Answer Happy

Question:
Fix Java code that reads in file "in.fasta" . Right now,the output is wrong. The output should should looklike Real Solution output at thevery bottom.
MY JAVA CODE
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.*;
import java.util.*;
public class Test1{
static StringBuilder buildStr (StringBuilder bStr) {
bStr.setLength(0);
StringBuilder str = new StringBuilder();
return str;
}
public static void main(String[] args) throws IOException {
File inputFile = new File("in.fasta");
File outputFile = new File("out.fasta");
try {
FileReader in = new FileReader(inputFile);
FileWriter out = new FileWriter(outputFile);
BufferedReader br = new BufferedReader(newInputStreamReader(new FileInputStream(inputFile)));
BufferedWriter bw = new BufferedWriter(newOutputStreamWriter(new FileOutputStream(outputFile)));
List<String> listOfStrings = newArrayList<String>();
String s = "";
int ct = 0;
while ((s = br.readLine()) !=null) {
listOfStrings.add(s);
}
br.close();
String[] array = listOfStrings.toArray(newString[0]);
StringBuilder str = new StringBuilder();
for (int i = 0; i < array.length; i++) {
if(array.startsWith(">"))
{
ct++;
array = ">REV_00000" +ct + " reversed";
bw.write(array);
bw.write ("\n");
}
else
{
for(int j = i ; j < array.length();j++) {
if(!array[j].startsWith(">")) {
str.append(array[j]);
}
else {
str.reverse();
array = str.toString();
bw.write(str.toString());
bw.write ("\n");
str.setLength(0);
str =buildStr(str);
break;
}
}
}
// System.out.println(array);
}
bw.flush();
bw.close();
} catch (Exception ex) {
ex.printStackTrace();
}
} // end of main
}// end of class
Wrong OUTPUT FILE ( "out.fasta " ) --this is wrong andis what the code is doing
>REV_000001 reversedHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSVIELLFALWYQLSIPLSMRSDLCFGWEKSLTYNLDDYSQHPTDDSIYYFQGQINPVKKPDRLARLALIHAWAVNGVYVPNVRSFKCHNTLIGNNNLAGHMYASLFPSGEGYIYMPRLACTYLTGGNKLAWGNAGLVAKEALKKSYPYPSSWASEHHEEERGDQIIERYSNPGAVEITSTHIFVPVSAQVCAELLLQTGKVNVNMITERPVANRVDIVSATHIVVSTGQCAGKLCQEDLIDGELLTLKIKSQLKSFEERVEPRFVKDLVRIEQLDKEEVLLCIIRQGLFGGGGTVLCSWGAHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSVIELLFALWYQLSIPLSMRSDLCFGWEKSLTYNLDDYSQHPTDDSIYYFQGQINPVKKPDRLARLALIHAWAVNGVYVPNVRSFKCHNTLIGNNNLAGHMYASLFPSGEGYIYMPRLACTYLTGGNKLAWGNAGLVAKEALKKSYPYPSSWASEHHEEERGDQIIERYSNPGAVEITSTHIFVPVSAQVCAELLLQTGKVNVNMITERPVANRVDIVSATHIVVSTGQCAGKLCQEDLIDHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSVIELLFALWYQLSIPLSMRSDLCFGWEKSLTYNLDDYSQHPTDDSIYYFQGQINPVKKPDRLARLALIHAWAVNGVYVPNVRSFKCHNTLIGNNNLAGHMYASLFPSGEGYIYMPRLACTYLTGGNKLAWGNAGLVAKEALKKSYPYPSSWASEHHEEERGDQIIERYSNPGAVEITSTHHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSVIELLFALWYQLSIPLSMRSDLCFGWEKSLTYNLDDYSQHPTDDSIYYFQGQINPVKKPDRLARLALIHAWAVNGVYVPNVRSFKCHNTLIGNNNLAGHMYASLFPSGEGYIYMPRLACTHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSVIELLFALWYQLSIPLSMRSDLCFGWEKSLTYNLDDYSQHPTDDSIYYFQGQINPVKKPDHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSHIKTKLTEKHQK>REV_000002 reversedEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSYRFKSGLALFKSKPITDTSTLRFFTHHEVCVKWLKKAARYSPLKFGITSEYQEQEGPRIKIFFSSRKYSIKLVKPWPFRNIRLKEKYVLLGSSCVGLIIDVGELDKAKHLDVGYMSLKKANELFELDAQAPTMSRYSKHLEMVKEELEKTQNPALKFDSVYDAGHLEPDYDGLESQITYSGLLALTAFSCPLRGSVIDQRLQLCLYYRTIDETLQAPDPPYFKVNFTFNWPVGRVQKKIEKASDLWTKSTANDWIALGFYDEELLNLHECVRKLLDQGKAHKEVVCEYVTDDLLSVKCHMEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSYRFKSGLALFKSKPITDTSTLRFFTHHEVCVKWLKKAARYSPLKFGITSEYQEQEGPRIKIFFSSRKYSIKLVKPWPFRNIRLKEKYVLLGSSCVGLIIDVGELDKAKHLDVGYMSLKKANELFELDAQAPTMSRYSKHLEMVKEELEKTQNPALKFDSVYDAGHLEPDYDGLESQITYSGLLALTAFSCPLRGSVIDQRLQLCLYYRTIDETLQAPDPPYFKVNFTFNWPVGRVQKKIEEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSYRFKSGLALFKSKPITDTSTLRFFTHHEVCVKWLKKAARYSPLKFGITSEYQEQEGPRIKIFFSSRKYSIKLVKPWPFRNIRLKEKYVLLGSSCVGLIIDVGELDKAKHLDVGYMSLKKANELFELDAQAPTMSRYSKHLEMVKEELEKTQNPALKFDSVYDAGHLEPDYDGLESQITYSEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSYRFKSGLALFKSKPITDTSTLRFFTHHEVCVKWLKKAARYSPLKFGITSEYQEQEGPRIKIFFSSRKYSIKLVKPWPFRNIRLKEKYVLLGSSCVGLIIDVGELDKAKHLDVGYMSLKKAEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSYRFKSGLALFKSKPITDTSTLRFFTHHEVCVKWLKKAARYSPLKFGITSEYQEQEGPRIKEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQ
-------------------------------
In.fasta
>3BHS_BOVIN (P14893) 3 beta-hydroxysteroiddehydrogenase/delta 5-->4-isomerase (3Beta-HSD) [Includes:3-beta-hydroxy-delta(5)-steroid dehydrogenase (EC 1.1.1.145)(3-beta-hydroxy-5-ene steroid dehydrogenase) (Progesteronereductase); Steroid delta-isomeraAGWSCLVTGGGGFLGQRIICLLVEEKDLQEIRVLDKVFRPEVREEFSKLQSKIKLTLLEGDILDEQCLKGACQGTSVVIHTASVIDVRNAVPRETIMNVNVKGTQLLLEACVQASVPVFIHTSTIEVAGPNSYREIIQDGREEEHHESAWSSPYPYSKKLAEKAVLGANGWALKNGGTLYTCALRPMYIYGEGSPFLSAYMHGALNNNGILTNHCKFSRVNPVYVGNVAWAHILALRALRDPKKVPNIQGQFYYISDDTPHQSYDDLNYTLSKEWGFCLDSRMSLPISLQYWLAFLLEIVSFLLSPIYKYNPCFNRHLVTLSNSVFTFSYKKAQRDLGYEPLYTWEEAKQKTKEWIGSLVKQHKETLKTKIH>41_BOVIN (Q9N179) Protein 4.1 (Band 4.1) (P4.1) (4.1R)MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAKEIKKQVRGVPWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVSGRLPCSFATLALLGSYTIQSELGDYDPELHGADYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLENAKKLSMYGVDLHKAKDLEGVDIILGVCSSGLLVYKEKLRINRFPWPKVLKISYKRSSFFIKIRPGEQEQYESTIGFKLPSYRAAKKLWKVCVEHHTFFRLTSTDTIPKSKFLALGSKFRYSGRTQAQTRQASALIDRPAPHFERTASKRASRSLDGAAAVEPADRTPRPTSAPAIAPSPAAEGGVPGAPVKKAQKETVQVEVKQEEAPPEDAEPEPSEAWKKKRERLDGENIYIRHSNLMLEDLDKSQEEIKKHHASISELKKNFMESVPEPRPSEWDKRLSTHSPFRTLNINGQIPTGEGPPLVKTQTVTISDTANAVKSEIPTKDVPIVHTETKTITYEAAQTDDSNGDLDPGVLLTAQTITSETTSSTTTTQITKTVKGGISETRIEKRIVITGDADIDHDQVLVQAIKEAKEQHPDMSVTKVVVHQETEISEE
Real Solution output ( this is what itsupposed to look like)
>REV_000001 reversedHIKTKLTEKHQKVLSGIWEKTKQKAEEWTYLPEYGLDRQAKKYSFTFVSNSLTVLHRNFCPNYKYIPSLLFSVIELLFALWYQLSIPLSMRSDLCFGWEKSLTYNLDDYSQHPTDDSIYYFQGQINPVKKPDRLARLALIHAWAVNGVYVPNVRSFKCHNTLIGNNNLAGHMYASLFPSGEGYIYMPRLACTYLTGGNKLAWGNAGLVAKEALKKSYPYPSSWASEHHEEERGDQIIERYSNPGAVEITSTHIFVPVSAQVCAELLLQTGKVNVNMITERPVANRVDIVSATHIVVSTGQCAGKLCQEDLIDGELLTLKIKSQLKSFEERVEPRFVKDLVRIEQLDKEEVLLCIIRQGLFGGGGTVLCSWGA>REV_000002 reversedEESIETEQHVVVKTVSMDPHQEKAEKIAQVLVQDHDIDADGTIVIRKEIRTESIGGKVTKTIQTTTTSSTTESTITQATLLVGPDLDGNSDDTQAAEYTITKTETHVIPVDKTPIESKVANATDSITVTQTKVLPPGEGTPIQGNINLTRFPSHTSLRKDWESPRPEPVSEMFNKKLESISAHHKKIEEQSKDLDELMLNSHRIYINEGDLRERKKKWAESPEPEADEPPAEEQKVEVQVTEKQAKKVPAGPVGGEAAPSPAIAPASTPRPTRDAPEVAAAGDLSRSARKSATREFHPAPRDILASAQRTQAQTRGSYRFKSGLALFKSKPITDTSTLRFFTHHEVCVKWLKKAARYSPLKFGITSEYQEQEGPRIKIFFSSRKYSIKLVKPWPFRNIRLKEKYVLLGSSCVGLIIDVGELDKAKHLDVGYMSLKKANELFELDAQAPTMSRYSKHLEMVKEELEKTQNPALKFDSVYDAGHLEPDYDGLESQITYSGLLALTAFSCPLRGSVIDQRLQLCLYYRTIDETLQAPDPPYFKVNFTFNWPVGRVQKKIEKASDLWTKSTANDWIALGFYDEELLNLHECVRKLLDQGKAHKEVVCEYVTDDLLSVKCHM