Functions
public void	found_match ()

public void	found_nomatch ()

Function Documentation

◆ found_match()

public void found_match ( )

  Arg[1]      : String $R_chr - reference toplevel seq_region name 
  Arg[2]      : String $A_chr - alternative toplevel seq_region name 
  Arg[3]      : Hashref $match - datastructure to store aligned blocks
  Arg[4]      : Hashref $nomatch - datastructure to store non-aligned blocks
  Arg[5]      : Bio::EnsEMBL::ProjectionSegment $A_seg - current alternative
                segment
  Arg[6]      : Bio::EnsEMBL::ProjectionSegment $last_A_seg - last alternative
                segment
  Arg[7]      : Bio::EnsEMBL::ProjectionSegment $R_seg - current reference
                segment
  Arg[8]      : Bio::EnsEMBL::ProjectionSegment $last_R_seg - last reference
                segment
  Arg[9]      : Boolean $match_flag - flag indicating if last clone was a match
  Arg[10]     : Int $i - reference clone count
  Arg[11]     : Int $j - alternative clone count
  Description : This function is called when two clones match (i.e. have the
                same name.version in both assemblies). Depending on the state
                of the last clone (match or nomatch), it extends aligned blocks
                or finishes the non-aligned block and creates a new aligned
                block.
  Return type : none
  Exceptions  : none
  Caller      : internal

Code:

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sub found_match {
  my ($R_chr, $A_chr, $match, $nomatch, $A_seg, $last_A_seg, $R_seg, $last_R_seg, $match_flag, $i, $j) = @_;
 
  # last clone was a match
  if ($match_flag) {
 
    # adjust align block end
    if ($match->{$R_chr}) {
 
      my $c = scalar(@{ $match->{$R_chr} }) - 1;
 
      # if the gaps between this clone and the last are different, start
      # a new block
      if (($A_seg->from_start - $match->{$R_chr}->[$c]->[1]) !=
          ($R_seg->from_start - $match->{$R_chr}->[$c]->[4])) {
 
        $support->log("Gap size mismatch at A:$A_chr:".$match->{$R_chr}->[$c]->[1].'-'.$A_seg->from_start.", R:$R_chr:".$match->{$R_chr}->[$c]->[4].'-'.$R_seg->from_start."\n", 2);
 
        # finish the last align block
        $match->{$R_chr}->[$c]->[1] = $last_A_seg->from_end;
        $match->{$R_chr}->[$c]->[2] = $j - $match->{$R_chr}->[$c]->[2];
        $match->{$R_chr}->[$c]->[4] = $last_R_seg->from_end;
        $match->{$R_chr}->[$c]->[5] = $i - $match->{$R_chr}->[$c]->[5];
 
        # start a new align block
        push @{ $match->{$R_chr} }, [
          $A_seg->from_start,
          $A_seg->from_end,
          $j,
          $R_seg->from_start,
          $R_seg->from_end,
          $i,
          $A_chr,
        ];
 
      # adjust align block end
      } else {
        $match->{$R_chr}->[$c]->[1] = $A_seg->from_end;
        $match->{$R_chr}->[$c]->[4] = $R_seg->from_end;
      }
    }
 
  # last clone was a non-match
  } else {
    
    # start a new align block
    push @{ $match->{$R_chr} }, [
      $A_seg->from_start,
      $A_seg->from_end,
      $j,
      $R_seg->from_start,
      $R_seg->from_end,
      $i,
      $A_chr,
    ];
 
    # finish the last non-align block
    if ($nomatch->{$R_chr} and $last_A_seg) {
      my $c = scalar(@{ $nomatch->{$R_chr} }) - 1;
      $nomatch->{$R_chr}->[$c]->[1] = $last_A_seg->from_end;
      $nomatch->{$R_chr}->[$c]->[2] = $j - $nomatch->{$R_chr}->[$c]->[2];
      $nomatch->{$R_chr}->[$c]->[4] = $last_R_seg->from_end;
      $nomatch->{$R_chr}->[$c]->[5] = $i - $nomatch->{$R_chr}->[$c]->[5];
    }
  }
}

◆ found_nomatch()

public void found_nomatch ( )

  Arg[1]      : String $R_chr - reference toplevel seq_region name 
  Arg[2]      : String $A_chr - alternative toplevel seq_region name 
  Arg[3]      : Hashref $match - datastructure to store aligned blocks
  Arg[4]      : Hashref $nomatch - datastructure to store non-aligned blocks
  Arg[5]      : Bio::EnsEMBL::ProjectionSegment $A_seg - current alternative
                segment
  Arg[6]      : Bio::EnsEMBL::ProjectionSegment $last_A_seg - last alternative
                segment
  Arg[7]      : Bio::EnsEMBL::ProjectionSegment $R_seg - current reference 
                segment
  Arg[8]      : Bio::EnsEMBL::ProjectionSegment $last_R_seg - last reference
                segment
  Arg[9]      : Boolean $match_flag - flag indicating if last clone was a match
  Arg[10]     : Int $i - reference clone count
  Arg[11]     : Int $j - alternative clone count
  Description : This function is called when two clones don't match (either
                different name.version or length mismatch in the two
                assemblies). Depending on the state of the last clone (nomatch
                or match), it extends non-aligned blocks or finishes the
                aligned block and creates a new non-aligned block.
  Return type : none
  Exceptions  : none
  Caller      : internal

Code:

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Functions

Function Documentation

◆ found_match()

◆ found_nomatch()