1A3B:H|PDBID|CHAIN|SEQUENCE IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISM LEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY THVFRLKKWIQKVIDQFGE 1A3B:I|PDBID|CHAIN|SEQUENCE GGQSHNDGDFEEIPEEYL 1A3B:L|PDBID|CHAIN|SEQUENCE TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

This is the data which is stored in a text file. How do i go about extracting the fasta sequence strictly between

">1A3B:I|PDBID|CHAIN|SEQUENCE" and ">1A3B:L|PDBID|CHAIN|SEQUENCE", when only

">1A3B:I|PDBID|CHAIN|SEQUENCE" is known to us.

Also, in this given example though the sequence to be retrieved is only of one line, it can vary upto many lines too. So far, i tried writing the entire content of the file to a string variable and using substring, but that logic seems to be flawed as the ending delimiter's index is unknown. Please help

import java.io.*; 
public class ReadingChainSpecificFastaSequence {

    public static void main(String[] args) {


            File file = new File("1A3B.fasta.txt");
            BufferedInputStream bin = null;

            try
            {

                    FileInputStream fin = new FileInputStream(file);


                    bin = new BufferedInputStream(fin);


                    byte[] contents = new byte[1024];

                    int bytesRead=0;
                    String strFileContents=null;

                    while( (bytesRead = bin.read(contents)) != -1){

                            strFileContents = new String(contents, 0, bytesRead);

                    }
                   // System.out.print(strFileContents); 
                    String search = ">1A3B:I|PDBID|CHAIN|SEQUENCE";
                    int start = (strFileContents.indexOf(search))+30;
                    String search2= ">1A3B:L|PDBID|CHAIN|SEQUENCE";
                    int end= (strFileContents.indexOf(search2));
                   String result = strFileContents.substring(start,end);

            }
        catch(FileNotFoundException e)
            {
                    System.out.println("File not found" + e);
            }
            catch(IOException ioe)
            {
                    System.out.println("Exception while reading the file "+ ioe);
            }
            finally
            {

                    try{
                            if(bin != null)
                                    bin.close();
                    }catch(IOException ioe)
                    {
                            System.out.println("Error while closing thestream:"+ioe);
                    }

            }
    }
   }