Hi Perlmonks. I have a database consists of records separated by // and \n.
I have a very terrible program consists of lots of flags. Now I have a problem about where to check one of them ( the siteflag). Well part of my input and output files looks like follow. 
Input files
 
TITLE     An excitatory scorpion toxin with a distinctive feature: an
            additional alpha helix at the C terminus and its implicati
+ons 
            for interaction with insect sodium channels
             /interaction_site="Q8, N9, Y10, N11, C12, F17, W38, R58, 
+V59 and K62 form the putative bioactive
                surface in mature toxin (Zilberberg et al., 1997)."
             /channel="Sodium channel"
             /target_cell="Insect specific (Excitatory)"
             /c_end="Free"
//
TITLE     Cloning and Sequencing of an Excitatory Insect-Selective Neu
+rotoxin
            BmKIT cDNA from Buthus martensii Karsch
            /interaction_site="Sequential deletions of C-terminal resi
+dues suggested Ile73 and Ile74 for toxicity. {Oren et al., 1999}"
            /channel="Sodium channel"
            /c_end="Free"        
//

Output

References:TITLE         "An excitatory scorpion toxin with a distinct
+ive feature: an additional alpha helix at the C terminus and its impl
+ications  for interaction 
with insect sodium channels"  
Interaction_site  "Q8, N9, Y10, N11, C12, F17, W38, R58, V59 and K62 f
+orm the putative bioactive surface in mature toxin (Zilberberg et al.
+, 1997)."
Channel  "Sodium channel"
Target_cell      "Insect specific (Excitatory)"
C_end    "Free" 

References:TITLE         "Cloning and Sequencing of an Excitatory Inse
+ct-Selecti
ve Neurotoxin BmKIT cDNA from Buthus martensii Karsch"    
Interaction_site  "Sequential deletions of C-terminal residues suggest
+ed Ile73 and Ile74 for toxicity. {Oren et al., 1999}"
Channel  "Sodium channel"
C_end    "Free"

[download]
The title, interaction_site and c_end are fixed element( appear in every record). The rest are optional.
For every record in the file I check them line by line, modify some input and print it to the output file.
The title and interaction site may consist of nothing (" "), a line, or multiple line
Therefore I must use flag to keep track of the input.
The problem is, there a quite a lot of elements after the interaction site which are optional ( not consist in every record ).I include only two of them. My code looks like follow: 
compile : perl  prog.pl  input.db  result
#! /usr/local/bin/perl -w

#initialize all the variable, initialize flags to 0 and line to ''

my $counter=1;
my $file1="$ARGV[0]";
my $result=">".$ARGV[1];
my $site='';
my $titleline='';
my $siteflag=0;
my $titleflag=0;

open(INFO1,$file1) or die "Can't open $file1.\n";   #open file1
open(OUT,$result) or die "Can't open $result.\n";   #open result  

#the input files has a separator :\r\n in each line
foreach(<INFO1>)
{                   

  if(/\s*TITLE\s*(.*)\r/){
    ######## check the title
        $titleflag=1;
        $titleline=$1;
    }                              
   elsif(/\s*\/interaction_site=(.*)\r/){
     ######## handle the title
        print OUT qq(References:TITLE\t "$titleline"\n);
        $titleflag=0;
        $titleline=''; 
     ########  check the site   
       $site=$1;
       $siteflag=1;
    }      
    elsif(/\s*(.*)\r/ && $titleflag==1){
        $titleline.=" "; # add a white space
        $titleline.=$1;  #concatenate the title with previous line
    }                      
                                           
    elsif(/\s*\/channel=(.*)\r/){
        if(check2($1)){
        print OUT "Channel\t $1\n";
        }
    }
    elsif(/\s*\/target_cell=(.*)\r/){
        if(check2($1)){
        print OUT "Target_cell\t $1\n";
        }
    }
    elsif(/\s*\/c_end=(.*)\r/){
    ######## handle interaction site
        $siteflag=0;
        $site='';
   
    ######## check c_end
        if(check2($1)){
            print OUT "C_end\t $1\n";
      }# end if
    }#end elsif
    
    ####elsif(/\s*(.*)\r && $siteflag==1){
    ####   $site.=" "; # add a white space
    ####    $site.=$1; #concatenatewith previous site
    ####    print "Site $site\n";
    ####    }    

} # end foreach

sub check2 { #check whether item = empty quotes
    if($1 =~ /" "/){
        return 0;}
    else{
        return 1;}
}

[download]
The last code preceded by #### is the one that need to be modified. If I use the code in that location it will only print the interaction site if there are more than one lines of site.
Where should I put the code in order I can print the interaction_site regardless they are consists of "" , a line or multiple line? Thanks so much...

In reply to about where to check the flag by gdnew

Title:
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