use warnings;
use strict;
#use Frontier::Daemon;
use lib '/opt/deepak/bioperl-1.5.1';

use Bio::Root::Exception;
use Bio::SimpleAlign;
use Bio::SearchIO;
use Bio::AlignIO;

#@NoCanDoException::ISA = qw( *Bio::Root::Exception* );
use Error qw(:try);
  

use lib 'lib/perl5/site_perl/5.8.5/';
use Config::Simple;
use Log::Log4perl;

Log::Log4perl::init('log4perl.conf');

my $logger = Log::Log4perl->get_logger('rootLogger');
$logger->debug("Logger Initialised");

my $isException = 1;

&blastParser;

sub blastParser
{
  #output file name to be send at the serverside
  my $outFileName = "OutPutFile";
  open (outFILE,">$outFileName") or die "can't Open output file file";
      
try{   
  print "\nInside...";
  $logger->debug("\nInside Method blastParser");
  
  my $hitCount = 0;
  $hitCount = $ARGV[0]; 
  my $hitAllignCnt = 0;
  my $seqCnt = 0;
  my $arrayCntr = 0;

  #This is the file that is transfered by to the xml-client to current working
  #directory
  my $file = "tempBlastFile";

  my $in = new Bio::SearchIO(-format => 'blast',
	 # comment out the next line to read STDIN
			   -file   => $file );
   
   while ( my $result = $in->next_result ) 
   { 
      print "\nInside result..";
      $logger->debug("\nAnalysing result...");
           
        my @stats =  $result->available_statistics;
        my @params = $result->available_parameters;
          
        while ( my $hit = $result->next_hit and $hitCount) 
        {     
            $hitCount--;
            $hitAllignCnt++;
            print "\n\nRecordcount ::\t$hitCount\n\n";   
            $logger->debug("\nAnalysing hit");
            $logger->debug("\nRecordCount $hitCount");
          	my $id =         $hit->matches('id');
          	my $cons =       $hit->matches('cons');
          	my @accs =       $hit->each_accession_number;
          	my @qidentical = $hit->seq_inds('query','identical');
          	my @qconserved = $hit->seq_inds('query','conserved');
          	my @hidentical = $hit->seq_inds('hit','identical');
          	my @hconserved = $hit->seq_inds('hit','conserved');
                
            $logger->debug("\nHit Name : ".$hit->name);
            $logger->debug("\nHit Accession".$hit->accession);
            $logger->debug("\nHit Row score :".$hit->raw_score);
            $logger->debug("\nHit Bits :".$hit->bits);
            $logger->debug("\nHit Gaps :".$hit->gaps);
     
            $seqCnt=0;
            while(my $hsp = $hit->next_hsp)
            {
            $logger->debug("Analysing Hsp");
            $seqCnt++;
     	      my ($qid,$qcons) = $hsp->matches('hit');
            my ($id,$cons) = $hsp->matches('query');
            @qidentical = $hsp->seq_inds('query','identical');
    	      @qconserved = $hsp->seq_inds('query','conserved');
	          @hidentical = $hsp->seq_inds('hit','identical');
      	    @hconserved = $hsp->seq_inds('hit','conserved');
      	    my @hrange =  $hsp->range('hit');
      	    my @qrange =  $hsp->range('query');
    	      my $aln =     $hsp->get_aln;
      	    my $alnIO =
            Bio::AlignIO->new(-format=>"clustalw",-file=>'>tempHitFile');
            print outFILE "\nHIT-NUMBER=$hitAllignCnt.$seqCnt";
            print outFILE "\nHIT-NAME=".$hit->name;
            print outFILE "\nHIT-ACCESSION=".$hit->accession;
            print outFILE "\nHIT-ROW-SCORE=".$hit->raw_score;
            print outFILE "\nHIT-BITS=".$hit->bits;
            print outFILE "\nHIT-GAPS=".$hit->gaps;            
            print outFILE "\nHIT-EVALUE=".$hsp->evalue;
            print outFILE "\nHIT-PERCENT-IDENTITY=".$hsp->percent_identity;
            
            $logger->debug("Evalue".$hsp->evalue);
            $logger->debug("Percent Identity".$hsp->percent_identity);           
            $logger->debug("\nHit Name : ".$hit->name);
            $logger->debug("\nHit Accession".$hit->accession);
            $logger->debug("\nHit Row score :".$hit->raw_score);
            $logger->debug("\nHit Bits :".$hit->bits);
            $logger->debug("\nHit Gaps :".$hit->gaps);                                                  

            #alnIO object is required to show the sequences in well format
            $alnIO->write_aln($aln);
            open hitFile, "tempHitFile" or die "Can't read file";
            undef $/;
            my $allignMent =  <hitFile>;
            close  hitFile;  
            
            print outFILE "\nALLIGNMENT=START";
            print outFILE "\n$allignMent";
            print outFILE "\nEND";
            undef $hsp;
            undef $allignMent;
            undef $alnIO;
            undef $aln;
            undef @qrange;
            undef @hrange;
            undef @hconserved;
            undef @hidentical;
            undef @qconserved;
            undef @qidentical;
         	}#hsp while ends
          undef $hit;
       }#hit while ends
       undef $result;
    }#result while end
     undef $in;
     print "\nReturning and Closing the OutPutFile\n";
     
     close outFILE;
     $isException = 0;        
  } 
  catch Bio::Root::Exception with 
  {
     my $ex = shift;
     print "\nDeepak Exception...:$ex\n";   
     print outFILE "\nERROR=START\n";
     print outFILE "$ex\n";
     print outFILE "ERROR=END\n";
     return;
  }
otherwise{
    my $exOtherwise = shift;
      $isException = 1;      
      print "Deepak Otherwise...:$exOtherwise\n";
    }
}