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revision 1.8, Sat Nov 5 22:59:44 2005 UTC revision 1.10, Mon Dec 5 18:56:37 2005 UTC
# Line 1  Line 1 
1  # -*- perl -*-  # -*- perl -*-
2    #
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    #
18    
19    
20  use FIG;  use FIG;
21  my $fig = new FIG;  my $fig = new FIG;
# Line 82  Line 99 
99    
100      for ($i=0; $i < @$x; ++$i)      for ($i=0; $i < @$x; ++$i)
101      {      {
102          unless (defined($overlaps{$x->[$i]->[FID]}))  { $overlaps{$x->[$i]->[FID]} = 0; }          unless (defined($overlap_boundary{$x->[$i]->[FID]}))
103            {
104                $overlap_boundary{$x->[$i]->[FID]} = $x->[$i]->[START];
105            }
106    
107          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)
108          {          {
# Line 90  Line 110 
110    
111              if ($x->[$j]->[STRAND] eq '+')              if ($x->[$j]->[STRAND] eq '+')
112              {              {
113                  $overlaps{$x->[$j]->[FID]} = &FIG::max( $overlap, $overlaps{$x->[$j]->[FID]} );                  $overlap_boundary{$x->[$j]->[FID]}
114                       = &FIG::max( $overlap, $overlap_boundary{$x->[$j]->[FID]} );
115              }              }
116    
117              if ($x->[$i]->[STRAND] eq '-')              if ($x->[$i]->[STRAND] eq '-')
118              {              {
119                  $overlaps{$x->[$i]->[FID]} = &FIG::max( $overlap, $overlaps{$x->[$i]->[FID]} );                  $overlap_boundary{$x->[$i]->[FID]} = &FIG::max( $overlap, $overlap_boundary{$x->[$i]->[FID]} );
120              }              }
121          }          }
122      }      }
# Line 208  Line 229 
229                  print "SEQ=$orf\n";                  print "SEQ=$orf\n";
230                  print "PREFIX=$pre_orf\n";                  print "PREFIX=$pre_orf\n";
231                  print "OLD_START_POS=", $len_pre_peg-$i-2, "\n";                  print "OLD_START_POS=", $len_pre_peg-$i-2, "\n";
232                  print "OVERLAP=$overlaps{$peg}\n";                  print "OVERLAP=$overlap_boundary{$peg}\n";
233                  print "///\n";                  print "///\n";
234                  $found = 1;                  $found = 1;
235              }              }

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