#!/usr/local/bin/perl -w

#Usage: t2k_non_lib_pairwise_alignments workdir target T2Kmlib  


    use FileHandle;
    STDERR->autoflush(1);
    use English;
    use File::Basename;
    use lib dirname($PROGRAM_NAME);
    use IdChecker;

    use lib qw(/projects/compbio/experiments/models.97/scripts);
    use SamT2k;	   # for run_prog, run_cmd


($WORKDIR, $TARGET, $T2K_MLIB) = @ARGV;


#fix path set by SamT2k to include pcb needed by get-pdb-info		      
my $oldPATH = $ENV{"PATH"};						      
$ENV{"PATH"} = "$oldPATH:/projects/compbio/bin";

$SAMBIN = "/projects/compbio/experiments/protein-predict/SAM_T02/bin_freeze/sam";
$T02_SCRIPTS = "/projects/compbio/experiments/protein-predict/SAM_T02/scripts";
$TARGET_AA_MOD = "$TARGET.t2k-w0.5.mod";
$TARGET_SEED_A2M = "$TARGET.a2m";
$PDB_DB = "/projects/compbio/data/pdb/all-protein";
#hmm built with only the target seq
$TARGET_SEED_MOD = "$TARGET.mod";

%hitshash = ();

# get ids of the top hits
while($line = <STDIN>)
{   chomp $line;
    @cols = split("\t", $line);
    #key is chainID of the hit and value is its FSSP rep
    $hitshash{$cols[0]} = $cols[1];
}


foreach $PRED (keys %hitshash)
{
    #destination file prefixes for joint alignments
    $TP = "$PRED/$TARGET-$PRED";

    #create directory for alignments to this hit
    if ( !(defined $WORKDIR) || !(defined  $PRED)){
	die "WORKDIR:$WORKDIR PRED:$PRED missing!\n";
    }

    #create directory for alignments to this hit
    $new_dir = $WORKDIR . "/" . $PRED;
    run_prog("mkdir $new_dir") if (! -e $new_dir);


    #the sequence is not in our library so we must
    #get the sequence from the pdb seqs file 
    run_prog( "$T02_SCRIPTS/get_one_seq $PRED < $PDB_DB > $WORKDIR/$PRED/$PRED.fa");
    $PRED_SEQ = "$WORKDIR/$PRED/$PRED.fa";

    #in this case we have the fasta sequence $PRED_SEQ only 
    #and our target models and sequences 
        $adpstyle = 1;
        &pw_viterbi($T2K_MLIB, $adpstyle);
        &pw_local($T2K_MLIB, $adpstyle);
        &pw_simple_SW($adpstyle);

        $adpstyle = 5;
        &pw_viterbi($T2K_MLIB, $adpstyle);
        &pw_local($T2K_MLIB, $adpstyle);
        &pw_simple_SW($adpstyle);

}

exit(0);


sub pw_viterbi{

    #no viterbi mlibs built yet so these are not calibrated
    #We pass in the MLIB argument just to be ready for the MLIBS
    #that we will build soon

    ($MLIB, $adp) = @_;
    
    #target-template
    
    #align stride-mixed sequence
    $cmd = "$SAMBIN/hmmscore $TP-vit-adpstyle$adp.pw -i $WORKDIR/$TARGET_AA_MOD -db $WORKDIR/$TARGET_SEED_A2M -db $PRED_SEQ -viterbi 1 -sw 2 -subtract_null 4  -select_align 8 -adpstyle $adp";
    run_prog("$cmd");
    $cmd = "gzip -f $TP-vit-adpstyle$adp.pw.a2m";
    run_prog("$cmd");

}

#do SW alignment of the template sequence to a HMM built
#with only the target sequence 
sub pw_simple_SW{
    ($adp) = @_;
    #target-template
    
    #align stride-mixed sequence 
    $cmd = "$SAMBIN/hmmscore $TP-simpleSW-adpstyle$adp.pw -i $WORKDIR/$TARGET_SEED_MOD  -db $WORKDIR/$TARGET_SEED_A2M -db $PRED_SEQ  -adpstyle $adp -sw 2 -subtract_null 4  -select_align 8";
    run_prog("$cmd");
    $cmd = "gzip -f $TP-simpleSW-adpstyle$adp.pw.a2m";
    run_prog("$cmd");
}

sub pw_local{
    ($MLIB, $adp) = @_;
    #target-template
    
    #align stride-mixed sequence 
    $cmd = "$SAMBIN/hmmscore $TP-local-adpstyle$adp.pw -i $WORKDIR/$TARGET_AA_MOD -modellibrary $WORKDIR/$MLIB -db $WORKDIR/$TARGET_SEED_A2M -db $PRED_SEQ  -adpstyle $adp -sw 2 -subtract_null 4  -select_align 8";
    run_prog("$cmd");
    $cmd = "gzip -f $TP-local-adpstyle$adp.pw.a2m";
    run_prog("$cmd");
}


sub print_usage_exit{
    print "Usage: t2k_non_lib_pairwise_alignments workdir target T2Kmlib < seed-top_hits_non_t2k\n";
    exit(-1);
}