[!INDEX]
- remaining part
- two occurance data
- finding weblinks
- Three stop codon return lenght
- ThreeStopCodonORAND + return -1
- Print All Gene Cls
- Storage Resource For All Gene
- c and g ration
1. remaining part
public class RemainingPart {
public String lastPart(String x,String y) {
String result ;
int pos = y.indexOf(x);
int len = x.length();
if(pos != -1){
String z = y.substring(pos+len);
result = z;
System.out.println(result);
}
else{
result =y;
System.out.println(result);
}
return result;
}
public void test2(){
String xx = lastPart("by","byA story by Abb Long");
}
}
2. two occurance data
// twoOccurrences(String a,String b) - method returns true if stringa appears at least twice in stringb,
import edu.duke.*;
public class TwoOccurrencesDna {
String output;
public String twoOccurrences(String a,String b){
int firstpos = b.indexOf(a);
if(firstpos != -1){
firstpos= firstpos+a.length()-1;
int secondpos = b.indexOf(a,firstpos);
if(secondpos != -1){
output = "yes";
}
}
return output;
}
public void checkOccurance () {
String xx = twoOccurrences("bye","aaabyedaaaby");
if(xx=="yes"){
System.out.println("it has two occurance , using method twooccurance");
}
else{
System.out.println("it has one occurance , using method twooccurance");
}
}
}
3. finding weblinks
import edu.duke.*;
public class FindingWebLinks {
public void checkurlwords(){
String url = "https://www.dukelearntoprogram.com/course2/data/manylinks.html";
String dq = "\"";
// Create a URLResource object to read from the URL
URLResource urlResource = new URLResource(url);
// Loop through each word in the file
for (String word : urlResource.words()) {
if(word.contains("www.youtube.com")){
int firstPos = word.indexOf(dq);
int lastPos = word.lastIndexOf(dq);
String toPrint = word.substring(firstPos+1,lastPos);
System.out.println(toPrint);
}
}
}
public void getData(){
FindingWebLinks reader = new FindingWebLinks();
reader.checkurlwords();
}
}4. three stop codon return lenght
public class ThreeStopCondon {
// finds the gene index , later we will match it
public int findStopCodon(String dnaStr, int startindex, String stopcodon ){
int currentindex = dnaStr.indexOf(stopcodon,startindex+3);
while(currentindex!= -1){
int diff = currentindex-startindex;
if(diff % 3 == 0){
return currentindex;
}
else{
currentindex = dnaStr.indexOf(stopcodon, currentindex+1);// if not ok then start form this index further
}
}
return dnaStr.length(); // this return the biggest number , easy for finding the smallest one
//return -1; // it is the samllest number it will not give proper result
}
public String findGene(String dna){
int startindex = dna.indexOf("ATG");
if(startindex == -1){
return "";
}
int taaindex = findStopCodon(dna,startindex,"TAA");
int tagindex = findStopCodon(dna,startindex,"TAG");
int tgaindex = findStopCodon(dna,startindex,"TGA");
//using one line
int temp = Math.min(taaindex,Math.min(tagindex,tgaindex));
int minIdex=0;
return dna.substring(startindex,minIdex+3);
}
// below is just for testing purpose
public void testFindGeneSimple(){
String dna = "*********TAA*********TAAs";
System.out.println("Dna strand is "+dna);
int getindex = findStopCodon(dna, 0, "TAA"); // must return 9
if(getindex != 9 )System.out.println("error on line 9 ");// 9 not equal to 9, false, dont print
getindex = findStopCodon(dna, 9, "TAA"); // must return 21
if(getindex != 21 )System.out.println("error on line 21 ");// 21 not equals to 21, false, dont print
getindex = findStopCodon(dna, 1, "TAA"); //
System.out.println(getindex);
// if(getindex != 26 )System.out.println("error on line 26 ");// true statement
System.out.println("Testing is done : All works fine" );
}
}
5. Three Stop Codon OR AND + return -1
public class ThreStopCodonORAND {
// finds the gene index , later we will match it
public int findStopCodon(String dnaStr, int startindex, String stopcodon ){
int currentindex = dnaStr.indexOf(stopcodon,startindex+3);
while(currentindex!= -1){
int diff = currentindex-startindex;
if(diff % 3 == 0){
return currentindex;
}
else{
currentindex = dnaStr.indexOf(stopcodon, currentindex+1);// if not ok then start form this index further
}
}
return -1; // it is the samllest number it will not give proper result
}
public String findGene(String dna){
int startindex = dna.indexOf("ATG");
if(startindex == -1){
return "";
}
int taaindex = findStopCodon(dna,startindex,"TAA");
int tagindex = findStopCodon(dna,startindex,"TAG");
int tgaindex = findStopCodon(dna,startindex,"TGA");
// using and or operators
int minIdex=0;
if(taaindex == -1 || (tgaindex != -1 && tgaindex < taaindex)){
minIdex=tgaindex;
}
else{
minIdex=taaindex;
}
if(minIdex == -1 || (tagindex !=-1 && tagindex < minIdex)){
minIdex = tagindex;
}
if(minIdex == -1){
return "";
}
return dna.substring(startindex,minIdex+3);
}
// below is just for testing purpose
public void testFindGeneSimple(){
String dna = "*********TAA*********TAAs";
System.out.println("Dna strand is "+dna);
int getindex = findStopCodon(dna, 0, "TAA"); // must return 9
if(getindex != 9 )System.out.println("error on line 9 ");// 9 not equal to 9, false, dont print
getindex = findStopCodon(dna, 9, "TAA"); // must return 21
if(getindex != 21 )System.out.println("error on line 21 ");// 21 not equals to 21, false, dont print
getindex = findStopCodon(dna, 1, "TAA"); //
if(getindex != -1 )System.out.println("error on line 26 ");// false statement
System.out.println("Testing is done : All works fine" );
}
}6. Print All Gene Cls
public class PrintAllGeneCls {
//finds the gene index , later we will match it
public int findStopCodon(String dnaStr, int startindex, String stopcodon ){
int currentindex = dnaStr.indexOf(stopcodon,startindex+3);
while(currentindex!= -1){
int diff = currentindex-startindex;
if(diff % 3 == 0){
return currentindex;
}
else{
currentindex = dnaStr.indexOf(stopcodon, currentindex+1);// if not ok then start form this index further
}
}
return -1; // it is the samllest number it will not give proper result
}
public void printAllGene(String dna){
int startindex = 0 ;
while(true){
String currentGene = findGene(dna, startindex) ;
if(currentGene.isEmpty()){
break;
}
System.out.println(currentGene);
startindex = dna.indexOf(currentGene,startindex)+currentGene.length();
}
}
//return the shortest gene with characters
public String findGene(String dna, int where){ // where to start lookin in the middle of the string
int startindex = dna.indexOf("ATG", where);
if(startindex == -1){
return "";
}
int taaindex = findStopCodon(dna,startindex,"TAA");
int tagindex = findStopCodon(dna,startindex,"TAG");
int tgaindex = findStopCodon(dna,startindex,"TGA");
// using and or operators
int minIdex=0;
if(taaindex == -1 || (tgaindex != -1 && tgaindex < taaindex)){
minIdex=tgaindex;
}
else{
minIdex=taaindex;
}
if(minIdex == -1 || (tagindex !=-1 && tagindex < minIdex)){
minIdex = tagindex;
}
if(minIdex == -1){
return "";
}
return dna.substring(startindex,minIdex+3);
}
public void testOn(String dna){
System.out.println("testing all gene");
printAllGene(dna);
}
// below is just for testing purpose
public void test(){
String dna = "ATG******TAA***ATG******TGA";
testOn(dna);
}
}7. Storage Resource For All Gene
import edu.duke.*;
public class StorageResourceForAllGene {
//finds the gene index , later we will match it
public int findStopCodon(String dnaStr, int startindex, String stopcodon ){
int currentindex = dnaStr.indexOf(stopcodon,startindex+3);
while(currentindex!= -1){
int diff = currentindex-startindex;
if(diff % 3 == 0){
return currentindex;
}
else{
currentindex = dnaStr.indexOf(stopcodon, currentindex+1);// if not ok then start form this index further
}
}
return -1; // it is the samllest number it will not give proper result
}
public void printAllGene(String dna){
int startindex = 0 ;
while(true){
String currentGene = findGene(dna, startindex) ;
if(currentGene.isEmpty()){
break;
}
System.out.println(currentGene);
startindex = dna.indexOf(currentGene,startindex)+currentGene.length();
}
}
public StorageResource getAllGenes(String dna){
StorageResource geneList = new StorageResource();
int startindex = 0 ;
while(true){
String currentGene = findGene(dna, startindex) ;
if(currentGene.isEmpty()){
break;
}
geneList.add(currentGene);
// System.out.println(currentGene);
startindex = dna.indexOf(currentGene,startindex)+currentGene.length();
}
return geneList;
}
//return the shortest gene with characters
public String findGene(String dna, int where){ // where to start lookin in the middle of the string
int startindex = dna.indexOf("ATG", where);
if(startindex == -1){
return "";
}
int taaindex = findStopCodon(dna,startindex,"TAA");
int tagindex = findStopCodon(dna,startindex,"TAG");
int tgaindex = findStopCodon(dna,startindex,"TGA");
// using and or operators
int minIdex=0;
if(taaindex == -1 || (tgaindex != -1 && tgaindex < taaindex)){
minIdex=tgaindex;
}
else{
minIdex=taaindex;
}
if(minIdex == -1 || (tagindex !=-1 && tagindex < minIdex)){
minIdex = tagindex;
}
if(minIdex == -1){
return "";
}
return dna.substring(startindex,minIdex+3);
}
public void testOn(String dna){
System.out.println("testing all gene");
StorageResource gene = getAllGenes(dna);
for(String g : gene.data()){
System.out.println(g);
}
}
// below is just for testing purpose
public void test(){
String dna = "ATG******TAA***ATG******TGA";
testOn(dna);
}
}8. c and g ration
import java.text.DecimalFormat;
public class CgRatioCls {
public double cgRation(String dna){
float dnalength = dna.length();
float cCount = (float)calculate("C",dna);
float gCount = (float)calculate("G",dna);
float result = (cCount+gCount)/dnalength;
double roundedValue = Math.round(result * 1000.0) / 1000.0;
return roundedValue;
}
public int calculate(String x, String dna){
int startindex = 0;
int count =0;
String Charcter = x;
while(true){
int findC = dna.indexOf(Charcter,startindex);
if(findC == -1){
break;
}
else{
count = count+1;
startindex = findC+1;
}
}
return count;
}
// for run the code
public void check(){
String dna = "ATGCCATAG"; //
System.out.println("cg ration is = " + cgRation(dna));
}
public void testcase(){
String dna = "ATGCCATAG"; //
if(cgRation(dna)!= 0.444 )System.out.println("error generate step-1 ");
dna = "ATGCCATAGG";
if(cgRation(dna)!= 0.5 )System.out.println("error generate step-2 ");
System.out.println("code is check and found ok");
}
}