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revision 1.11, Mon Jun 11 17:27:54 2007 UTC revision 1.12, Thu Dec 6 13:59:34 2007 UTC
# Line 73  Line 73 
73    
74  =head3 new  =head3 new
75    
76  C<< my $loc = FullLocation->new($fig, $genomeID, $locList, $translation); >>      my $loc = FullLocation->new($fig, $genomeID, $locList, $translation);
77    
78  Construct a new FullLocation object.  Construct a new FullLocation object.
79    
# Line 146  Line 146 
146    
147  =head3 Locs  =head3 Locs
148    
149  C<< my $locObject = $loc->Locs->[$idx]; >>      my $locObject = $loc->Locs->[$idx];
150    
151  Return a reference to the array of location objects.  Return a reference to the array of location objects.
152    
# Line 158  Line 158 
158    
159  =head3 Contig  =head3 Contig
160    
161  C<< my $contigID = $loc->Contig(); >>      my $contigID = $loc->Contig();
162    
163  Return the ID of the base contig for this location list. The base contig is the  Return the ID of the base contig for this location list. The base contig is the
164  contig used for most of the locations in the list.  contig used for most of the locations in the list.
# Line 174  Line 174 
174    
175  =head3 Dir  =head3 Dir
176    
177  C<< my $dir = $loc->Dir; >>      my $dir = $loc->Dir;
178    
179  Return the base direction for this location list. The base direction is the direction  Return the base direction for this location list. The base direction is the direction
180  (C<+> or C<->) used for most of the locations in the list.  (C<+> or C<->) used for most of the locations in the list.
# Line 190  Line 190 
190    
191  =head3 NextPoint  =head3 NextPoint
192    
193  C<< my $offset = $loc->NextPoint; >>      my $offset = $loc->NextPoint;
194    
195  Return the location immediately after the end point of the last location.  Return the location immediately after the end point of the last location.
196    
# Line 207  Line 207 
207    
208  =head3 PrevPoint  =head3 PrevPoint
209    
210  C<< my $offset = $loc->PrevPoint; >>      my $offset = $loc->PrevPoint;
211    
212  Return the location immediately before the begin point of the first location.  Return the location immediately before the begin point of the first location.
213    
# Line 224  Line 224 
224    
225  =head3 Begin  =head3 Begin
226    
227  C<< my $offset = $loc->Begin; >>      my $offset = $loc->Begin;
228    
229  Return the begin point of the first location.  Return the begin point of the first location.
230    
# Line 241  Line 241 
241    
242  =head3 EndPoint  =head3 EndPoint
243    
244  C<< my $offset = $loc->EndPoint; >>      my $offset = $loc->EndPoint;
245    
246  Return the end point of the last location.  Return the end point of the last location.
247    
# Line 258  Line 258 
258    
259  =head3 SeedString  =head3 SeedString
260    
261  C<< my $string = $loc->SeedString; >>      my $string = $loc->SeedString;
262    
263  Return a comma-delimited list of this object's basic locations, in SEED format.  Return a comma-delimited list of this object's basic locations, in SEED format.
264    
# Line 275  Line 275 
275    
276  =head3 Adjusted  =head3 Adjusted
277    
278  C<< my $offset = $loc->Adjusted($oldOffset, $distance); >>      my $offset = $loc->Adjusted($oldOffset, $distance);
279    
280  Adjust the specified offset by the specified distance in the direction of this  Adjust the specified offset by the specified distance in the direction of this
281  location. If this is a forward location, the distance is added; if it is a backward  location. If this is a forward location, the distance is added; if it is a backward
# Line 309  Line 309 
309    
310  =head3 GetBest  =head3 GetBest
311    
312  C<< my $bestKey = FullLocation::GetBest(%hash); >>      my $bestKey = FullLocation::GetBest(%hash);
313    
314  Return the key of the hash element with the highest positive numeric value.  Return the key of the hash element with the highest positive numeric value.
315    
# Line 347  Line 347 
347    
348  =head3 DNA  =head3 DNA
349    
350  C<< my $dnaString = $loc->DNA; >>      my $dnaString = $loc->DNA;
351    
352  Return the complete DNA string for this location.  Return the complete DNA string for this location.
353    
# Line 365  Line 365 
365    
366  =head3 Codon  =head3 Codon
367    
368  C<< my $codon = $loc->Codon($point); >>      my $codon = $loc->Codon($point);
369    
370  Return the DNA codon at the specified point on this location's contig in this  Return the DNA codon at the specified point on this location's contig in this
371  location's direction.  location's direction.
# Line 397  Line 397 
397    
398  =head3 Translation  =head3 Translation
399    
400  C<< my $proteinString = $loc->Translation($code, $fixStart); >>      my $proteinString = $loc->Translation($code, $fixStart);
401    
402  Return the protein translation of this location's DNA. The first time a  Return the protein translation of this location's DNA. The first time a
403  translation is requested, it will be cached in the object, and returned  translation is requested, it will be cached in the object, and returned
# Line 450  Line 450 
450    
451  =head3 Constrain  =head3 Constrain
452    
453  C<< my $constrainedPoint = $loc->Constrain($point); >>      my $constrainedPoint = $loc->Constrain($point);
454    
455  Change a point location value so that it fits inside the base contig. If the point  Change a point location value so that it fits inside the base contig. If the point
456  location is less than 1, it will be set to 1. If it's greater than the length of  location is less than 1, it will be set to 1. If it's greater than the length of
# Line 496  Line 496 
496    
497  =head3 Search  =head3 Search
498    
499  C<< my $newPoint = $loc->Search(\@pattern, $point, $dir, $limit); >>      my $newPoint = $loc->Search(\@pattern, $point, $dir, $limit);
500    
501  Search for a DNA codons in the specified direction from the specified  Search for a DNA codons in the specified direction from the specified
502  point. The search is limited to the specified number of positions.  point. The search is limited to the specified number of positions.
# Line 568  Line 568 
568    
569  =head3 ExtremeCodon  =head3 ExtremeCodon
570    
571  C<< my $loc->ExtremeCodon($dir); >>      my $loc->ExtremeCodon($dir);
572    
573  Return the most extreme codon in the specified direction. This is not always the most  Return the most extreme codon in the specified direction. This is not always the most
574  extreme location, since the distance to the appropriate edge of the location must be  extreme location, since the distance to the appropriate edge of the location must be
# Line 630  Line 630 
630    
631  =head3 Extend  =head3 Extend
632    
633  C<< my  = $loc->Extend($newBegin, $newEnd, $trimFlag); >>      my  = $loc->Extend($newBegin, $newEnd, $trimFlag);
634    
635  Extend this gene to a new begin point and a new end point. If a translation exists,  Extend this gene to a new begin point and a new end point. If a translation exists,
636  it will be updated to match the new locations. The I<$trimFlag> indicates whether  it will be updated to match the new locations. The I<$trimFlag> indicates whether

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