/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+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 java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class NJTree
{
- Vector cluster;
+ Vector<Cluster> cluster;
+
SequenceI[] sequence;
- //SequenceData is a string representation of what the user
- //sees. The display may contain hidden columns.
+ // SequenceData is a string representation of what the user
+ // sees. The display may contain hidden columns.
public AlignmentView seqData = null;
int[] done;
+
int noseqs;
+
int noClus;
+
float[][] distance;
+
int mini;
+
int minj;
+
float ri;
+
float rj;
- Vector groups = new Vector();
+
+ Vector<SequenceNode> groups = new Vector<SequenceNode>();
+
SequenceNode maxdist;
+
SequenceNode top;
+
float maxDistValue;
+
float maxheight;
+
int ycount;
- Vector node;
+
+ Vector<SequenceNode> node;
+
String type;
+
String pwtype;
+
Object found = null;
- Object leaves = null;
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
+ *
+ * @param seqs
+ * SequenceI[]
+ * @param odata
+ * Cigar[]
+ * @param treefile
+ * NewickFile
*/
public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
{
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();
- } */
+ * 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
+ *
+ * @param seqs
+ * SequenceI which should be associated with leafs of treefile
+ * @param treefile
+ * A parsed tree
*/
public NJTree(SequenceI[] seqs, NewickFile treefile)
{
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();
- }
- }
+ * 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();
SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
- Vector leaves = new Vector();
- findLeaves(top, leaves);
+ Vector<SequenceNode> leaves = findLeaves(top);
int i = 0;
int namesleft = seqs.length;
SequenceNode j;
SequenceI nam;
String realnam;
- Vector one2many = new Vector();
+ Vector<SequenceI> one2many = new Vector<SequenceI>();
int countOne2Many = 0;
while (i < leaves.size())
{
- j = (SequenceNode) leaves.elementAt(i++);
+ j = leaves.elementAt(i++);
realnam = j.getName();
nam = null;
if (one2many.contains(nam))
{
countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
+ // if (jalview.bin.Cache.log.isDebugEnabled())
+ // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // "+nam.getName());
}
else
{
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();
+ // 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();
}
/**
* Creates a new NJTree object.
- *
- * @param sequence DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- * @param start DOCUMENT ME!
- * @param end DOCUMENT ME!
+ *
+ * @param sequence
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ * @param start
+ * DOCUMENT ME!
+ * @param end
+ * DOCUMENT ME!
*/
- public NJTree(SequenceI[] sequence,
- AlignmentView seqData,
- String type,
- String pwtype,
- int start, int end)
+ public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
+ String pwtype, ScoreModelI sm, int start, int end)
{
this.sequence = sequence;
- this.node = new Vector();
+ this.node = new Vector<SequenceNode>();
this.type = type;
this.pwtype = pwtype;
if (seqData != null)
sdata.addOperation(CigarArray.M, end - start + 1);
this.seqData = new AlignmentView(sdata, start);
}
-
- if (! (type.equals("NJ")))
+ // System.err.println("Made seqData");// dbg
+ if (!(type.equals("NJ")))
{
type = "AV";
}
- if (! (pwtype.equals("PID")))
+ if (sm == null && !(pwtype.equals("PID")))
{
- if (ResidueProperties.getScoreMatrix(pwtype) == null)
+ if (ScoreModels.getInstance().forName(pwtype) == null)
{
- type = "BLOSUM62";
+ pwtype = "BLOSUM62";
}
}
done = new int[sequence.length];
- while ( (i < sequence.length) && (sequence[i] != null))
+ while ((i < sequence.length) && (sequence[i] != null))
{
done[i] = 0;
i++;
noseqs = i++;
- distance = findDistances(this.seqData.getSequenceStrings(Comparison.
- GapChars.charAt(0)));
-
+ distance = findDistances(sm);
+ // System.err.println("Made distances");// dbg
makeLeaves();
+ // System.err.println("Made leaves");// dbg
noClus = cluster.size();
cluster();
+ // System.err.println("Made clusters");// dbg
+
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Generate a string representation of the Tree
+ *
+ * @return Newick File with all tree data available
*/
+ @Override
public String toString()
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
- return fout.print(false, true); // distances only
+ return fout.print(isHasBootstrap(), isHasDistances(),
+ isHasRootDistance()); // output all data available for tree
}
/**
- *
+ *
* used when the alignment associated to a tree has changed.
- *
- * @param alignment Vector
+ *
+ * @param list
+ * Sequence set to be associated with tree nodes
*/
- public void UpdatePlaceHolders(Vector alignment)
+ public void UpdatePlaceHolders(List<SequenceI> list)
{
- Vector leaves = new Vector();
- findLeaves(top, leaves);
+ Vector<SequenceNode> leaves = findLeaves(top);
int sz = leaves.size();
SequenceIdMatcher seqmatcher = null;
while (i < sz)
{
- SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+ SequenceNode leaf = leaves.elementAt(i++);
- if (alignment.contains(leaf.element()))
+ if (list.contains(leaf.element()))
{
leaf.setPlaceholder(false);
}
if (seqmatcher == null)
{
// Only create this the first time we need it
- SequenceI[] seqs = new SequenceI[alignment.size()];
+ SequenceI[] seqs = new SequenceI[list.size()];
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) alignment.elementAt(j);
+ seqs[j] = list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);
{
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)
+ // 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);
if (!leaf.isPlaceholder())
{
// Construct a new placeholder sequence object for this leaf
- leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+ 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());
+ }
+ }
+ });
+ }
+
+ /**
* DOCUMENT ME!
*/
public void cluster()
}
joinClusters(one, two);
- top = (SequenceNode) (node.elementAt(one));
+ top = (node.elementAt(one));
reCount(top);
findHeight(top);
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public Cluster joinClusters(int i, int j)
{
float dist = distance[i][j];
- int noi = ( (Cluster) cluster.elementAt(i)).value.length;
- int noj = ( (Cluster) cluster.elementAt(j)).value.length;
+ int noi = cluster.elementAt(i).value.length;
+ int noj = cluster.elementAt(j).value.length;
int[] value = new int[noi + noj];
for (int ii = 0; ii < noi; ii++)
{
- value[ii] = ( (Cluster) cluster.elementAt(i)).value[ii];
+ value[ii] = cluster.elementAt(i).value[ii];
}
for (int ii = noi; ii < (noi + noj); ii++)
{
- value[ii] = ( (Cluster) cluster.elementAt(j)).value[ii - noi];
+ value[ii] = cluster.elementAt(j).value[ii - noi];
}
Cluster c = new Cluster(value);
SequenceNode sn = new SequenceNode();
- sn.setLeft( (SequenceNode) (node.elementAt(i)));
- sn.setRight( (SequenceNode) (node.elementAt(j)));
+ sn.setLeft((node.elementAt(i)));
+ sn.setRight((node.elementAt(j)));
- SequenceNode tmpi = (SequenceNode) (node.elementAt(i));
- SequenceNode tmpj = (SequenceNode) (node.elementAt(j));
+ SequenceNode tmpi = (node.elementAt(i));
+ SequenceNode tmpj = (node.elementAt(j));
if (type.equals("NJ"))
{
/**
* DOCUMENT ME!
- *
- * @param tmpi DOCUMENT ME!
- * @param tmpj DOCUMENT ME!
- * @param dist DOCUMENT ME!
+ *
+ * @param tmpi
+ * DOCUMENT ME!
+ * @param tmpj
+ * DOCUMENT ME!
+ * @param dist
+ * DOCUMENT ME!
*/
public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
+ float dist)
{
- tmpi.dist = ( (dist + ri) - rj) / 2;
+ tmpi.dist = ((dist + ri) - rj) / 2;
tmpj.dist = (dist - tmpi.dist);
if (tmpi.dist < 0)
/**
* DOCUMENT ME!
- *
- * @param tmpi DOCUMENT ME!
- * @param tmpj DOCUMENT ME!
- * @param dist DOCUMENT ME!
+ *
+ * @param tmpi
+ * DOCUMENT ME!
+ * @param tmpj
+ * DOCUMENT ME!
+ * @param dist
+ * DOCUMENT ME!
*/
public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
- float dist)
+ float dist)
{
float ih = 0;
float jh = 0;
snj = (SequenceNode) snj.left();
}
- tmpi.dist = ( (dist / 2) - ih);
- tmpj.dist = ( (dist / 2) - jh);
+ tmpi.dist = ((dist / 2) - ih);
+ tmpj.dist = ((dist / 2) - jh);
}
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
*/
public void findClusterDistance(int i, int j)
{
- int noi = ( (Cluster) cluster.elementAt(i)).value.length;
- int noj = ( (Cluster) cluster.elementAt(j)).value.length;
+ int noi = cluster.elementAt(i).value.length;
+ int noj = cluster.elementAt(j).value.length;
// New distances from cluster to others
float[] newdist = new float[noseqs];
for (int l = 0; l < noseqs; l++)
{
- if ( (l != i) && (l != j))
+ if ((l != i) && (l != j))
{
- newdist[l] = ( (distance[i][l] * noi) + (distance[j][l] * noj)) / (noi +
- noj);
+ newdist[l] = ((distance[i][l] * noi) + (distance[j][l] * noj))
+ / (noi + noj);
}
else
{
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
*/
public void findClusterNJDistance(int i, int j)
{
for (int l = 0; l < noseqs; l++)
{
- if ( (l != i) && (l != j))
+ if ((l != i) && (l != j))
{
- newdist[l] = ( (distance[i][l] + distance[j][l]) -
- distance[i][j]) / 2;
+ newdist[l] = ((distance[i][l] + distance[j][l]) - distance[i][j]) / 2;
}
else
{
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public float findr(int i, int j)
for (int k = 0; k < noseqs; k++)
{
- if ( (k != i) && (k != j) && (done[k] != 1))
+ if ((k != i) && (k != j) && (done[k] != 1))
{
tmp = tmp + distance[i][k];
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public float findMinNJDistance()
{
for (int j = i + 1; j < noseqs; j++)
{
- if ( (done[i] != 1) && (done[j] != 1))
+ if ((done[i] != 1) && (done[j] != 1))
{
float tmp = distance[i][j] - (findr(i, j) + findr(j, i));
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public float findMinDistance()
{
for (int j = i + 1; j < noseqs; j++)
{
- if ( (done[i] != 1) && (done[j] != 1))
+ if ((done[i] != 1) && (done[j] != 1))
{
if (distance[i][j] < min)
{
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Calculate a distance matrix given the sequence input data and score model
+ *
+ * @return similarity matrix used to compute tree
*/
- public float[][] findDistances(String[] sequenceString)
+ public float[][] findDistances(ScoreModelI _pwmatrix)
{
- float[][] distance = new float[noseqs][noseqs];
- if (pwtype.equals("PID"))
+ float[][] dist = new float[noseqs][noseqs];
+ if (_pwmatrix == null)
{
- for (int i = 0; i < (noseqs - 1); i++)
+ // Resolve substitution model
+ _pwmatrix = ScoreModels.getInstance().forName(pwtype);
+ if (_pwmatrix == null)
{
- for (int j = i; j < noseqs; j++)
- {
- if (j == i)
- {
- distance[i][i] = 0;
- }
- else
- {
- distance[i][j] = 100 -
- Comparison.PID(sequenceString[i], sequenceString[j]);
-
- distance[j][i] = distance[i][j];
- }
- }
+ _pwmatrix = ScoreModels.getInstance().forName("BLOSUM62");
}
}
- else
- {
- // Pairwise substitution score (with no gap penalties)
- ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
- if (pwmatrix == null)
- {
- pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
- }
- int maxscore = 0;
- int end = sequenceString[0].length();
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- int score = 0;
-
- for (int k = 0; k < end; k++)
- {
- try
- {
- score += pwmatrix.getPairwiseScore(sequenceString[i].charAt(k),
- sequenceString[j].charAt(k));
- }
- catch (Exception ex)
- {
- System.err.println("err creating BLOSUM62 tree");
- ex.printStackTrace();
- }
- }
-
- distance[i][j] = (float) score;
+ dist = _pwmatrix.findDistances(seqData);
+ return dist;
- if (score > maxscore)
- {
- maxscore = score;
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = (float) maxscore - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
-
- }
- return distance;
-
- // else
- /* else if (pwtype.equals("SW"))
- {
- float max = -1;
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
- as.calcScoreMatrix();
- as.traceAlignment();
- as.printAlignment(System.out);
- distance[i][j] = (float) as.maxscore;
-
- if (max < distance[i][j])
- {
- max = distance[i][j];
- }
- }
- }
-
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = max - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
- }/*/
}
/**
*/
public void makeLeaves()
{
- cluster = new Vector();
+ cluster = new Vector<Cluster>();
for (int i = 0; i < noseqs; i++)
{
}
/**
+ * 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 node root node to search from
- * @param leaves Vector of leaves to add leaf node objects too.
- *
+ *
+ * @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
*/
- public Vector findLeaves(SequenceNode node, Vector leaves)
+ Vector<SequenceNode> findLeaves(SequenceNode nd,
+ Vector<SequenceNode> leaves)
{
- if (node == null)
+ if (nd == null)
{
return leaves;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null)) // Interior node
+ // detection
{
- leaves.addElement(node);
+ leaves.addElement(nd);
return leaves;
}
else
{
- findLeaves( (SequenceNode) node.left(), leaves);
- findLeaves( (SequenceNode) node.right(), leaves);
+ /*
+ * TODO: Identify internal nodes... if (node.isSequenceLabel()) {
+ * leaves.addElement(node); }
+ */
+ findLeaves((SequenceNode) nd.left(), leaves);
+ findLeaves((SequenceNode) nd.right(), leaves);
}
return leaves;
}
/**
- * Find the leaf node with a particular ycount
- *
- * @param node initial point on tree to search from
- * @param count value to search for
- *
+ * Find the leaf node with a particular ycount
+ *
+ * @param nd
+ * initial point on tree to search from
+ * @param count
+ * value to search for
+ *
* @return null or the node with ycound=count
*/
- public Object findLeaf(SequenceNode node, int count)
+ public Object findLeaf(SequenceNode nd, int count)
{
- found = _findLeaf(node, count);
+ found = _findLeaf(nd, count);
return found;
}
- /*#see findLeaf(SequenceNode node, count)
- *
+ /*
+ * #see findLeaf(SequenceNode node, count)
*/
- public Object _findLeaf(SequenceNode node, int count)
+ public Object _findLeaf(SequenceNode nd, int count)
{
- if (node == null)
+ if (nd == null)
{
return null;
}
- if (node.ycount == count)
+ if (nd.ycount == count)
{
- found = node.element();
+ found = nd.element();
return found;
}
else
{
- _findLeaf( (SequenceNode) node.left(), count);
- _findLeaf( (SequenceNode) node.right(), count);
+ _findLeaf((SequenceNode) nd.left(), count);
+ _findLeaf((SequenceNode) nd.right(), count);
}
return found;
/**
* printNode is mainly for debugging purposes.
- *
- * @param node SequenceNode
+ *
+ * @param nd
+ * SequenceNode
*/
- public void printNode(SequenceNode node)
+ public void printNode(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null))
{
- System.out.println("Leaf = " +
- ( (SequenceI) node.element()).getName());
- System.out.println("Dist " + ( (SequenceNode) node).dist);
- System.out.println("Boot " + node.getBootstrap());
+ 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 " + ( (SequenceNode) node).dist);
- printNode( (SequenceNode) node.left());
- printNode( (SequenceNode) node.right());
+ System.out.println("Dist " + nd.dist);
+ printNode((SequenceNode) nd.left());
+ printNode((SequenceNode) nd.right());
}
}
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
*/
- public void findMaxDist(SequenceNode node)
+ public void findMaxDist(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null))
{
- float dist = ( (SequenceNode) node).dist;
+ float dist = nd.dist;
if (dist > maxDistValue)
{
- maxdist = (SequenceNode) node;
+ maxdist = nd;
maxDistValue = dist;
}
}
else
{
- findMaxDist( (SequenceNode) node.left());
- findMaxDist( (SequenceNode) node.right());
+ findMaxDist((SequenceNode) nd.left());
+ findMaxDist((SequenceNode) nd.right());
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ public Vector<SequenceNode> getGroups()
{
return groups;
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public float getMaxHeight()
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param threshold DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ * @param threshold
+ * DOCUMENT ME!
*/
- public void groupNodes(SequenceNode node, float threshold)
+ public void groupNodes(SequenceNode nd, float threshold)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ( (node.height / maxheight) > threshold)
+ if ((nd.height / maxheight) > threshold)
{
- groups.addElement(node);
+ groups.addElement(nd);
}
else
{
- groupNodes( (SequenceNode) node.left(), threshold);
- groupNodes( (SequenceNode) node.right(), threshold);
+ groupNodes((SequenceNode) nd.left(), threshold);
+ groupNodes((SequenceNode) nd.right(), threshold);
}
}
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- *
+ *
+ * @param nd
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
- public float findHeight(SequenceNode node)
+ public float findHeight(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return maxheight;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ((nd.left() == null) && (nd.right() == null))
{
- node.height = ( (SequenceNode) node.parent()).height + node.dist;
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
- if (node.height > maxheight)
+ if (nd.height > maxheight)
{
- return node.height;
+ return nd.height;
}
else
{
}
else
{
- if (node.parent() != null)
+ if (nd.parent() != null)
{
- node.height = ( (SequenceNode) node.parent()).height +
- node.dist;
+ nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
}
else
{
maxheight = 0;
- node.height = (float) 0.0;
+ nd.height = (float) 0.0;
}
- maxheight = findHeight( (SequenceNode) (node.left()));
- maxheight = findHeight( (SequenceNode) (node.right()));
+ maxheight = findHeight((SequenceNode) (nd.left()));
+ maxheight = findHeight((SequenceNode) (nd.right()));
}
return maxheight;
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceNode reRoot()
}
/**
- *
+ *
* @return true if original sequence data can be recovered
*/
public boolean hasOriginalSequenceData()
}
/**
- * Returns original alignment data used for calculation - or null where
- * not available.
- *
+ * Returns original alignment data used for calculation - or null where not
+ * available.
+ *
* @return null or cut'n'pasteable alignment
*/
public String printOriginalSequenceData(char gapChar)
String[] seqdatas = seqData.getSequenceStrings(gapChar);
for (int i = 0; i < seqdatas.length; i++)
{
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(
- sequence[i].getName()));
+ sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
+ .getName()));
sb.append(" " + seqdatas[i] + "\n");
}
return sb.toString();
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
*/
- public void printN(SequenceNode node)
+ public void printN(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if ( (node.left() != null) && (node.right() != null))
+ if ((nd.left() != null) && (nd.right() != null))
{
- printN( (SequenceNode) node.left());
- printN( (SequenceNode) node.right());
+ printN((SequenceNode) nd.left());
+ printN((SequenceNode) nd.right());
}
else
{
- System.out.println(" name = " +
- ( (SequenceI) node.element()).getName());
+ System.out.println(" name = " + ((SequenceI) nd.element()).getName());
}
- System.out.println(" dist = " + ( (SequenceNode) node).dist + " " +
- ( (SequenceNode) node).count + " " +
- ( (SequenceNode) node).height);
+ System.out.println(" dist = " + nd.dist + " " + nd.count + " "
+ + nd.height);
}
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
*/
- public void reCount(SequenceNode node)
+ public void reCount(SequenceNode nd)
{
ycount = 0;
- _reCount(node);
+ _lycount = 0;
+ // _lylimit = this.node.size();
+ _reCount(nd);
}
+ private long _lycount = 0, _lylimit = 0;
+
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
*/
- public void _reCount(SequenceNode node)
+ public void _reCount(SequenceNode nd)
{
- if (node == null)
+ // if (_lycount<_lylimit)
+ // {
+ // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // }
+ if (nd == null)
{
return;
}
+ _lycount++;
- if ( (node.left() != null) && (node.right() != null))
+ if ((nd.left() != null) && (nd.right() != null))
{
- _reCount( (SequenceNode) node.left());
- _reCount( (SequenceNode) node.right());
- SequenceNode l = (SequenceNode) node.left();
- SequenceNode r = (SequenceNode) node.right();
+ _reCount((SequenceNode) nd.left());
+ _reCount((SequenceNode) nd.right());
+
+ SequenceNode l = (SequenceNode) nd.left();
+ SequenceNode r = (SequenceNode) nd.right();
- ( (SequenceNode) node).count = l.count + r.count;
- ( (SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+ nd.count = l.count + r.count;
+ nd.ycount = (l.ycount + r.ycount) / 2;
}
else
{
- ( (SequenceNode) node).count = 1;
- ( (SequenceNode) node).ycount = ycount++;
+ nd.count = 1;
+ nd.ycount = ycount++;
}
+ _lycount--;
}
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
*/
- public void swapNodes(SequenceNode node)
+ public void swapNodes(SequenceNode nd)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- SequenceNode tmp = (SequenceNode) node.left();
+ SequenceNode tmp = (SequenceNode) nd.left();
- node.setLeft(node.right());
- node.setRight(tmp);
+ nd.setLeft(nd.right());
+ nd.setRight(tmp);
}
/**
* DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param dir DOCUMENT ME!
+ *
+ * @param nd
+ * DOCUMENT ME!
+ * @param dir
+ * DOCUMENT ME!
*/
- public void changeDirection(SequenceNode node, SequenceNode dir)
+ public void changeDirection(SequenceNode nd, SequenceNode dir)
{
- if (node == null)
+ if (nd == null)
{
return;
}
- if (node.parent() != top)
+ if (nd.parent() != top)
{
- changeDirection( (SequenceNode) node.parent(), node);
+ changeDirection((SequenceNode) nd.parent(), nd);
- SequenceNode tmp = (SequenceNode) node.parent();
+ SequenceNode tmp = (SequenceNode) nd.parent();
- if (dir == node.left())
+ if (dir == nd.left())
{
- node.setParent(dir);
- node.setLeft(tmp);
+ nd.setParent(dir);
+ nd.setLeft(tmp);
}
- else if (dir == node.right())
+ else if (dir == nd.right())
{
- node.setParent(dir);
- node.setRight(tmp);
+ nd.setParent(dir);
+ nd.setRight(tmp);
}
}
else
{
- if (dir == node.left())
+ if (dir == nd.left())
{
- node.setParent(node.left());
+ nd.setParent(nd.left());
- if (top.left() == node)
+ if (top.left() == nd)
{
- node.setRight(top.right());
+ nd.setRight(top.right());
}
else
{
- node.setRight(top.left());
+ nd.setRight(top.left());
}
}
else
{
- node.setParent(node.right());
+ nd.setParent(nd.right());
- if (top.left() == node)
+ if (top.left() == nd)
{
- node.setLeft(top.right());
+ nd.setLeft(top.right());
}
else
{
- node.setLeft(top.left());
+ nd.setLeft(top.left());
}
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceNode getMaxDist()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public SequenceNode getTopNode()
}
/**
- *
+ *
* @return true if tree has real distances
*/
public boolean isHasDistances()
}
/**
- *
+ *
* @return true if tree has real bootstrap values
*/
public boolean isHasBootstrap()
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()))
+ {
+ ;
+ }
+ }
}
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
/**
* Creates a new Cluster object.
- *
- * @param value DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
*/
public Cluster(int[] value)
{
git://source.jalview.org / jalview.git / blobdiff