test.java

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package org.clothocad.algorithm.seqanalyzer.sequencing;

import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.BufferedReader;
import java.io.FileReader;
import java.util.Hashtable;
import java.net.URL;
import java.util.ArrayList;
//import sequencing.ABITrace;
//import sequencing.seqAnalysis;
/**
 *
 * @author benjaminbubenheim
 */
public class test {
    public static void main(String[] args){
        ABITrace abi1=null, abi2=null, abi3=null, abi4=null, abi5=null, abiC=null, abiC1=null;
        ArrayList<ABITrace> abis=new ArrayList<ABITrace>();
        String actual="GAATTCATGAGATCTCAGCTGAAGTGACCGCATTAGCAACGCAGTAACCCGAAATCCTCTTTGACAAAGACAAAGCGTGTCAGGCTGATTCTGATGCGCTTTTTTTTGAAATGTCACAAAAATTCCATGCGGGAGATGAGAGCTAAAATCCCCGTGCAGAACTTTCCACCCAGGGCGAGAAAACTTGTCATTTTGACCTGTTCGCCCTTCGGAACAGTCGAAATCGATCGCGCATCGCTTTCGTGCATAGTTATGCAGCCCTCTAAAAACGATTCTGGCGCGTTTTTCTGGTTTGGCCTGGTGTTTTCTTGTCTTTTTGCGTTTTTTGCGCCAGAAAGCGACTGAGGGCGTTTTAAGGGGTACGTACAACGGGAGTTATGGTAAATGGATCGGGTTTTCGGGAAGGTTCGACAGGATTTGCCGTTGGGTGTACTGTAAGCGACTGAAAAACAAACGCCCCTGAAATCATGTCCAGATCCGGCAAGATTCAACATGAAATACAGAGGGCGTGTAGGTCGCATAACCCGGAGAGAATCGTAACACATGAGCGCCGCGCTTCAATACTTCGACGAAAATTTACCCCATCGTCCCTATCACACGGATGATCTCGCTTTTGGTCTTCGCATCTCCGGCAAAGGGCGTGCGCTTCTTGCGCGGTACATACAGCAGAACCAGCCTCATGCGCAGTTCTGGCTGGTTTTTGATGTTGACCGCGAGGGGGCTGCGATTGACTGGAGCGACCTGAACGCCCCCGCACCGAACATCACCATAAAAAATCCCGTGAACGGTCACGCCCACCTGCTCTACGCACTCAATATCGCCGTGAGAACCGCGCCTGATGCTTCGGTTAAGGCGCTGAAATACGCCGCCGCGATTGAACGTGCGTTGTGTGAAAAACTGGGCGCAGATGTAAACTACAGCGGCCTGATTTGCAAAAATCCGTTCCATCTGGAATGGCAGGTGATGGAGTGGCGTGAGGAAGCCTATACCCTCGATGAACTGGCTGATTATCTTGATTTGAGCACTTCAGCGCGCCGTAGCATCGATAAACATTACGGGATGGGGCGAAACTGCCATCTGTTCGAAATGACGCGCAAATGGGCTTACAGGGCGATTCGTCAGGGCTGGCCAGCATTCTCACAGTGGCTTGATGCCGAGATTCAGCGTGTCGAAATGTACAACGCATCGCTTCCCGTTCCGCTTTCACCTCCTGAATGTCGGGCTATTGGCAAGAGTATTGCGAAATACACGCACAGGAACTTCACGGCGGAAACTTTCGCACAGTATGTGGCTGATACGCACACGCCAGAAATACAGGCCAAGAGAGGCAGGAAAGGTGGCATCGCTAAAGGCGAAGCCTACGATGACAAGCGTTTCATGGCGCTATGTATGCTGGAGAATGGATATTCTCAGAAAGCTATTGCGGCGATGTTGGAGGTTTCTACTCGAACCATTCGAAACTGGAAAAGCGGAAAATAGGGATCC";
        String actual1="GAATTCATGAGATCTTGTTCGGAGCCGCTTTAACCCACTCTGTGGAAGTGCTGGATCC";
        String actual2="GAATTCATGAGATCTAGAACCGCAACTCCCAATAAACGCAAACCCAAAACTCCAACGGATAATCGCTGATGGCTGCTAGACCCCGATCTCACAAAATCTCTATACCCAATTTATATTGCAAATTAGATAAGCGAACCGGAAAGGTATATTGGCAATACAAACATCCACTATCCGGTCGTTTTCATAGCTTAGGAACTGATGAGAATGAAGCAAAACAAGTTGCTACTGAAGCAAATACCATTATTGCTGAACAACGTACCAGACAAATATTAAGCGTCAATGAGCGTCTGGAAAGAATGAAAGGCAGGCGCTCAGACATTACGGTGACAGAATGGCTTGATAAATATATTTCTATCCAGGAGGACAGGCTGCAACATAATGAACTAAGACCCAACTCCTATCGGCAAAAAGGCAAACCCATTCGTCTTTTCCGTGAGCATTGTGGAATGCAACACCTCAAGGATATTACCGCACTTGATATTGCCGAAATAATTGATGCTGTAAAGGCTGAAGGTCATAACAGGATGGCGCAAGTCGTGAGAATGGTGTTGATCGACGTCTTCAAAGAAGCACAACACGCAGGACATGTTCCGCCAGGATTTAACCCAGCGCAGGCAACAAAACAACCGCGAAATCGAGTAAACCGCCAAAGATTGTCACTGCTCGAATGGCAGGCAATATTTGAAAGCGTAAGCAGACGGCAGCCCTATTTAAAATGCGGCATGCTACTTGCTCTTGTTACTGGACAACGTTTAGGCGATATCTGCAATTTGAAATTCTCTGATATATGGGACGACATGTTGCACATTACTCAGGAAAAAACCGGTTCAAAACTTGCTATTCCGCTTAACCTGAAATGCGATGCTCTGAATATTACCCTTCGTGAAGTTATATCTCAGTGCAGGGATGCTGTTGTTAGTAAATATCTGGTCCATTACCGTCACACTACCTCTCAAGCAAACAGAGGAGACCAGGTTTCTGCAAATACTCTGACAACGGCTTTTAAAAAGGCCAAGGAAAAATGTGGCATAAAATGGGAGCAAGGAACTGCGCCCACATTTCATGAACAGCGATCTCTGTCAGAACGATTATATCGGGAACAGGGTCTGGATACGCAAAAGTTGTTAGGCCATAAATCCAGAAAAATGACCGACCGATACAATGATGATCGTGGTAAAGACTGGATTATCGTAGATATCAAAACAGCATAGGGATCC";
        String c="GATCTCAGATCATATATAAGGAGGTACATATGGACACGTACGCGGGTGCTTACGACCGTCAGTCGCGCGAGCGCGAAAATTCGAGCGCAGCAAGCCCAGCGACACAGCGTAGCGCCAACGAAGACAAGGCGGCCGACCTCCAGCGCGAAGTCGAGCGCGACGGGGGCCGGTTCAGGTTCGTCGGGCATTTCAGCGAAGCGCCGGGCACGTCGGCGTTCGGGACGGCGGAGCGCCCGGAGTTCGAACGCATCCTGAACGAATGCCGCGCCGGGCGGCTCAACATGATCATTGTCTATGACGTGTCGCGCTTCTCGCGCCTCAAGGTCATGGACGCGATTCCGATTGTCTCGGAATTGCTCGCCCTGGGCGTGACGATTGTTTCCACTCAGGAAGGCGTCTTCCGGCAGGGAAACGTCATGGACCTGATTCACCTGATTATGCGGCTCGACGCGTCGCACAAAGAATCTTCGCTCAAGTCGGCGAAGATTCTCGACACGAAGAACCTCCAGCGCGAATTGGGCGGGTACGTCGGCGGGAAGGCGCCTTACGGCTTCGAGCTTGTTTCGGAGACGAAGGAGATCACGCGCAACGGCCGAATGGTCAATGTCGTCATCAACAAGCTTGCGCACTCGACCACTCCCCTTACCGGACCCTTCGAGTTCGAGCCCGACGTAATCCGGTGGTGGTGGCGTGAGATCAAGACGCACAAACACCTTCCCTTCAAGCCGGGCAGTCAAGCCGCCATTCACCCGGGCAGCATCACGGGGCTTTGTAAGCGCATGGACGCTGACGCCGTGCCGACCCGGGGCGAGACGATTGGGAAGAAGACCGCTTCAAGCGCCTGGGACCCGGCAACCGTTATGCGAATCCTTCGGGACCCGCGTATTGCGGGCTTCGCCGCTGAGGTGATCTACAAGAAGAAGCCGGACGGCACGCCGACCACGAAGATTGAGGGTTACCGCATTCAGCGCGACCCGATCACGCTCCGGCCGGTCGAGCTTGATTGCGGACCGATCATCGAGCCCGCTGAGTGGTATGAGCTCCAGGCGTGGTTGGACGGCAGGGGGCGCGGCAAGGGGCTTTCCCGGGGGCAAGCCATTCTGTCCGCCATGGACAAGCTGTACTGCGAGTGTGGCGCCGTCATGACTTCGAAGCGCGGGGAAGAATCGATCAAGGACTCTTACCGCTGCCGTCGCCGGAAGGTGGTCGACCCGTCCGCACCTGGGCAGCACGAAGGCACGTGCAACGTCAGCATGGCGGCACTCGACAAGTTCGTTGCGGAACGCATCTTCAACAAGATCAGGCACGCCGAAGGCGACGAAGAGACGTTGGCGCTTCTGTGGGAAGCCGCCCGACGCTTCGGCAAGCTCACTGAGGCGCCTGAGAAGAGCGGCGAACGGGCGAACCTTGTTGCGGAGCGCGCCGACGCCCTGAACGCCCTTGAAGAGCTGTACGAAGACCGCGCGGCAGGCGCGTACGACGGACCCGTTGGCAGGAAGCACTTCCGGAAGCAACAGGCAGCGCTGACGCTCCGGCAGCAAGGGGCGGAAGAGCGGCTTGCCGAACTTGAAGCCGCCGAAGCCCCGAAGCTTCCCCTTGACCAATGGTTCCCCGAAGACGCCGACGCTGACCCGACCGGCCCTAAGTCGTGGTGGGGGCGCGCGTCAGTAGACGACAAGCGCGTGTTCGTCGGGCTCTTCGTAGACAAGATCGTTGTCACGAAGTCGACTACGGGCAGGGGGCAGGGAACGCCCATCGAGAAGCGCGCTTCGATCACGTGGGCGAAGCCGCCGACCGACGACGACGAAGACGACGCCCAGGACGGCACGGAAGACGTAGCGGCGGGATCTCCGCCGAAAAAAAAACGTAAAGTTtaag";
        String c2="GATCTaaaaaaaaaccccgcccctgacagggcggggttttttattaGGATCTAATTGAAGAACCGCTGACCACCTCCCATCCGACAATGCAAGGGTGCCCCGCTCCCAGCGCGACACGGTTGCCTGATCCACACCCATTAATTCAGCTAGGTGACTTTGCTTCATATGACGAAGCAACCGCGCCCTCCGCACCTGCCGCCCCCTGTCATTCGTCAACATTCTTCAGCACCTCAATGTCGTTCGTAGTGAGCCTCATTTTTTCAAGACCGCCGATGATGAGAGCCAGGCCTCGCTCGAATGCCGCGTCCGGACCGCCTTCGTAGACGATTTTCATCGCGCTCTGTAGGCGCGCCGGCATCGTAGACGCTGAGGTGGTCAACTGATCTTCGCCCCGCTCCTCGGCGTCTGCCTCGCTAGCTTGCTGCTCAAGAACAGCGCCGACGGTGAAGTAGCTGATTGCCATCAACGCATAGGTCGCGTCACCTGCCGAAAAGCCAGCATCGCAAAGGAAGCGAAGCTGCGCGTCGGCTTTTTCCATCTGCGGCGCGGCTGGCCGCGTCCCGGCATGAATACGCGCGCCATCGCGATAAGCGAGCAACGCCCGTCGAAAACTGCATGCATTGCCCTTCAGGAACGAACGCCAGTCGTCGTCATCCCTTGGCGTCGAATGCGTGTGATTTATCGTCAGCATGGCTTCGGCAAGTGCGTCGAGCAACGCACGCTTGTTCTTGAAATGCCAGTAGAGCGCTGGCTGTTGCACCCCGAGGCGCTCAGCCAGTCGGCGCGTCGTTAGACCTTCCATGCCCACGTCGTTAAGCAGTTCGAGCGCGGTTCGGATCACGGCCTCGCGTTGGAGCTTGTTCATTCGCcAATTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATAGGATCTaaaaaagccggagtagaagatggtagaaatcaataatcaacgtaaggcgttcctcgatatgctggcgtggtcggagggaactgataacggacgtcagaaaaccagaaatcatggttatgacgtcattgtaggcggagagctattCactgattactccgatcaccctcgcaaacttgtcacgctaaacccaaaactcaaatcaacaggcgccggacgctaccagcttctttcccgttggtgggatgcctaccgcaagcagcttggcctgaaagacttctctccgaaaagtcaggacgctgtggcattgcagcagattaaggagcgtggcgctttacctatgattgatcgtggtgatatccgtcaggcaatcgaccgttgcagcaatatctgggcttcactgccgggcgctggttatggtcagttcgagcataaggctgacagcctgattgcaaaattcaaagaagcgggcggaacggtcagagagattgatgtatgaGGATCTattgggggtaagacCtgaagatgccagaaaaacatgacctgttggccgccattctcgcggcaaaggaacaaggcatcggggcaatccttgcgtttgcaatggcgtaccttcgcggcagatataatggcggtgcgtttacaaaaacagtaatcgacgcaacgatgtgcgccattatcgcctggttcattcgtgaccttctcgacttcgccggactaagtagcaatctcgcttatataacgagcgtgtttatcggctacatcggtactgactcgattggttcgcttatcaaacgcttcgctgctaaaaaagccggagtagaagatggtagaaatcaataaGGATCTccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttataGGATCTCTTACGGCTAGCTCAGTCCTAGGCACTTTGCTAGCGGATCTccccttattgggggtaagacatgaagCtgccagaaaaacatgacctgttggccgccattctcgcggcaaaggaacaaggcatcggggcaatccttgcgtttgcaatggcgtaccttcgcggcagatataatggcggtgcgtttacaaaaacagtaatcgacgcaacgatgtgcgccattatcgcctggttcattcgtgaccttctcgacttcgccggactaagtagcaatctcgcttatataacgagcgtgtttatcggctacatcggtactgactcgattggttcgcttatcaaacgcttcgctgctaaaaaagccggagtagaagatggtagaaatcaataaGGATCTgCcggcttatcGgtcagtttcacctgatttacgtaaaaacccgcttcggcgggtttttgcttttggaggggcagaaagatgaatgactgtccacgacgctatacccaaaagaaatG";
        try{
        abi1=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//sequencing//BG4_ca998_2010-03-20_B03_029.ab1"));
        abi2=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//sequencing//BG4_G00101_2010-03-19_E10_072.ab1"));

        abi3=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//032510_jca//CF8_ca998_2010-03-25_C09_075.ab1"));

        abi4=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//sequencing//CC4_ca998_2010-03-27_A10_080.ab1"));
        abi5=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//sequencing//CC4_G00101_2010-03-26_C02_012.ab1"));

        abiC=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//071410_iGEM//iGEM43_g00101_2010-07-14_G10.ab1"));
        abiC1=new ABITrace(new File("//Users//benjaminbubenheim//Downloads//071410_iGEM//iGEM44_ca998_2010-07-14_H10.ab1"));
        }
        catch(IOException e){
            System.out.println("OOPS");
        }
        
        Hashtable hash=new Hashtable(200);
        File xls = new File("//Users//benjaminbubenheim//Downloads//sequencingmatching.csv");
        try{
        BufferedReader in=new BufferedReader(new FileReader(xls));
        String str="";
        while((str=in.readLine())!=null){
            //System.out.println(str);
            String temp1=str.substring(0, str.indexOf(","));
            String temp2=str.substring(str.indexOf(",")+1);
            hash.put(temp1, temp2);
        }
        }
        catch(Exception e){
            System.out.println(e);
            e.printStackTrace();
        }
        
        File folder = new File("//Users//benjaminbubenheim//Downloads//seqTest//");
        File[] listOfFiles = folder.listFiles();
        ArrayList<String> seenB4=new ArrayList<String>();
        Hashtable fileHash=new Hashtable(200);
        for (int i = 0; i < listOfFiles.length; i++) {
            if (listOfFiles[i].isFile()&&listOfFiles[i].getName().contains(".ab1")) {
                System.out.println("File " + listOfFiles[i].getName());
                if(!seenB4.contains(listOfFiles[i].getName().substring(0, 3))){
                    seenB4.add(listOfFiles[i].getName().substring(0, 3));
                    ArrayList<ABITrace> temp=new ArrayList<ABITrace>();
                    
                    try{
                        temp.add(new ABITrace(listOfFiles[i]));
                        fileHash.put(listOfFiles[i].getName().substring(0, 3), temp);
                        //abis.add(new ABITrace(listOfFiles[i]));
                    }
                    catch(IOException e){
                        System.out.println("OOPS");
                    }
                }
                else{
                    try{
                    ((ArrayList<ABITrace>)fileHash.get(listOfFiles[i].getName().substring(0, 3))).add(new ABITrace(listOfFiles[i]));
                    }
                    catch(IOException e){
                        System.out.println("OOPS");
                    }
                }
            }
        }

        
        
        ArrayList<ABITrace> a=new ArrayList<ABITrace>();
        a.add(abi1);
        a.add(abi2);
        //a.add(abiC);
        //a.add(abiC1);
        //System.out.println(((String)hash.get("BG4")).toUpperCase());
        //System.out.println(actual);
        String f="CE2";
        seqAnalysis s=new seqAnalysis((ArrayList<ABITrace>)fileHash.get(f), (String)hash.get(f), null, null, true);//((String)hash.get("BG4")).toUpperCase());
        //seqAnalysis s=new seqAnalysis(a, actual, null, null, true);

        
        
    }
}