Java passing method help

Make a copy of the printAll method called getAll. Instead of printing the genes found, this method should create and return a StorageResource containing the genes found. Remember to import the edu.duke libraries otherwise you will get an error message cannot find the class StorageResource.

Here is what I have.

import edu.duke.*;

public class Part1 {

public int findStop(String dnaStr, int startIndex,

String stopCodon){

//Find stop codon from end of ATG

int currIndex=dnaStr.indexOf(stopCodon, startIndex+3);

//as long as curr index not -1

while(currIndex !=-1){

//check for multiple of 3

if((currIndex - startIndex) % 3==0){

//if so, text between is substring

return currIndex;

}

else{

//if not,Update currIndex

currIndex=dnaStr.indexOf(stopCodon,currIndex+1);

}

}

return dnaStr.length();

}

public String findGene(String dna){

//First occurrence of ATG

int startIndex =dna.indexOf("ATG");

//if no ATG is found return null

if(startIndex == -1){

return "";

}

//stop codons to look for in index of dna string

int taaIndex=findStop(dna, startIndex, "TAA");

int tagIndex=findStop(dna, startIndex, "TAG");

int tgaIndex=findStop(dna, startIndex, "TGA");

//store smallest index of ending codon values

int min1;

int min2=0;

if(taaIndex == -1 ||(tgaIndex!=-1 &&

tgaIndex< taaIndex)){

min2 = tgaIndex;

}

else{

min2 = taaIndex;

}

if(min2 ==-1 ||(tagIndex!=-1 && tagIndex < min2)){

min2=tagIndex;

}

//is full dna string none were found so print null

if(min2 == -1){

return "";

}

else{

return dna.substring(startIndex, min2+3);

}

}

public void printGenes(String dna) {

//set start index

int startIndex =0;

//loop

while (true){

//find next gene after start index

String currGene =findGene(dna);

// no gene found leave loop

if(currGene.isEmpty()){

break;

}

//Print gene out

System.out.println(currGene);

//Set start index to 1 past end of last gene

startIndex= dna.indexOf(currGene, startIndex) +

currGene.length();

}

}

public void testfindStop(){

String dna="ACTATGGAAGCATAA";

System.out.println("DNA strand is "+ dna);

int gene=findStop(dna,0,"TAA");

System.out.println("Gene is "+ gene);

dna="ACTATGTAAGCATGATAA";

System.out.println("DNA strand is "+ dna);

gene=findStop(dna,0,"TGA");

System.out.println("Gene is "+ gene);

dna="ACTATGTACCATAACTAG";

System.out.println("DNA strand is "+ dna);

gene=findStop(dna,0,"TAG");

System.out.println("Gene is "+ gene);

}

public void testfindGene(){

String dna = "ATTATGGTCTAGTAA";

System.out.println("DNA strand is "+ dna);

String gene= findGene(dna);

if(gene.isEmpty()){

System.out.println ("");}

else{

System.out.println("Gene is "+ gene);

}

}

public void testprintGenes(String dna){

System.out.println("DNA strand is "+ dna);

printGenes(dna);

}

public void printAll(String dna){

int index=0;

while(true){

int startIndex=dna.indexOf("ATG",index);

if(startIndex!=-1)

System.out.println("start:" + startIndex);

index+=startIndex+3;

if(startIndex ==-1){

System.out.println("");

break;

}

}

}

public StorageResource getAll(String dna){

StorageResource store = new StorageResource();

int index=0;

while(true){

int startIndex=dna.indexOf("ATG",index);

if(startIndex!=-1)

System.out.println("start:" + startIndex);

index += startIndex+3;

if(startIndex ==-1){

System.out.println("");

break;

}

int stopIndex = findStop.(dna,startIndex+3 );

System.out.println("STOP: " + (stopIndex));

// If stop codon is found, save gene as a variable

// and add gene to StorageResource object

if (stopIndex != -1) {

String gene = dna.substring(startIndex, stopIndex + 3);

System.out.println(gene);

store.add(gene);

// Update region to dna to look for codon in,

//setting it to the index right after the stop codon

index = stopIndex + 3;

} else {

// Update region of dna to look for codon in

index = startIndex + 1;

}

}

return store;

}

public void testprintAll(){

String dna = "ATGGAATAGTCGATGGCTTAA";

System.out.println("DNA is "+ dna);

printAll(dna);

}

public void testgetAll(){

String dna = "ATGGAATAGTCGATGGCTTAA";

System.out.println("DNA is "+ dna);

getAll(dna);

}

}