- Matrix eigenvector;
-
- StringBuffer details = new StringBuffer();
-
- /**
- * Creates a new PCA object.
- *
- * @param s
- * Set of sequences to perform PCA on
- */
- public PCA(String[] s)
- {
-
- BinarySequence[] bs = new BinarySequence[s.length];
- int ii = 0;
-
- while ((ii < s.length) && (s[ii] != null))
- {
- bs[ii] = new BinarySequence(s[ii]);
- bs[ii].encode();
- ii++;
- }
-
- BinarySequence[] bs2 = new BinarySequence[s.length];
- ii = 0;
-
- while ((ii < s.length) && (s[ii] != null))
- {
- bs2[ii] = new BinarySequence(s[ii]);
- bs2[ii].blosumEncode();
- ii++;
- }
-
- // System.out.println("Created binary encoding");
- // printMemory(rt);
- int count = 0;
-
- while ((count < bs.length) && (bs[count] != null))
- {
- count++;
- }
-
- double[][] seqmat = new double[count][bs[0].getDBinary().length];
- double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
- int i = 0;