- Vector cluster;
- SequenceI[] sequence;
-
- //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();
- SequenceNode maxdist;
- SequenceNode top;
- float maxDistValue;
- float maxheight;
- int ycount;
- Vector 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
- */
- 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.sequence = 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();
- }
- }
- */