=head1 LICENSE

  Copyright (c) 1999-2013 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <dev@ensembl.org>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut

=head1 NAME

Bio::EnsEMBL::BaseAlignFeature - Baseclass providing a common abstract
implmentation for alignment features

=head1 SYNOPSIS

  my $feat = new Bio::EnsEMBL::DnaPepAlignFeature(
    -slice        => $slice,
    -start        => 100,
    -end          => 120,
    -strand       => 1,
    -hseqname     => 'SP:RF1231',
    -hstart       => 200,
    -hend         => 220,
    -analysis     => $analysis,
    -cigar_string => '10M3D5M2I'
  );

  where $analysis is a Bio::EnsEMBL::Analysis object.

  Alternatively if you have an array of ungapped features:

    my $feat =
      new Bio::EnsEMBL::DnaPepAlignFeature( -features => \@features );

  where @features is an array of Bio::EnsEMBL::FeaturePair objects.

  There is a method to (re)create ungapped features from the cigar_string:

    my @ungapped_features = $feat->ungapped_features();

  where @ungapped_features is an array of Bio::EnsEMBL::FeaturePair's.

  Bio::EnsEMBL::BaseAlignFeature inherits from:
    Bio::EnsEMBL::FeaturePair, which in turn inherits from:
      Bio::EnsEMBL::Feature,
  thus methods from both parent classes are available.


  The cigar_string is a condensed representation of the matches and gaps
  which make up the gapped alignment (where CIGAR stands for
  Concise Idiosyncratic Gapped Alignment Report).

  CIGAR format is: n <matches> [ x <deletes or inserts> m <matches> ]*
  where M = match, D = delete, I = insert; n, m are match lengths;
  x is delete or insert length.

  Spaces are omitted, thus: "23M4I12M2D1M"
  as are counts for any lengths of 1, thus 1M becomes M: "23M4I12M2DM"


  To make things clearer this is how a blast HSP would be parsed:

  >AK014066
         Length = 146

    Minus Strand HSPs:

    Score = 76 (26.8 bits), Expect = 1.4, P = 0.74
    Identities = 20/71 (28%), Positives = 29/71 (40%), Frame = -1

  Query:   479 GLQAPPPTPQGCRLIPPPPLGLQAPLPTLRAVGSSHHHP*GRQGSSLSSFRSSLASKASA 300
               G  APPP PQG R   P P G + P   L             + + ++  R  +A   +
  Sbjct:     7 GALAPPPAPQG-RWAFPRPTG-KRPATPLHGTARQDRQVRRSEAAKVTGCRGRVAPHVAP 64

  Query:   299 SSPHNPSPLPS 267
                  H P+P P+
  Sbjct:    65 PLTHTPTPTPT 75

  The alignment goes from 479 down to 267 in the query sequence on the reverse
  strand, and from 7 to 75 in the subject sequence.

  The alignment is made up of the following ungapped pieces:

  query_seq start 447 , sbjct_seq hstart  7 , match length  33 , strand -1
  query_seq start 417 , sbjct_seq hstart 18 , match length  27 , strand -1
  query_seq start 267 , sbjct_seq hstart 27 , match length 147 , strand -1

  When assembled into a DnaPepAlignFeature where:
    (seqname, start, end, strand) refer to the query sequence,
    (hseqname, hstart, hend, hstrand) refer to the subject sequence,
  these ungapped pieces are represented by the cigar string:
    33M3I27M3I147M
  with start 267, end 479, strand -1, and hstart 7, hend 75, hstrand 1.

=head1 CAVEATS

  AlignFeature cigar strings have the opposite 'sense'
  ('D' and 'I' swapped) compared with Exonerate cigar strings.

  Exonerate modules in Bio::EnsEMBL::Analysis use this convention:

   The longer genomic sequence specified by:
      exonerate:    target
      AlignFeature: (sequence, start, end, strand)

   A shorter sequence (such as EST or protein) specified by:
      exonerate:    query
      AlignFeature: (hsequence, hstart, hend, hstrand)

  The resulting AlignFeature cigar strings have 'D' and 'I'
  swapped compared with the Exonerate output, i.e.:

    exonerate:    M 123 D 1 M 11 I 1 M 39
    AlignFeature: 123MI11MD39M

=head1 METHODS

=cut


package Bio::EnsEMBL::BaseAlignFeature;

use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);

use vars qw(@ISA);
use strict;

@ISA = qw(Bio::EnsEMBL::FeaturePair);


=head2 new

  Arg [..]   : List of named arguments. (-cigar_string , -features) defined
               in this constructor, others defined in FeaturePair and 
               SeqFeature superclasses.  Either cigar_string or a list
               of ungapped features should be provided - not both.
  Example    : $baf = new BaseAlignFeatureSubclass(-cigar_string => '3M3I12M');
  Description: Creates a new BaseAlignFeature using either a cigar string or
               a list of ungapped features.  BaseAlignFeature is an abstract
               baseclass and should not actually be instantiated - rather its
               subclasses should be.
  Returntype : Bio::EnsEMBL::BaseAlignFeature
  Exceptions : thrown if both feature and cigar string args are provided
               thrown if neither feature nor cigar string args are provided
  Caller     : general
  Status     : Stable

=cut

sub new {
  
  my $caller = shift;

  my $class = ref($caller) || $caller;

  my $self = $class->SUPER::new(@_);

  my ($cigar_string,$features) = rearrange([qw(CIGAR_STRING FEATURES)], @_);

  if (defined($cigar_string) && defined($features)) {
    throw("CIGAR_STRING or FEATURES argument is required - not both.");
  } elsif (defined($features)) {
    $self->_parse_features($features);
    
  } elsif (defined($cigar_string)) {
    $self->{'cigar_string'} = $cigar_string;
  } else {
    throw("CIGAR_STRING or FEATURES argument is required");
  }
  
  return $self;
}


=head2 cigar_string

  Arg [1]    : string $cigar_string
  Example    : $feature->cigar_string( "12MI3M" );
  Description: get/set for attribute cigar_string.
               cigar_string describes the alignment:
                 "xM" stands for x matches (or mismatches),
                 "xI" for x inserts into the query sequence,
                 "xD" for x deletions from the query sequence
                 where the query sequence is specified by (seqname, start, ...)
                 and the subject sequence by (hseqname, hstart, ...).
               An "x" that is 1 can be omitted.
               See the SYNOPSIS for an example.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub cigar_string {
  my $self = shift;
  $self->{'cigar_string'} = shift if(@_);
  return $self->{'cigar_string'};
}


=head2 alignment_length

  Arg [1]    : None
  Description: return the alignment length (including indels) based on the cigar_string
  Returntype : int
  Exceptions : 
  Caller     : 
  Status     : Stable

=cut

sub alignment_length {
  my $self = shift;

  if (! defined $self->{'_alignment_length'} && defined $self->cigar_string) {
    
    my @pieces = ( $self->cigar_string =~ /(\d*[MDI])/g );
    unless (@pieces) {
      print STDERR "Error parsing cigar_string\n";
    }
    my $alignment_length = 0;
    foreach my $piece (@pieces) {
      my ($length) = ( $piece =~ /^(\d*)/ );
      if (! defined $length || $length eq "") {
        $length = 1;
      }
      $alignment_length += $length;
    }
    $self->{'_alignment_length'} = $alignment_length;
  }
  return $self->{'_alignment_length'};
}

=head2 ungapped_features

  Args       : none
  Example    : @ungapped_features = $align_feature->get_feature
  Description: converts the internal cigar_string into an array of
               ungapped feature pairs
  Returntype : list of Bio::EnsEMBL::FeaturePair
  Exceptions : cigar_string not set internally
  Caller     : general
  Status     : Stable

=cut

sub ungapped_features {
  my ($self) = @_;

  if (!defined($self->{'cigar_string'})) {
    throw("No cigar_string defined.  Can't return ungapped features");
  }

  return @{$self->_parse_cigar()};
}

=head2 strands_reversed
 
  Arg [1]    : int $strands_reversed
  Description: get/set for attribute strands_reversed
               0 means that strand and hstrand are the original strands obtained
                 from the alignment program used
               1 means that strand and hstrand have been flipped as compared to
                 the original result provided by the alignment program used.
                 You may want to use the reverse_complement method to restore the
                 original strandness.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut

sub strands_reversed {
   my ($self, $arg) = @_;
 
   if ( defined $arg ) {
      $self->{'strands_reversed'} = $arg ;
   }

   $self->{'strands_reversed'} = 0 unless (defined $self->{'strands_reversed'});

   return $self->{'strands_reversed'};
}

=head2 reverse_complement

  Args       : none
  Description: reverse complement the FeaturePair,
               modifing strand, hstrand and cigar_string in consequence
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub reverse_complement {
  my ($self) = @_;

  # reverse strand in both sequences
  $self->strand($self->strand * -1);
  $self->hstrand($self->hstrand * -1);

  # reverse cigar_string as consequence
  my $cigar_string = $self->cigar_string;
  $cigar_string =~ s/(D|I|M)/$1 /g;
  my @cigar_pieces = split / /,$cigar_string;
  $cigar_string = "";
  while (my $piece = pop @cigar_pieces) {
    $cigar_string .= $piece;
  }
  
  $self->{'strands_reversed'} = 0 unless (defined $self->{'strands_reversed'});

  if ($self->strands_reversed) {
    $self->strands_reversed(0)
  } else {
    $self->strands_reversed(1);
  }

  $self->cigar_string($cigar_string);
}



=head2 transform

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Example    : $feature = $feature->transform('contig');
               $feature = $feature->transform('chromosome', 'NCBI33');
  Description: Moves this AlignFeature to the given coordinate system.
               If the feature cannot be transformed to the destination 
               coordinate system undef is returned instead.
  Returntype : Bio::EnsEMBL::BaseAlignFeature;
  Exceptions : wrong parameters
  Caller     : general
  Status     : Medium Risk
             : deprecation needs to be removed at some time

=cut

sub transform {
  my $self = shift;

  # catch for old style transform calls
  if( ref $_[0] eq 'HASH') {
    deprecate("Calling transform with a hashref is deprecate.\n" .
              'Use $feat->transfer($slice) or ' .
              '$feat->transform("coordsysname") instead.');
    my (undef, $new_feat) = each(%{$_[0]});
    return $self->transfer($new_feat->slice);
  }

  my $new_feature = $self->SUPER::transform(@_);
  if ( !defined($new_feature)
    || $new_feature->length() != $self->length() )
  {
    my @segments = @{ $self->project(@_) };

    if ( !@segments ) {
      return undef;
    }

    my @ungapped;
    foreach my $f ( $self->ungapped_features() ) {
      $f = $f->transform(@_);
      if ( defined($f) ) {
        push( @ungapped, $f );
      } else {
        warning( "Failed to transform alignment feature; "
            . "ungapped component could not be transformed" );
        return undef;
      }
    }

    eval { $new_feature = $self->new( -features => \@ungapped ); };

    if ($@) {
      warning($@);
      return undef;
    }
  } ## end if ( !defined($new_feature...))

  return $new_feature;
}


=head2 _parse_cigar

  Args       : none
  Description: PRIVATE (internal) method - creates ungapped features from 
               internally stored cigar line
  Returntype : list of Bio::EnsEMBL::FeaturePair
  Exceptions : none
  Caller     : ungapped_features
  Status     : Stable

=cut

sub _parse_cigar {
  my ( $self ) = @_;

  my $query_unit = $self->_query_unit();
  my $hit_unit = $self->_hit_unit();

  my $string = $self->{'cigar_string'};

  throw("No cigar string defined in object") if(!defined($string));

  my @pieces = ( $string =~ /(\d*[MDI])/g );
  #print "cigar: ",join ( ",", @pieces ),"\n";

  my @features;
  my $strand1 = $self->{'strand'} || 1;
  my $strand2 = $self->{'hstrand'}|| 1;

  my ( $start1, $start2 );

  if( $strand1 == 1 ) {
    $start1 = $self->{'start'};
  } else {
    $start1 = $self->{'end'};
  }

  if( $strand2 == 1 ) {
    $start2 = $self->{'hstart'};
  } else {
    $start2 = $self->{'hend'};
  }

  #
  # Construct ungapped blocks as FeaturePairs objects for each MATCH
  #
  foreach my $piece (@pieces) {

    my ($length) = ( $piece =~ /^(\d*)/ );
    if( $length eq "" ) { $length = 1 }
    my $mapped_length;

    # explicit if statements to avoid rounding problems
    # and make sure we have sane coordinate systems
    if( $query_unit == 1 && $hit_unit == 3 ) {
      $mapped_length = $length*3;
    } elsif( $query_unit == 3 && $hit_unit == 1 ) {
      $mapped_length = $length / 3;
    } elsif ( $query_unit == 1 && $hit_unit == 1 ) {
      $mapped_length = $length;
    } else {
      throw("Internal error $query_unit $hit_unit, currently only " .
            "allowing 1 or 3 ");
    }

    if( int($mapped_length) != $mapped_length and
        ($piece =~ /M$/ or $piece =~ /D$/)) {
      throw("Internal error with mismapped length of hit, query " .
            "$query_unit, hit $hit_unit, length $length");
    }

    if( $piece =~ /M$/ ) {
      #
      # MATCH
      #
      my ( $qstart, $qend);
      if( $strand1 == 1 ) {
        $qstart = $start1;
        $qend = $start1 + $length - 1;
        $start1 = $qend + 1;
      } else {
        $qend = $start1;
        $qstart = $start1 - $length + 1;
        $start1 = $qstart - 1;
      }

      my ($hstart, $hend);
      if( $strand2 == 1 ) {
        $hstart = $start2;
        $hend = $start2 + $mapped_length - 1;
        $start2 = $hend + 1;
      } else {
        $hend = $start2;
        $hstart = $start2 - $mapped_length + 1;
        $start2 = $hstart - 1;
      }


      push @features, Bio::EnsEMBL::FeaturePair->new
        (-SLICE      => $self->{'slice'},
         -SEQNAME   => $self->{'seqname'},
         -START      => $qstart,
         -END        => $qend,
         -STRAND     => $strand1,
         -HSLICE      => $self->{'hslice'},
         -HSEQNAME   => $self->{'hseqname'},
         -HSTART     => $hstart,
         -HEND       => $hend,
         -HSTRAND    => $strand2,
         -SCORE      => $self->{'score'},
         -PERCENT_ID => $self->{'percent_id'},
         -ANALYSIS   => $self->{'analysis'},
         -P_VALUE    => $self->{'p_value'},
         -EXTERNAL_DB_ID => $self->{'external_db_id'}, 
         -HCOVERAGE   => $self->{'hcoverage'},
         -GROUP_ID    => $self->{'group_id'},
         -LEVEL_ID    => $self->{'level_id'});
      

      # end M cigar bits 
    } elsif( $piece =~ /I$/ ) {
      #
      # INSERT
      #
      if( $strand1 == 1 ) {
        $start1 += $length;
      } else {
        $start1 -= $length;
      }
    } elsif( $piece =~ /D$/ ) {
      #
      # DELETION
      #
      if( $strand2 == 1 ) {
        $start2 += $mapped_length;
      } else {
        $start2 -= $mapped_length;
      }
    } else {
      throw( "Illegal cigar line $string!" );
    }
  }

  return \@features;
}




=head2 _parse_features

  Arg  [1]   : listref Bio::EnsEMBL::FeaturePair $ungapped_features
  Description: creates internal cigar_string and start,end hstart,hend
               entries.
  Returntype : none, fills in values of self
  Exceptions : argument list undergoes many sanity checks - throws under many
               invalid conditions
  Caller     : new
  Status     : Stable

=cut

my $message_only_once = 1;

sub _parse_features {
  my ($self,$features ) = @_;

  my $query_unit = $self->_query_unit();
  my $hit_unit = $self->_hit_unit();

  if (ref($features) ne "ARRAY") {
    throw("features must be an array reference not a [".ref($features)."]");
  }

  my $strand  = $features->[0]->strand;

  throw ('FeaturePair needs to have strand == 1 or strand == -1') if(!$strand);

  my @f;

  #
  # Sort the features on their start position
  # Ascending order on positive strand, descending on negative strand
  #
  if( $strand == 1 ) {
    @f = sort {$a->start <=> $b->start} @$features;
  } else {
    @f = sort { $b->start <=> $a->start} @$features;
  }

  my $hstrand     = $f[0]->hstrand;
  my $slice       = $f[0]->slice();
  my $hslice       = $f[0]->hslice();
  my $name        = $slice ? $slice->name() : undef;
  my $hname       = $f[0]->hseqname;
  my $score       = $f[0]->score;
  my $percent     = $f[0]->percent_id;
  my $analysis    = $f[0]->analysis;
  my $pvalue      = $f[0]->p_value();
  my $external_db_id = $f[0]->external_db_id;
  my $hcoverage   = $f[0]->hcoverage;
  my $group_id    = $f[0]->group_id;
  my $level_id    = $f[0]->level_id;

  my $seqname = $f[0]->seqname;
  # implicit strand 1 for peptide sequences
  $strand  ||= 1;
  $hstrand ||= 1;
  my $ori = $strand * $hstrand;

  throw("No features in the array to parse") if(scalar(@f) == 0);

  my $prev1; # where last feature q part ended
  my $prev2; # where last feature s part ended

  my $string;

  # Use strandedness info of query and hit to make sure both sets of 
  # start and end  coordinates are oriented the right way around.
  my $f1start;
  my $f1end;
  my $f2end;
  my $f2start;

  if ($strand == 1) {
    $f1start = $f[0]->start;
    $f1end = $f[-1]->end;
  } else {
    $f1start = $f[-1]->start;
    $f1end = $f[0]->end;
  }

  if ($hstrand == 1) {
    $f2start = $f[0]->hstart;
    $f2end = $f[-1]->hend;
  } else {
    $f2start = $f[-1]->hstart;
    $f2end = $f[0]->hend;
  }

  #
  # Loop through each portion of alignment and construct cigar string
  #

  foreach my $f (@f) {
    #
    # Sanity checks
    #

    if (!$f->isa("Bio::EnsEMBL::FeaturePair")) {
      throw("Array element [$f] is not a Bio::EnsEMBL::FeaturePair");
    }
    if( defined($f->hstrand()) && $f->hstrand() != $hstrand ) {
      throw("Inconsistent hstrands in feature array");
    }
    if( defined($f->strand()) && ($f->strand != $strand)) {
      throw("Inconsistent strands in feature array");
    }
    if ( defined($name) && $name ne $f->slice->name()) {
      throw("Inconsistent names in feature array [$name - ".
            $f->slice->name()."]");
    }
    if ( defined($hname) && $hname ne $f->hseqname) {
      throw("Inconsistent hit names in feature array [$hname - ".
            $f->hseqname . "]");
    }
    if ( defined($score) && $score ne $f->score) {
      throw("Inconsisent scores in feature array [$score - " .
            $f->score . "]");
    }
    if (defined($f->percent_id) && $percent ne $f->percent_id) {
      throw("Inconsistent pids in feature array [$percent - " .
            $f->percent_id . "]");
    }
    if(defined($pvalue) && $pvalue != $f->p_value()) {
      throw("Inconsistant p_values in feature arraw [$pvalue " .
            $f->p_value() . "]");
    }
    if($seqname && $seqname ne $f->seqname){
      throw("Inconsistent seqname in feature array [$seqname - ".
            $f->seqname . "]");
    }
    my $start1 = $f->start;      #source sequence alignment start
    my $start2 = $f->hstart();   #hit sequence alignment start

    #
    # More sanity checking
    #
    if (defined($prev1)) {
      if ( $strand == 1 ) {
        if ($f->start < $prev1) {
          throw("Inconsistent coords in feature array (forward strand).\n" .
		       "Start [".$f->start()."] in current feature should be greater " .
           "than previous feature end [$prev1].");
        }
      } else {
        if ($f->end > $prev1) {
          throw("Inconsistent coords in feature array (reverse strand).\n" .
                "End [".$f->end() ."] should be less than previous feature " .
                "start [$prev1].");
        }
      }
    }

    my $length = ($f->end - $f->start + 1);    #length of source seq alignment
    my $hlength = ($f->hend - $f->hstart + 1); #length of hit seq alignment

    # using multiplication to avoid rounding errors, hence the
    # switch from query to hit for the ratios

    #
    # Yet more sanity checking
    #
    if($query_unit > $hit_unit){
      # I am going to make the assumption here that this situation will 
      # only occur with DnaPepAlignFeatures, this may not be true
      my $query_p_length = sprintf "%.0f", ($length/$query_unit);
      my $hit_p_length = sprintf "%.0f", ($hlength * $hit_unit);
      if( $query_p_length != $hit_p_length) {
        throw( "Feature lengths not comparable Lengths:" .$length .
               " " . $hlength . " Ratios:" . $query_unit . " " .
               $hit_unit );
      }
    } else{
      my $query_d_length = sprintf "%.0f", ($length*$hit_unit);
      my $hit_d_length = sprintf "%.0f", ($hlength * $query_unit);
      if( $length * $hit_unit != $hlength * $query_unit ) {
        throw( "Feature lengths not comparable Lengths:" . $length .
               " " . $hlength . " Ratios:" . $query_unit . " " .
               $hit_unit );
      }
    }

    my $hlengthfactor = ($query_unit/$hit_unit);

    #
    # Check to see if there is an I type (insertion) gap:
    #   If there is a space between the end of the last source sequence 
    #   alignment and the start of this one, then this is an insertion
    #

    my $insertion_flag = 0;
    if( $strand == 1 ) {
      if( ( defined $prev1 ) && ( $f->start > $prev1 + 1  )) {

        #there is an insertion
        $insertion_flag = 1;
        my $gap = $f->start - $prev1 - 1;
        if( $gap == 1 ) {
          $gap = ""; # no need for a number if gap length is 1
        }
        $string .= "$gap"."I";

      }

      #shift our position in the source seq alignment
      $prev1 = $f->end();
    } else {

      if(( defined $prev1 ) && ($f->end + 1 < $prev1 )) {

        #there is an insertion
        $insertion_flag = 1;
        my $gap = $prev1 - $f->end() - 1;
        if( $gap == 1 ) {
          $gap = ""; # no need for a number if gap length is 1
        }
        $string .= "$gap"."I";
      }

      #shift our position in the source seq alignment
      $prev1 = $f->start();
    }

    #
    # Check to see if there is a D type (deletion) gap
    #   There is a deletion gap if there is a space between the end of the
    #   last portion of the hit sequence alignment and this one
    #
    if( $hstrand == 1 ) {
      if((  defined $prev2 ) && ( $f->hstart() > $prev2 + 1 )) {

        #there is a deletion
        my $gap = $f->hstart - $prev2 - 1;
        my $gap2 = int( $gap * $hlengthfactor + 0.5 );
	
        if( $gap2 == 1 ) {
          $gap2 = "";  # no need for a number if gap length is 1
        }
        $string .= "$gap2"."D";

        #sanity check,  Should not be an insertion and deletion
        if($insertion_flag) {
          if ($message_only_once) {
            warning("Should not be an deletion and insertion on the " .
                    "same alignment region. cigar_line=$string\n");
            $message_only_once = 0;
          }
        }
      }
      #shift our position in the hit seq alignment
      $prev2 = $f->hend();

     } else {
      if( ( defined $prev2 ) && ( $f->hend() + 1 < $prev2 )) {

        #there is a deletion
        my $gap = $prev2 - $f->hend - 1;
        my $gap2 = int( $gap * $hlengthfactor + 0.5 );
	
        if( $gap2 == 1 ) {
          $gap2 = "";  # no need for a number if gap length is 1
        }
        $string .= "$gap2"."D";

        #sanity check,  Should not be an insertion and deletion
        if($insertion_flag) {
          if ($message_only_once) {
            warning("Should not be an deletion and insertion on the " .
                    "same alignment region. prev2 = $prev2; f->hend() = " .
                    $f->hend() . "; cigar_line = $string;\n");
            $message_only_once = 0;
          }
        }
      }
      #shift our position in the hit seq alignment
      $prev2 = $f->hstart();
    }

    my $matchlength = $f->end() - $f->start() + 1;
    if( $matchlength == 1 ) {
      $matchlength = "";
    }
    $string .= $matchlength."M";
  }

  $self->{'start'}      = $f1start;
  $self->{'end'}        = $f1end;
  $self->{'seqname'}    = $seqname;
  $self->{'strand'}     = $strand;
  $self->{'score'}      = $score;
  $self->{'percent_id'} = $percent;
  $self->{'analysis'}   = $analysis;
  $self->{'slice'}      = $slice;
  $self->{'hslice'}     = $hslice;
  $self->{'hstart'}     = $f2start;
  $self->{'hend'}       = $f2end;
  $self->{'hstrand'}    = $hstrand;
  $self->{'hseqname'}   = $hname;
  $self->{'cigar_string'} = $string;
  $self->{'p_value'}      = $pvalue;
  $self->{'external_db_id'} = $external_db_id; 
  $self->{'hcoverage'}    = $hcoverage; 
  $self->{'group_id'}     = $group_id;
  $self->{'level_id'}     = $level_id;
}






=head2 _hit_unit

  Args       : none
  Description: abstract method, overwrite with something that returns
               one or three
  Returntype : int 1,3
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut

sub _hit_unit {
  my $self = shift;
  throw( "Abstract method call!" );
}



=head2 _query_unit

  Args       : none
  Description: abstract method, overwrite with something that returns
               one or three
  Returntype : int 1,3
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut

sub _query_unit {
  my $self = shift;
  throw( "Abstract method call!" );
}




1;