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revision 1.8, Sat Nov 5 22:59:44 2005 UTC revision 1.9, Tue Nov 22 14:57:50 2005 UTC
# Line 82  Line 82 
82    
83      for ($i=0; $i < @$x; ++$i)      for ($i=0; $i < @$x; ++$i)
84      {      {
85          unless (defined($overlaps{$x->[$i]->[FID]}))  { $overlaps{$x->[$i]->[FID]} = 0; }          unless (defined($overlap_boundary{$x->[$i]->[FID]}))
86            {
87                $overlap_boundary{$x->[$i]->[FID]} = $x->[$i]->[START];
88            }
89    
90          for ($j=$i+1; (($j < @$x) && ($overlap = &entries_overlap($x, $i, $j))); ++$j)          for ($j=$i+1; (($j < @$x) && ($overlap = &entries_overlap($x, $i, $j))); ++$j)
91          {          {
# Line 90  Line 93 
93    
94              if ($x->[$j]->[STRAND] eq '+')              if ($x->[$j]->[STRAND] eq '+')
95              {              {
96                  $overlaps{$x->[$j]->[FID]} = &FIG::max( $overlap, $overlaps{$x->[$j]->[FID]} );                  $overlap_boundary{$x->[$j]->[FID]}
97                       = &FIG::max( $overlap, $overlap_boundary{$x->[$j]->[FID]} );
98              }              }
99    
100              if ($x->[$i]->[STRAND] eq '-')              if ($x->[$i]->[STRAND] eq '-')
101              {              {
102                  $overlaps{$x->[$i]->[FID]} = &FIG::max( $overlap, $overlaps{$x->[$i]->[FID]} );                  $overlap_boundary{$x->[$i]->[FID]} = &FIG::max( $overlap, $overlap_boundary{$x->[$i]->[FID]} );
103              }              }
104          }          }
105      }      }
# Line 208  Line 212 
212                  print "SEQ=$orf\n";                  print "SEQ=$orf\n";
213                  print "PREFIX=$pre_orf\n";                  print "PREFIX=$pre_orf\n";
214                  print "OLD_START_POS=", $len_pre_peg-$i-2, "\n";                  print "OLD_START_POS=", $len_pre_peg-$i-2, "\n";
215                  print "OVERLAP=$overlaps{$peg}\n";                  print "OVERLAP=$overlap_boundary{$peg}\n";
216                  print "///\n";                  print "///\n";
217                  $found = 1;                  $found = 1;
218              }              }

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