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misterpandaamisterpandaa
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add week2 solution
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‎Week2/StringsFirstAssignments/Part1.java

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/**
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* Finding a Gene - Using the Simplified Algorithm
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*
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* @author Deny Kiantono
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* @version 1.0
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*/
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public class Part1 {
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public String findSimpleGene(String dna) {
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String result = "";
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int startIndex = dna.indexOf("ATG");
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int stopIndex = dna.indexOf("TAA", startIndex + 3);
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if (startIndex == -1 || stopIndex == -1) {
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return result;
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}
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if ((stopIndex - startIndex) % 3 == 0) {
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result = dna.substring(startIndex, stopIndex + 3);
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}
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return result;
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}
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public void testSimpleGene() {
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// DNA with no ATG
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String dna = "ATCTAACATC";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna));
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// DNA with no TAA
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dna = "ATTATCATGTTA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna));
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// DNA with no “ATG” and “TAA”
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dna = "ATTAGTGTA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna));
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// DNA with ATG, TAA and the substring between them is not a multiple of 3
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dna = "GAAATGGATAGTAA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna));
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// DNA with ATG, TAA and the substring between them is a multiple of 3 (a gene)
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dna = "TAAGATATGGTGAAGTAA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna));
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}
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}

‎Week2/StringsFirstAssignments/Part2.java

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/**
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* Finding a Gene - Using the Simplified Algorithm Reorganized
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*
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* @author Deny Kiantono
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* @version 1.0
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*/
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public class Part2 {
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public String findSimpleGene(String dna, String startCodon, String stopCodon) {
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String result = "";
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int startIndex = dna.toUpperCase().indexOf(startCodon);
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int stopIndex = dna.toUpperCase().indexOf(stopCodon, startIndex + 3);
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if (startIndex == -1 || stopIndex == -1) {
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return result;
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}
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if ((stopIndex - startIndex) % 3 == 0) {
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result = dna.substring(startIndex, stopIndex + 3);
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}
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return result;
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}
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public void testSimpleGene() {
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String startCodon = "ATG";
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String stopCodon = "TAA";
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// DNA with no ATG
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String dna = "ATCTAACATC";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon,stopCodon));
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// DNA with no TAA
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dna = "ATTATCATGTTA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon, stopCodon));
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// DNA with no “ATG” and “TAA”
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dna = "ATTAGTGTA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon, stopCodon));
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// DNA with ATG, TAA and the substring between them is not a multiple of 3
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dna = "GAAATGGATAGTAA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon, stopCodon));
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// DNA with ATG, TAA and the substring between them is a multiple of 3 (a gene)
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dna = "TAAGATATGGTGAAGTAA";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon, stopCodon));
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dna = "ATGGGTTAAGTC";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon, stopCodon));
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dna = "gatgctataat";
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System.out.println("DNA strand is " + dna);
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System.out.println("Gene is " + findSimpleGene(dna, startCodon, stopCodon));
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}
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}
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‎Week2/StringsFirstAssignments/Part3.java

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/**
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* Problem Solving with Strings
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*
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* @author Deny Kiantono
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* @version 1.0
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*/
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public class Part3 {
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public boolean twoOccurrences(String stringa, String stringb) {
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int firstIndex = stringb.indexOf(stringa);
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int lastIndex = stringb.lastIndexOf(stringa);
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if (firstIndex != lastIndex) {
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return true;
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} else {
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return false;
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}
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}
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public String lastPart(String stringa, String stringb) {
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int index = stringb.indexOf(stringa);
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if (index == -1) {
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return stringb;
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} else {
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return stringb.substring(index + stringa.length());
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}
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}
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public void test() {
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String stringa;
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String stringb;
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System.out.println("Testing twoOccurences");
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System.out.println("=====================");
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stringa = "by";
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stringb = "A story by Abby Long";
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System.out.println(stringa + " appears at least twice in " + stringb + " = " + twoOccurrences(stringa, stringb));
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stringa = "a";
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stringb = "banana";
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System.out.println(stringa + " appears at least twice in " + stringb + " = " + twoOccurrences(stringa, stringb));
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stringa = "atg";
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stringb = "ctgtatgta";
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System.out.println(stringa + " appears at least twice in " + stringb + " = " + twoOccurrences(stringa, stringb));
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System.out.println("\n\nTesting lastPart:");
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System.out.println("=================");
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stringa = "an";
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stringb = "banana";
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System.out.println("The part of the string after " + stringa + " in " + stringb + " is " + lastPart(stringa, stringb));
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stringa = "zoo";
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stringb = "forest";
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System.out.println("The part of the string after " + stringa + " in " + stringb + " is " + lastPart(stringa, stringb));
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}
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}

‎Week2/StringsFirstAssignments/Part4.java

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/**
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* Finding Web Links
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*
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* @author Deny Kiantono
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* @version 1.0
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*/
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import edu.duke.*;
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public class Part4 {
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public void findLinks(String url) {
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URLResource urlResource = new URLResource(url);
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for (String line : urlResource.lines()) {
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int youtubeIndex = line.toLowerCase().indexOf("youtube.com");
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if (youtubeIndex != -1) {
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int startIndex = line.lastIndexOf("\"", youtubeIndex);
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int lastIndex = line.indexOf("\"", youtubeIndex);
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System.out.println("Youtube link: " + line.substring(startIndex + 1, lastIndex));
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}
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}
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}
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public void test() {
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String url = "http://www.dukelearntoprogram.com/course2/data/manylinks.html";
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findLinks(url);
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}
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}

‎Week2/StringsSecondAssignments/Part1.java

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/**
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* Finding many Genes
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*
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* @author Deny Kiantono
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* @version 1
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*/
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public class Part1 {
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public int findStopCodon(String dna, int startIndex, String stopCodon) {
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int index = 0;
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while(true) {
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index = dna.indexOf(stopCodon, startIndex + 3);
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if (index == -1 || (index - startIndex) % 3 == 0) {
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break;
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}
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startIndex += 3;
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}
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if (index != -1) {
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return index;
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} else {
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return dna.length();
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}
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}
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public void testFindStopCodon() {
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String dna = "xxxyyyzzzTAAxxxyyyzzzTAAxx";
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int index = findStopCodon(dna, 0, "TAA");
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System.out.println("Index = " + index);
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index = findStopCodon(dna, 9, "TAA");
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System.out.println("Index = " + index);
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index = findStopCodon(dna, 1, "TAA");
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System.out.println("Index = " + index);
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index = findStopCodon(dna, 0, "TAG");
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System.out.println("Index = " + index);
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}
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public String findGene(String dna, int start) {
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final String START_CODON = "ATG";
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int startIndex = dna.indexOf(START_CODON, start);
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if (startIndex == -1) {
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return "";
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}
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int taaIndex = findStopCodon(dna, startIndex, "TAA");
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int tagIndex = findStopCodon(dna, startIndex, "TAG");
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int tgaIndex = findStopCodon(dna, startIndex, "TGA");
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int minIndex = Math.min(taaIndex, Math.min(tagIndex, tgaIndex));
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if (minIndex == dna.length()) {
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return "";
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} else {
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return dna.substring(startIndex, minIndex + 3);
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}
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}
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public void testFindGene() {
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String dna = "GTTAATGTAGCTTAAACCTTTAAAGCAAGGCACTGAAAATGCCTAGATGA";
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System.out.println("Gene: " + findGene(dna, 0));
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dna = "GTGAGCTCACTCCATAGACACAAAGGTTTGGTCCTGGCCTTCTTATTAGT";
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System.out.println("Gene: " + findGene(dna, 0));
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dna = "TTTCAGTGAGCTTACACATGCAAGTATCCGCGCGCCAGTGAAAATGCCCT";
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System.out.println("Gene: " + findGene(dna, 0));
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dna = "TCAAATCATTACTGACCATAAAGGAGCGGGTATCAAGCACACACCTATGT";
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System.out.println("Gene: " + findGene(dna, 0));
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dna = "AGCTCACAACACCTTGCTTAGCCACACCCCCACGGGATACAGCAGTGATA";
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System.out.println("Gene: " + findGene(dna, 0));
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}
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public void printAllGenes(String dna) {
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int start = 0;
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while (true) {
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String gene = findGene(dna, start);
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if (gene.isEmpty()) {
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break;
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}
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System.out.println("Gene: " + gene);
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start = dna.indexOf(gene, start) + gene.length();
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}
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}
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public void testPrintAllGenes() {
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String dna = "ATGATCTAATTTATGCTGCAACGGTGAAGA";
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printAllGenes(dna);
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}
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}

‎Week2/StringsSecondAssignments/Part2.java

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/**
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* HowMany - Finding Multiple Occurrences
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*
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* @author Deny Kiantono
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* @version 1.0
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*/
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public class Part2 {
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public int howMany(String stringa, String stringb) {
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int totalOccurences = 0;
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int start = 0;
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while (true) {
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int index = stringb.indexOf(stringa, start);
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if (index == -1) {
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break;
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}
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totalOccurences++;
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start = index + stringa.length();
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}
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return totalOccurences;
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}
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public void testHowMany() {
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String stringa = "GAA";
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String stringb = "ATGAACGAATTGAATC";
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System.out.println("Total occurences of " + stringa + " in " + stringb + " = " + howMany(stringa, stringb));
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stringa = "AA";
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stringb = "ATAAAA";
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System.out.println("Total occurences of " + stringa + " in " + stringb + " = " + howMany(stringa, stringb));
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}
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}

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