Clones - import java.io.BufferedReader import...

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import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.util.Random; import java.util.StringTokenizer; //updated on 10/7/2010 Bassam Tork //I don't remeber if it is the same as ExactCpies.java //As I remeber it creates clones from qusi species, those clones are similar to clouds generated by Evolve11.java //in myjavaprograms project, but indels={insertions,deletions,mismatches,matches} are not calculated according to collected //statistics from quasi species, but above indels are randomly decided. And the number of generated offsprings from //the parent is decided by the geometric progression / public class Clones { public static void main(String[] args){ CalcStatistics1 calcStatistics=new CalcStatistics1(); int[] insertionArray=new int[50]; int[] deletionArray=new int[4]; int[] mismatchArray={0}; int[] matchArray={0}; int[] ignoredII={0}; String file1="", file2=""; S int insertionSize=0; int deletionSize=0; int r2=0; String line=""; int value=0;//generated from r:Random int[] errors={0}; int clonesCount=0; //calcStatistics.calc(insertionArray,deletionArray,mismatchArray,matchA rray,ignoredII,errors,"NewReads.txt","ref.txt"); //calcStatistics.accumulateArrays(insertionArray,deletionArray,mismatch Array,matchArray);//returns accumulative contents for InsertionArray followed by deletionArray followed by mismatchArray d int upperBound=matchArray[0];//no need for upperBound variable , just use matchArray[0] as upperBound //**System.out.println("Evolve Upper Bound="+upperBound); / for(int i=1;i<insertionArray.length;i++){//i should be i=1 not i=2 by 8_16_2010 bcs in deletions we add biggest accumulative insertions to D[1] and not to D[2] if (insertionArray[i]!=0){
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This note was uploaded on 12/17/2010 for the course CSC 8550 taught by Professor Alex during the Spring '10 term at Georgia State.

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Clones - import java.io.BufferedReader import...

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