\r
//SequenceData is a string representation of what the user\r
//sees. The display may contain hidden columns.\r
- CigarArray seqData=null;\r
+ public AlignmentView seqData=null;\r
\r
int[] done;\r
int noseqs;\r
* @param odata Cigar[]\r
* @param treefile NewickFile\r
*/\r
- public NJTree(SequenceI[] seqs, CigarArray odata, NewickFile treefile) {\r
+ public NJTree(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) {\r
this(seqs, treefile);\r
if (odata!=null)\r
seqData = odata;\r
* @param end DOCUMENT ME!\r
*/\r
public NJTree(SequenceI[] sequence,\r
- CigarArray seqData,\r
+ AlignmentView seqData,\r
String type,\r
String pwtype,\r
int start, int end)\r
{\r
seqs[i] = new SeqCigar(sequence[i], start, end);\r
}\r
- this.seqData = new CigarArray(seqs);\r
- this.seqData.addOperation(CigarArray.M, end-start+1);\r
+ CigarArray sdata = new CigarArray(seqs);\r
+ sdata.addOperation(CigarArray.M, end-start+1);\r
+ this.seqData = new AlignmentView(sdata);\r
}\r
\r
if (!(type.equals("NJ")))\r
}\r
return sb.toString();\r
}\r
-\r
/**\r
* DOCUMENT ME!\r
*\r