/**
* A method that indicates the end of a gene, which is found in a dna.
*
* @param dna The dna strand to search for gene's end.
* @param startIndex The index of the searching start.
* @return The index of end.
*/
public int stopIndex(String dna, int startIndex) {
int stopTAG = dna.indexOf("TAG", startIndex);
if (stopTAG == -1 || (stopTAG - startIndex) % 3 != 0) stopTAG = dna.length();
int stopTGA = dna.indexOf("TGA", startIndex);
if (stopTGA == -1 || (stopTGA - startIndex) % 3 != 0) stopTGA = dna.length();
int stopTAA = dna.indexOf("TAA", startIndex);
if (stopTAA == -1 || (stopTAA - startIndex) % 3 != 0) stopTAA = dna.length();
return Math.min(stopTAG + 3, Math.min(stopTGA + 3, stopTAA + 3));
}
/**
* A method that find the length of longest gene.
*
* @param genes The genes of a dna strand.
* @return The Length of longer gene.
*/
public int longestGene(StorageResource sr) {
int maxlength = 0;
for (String a : sr.data()) {
maxlength = Math.max(a.length(), maxlength);
}
return maxlength;
}
/**
* A method that calculates the CG ratio.
*
* @param dna The dna strand to search for genes.
* @return The CG Ratio.
*/
public float cgRatio(String dna) {
dna = dna.toUpperCase();
int i = 0, counter = 0;
while (true) {
int cid = dna.indexOf("C", i);
if (cid == -1) cid = dna.length() + 1;
int gid = dna.indexOf("G", i);
if (gid == -1) gid = dna.length() + 1;
int pos = Math.min(cid, gid);
if (pos == dna.length() + 1) break;
else counter++;
i = pos + 1;
}
return (float) counter / dna.length();
}