+ * Returns original alignment data used for calculation - or null where not
+ * available.
+ *
+ * @return null or cut'n'pasteable alignment
+ */
+ public String printOriginalSequenceData(char gapChar)
+ {
+ if (seqData == null)
+ {
+ return null;
+ }
+
+ StringBuffer sb = new StringBuffer();
+ String[] seqdatas = seqData.getSequenceStrings(gapChar);
+ for (int i = 0; i < seqdatas.length; i++)
+ {
+ sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequences[i]
+ .getName()));
+ sb.append(" " + seqdatas[i] + "\n");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ void printN(SequenceNode nd)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ if ((nd.left() != null) && (nd.right() != null))
+ {
+ printN((SequenceNode) nd.left());
+ printN((SequenceNode) nd.right());
+ }
+ else
+ {
+ System.out.println(" name = " + ((SequenceI) nd.element()).getName());
+ }
+
+ System.out.println(" dist = " + nd.dist + " " + nd.count + " "
+ + nd.height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ public void reCount(SequenceNode nd)
+ {
+ ycount = 0;
+ // _lycount = 0;
+ // _lylimit = this.node.size();
+ _reCount(nd);
+ }
+
+ // private long _lycount = 0, _lylimit = 0;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ void _reCount(SequenceNode nd)
+ {
+ // if (_lycount<_lylimit)
+ // {
+ // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // }
+ if (nd == null)
+ {
+ return;
+ }
+ // _lycount++;
+
+ if ((nd.left() != null) && (nd.right() != null))
+ {
+
+ _reCount((SequenceNode) nd.left());
+ _reCount((SequenceNode) nd.right());
+
+ SequenceNode l = (SequenceNode) nd.left();
+ SequenceNode r = (SequenceNode) nd.right();
+
+ nd.count = l.count + r.count;
+ nd.ycount = (l.ycount + r.ycount) / 2;
+ }
+ else
+ {
+ nd.count = 1;
+ nd.ycount = ycount++;
+ }
+ // _lycount--;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ */
+ public void swapNodes(SequenceNode nd)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ SequenceNode tmp = (SequenceNode) nd.left();
+
+ nd.setLeft(nd.right());
+ nd.setRight(tmp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ * @param dir
+ * DOCUMENT ME!
+ */
+ void changeDirection(SequenceNode nd, SequenceNode dir)
+ {
+ if (nd == null)
+ {
+ return;
+ }
+
+ if (nd.parent() != top)
+ {
+ changeDirection((SequenceNode) nd.parent(), nd);
+
+ SequenceNode tmp = (SequenceNode) nd.parent();
+
+ if (dir == nd.left())
+ {
+ nd.setParent(dir);
+ nd.setLeft(tmp);
+ }
+ else if (dir == nd.right())
+ {
+ nd.setParent(dir);
+ nd.setRight(tmp);
+ }
+ }
+ else
+ {
+ if (dir == nd.left())
+ {
+ nd.setParent(nd.left());
+
+ if (top.left() == nd)
+ {
+ nd.setRight(top.right());
+ }
+ else
+ {
+ nd.setRight(top.left());
+ }
+ }
+ else
+ {
+ nd.setParent(nd.right());
+
+ if (top.left() == nd)
+ {
+ nd.setLeft(top.right());
+ }
+ else
+ {
+ nd.setLeft(top.left());
+ }
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getTopNode()
+ {
+ return top;
+ }
+
+ /**
+ *
+ * @return true if tree has real distances
+ */
+ public boolean hasDistances()
+ {
+ return hasDistances;
+ }
+
+ /**
+ *
+ * @return true if tree has real bootstrap values
+ */
+ public boolean hasBootstrap()
+ {
+ return hasBootstrap;
+ }
+
+ public boolean hasRootDistance()
+ {
+ return hasRootDistance;
+ }
+
+ /**
+ * apply the given transform to all the nodes in the tree.
+ *
+ * @param nodeTransformI
+ */
+ public void applyToNodes(NodeTransformI nodeTransformI)
+ {
+ for (Enumeration<SequenceNode> nodes = node.elements(); nodes
+ .hasMoreElements(); nodeTransformI.transform(nodes
+ .nextElement()))
+ {
+ ;
+ }
+ }
+}
*/
package jalview.appletgui;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.JalviewLite;
boolean validCharWidth = true;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
public jalview.bin.JalviewLite applet;
setEndSeq(height / getCharHeight());
}
- public void setCurrentTree(NJTree tree)
+ public void setCurrentTree(TreeModel tree)
{
currentTree = tree;
}
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
package jalview.appletgui;
import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import java.awt.event.MouseMotionListener;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class TreeCanvas extends Panel implements MouseListener,
MouseMotionListener
{
- NJTree tree;
+ TreeModel tree;
ScrollPane scrollPane;
selected.addOrRemove(sequence, true);
}
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree2)
{
- this.tree = tree;
- tree.findHeight(tree.getTopNode());
+ this.tree = tree2;
+ tree2.findHeight(tree2.getTopNode());
// Now have to calculate longest name based on the leaves
- Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
+ Vector<SequenceNode> leaves = tree2.findLeaves(tree2.getTopNode());
boolean has_placeholders = false;
longestName = "";
threshold = (float) (x - offx)
/ (float) (getSize().width - labelLength - 2 * offx);
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<SequenceNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
av.setSelectionGroup(null);
codingComplement.clearSequenceColours();
}
- colourGroups();
+ colourGroups(groups);
}
}
}
- void colourGroups()
+ void colourGroups(List<SequenceNode> groups)
{
- for (int i = 0; i < tree.getGroups().size(); i++)
+ for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor(tree.getGroups().elementAt(i), col.brighter());
+ setColor(groups.get(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
- .elementAt(i));
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)
*/
package jalview.appletgui;
+import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignmentPanel ap;
AlignViewport av;
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}
{
if (odata == null)
{
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ tree = new TreeModel(av.getAlignment().getSequencesArray(),
+ newtree);
}
else
{
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
+ tree = new TreeModel(av.getAlignment().getSequencesArray(),
+ odata, newtree);
}
}
else
{
ScoreModelI sm = configureScoreModel(pwtype);
- tree = new NJTree(av, type, sm, SimilarityParams.Jalview);
+ TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+ av, sm, SimilarityParams.Jalview)
+ : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
+ tree = new TreeModel(njtree);
}
tree.reCount(tree.getTopNode());
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
{
Font font;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
boolean cursorMode = false;
* @param tree
* DOCUMENT ME!
*/
- public void setCurrentTree(NJTree tree)
+ public void setCurrentTree(TreeModel tree)
{
currentTree = tree;
}
*
* @return DOCUMENT ME!
*/
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
tree.setCurrentTree((av.currentTree == tp.getTree()));
- tree.setNewick(tp.getTree().toString());
+ tree.setNewick(tp.getTree().print());
tree.setThreshold(tp.treeCanvas.threshold);
tree.setFitToWindow(tp.fitToWindow.getState());
package jalview.gui;
import jalview.analysis.Conservation;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import java.awt.print.PrinterJob;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
import javax.swing.JColorChooser;
/** DOCUMENT ME!! */
public static final String PLACEHOLDER = " * ";
- NJTree tree;
+ TreeModel tree;
JScrollPane scrollPane;
* @param tree
* DOCUMENT ME!
*/
- public void setTree(NJTree tree)
+ public void setTree(TreeModel tree)
{
this.tree = tree;
tree.findHeight(tree.getTopNode());
threshold = (float) (x - offx)
/ (float) (getWidth() - labelLength - (2 * offx));
- tree.getGroups().removeAllElements();
- tree.groupNodes(tree.getTopNode(), threshold);
+ List<SequenceNode> groups = tree.groupNodes(threshold);
setColor(tree.getTopNode(), Color.black);
AlignmentPanel[] aps = getAssociatedPanels();
aps[a].av.getCodingComplement().clearSequenceColours();
}
}
- colourGroups();
+ colourGroups(groups);
}
PaintRefresher.Refresh(tp, ap.av.getSequenceSetId());
}
- void colourGroups()
+ void colourGroups(List<SequenceNode> groups)
{
AlignmentPanel[] aps = getAssociatedPanels();
- for (int i = 0; i < tree.getGroups().size(); i++)
+ for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor(tree.getGroups().elementAt(i), col.brighter());
+ setColor(groups.get(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
- .elementAt(i));
+ Vector<SequenceNode> l = tree.findLeaves(groups.get(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
{
matchGaps.setEnabled(false);
}
+ if (tree.isSelected())
+ {
+ // ?? tree requires specific parameter settings??
+ includeGaps.setSelected(true);
+ includeGaps.setEnabled(false);
+ matchGaps.setSelected(true);
+ includeGappedColumns.setSelected(true);
+ includeGappedColumns.setEnabled(false);
+ shorterSequence.setSelected(false);
+ shorterSequence.setEnabled(false);
+ }
}
/**
package jalview.gui;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.analysis.ViewBasedAnalysisI;
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignViewport av;
{
if (odata == null)
{
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ tree = new TreeModel(av.getAlignment().getSequencesArray(),
+ newtree);
}
else
{
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
+ tree = new TreeModel(av.getAlignment().getSequencesArray(),
+ odata, newtree);
}
if (!tree.hasOriginalSequenceData())
{
else
{
ScoreModelI sm = configureScoreModel();
- tree = new NJTree(av, treeType, sm, similarityParams);
+ TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+ av, sm, similarityParams) : new AverageDistanceTree(av, sm,
+ similarityParams);
+ tree = new TreeModel(njtree);
showDistances(true);
}
*
* @return DOCUMENT ME!
*/
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}
{
// the following works because all trees are already had node/SequenceI
// associations created.
- jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
+ jalview.analysis.TreeModel njt = new jalview.analysis.TreeModel(
al.getSequencesArray(), nf);
// this just updates the displayed leaf name on the tree according to
// the SequenceIs.
package jalview.io.vamsas;
import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
/**
* 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<SequenceNode> leaves = ntree.findLeaves(ntree.getTopNode());
+ Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
+ .getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
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));
import static org.testng.ConversionUtils.wrapDataProvider;
-import jalview.analysis.NJTree;
import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.gui.JvOptionPane;
stage = "Compare original and generated tree" + treename;
Vector<SequenceNode> oseqs, nseqs;
- oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree());
+ oseqs = new TreeModel(new SequenceI[0], nf).findLeaves(nf.getTree());
AssertJUnit.assertTrue(stage + "No nodes in original tree.",
oseqs.size() > 0);
SequenceI[] olsqs = new SequenceI[oseqs.size()];
{
olsqs[i] = (SequenceI) oseqs.get(i).element();
}
- nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(nf_regen
+ nseqs = new TreeModel(new SequenceI[0], nf_regen).findLeaves(nf_regen
.getTree());
AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
nseqs.size() > 0);
git://source.jalview.org / jalview.git / commitdiff