/**
* A method that finds all genes in a dna strand strarting with ATG coden and ending with TAG, TGA
* or TAA coden.
*
* @param dna The dna strand to search for genes.
* @return all found genes in StorageResource datatype.
*/
public StorageResource storeAll(String dna) {
StorageResource sr = new StorageResource();
int start = 0;
int stop = 0;
int loc = 0;
String dna1 = dna.toUpperCase();
// System.out.println(dna1);
while (true) {
loc = dna1.indexOf("ATG", start);
if (loc == -1) break;
int sloc = stopIndex(dna1, loc + 3);
if (sloc > dna.length()) {
// continue;
// System.out.println("");
} else {
sr.add(dna.substring(loc, sloc));
// System.out.println(dna.substring(loc,sloc));
loc = sloc - 3;
}
// System.out.println(loc);
start = loc + 3;
}
return sr;
}
public void testStorageFinder() {
String dnaString = "";
// FileResource dna = new FileResource("dna/brca1line.fa");
FileResource dna = new FileResource("dna/GRch38dnapart.fa");
dnaString = dna.asString();
// String dnaString="ATGCCATAG";
StorageResource sr = storeAll(dnaString);
printGenes(sr);
System.out.println("Number of genes: " + sr.size());
System.out.println("Number of CTG : " + ctgCounter(dnaString));
System.out.println("The length of longer gene is : " + longestGene(sr));
}
/**
* 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;
}
public void printGenes(StorageResource sr) {
int counter60 = 0;
int counter035 = 0;
for (String a : sr.data()) {
if (a.length() > 60) {
System.out.println("String length longer than 60 : " + a);
counter60++;
}
if (cgRatio(a) > 0.35) {
System.out.println("CG Ratio greater than 0.35 : " + a);
counter035++;
}
}
System.out.println("Number of elements with length greater than 60 : " + counter60);
System.out.println("Number of elements with CG ratio greater than 0.35 : " + counter035);
}