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untabify, remove extra spacing

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commit feece49067eda9185a055b012e0938cd05edbb2a 1 parent 39585f9
authored March 21, 2012
31  lib/Bio/Coordinate/Chain.pm
... ...
@@ -1,7 +1,7 @@
1 1
 #
2 2
 # bioperl module for Bio::Coordinate::Chain
3 3
 #
4  
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
  4
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
5 5
 #
6 6
 # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
7 7
 #
@@ -64,15 +64,15 @@ Bioperl mailing lists  Your participation is much appreciated.
64 64
   bioperl-l@bioperl.org                  - General discussion
65 65
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
66 66
 
67  
-=head2 Support 
  67
+=head2 Support
68 68
 
69 69
 Please direct usage questions or support issues to the mailing list:
70 70
 
71 71
 I<bioperl-l@bioperl.org>
72 72
 
73  
-rather than to the module maintainer directly. Many experienced and 
74  
-reponsive experts will be able look at the problem and quickly 
75  
-address it. Please include a thorough description of the problem 
  73
+rather than to the module maintainer directly. Many experienced and
  74
+reponsive experts will be able look at the problem and quickly
  75
+address it. Please include a thorough description of the problem
76 76
 with code and data examples if at all possible.
77 77
 
78 78
 =head2 Reporting Bugs
@@ -126,19 +126,19 @@ sub map {
126 126
     my ($self,$value) = @_;
127 127
 
128 128
     $self->throw("Need to pass me a value.")
129  
-	unless defined $value;
  129
+        unless defined $value;
130 130
     $self->throw("I need a Bio::Location, not [$value]")
131  
-	unless $value->isa('Bio::LocationI');
  131
+        unless $value->isa('Bio::LocationI');
132 132
     $self->throw("No coordinate mappers!")
133  
-	unless $self->each_mapper;
  133
+        unless $self->each_mapper;
134 134
 
135 135
     my $res = Bio::Coordinate::Result->new();
136 136
 
137 137
     foreach my $mapper ($self->each_mapper) {
138 138
 
139  
-	my $res = $mapper->map($value);
140  
-	return unless $res->each_match;
141  
-	$value = $res->match;
  139
+        my $res = $mapper->map($value);
  140
+        return unless $res->each_match;
  141
+        $value = $res->match;
142 142
     }
143 143
 
144 144
    return $value;
@@ -155,7 +155,7 @@ sub map {
155 155
  Usage   : $obj->add_mapper($mapper)
156 156
  Function: Pushes one Bio::Coodinate::MapperI into the list of mappers.
157 157
            Sets _is_sorted() to false.
158  
- Example : 
  158
+ Example :
159 159
  Returns : 1 when succeeds, 0 for failure.
160 160
  Args    : mapper object
161 161
 
@@ -166,7 +166,7 @@ sub map {
166 166
  Title   : mappers
167 167
  Usage   : $obj->mappers();
168 168
  Function: Returns or sets a list of mappers.
169  
- Example : 
  169
+ Example :
170 170
  Returns : array of mappers
171 171
  Args    : array of mappers
172 172
 
@@ -177,7 +177,7 @@ sub map {
177 177
  Title   : each_mapper
178 178
  Usage   : $obj->each_mapper();
179 179
  Function: Returns a list of mappers.
180  
- Example : 
  180
+ Example :
181 181
  Returns : array of mappers
182 182
  Args    : none
183 183
 
@@ -190,7 +190,7 @@ sub map {
190 190
  Function: Swap the direction of mapping;input <-> output
191 191
  Example :
192 192
  Returns : 1
193  
- Args    : 
  193
+ Args    :
194 194
 
195 195
 =cut
196 196
 
@@ -214,4 +214,3 @@ sub sort{
214 214
 }
215 215
 
216 216
 1;
217  
-
68  lib/Bio/Coordinate/Collection.pm
@@ -119,13 +119,13 @@ sub new {
119 119
     $self->{'_mappers'} = [];
120 120
 
121 121
     my($in, $out, $strict, $mappers, $return_match) =
122  
-	$self->_rearrange([qw(IN
  122
+        $self->_rearrange([qw(IN
123 123
                               OUT
124 124
                               STRICT
125 125
                               MAPPERS
126 126
                               RETURN_MATCH
127  
-			     )],
128  
-			 @args);
  127
+                             )],
  128
+                         @args);
129 129
 
130 130
     $in  && $self->in($in);
131 131
     $out  && $self->out($out);
@@ -155,8 +155,8 @@ sub add_mapper {
155 155
 
156 156
   # test pair range lengths
157 157
   $self->warn("Coordinates in pair [". $value . ":" .
158  
-	      $value->in->seq_id . "/". $value->out->seq_id .
159  
-	      "] are not right.")
  158
+              $value->in->seq_id . "/". $value->out->seq_id .
  159
+              "] are not right.")
160 160
       unless $value->test;
161 161
 
162 162
   $self->_is_sorted(0);
@@ -175,18 +175,18 @@ sub add_mapper {
175 175
 =cut
176 176
 
177 177
 sub mappers{
178  
-	my ($self,@args) = @_;
179  
-
180  
-	if (@args) {
181  
-		if (@args == 1 && ref $args[0] eq 'ARRAY') {
182  
-			@args = @{$args[0]};
183  
-		}
184  
-		$self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
185  
-			unless defined $args[0] && $args[0]->isa('Bio::Coordinate::MapperI');
186  
-		push(@{$self->{'_mappers'}}, @args);
187  
-	}
188  
-
189  
-	return @{$self->{'_mappers'}};
  178
+        my ($self,@args) = @_;
  179
+
  180
+        if (@args) {
  181
+                if (@args == 1 && ref $args[0] eq 'ARRAY') {
  182
+                        @args = @{$args[0]};
  183
+                }
  184
+                $self->throw("Is not a Bio::Coordinate::MapperI but a [$self]")
  185
+                        unless defined $args[0] && $args[0]->isa('Bio::Coordinate::MapperI');
  186
+                push(@{$self->{'_mappers'}}, @args);
  187
+        }
  188
+
  189
+        return @{$self->{'_mappers'}};
190 190
 }
191 191
 
192 192
 
@@ -266,10 +266,10 @@ sub test {
266 266
 
267 267
    foreach my $mapper ($self->each_mapper) {
268 268
        unless( $mapper->test ) {
269  
-	   $self->warn("Coordinates in pair [". $mapper . ":" .
270  
-		       $mapper->in->seq_id . "/". $mapper->out->seq_id .
271  
-		       "] are not right.");
272  
-	   $res = 0;
  269
+           $self->warn("Coordinates in pair [". $mapper . ":" .
  270
+                       $mapper->in->seq_id . "/". $mapper->out->seq_id .
  271
+                       "] are not right.");
  272
+           $res = 0;
273 273
        }
274 274
    }
275 275
    $res;
@@ -343,20 +343,20 @@ IDMATCH: {
343 343
        # bail out now we if are forcing the use of an ID
344 344
        # and it is not in this collection
345 345
        last IDMATCH if defined $value->seq_id &&
346  
-	   ! $self->{'_in_ids'}->{$value->seq_id};
  346
+           ! $self->{'_in_ids'}->{$value->seq_id};
347 347
 
348 348
        foreach my $pair ($self->each_mapper) {
349 349
 
350  
-	   # if we are limiting input to a certain ID
351  
-	   next if defined $value->seq_id && $value->seq_id ne $pair->in->seq_id;
  350
+           # if we are limiting input to a certain ID
  351
+           next if defined $value->seq_id && $value->seq_id ne $pair->in->seq_id;
352 352
 
353  
-	   # if we haven't even reached the start, move on
354  
-	   next if $pair->in->end < $value->start;
355  
-	   # if we have over run, break
356  
-	   last if $pair->in->start > $value->end;
  353
+           # if we haven't even reached the start, move on
  354
+           next if $pair->in->end < $value->start;
  355
+           # if we have over run, break
  356
+           last if $pair->in->start > $value->end;
357 357
 
358  
-	   my $subres = $pair->map($value);
359  
-	   $result->add_result($subres);
  358
+           my $subres = $pair->map($value);
  359
+           $result->add_result($subres);
360 360
        }
361 361
    }
362 362
 
@@ -364,10 +364,10 @@ IDMATCH: {
364 364
    unless ($result->each_Location) {
365 365
        #build one gap;
366 366
        my $gap = Bio::Location::Simple->new(-start => $value->start,
367  
-					    -end => $value->end,
368  
-					    -strand => $value->strand,
369  
-					    -location_type => $value->location_type
370  
-					   );
  367
+                                            -end => $value->end,
  368
+                                            -strand => $value->strand,
  369
+                                            -location_type => $value->location_type
  370
+                                           );
371 371
        $gap->seq_id($value->seq_id) if defined $value->seq_id;
372 372
        bless $gap, 'Bio::Coordinate::Result::Gap';
373 373
        $result->seq_id($value->seq_id) if defined $value->seq_id;
34  lib/Bio/Coordinate/ExtrapolatingPair.pm
... ...
@@ -1,7 +1,7 @@
1 1
 #
2 2
 # bioperl module for Bio::Coordinate::ExtrapolatingPair
3 3
 #
4  
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
  4
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
5 5
 #
6 6
 # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
7 7
 #
@@ -22,18 +22,18 @@ Bio::Coordinate::ExtrapolatingPair - Continuous match between two coordinate set
22 22
   use Bio::Coordinate::ExtrapolatingPair;
23 23
 
24 24
 
25  
-  $match1 = Bio::Location::Simple->new 
  25
+  $match1 = Bio::Location::Simple->new
26 26
     (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
27 27
   $match2 = Bio::Location::Simple->new
28 28
     (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
29 29
 
30 30
   $pair = Bio::Coordinate::ExtrapolatingPair->
31 31
     new(-in => $match1,
32  
-    	-out => $match2,
33  
-    	-strict => 1
  32
+        -out => $match2,
  33
+        -strict => 1
34 34
        );
35 35
 
36  
-  $pos = Bio::Location::Simple->new 
  36
+  $pos = Bio::Location::Simple->new
37 37
       (-start => 40, -end => 60, -strand=> 1 );
38 38
   $res = $pair->map($pos);
39 39
   $res->start eq 20;
@@ -67,15 +67,15 @@ Bioperl mailing lists  Your participation is much appreciated.
67 67
   bioperl-l@bioperl.org                  - General discussion
68 68
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
69 69
 
70  
-=head2 Support 
  70
+=head2 Support
71 71
 
72 72
 Please direct usage questions or support issues to the mailing list:
73 73
 
74 74
 I<bioperl-l@bioperl.org>
75 75
 
76  
-rather than to the module maintainer directly. Many experienced and 
77  
-reponsive experts will be able look at the problem and quickly 
78  
-address it. Please include a thorough description of the problem 
  76
+rather than to the module maintainer directly. Many experienced and
  77
+reponsive experts will be able look at the problem and quickly
  78
+address it. Please include a thorough description of the problem
79 79
 with code and data examples if at all possible.
80 80
 
81 81
 =head2 Reporting Bugs
@@ -115,9 +115,9 @@ sub new {
115 115
     my $self = $class->SUPER::new(@args);
116 116
 
117 117
     my($strict) =
118  
-	$self->_rearrange([qw(STRICT
119  
-			     )],
120  
-			 @args);
  118
+        $self->_rearrange([qw(STRICT
  119
+                             )],
  120
+                         @args);
121 121
 
122 122
     $strict  && $self->strict($strict);
123 123
     return $self;
@@ -230,11 +230,11 @@ sub _map {
230 230
 
231 231
    my $match = Bio::Location::Simple->
232 232
        new(-start => $start,
233  
-	   -end => $end,
234  
-	   -strand => $self->strand,
235  
-	   -seq_id => $self->out->seq_id,
236  
-	   -location_type => $value->location_type
237  
-	  );
  233
+           -end => $end,
  234
+           -strand => $self->strand,
  235
+           -seq_id => $self->out->seq_id,
  236
+           -location_type => $value->location_type
  237
+          );
238 238
    $match->strand($match->strand * $value->strand) if $value->strand;
239 239
    bless $match, 'Bio::Coordinate::Result::Match';
240 240
 
543  lib/Bio/Coordinate/GeneMapper.pm
... ...
@@ -1,7 +1,7 @@
1 1
 #
2 2
 # bioperl module for Bio::Coordinate::GeneMapper
3 3
 #
4  
-# Please direct questions and support issues to <bioperl-l@bioperl.org> 
  4
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
5 5
 #
6 6
 # Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
7 7
 #
@@ -118,15 +118,15 @@ Bioperl mailing lists  Your participation is much appreciated.
118 118
   bioperl-l@bioperl.org                  - General discussion
119 119
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
120 120
 
121  
-=head2 Support 
  121
+=head2 Support
122 122
 
123 123
 Please direct usage questions or support issues to the mailing list:
124 124
 
125 125
 I<bioperl-l@bioperl.org>
126 126
 
127  
-rather than to the module maintainer directly. Many experienced and 
128  
-reponsive experts will be able look at the problem and quickly 
129  
-address it. Please include a thorough description of the problem 
  127
+rather than to the module maintainer directly. Many experienced and
  128
+reponsive experts will be able look at the problem and quickly
  129
+address it. Please include a thorough description of the problem
130 130
 with code and data examples if at all possible.
131 131
 
132 132
 =head2 Reporting Bugs
@@ -170,45 +170,45 @@ use base qw(Bio::Root::Root Bio::Coordinate::MapperI);
170 170
 # first set internal values for all translation tables
171 171
 
172 172
 %COORDINATE_SYSTEMS = (
173  
-		       peptide          => 10,
174  
-		       propeptide       => 9,
175  
-		       frame            => 8,
176  
-		       cds              => 7,
177  
-		       negative_intron  => 6,
178  
-		       intron           => 5,
179  
-		       exon             => 4,
180  
-		       inex             => 3,
181  
-		       gene             => 2,
182  
-		       chr              => 1
183  
-		      );
  173
+                       peptide          => 10,
  174
+                       propeptide       => 9,
  175
+                       frame            => 8,
  176
+                       cds              => 7,
  177
+                       negative_intron  => 6,
  178
+                       intron           => 5,
  179
+                       exon             => 4,
  180
+                       inex             => 3,
  181
+                       gene             => 2,
  182
+                       chr              => 1
  183
+                      );
184 184
 
185 185
 %COORDINATE_INTS = (
186  
-		    10 => 'peptide',
187  
-		    9 => 'propeptide',
188  
-		    8 => 'frame',
189  
-		    7 => 'cds',
190  
-		    6 => 'negative_intron',
191  
-		    5 => 'intron',
192  
-		    4 => 'exon',
193  
-		    3 => 'inex',
194  
-		    2 => 'gene',
195  
-		    1 => 'chr'
196  
-		   );
  186
+                    10 => 'peptide',
  187
+                    9 => 'propeptide',
  188
+                    8 => 'frame',
  189
+                    7 => 'cds',
  190
+                    6 => 'negative_intron',
  191
+                    5 => 'intron',
  192
+                    4 => 'exon',
  193
+                    3 => 'inex',
  194
+                    2 => 'gene',
  195
+                    1 => 'chr'
  196
+                   );
197 197
 
198 198
 $TRANSLATION = $COORDINATE_SYSTEMS{'cds'}. "-".
199 199
     $COORDINATE_SYSTEMS{'propeptide'};
200 200
 
201 201
 $DAG = {
202  
-	10 => [],
203  
-	9  => [10],
204  
-	8  => [],
205  
-	7  => [8, 9],
206  
-	6  => [],
207  
-	5  => [6],
208  
-	4  => [7],
209  
-	3  => [4, 5],
210  
-	2  => [3, 4, 5, 7],
211  
-	1  => [2]
  202
+        10 => [],
  203
+        9  => [10],
  204
+        8  => [],
  205
+        7  => [8, 9],
  206
+        6  => [],
  207
+        5  => [6],
  208
+        4  => [7],
  209
+        3  => [4, 5],
  210
+        2  => [3, 4, 5, 7],
  211
+        1  => [2]
212 212
        };
213 213
 
214 214
 $NOZERO_VALUES = {0 => 0, 'in' => 1, 'out' => 2, 'in&out' => 3 };
@@ -226,15 +226,15 @@ sub new {
226 226
 
227 227
     my($in, $out, $peptide_offset, $exons,
228 228
        $cds, $nozero, $strict) =
229  
-	$self->_rearrange([qw(IN
  229
+        $self->_rearrange([qw(IN
230 230
                               OUT
231 231
                               PEPTIDE_OFFSET
232 232
                               EXONS
233 233
                               CDS
234 234
                               NOZERO
235 235
                               STRICT
236  
-			     )],
237  
-			 @args);
  236
+                             )],
  237
+                         @args);
238 238
 
239 239
     # direction of mapping when going chr to protein
240 240
     $self->{_direction} = 1;
@@ -265,8 +265,8 @@ sub in {
265 265
    my ($self,$value) = @_;
266 266
    if( defined $value) {
267 267
        $self->throw("Not a valid input coordinate system name [$value]\n".
268  
-		    "Valid values are ". join(", ", keys %COORDINATE_SYSTEMS ))
269  
-	   unless defined $COORDINATE_SYSTEMS{$value};
  268
+                    "Valid values are ". join(", ", keys %COORDINATE_SYSTEMS ))
  269
+           unless defined $COORDINATE_SYSTEMS{$value};
270 270
 
271 271
        $self->{'_in'} = $COORDINATE_SYSTEMS{$value};
272 272
    }
@@ -289,8 +289,8 @@ sub out {
289 289
    my ($self,$value) = @_;
290 290
    if( defined $value) {
291 291
        $self->throw("Not a valid input coordinate system name [$value]\n".
292  
-		    "Valid values are ". join(", ", keys %COORDINATE_SYSTEMS ))
293  
-	   unless defined $COORDINATE_SYSTEMS{$value};
  292
+                    "Valid values are ". join(", ", keys %COORDINATE_SYSTEMS ))
  293
+           unless defined $COORDINATE_SYSTEMS{$value};
294 294
 
295 295
        $self->{'_out'} = $COORDINATE_SYSTEMS{$value};
296 296
    }
@@ -339,8 +339,8 @@ sub nozero {
339 339
 
340 340
    if (defined $value) {
341 341
        $self->throw("Not a valid value for nozero [$value]\n".
342  
-		    "Valid values are ". join(", ", keys %{$NOZERO_VALUES} ))
343  
-	   unless defined $NOZERO_VALUES->{$value};
  342
+                    "Valid values are ". join(", ", keys %{$NOZERO_VALUES} ))
  343
+           unless defined $NOZERO_VALUES->{$value};
344 344
        $self->{'_nozero'} = $NOZERO_VALUES->{$value};
345 345
    }
346 346
 
@@ -364,7 +364,7 @@ sub graph {
364 364
    my ($self,$value) = @_;
365 365
    if( defined $value) {
366 366
        $self->throw("Not a valid graph [$value]\n")
367  
-	   unless $value->isa('Bio::Coordinate::Graph');
  367
+           unless $value->isa('Bio::Coordinate::Graph');
368 368
        $self->{'_graph'} = $value;
369 369
    }
370 370
    return $self->{'_graph'};
@@ -385,29 +385,29 @@ sub peptide {
385 385
    my ($self, $value) = @_;
386 386
    if( defined $value) {
387 387
        $self->throw("I need a Bio::LocationI, not  [". $value. "]")
388  
-	   unless $value->isa('Bio::LocationI');
  388
+           unless $value->isa('Bio::LocationI');
389 389
 
390 390
        $self->throw("Peptide start not defined")
391  
-	   unless defined $value->start;
  391
+           unless defined $value->start;
392 392
        $self->{'_peptide_offset'} = $value->start - 1;
393 393
 
394 394
        $self->throw("Peptide end not defined")
395  
-	   unless defined $value->end;
  395
+           unless defined $value->end;
396 396
        $self->{'_peptide_length'} = $value->end - $self->{'_peptide_offset'};
397 397
 
398 398
 
399 399
        my $a = $self->_create_pair
400  
-	   ('propeptide', 'peptide', $self->strict,
401  
-	    $self->{'_peptide_offset'}, $self->{'_peptide_length'} );
  400
+           ('propeptide', 'peptide', $self->strict,
  401
+            $self->{'_peptide_offset'}, $self->{'_peptide_length'} );
402 402
        my $mapper =  $COORDINATE_SYSTEMS{'propeptide'}. "-".  $COORDINATE_SYSTEMS{'peptide'};
403 403
        $self->{'_mappers'}->{$mapper} = $a;
404 404
    }
405 405
    return  Bio::Location::Simple->new
406 406
        (-seq_id => 'propeptide',
407  
-	-start => $self->{'_peptide_offset'} + 1 ,
408  
-	-end => $self->{'_peptide_length'} + $self->{'_peptide_offset'},
409  
-	-strand => 1,
410  
-	-verbose => $self->verbose,
  407
+        -start => $self->{'_peptide_offset'} + 1 ,
  408
+        -end => $self->{'_peptide_length'} + $self->{'_peptide_offset'},
  409
+        -strand => 1,
  410
+        -verbose => $self->verbose,
411 411
        );
412 412
 }
413 413
 
@@ -425,17 +425,17 @@ sub peptide_offset {
425 425
    my ($self,$offset, $len) = @_;
426 426
    if( defined $offset) {
427 427
        $self->throw("I need an integer, not [$offset]")
428  
-	   unless $offset =~ /^[+-]?\d+$/;
  428
+           unless $offset =~ /^[+-]?\d+$/;
429 429
        $self->{'_peptide_offset'} = $offset;
430 430
 
431 431
        if (defined $len) {
432  
-	   $self->throw("I need an integer, not [$len]")
433  
-	       unless $len =~ /^[+-]?\d+$/;
434  
-	   $self->{'_peptide_length'} = $len;
  432
+           $self->throw("I need an integer, not [$len]")
  433
+               unless $len =~ /^[+-]?\d+$/;
  434
+           $self->{'_peptide_length'} = $len;
435 435
        }
436 436
 
437 437
        my $a = $self->_create_pair
438  
-	   ('propeptide', 'peptide', $self->strict, $offset, $self->{'_peptide_length'} );
  438
+           ('propeptide', 'peptide', $self->strict, $offset, $self->{'_peptide_length'} );
439 439
        my $mapper =  $COORDINATE_SYSTEMS{'propeptide'}. "-". $COORDINATE_SYSTEMS{'peptide'};
440 440
        $self->{'_mappers'}->{$mapper} = $a;
441 441
    }
@@ -457,7 +457,7 @@ sub peptide_length {
457 457
    my ($self, $len) = @_;
458 458
    if( defined $len) {
459 459
        $self->throw("I need an integer, not [$len]")
460  
-	   if defined $len && $len !~ /^[+-]?\d+$/;
  460
+           if defined $len && $len !~ /^[+-]?\d+$/;
461 461
        $self->{'_peptide_length'} = $len;
462 462
    }
463 463
    return $self->{'_peptide_length'};
@@ -493,51 +493,51 @@ sub exons {
493 493
 
494 494
    if(@value) {
495 495
        if (ref($value[0]) &&
496  
-	   $value[0]->isa('Bio::SeqFeatureI') and
497  
-	   $value[0]->location->isa('Bio::Location::SplitLocationI')) {
498  
-	   @value = $value[0]->location->each_Location;
  496
+           $value[0]->isa('Bio::SeqFeatureI') and
  497
+           $value[0]->location->isa('Bio::Location::SplitLocationI')) {
  498
+           @value = $value[0]->location->each_Location;
499 499
        } else {
500  
-	   $self->throw("I need an array , not [@value]")
501  
-	       unless ref \@value eq 'ARRAY';
502  
-	   $self->throw("I need a reference to an array of Bio::LocationIs, not to [".
503  
-			$value[0]. "]")
504  
-	       unless ref $value[0] and $value[0]->isa('Bio::LocationI');
  500
+           $self->throw("I need an array , not [@value]")
  501
+               unless ref \@value eq 'ARRAY';
  502
+           $self->throw("I need a reference to an array of Bio::LocationIs, not to [".
  503
+                        $value[0]. "]")
  504
+               unless ref $value[0] and $value[0]->isa('Bio::LocationI');
505 505
        }
506 506
 
507 507
        #
508 508
        # sort the input array
509 509
        #
510 510
        # and if the used has not defined CDS assume it is the complete exonic range
511  
-       if (defined $value[0]->strand && 
512  
-	   $value[0]->strand == - 1) {  #reverse strand
513  
-	   @value = map { $_->[0] }
514  
-	            sort { $b->[1] <=> $a->[1] }
515  
-	            map { [ $_, $_->start] }
  511
+       if (defined $value[0]->strand &&
  512
+           $value[0]->strand == - 1) {  #reverse strand
  513
+           @value = map { $_->[0] }
  514
+                    sort { $b->[1] <=> $a->[1] }
  515
+                    map { [ $_, $_->start] }
516 516
                     @value;
517 517
 
518 518
            unless ($self->cds) {
519 519
                $self->cds(Bio::Location::Simple->new
520  
-			  (-start   => $value[-1]->start,
521  
-			   -end     => $value[0]->end,
522  
-			   -strand  => $value[0]->strand,
523  
-			   -seq_id  => $value[0]->seq_id,
524  
-			   -verbose => $self->verbose,
525  
-			   )
526  
-			  );
  520
+                          (-start   => $value[-1]->start,
  521
+                           -end     => $value[0]->end,
  522
+                           -strand  => $value[0]->strand,
  523
+                           -seq_id  => $value[0]->seq_id,
  524
+                           -verbose => $self->verbose,
  525
+                           )
  526
+                          );
527 527
            }
528 528
        } else {               # undef or forward strand
529  
-	   @value = map { $_->[0] }
530  
-	            sort { $a->[1] <=> $b->[1] }
  529
+           @value = map { $_->[0] }
  530
+                    sort { $a->[1] <=> $b->[1] }
531 531
                     map { [ $_, $_->start] }
532 532
                     @value;
533 533
            unless ($self->cds) {
534 534
                $self->cds(Bio::Location::Simple->new
535  
-			  (-start   => $value[0]->start,
536  
-			   -end     => $value[-1]->end,
537  
-			   -strand  => $value[0]->strand,
538  
-			   -seq_id  => $value[0]->seq_id,
539  
-			   -verbose => $self->verbose,
540  
-			   )
  535
+                          (-start   => $value[0]->start,
  536
+                           -end     => $value[-1]->end,
  537
+                           -strand  => $value[0]->strand,
  538
+                           -seq_id  => $value[0]->seq_id,
  539
+                           -verbose => $self->verbose,
  540
+                           )
541 541
                          );
542 542
            }
543 543
 
@@ -552,20 +552,20 @@ sub exons {
552 552
        my $gene_mapper = "1-2";
553 553
        if (defined $self->{'_mappers'}->{$gene_mapper} ) {
554 554
 
555  
-	   my $tmp_in = $self->{'_in'};
556  
-	   my $tmp_out = $self->{'_out'};
557  
-	   my $tmp_verb = $self->verbose;
558  
-	   $self->verbose(0);
  555
+           my $tmp_in = $self->{'_in'};
  556
+           my $tmp_out = $self->{'_out'};
  557
+           my $tmp_verb = $self->verbose;
  558
+           $self->verbose(0);
559 559
 
560  
-	   $self->in('chr');
561  
-	   $self->out('gene');
562  
-	   @exons = map {$self->map($_) } @value;
  560
+           $self->in('chr');
  561
+           $self->out('gene');
  562
+           @exons = map {$self->map($_) } @value;
563 563
 
564  
-	   $self->{'_in'} = ($tmp_in);
565  
-	   $self->{'_out'} = ($tmp_out);
566  
-	   $self->verbose($tmp_verb);
  564
+           $self->{'_in'} = ($tmp_in);
  565
+           $self->{'_out'} = ($tmp_out);
  566
+           $self->verbose($tmp_verb);
567 567
        } else {
568  
-	   @exons = @value;
  568
+           @exons = @value;
569 569
        }
570 570
 
571 571
        my $cds_map = Bio::Coordinate::Collection->new;
@@ -581,106 +581,106 @@ sub exons {
581 581
        my $prev_exon_end;
582 582
 
583 583
        for my $exon ( @exons ) {
584  
-	   $exon_counter++;
585  
-
586  
-	   #
587  
-	   # gene -> cds
588  
-	   #
589  
-
590  
-	   my $match1 = Bio::Location::Simple->new
591  
-	       (-seq_id =>'gene' ,
592  
-		-start  => $exon->start,
593  
-		-end    => $exon->end, 
594  
-		-strand => 1,
595  
-		-verbose=> $self->verbose);
596  
-
597  
-	   my $match2 = Bio::Location::Simple->new
598  
-	       (-seq_id => 'cds',
599  
-		-start => $tr_end + 1,
600  
-		-end => $tr_end + $exon->end - $exon->start +1,
601  
-		-strand=>$exon->strand,
602  
-		-verbose=>$self->verbose);
603  
-
604  
-	   $cds_map->add_mapper(Bio::Coordinate::Pair->new
  584
+           $exon_counter++;
  585
+
  586
+           #
  587
+           # gene -> cds
  588
+           #
  589
+
  590
+           my $match1 = Bio::Location::Simple->new
  591
+               (-seq_id =>'gene' ,
  592
+                -start  => $exon->start,
  593
+                -end    => $exon->end,
  594
+                -strand => 1,
  595
+                -verbose=> $self->verbose);
  596
+
  597
+           my $match2 = Bio::Location::Simple->new
  598
+               (-seq_id => 'cds',
  599
+                -start => $tr_end + 1,
  600
+                -end => $tr_end + $exon->end - $exon->start +1,
  601
+                -strand=>$exon->strand,
  602
+                -verbose=>$self->verbose);
  603
+
  604
+           $cds_map->add_mapper(Bio::Coordinate::Pair->new
605 605
                                 (-in => $match1,
606 606
                                  -out => $match2,
607 607
                                 )
608 608
                                );
609 609
 
610  
-	   if ($exon->start <= 1 and $exon->end >= 1) {
611  
-	       $coffset = $tr_end - $exon->start + 1;
612  
-	   }
613  
-	   $tr_end = $tr_end  + $exon->end - $exon->start + 1;
614  
-
615  
-	   #
616  
-	   # gene -> intron
617  
-	   #
618  
-
619  
-	   if (defined $prev_exon_end) {
620  
-	       my $match3 = Bio::Location::Simple->new
621  
-		   (-seq_id  => 'gene',
622  
-		    -start   => $prev_exon_end + 1,
623  
-		    -end     => $exon->start -1, 
624  
-		    -strand  => $exon->strand,
625  
-		    -verbose => $self->verbose);
626  
-
627  
-	       my $match4 = Bio::Location::Simple->new
628  
-		   (-seq_id  => 'intron'. ($exon_counter -1),
629  
-		    -start   => 1,
630  
-		    -end     => $exon->start - 1 - $prev_exon_end,
631  
-		    -strand  =>$exon->strand,
632  
-		    -verbose => $self->verbose,);
633  
-
634  
-	       # negative intron coordinates
635  
-	       my $match5 = Bio::Location::Simple->new
636  
-		   (-seq_id  => 'intron'. ($exon_counter -1),
637  
-		    -start   => -1 * ($exon->start - 2 - $prev_exon_end) -1,
638  
-		    -end     => -1,
639  
-		    -strand  => $exon->strand,
640  
-		    -verbose => $self->verbose);
641  
-
642  
-	       $inex_map->add_mapper(Bio::Coordinate::Pair->new
  610
+           if ($exon->start <= 1 and $exon->end >= 1) {
  611
+               $coffset = $tr_end - $exon->start + 1;
  612
+           }
  613
+           $tr_end = $tr_end  + $exon->end - $exon->start + 1;
  614
+
  615
+           #
  616
+           # gene -> intron
  617
+           #
  618
+
  619
+           if (defined $prev_exon_end) {
  620
+               my $match3 = Bio::Location::Simple->new
  621
+                   (-seq_id  => 'gene',
  622
+                    -start   => $prev_exon_end + 1,
  623
+                    -end     => $exon->start -1,
  624
+                    -strand  => $exon->strand,
  625
+                    -verbose => $self->verbose);
  626
+
  627
+               my $match4 = Bio::Location::Simple->new
  628
+                   (-seq_id  => 'intron'. ($exon_counter -1),
  629
+                    -start   => 1,
  630
+                    -end     => $exon->start - 1 - $prev_exon_end,
  631
+                    -strand  =>$exon->strand,
  632
+                    -verbose => $self->verbose,);
  633
+
  634
+               # negative intron coordinates
  635
+               my $match5 = Bio::Location::Simple->new
  636
+                   (-seq_id  => 'intron'. ($exon_counter -1),
  637
+                    -start   => -1 * ($exon->start - 2 - $prev_exon_end) -1,
  638
+                    -end     => -1,
  639
+                    -strand  => $exon->strand,
  640
+                    -verbose => $self->verbose);
  641
+
  642
+               $inex_map->add_mapper(Bio::Coordinate::Pair->new
643 643
                                      (-in => $match3,
644 644
                                       -out => $match4
645 645
                                      )
646 646
                                     );
647  
-	       $intron_map->add_mapper(Bio::Coordinate::Pair->new
  647
+               $intron_map->add_mapper(Bio::Coordinate::Pair->new
648 648
                                        (-in => $self->_clone_loc($match3),
649 649
                                         -out => $self->_clone_loc($match4)
650 650
                                        )
651 651
                                       );
652  
-	       $negative_intron_map->add_mapper(Bio::Coordinate::Pair->new
  652
+               $negative_intron_map->add_mapper(Bio::Coordinate::Pair->new
653 653
                                                 (-in => $self->_clone_loc($match4),
654 654
                                                  -out => $match5
655 655
                                                 ));
656 656
 
657  
-	   }
658  
-
659  
-	   # store the value
660  
-	   $prev_exon_end = $exon->end;
661  
-
662  
-	   #
663  
-	   # gene -> exon
664  
-	   #
665  
-	   my $match6 = Bio::Location::Simple->new
666  
-	       (-seq_id => 'exon'. $exon_counter,
667  
-		-start  => 1,
668  
-		-end    => $exon->end - $exon->start +1,
669  
-		-strand => $exon->strand,
670  
-		-verbose=> $self->verbose,);
671  
-
672  
-	   my $pair2 = Bio::Coordinate::Pair->new(-in => $self->_clone_loc($match1),
673  
-						  -out => $match6
674  
-						 );
675  
-	   my $pair3 = Bio::Coordinate::Pair->new(-in => $self->_clone_loc($match6),
676  
-						  -out => $self->_clone_loc($match2)
677  
-						 );
678  
-	   $inex_map->add_mapper(Bio::Coordinate::Pair->new
  657
+           }
  658
+
  659
+           # store the value
  660
+           $prev_exon_end = $exon->end;
  661
+
  662
+           #
  663
+           # gene -> exon
  664
+           #
  665
+           my $match6 = Bio::Location::Simple->new
  666
+               (-seq_id => 'exon'. $exon_counter,
  667
+                -start  => 1,
  668
+                -end    => $exon->end - $exon->start +1,
  669
+                -strand => $exon->strand,
  670
+                -verbose=> $self->verbose,);
  671
+
  672
+           my $pair2 = Bio::Coordinate::Pair->new(-in => $self->_clone_loc($match1),
  673
+                                                  -out => $match6
  674
+                                                 );
  675
+           my $pair3 = Bio::Coordinate::Pair->new(-in => $self->_clone_loc($match6),
  676
+                                                  -out => $self->_clone_loc($match2)
  677
+                                                 );
  678
+           $inex_map->add_mapper(Bio::Coordinate::Pair->new
679 679
                                  (-in => $self->_clone_loc($match1),
680 680
                                   -out => $match6
681 681
                                  )
682 682
                                 );
683  
-	   $exon_map->add_mapper(Bio::Coordinate::Pair->new
  683
+           $exon_map->add_mapper(Bio::Coordinate::Pair->new
684 684
                                  (-in => $self->_clone_loc($match1),
685 685
                                   -out => $self->_clone_loc($match6)
686 686
                                  )
@@ -695,10 +695,10 @@ sub exons {
695 695
 
696 696
        # move coordinate start if exons have negative values
697 697
        if ($coffset) {
698  
-	   foreach my $m ($cds_map->each_mapper) {
699  
-	       $m->out->start($m->out->start - $coffset);
700  
-	       $m->out->end($m->out->end - $coffset);
701  
-	   }
  698
+           foreach my $m ($cds_map->each_mapper) {
  699
+               $m->out->start($m->out->start - $coffset);
  700
+               $m->out->end($m->out->end - $coffset);
  701
+           }
702 702
 
703 703
        }
704 704
 
@@ -731,7 +731,7 @@ sub _clone_loc { # clone a simple location
731 731
 
732 732
    return  Bio::Location::Simple->new
733 733
        (-verbose       => $self->verbose,
734  
-	-seq_id        => $loc->seq_id,
  734
+        -seq_id        => $loc->seq_id,
735 735
         -start         => $loc->start,
736 736
         -end           => $loc->end,
737 737
         -strand        => $loc->strand,
@@ -762,32 +762,32 @@ sub cds {
762 762
    my ($self,$value) = @_;
763 763
    if( defined $value) {
764 764
        if ($value =~ /^[+-]?\d+$/ ) {
765  
-	   my $loc = Bio::Location::Simple->new(-start=>$value, -end => $value,
766  
-						-verbose=>$self->verbose);
767  
-	   $self->{'_cds'} = $loc;
  765
+           my $loc = Bio::Location::Simple->new(-start=>$value, -end => $value,
  766
+                                                -verbose=>$self->verbose);
  767
+           $self->{'_cds'} = $loc;
768 768
        }
769 769
        elsif (ref $value &&  $value->isa('Bio::RangeI') ) {
770  
-	   $self->{'_cds'} = $value;
  770
+           $self->{'_cds'} = $value;
771 771
        } else {
772  
-	   $self->throw("I need an integer or Bio::RangeI, not [$value]")
  772
+           $self->throw("I need an integer or Bio::RangeI, not [$value]")
773 773
        }
774 774
        # strand !!
775 775
        my $len;
776 776
 
777 777
        $len = $self->{'_cds'}->end - $self->{'_cds'}->start +1
778  
-	   if defined $self->{'_cds'}->end;
  778
+           if defined $self->{'_cds'}->end;
779 779
 
780 780
        my $a = $self->_create_pair
781  
-	   ('chr', 'gene', 0,
782  
-	    $self->{'_cds'}->start-1,
783  
-	    $len,
784  
-	    $self->{'_cds'}->strand);
  781
+           ('chr', 'gene', 0,
  782
+            $self->{'_cds'}->start-1,
  783
+            $len,
  784
+            $self->{'_cds'}->strand);
785 785
        my $mapper =  $COORDINATE_SYSTEMS{'chr'}. "-". $COORDINATE_SYSTEMS{'gene'};
786 786
        $self->{'_mappers'}->{$mapper} = $a;
787 787
 
788 788
        # recalculate exon-based mappers
789 789
        if ( defined $self->{'_chr_exons'} ) {
790  
-	   $self->exons(@{$self->{'_chr_exons'}});
  790
+           $self->exons(@{$self->{'_chr_exons'}});
791 791
        }
792 792
 
793 793
    }
@@ -812,80 +812,80 @@ sub map {
812 812
    my ($res);
813 813
    $self->throw("Need to pass me a Bio::Location::Simple or ".
814 814
                 "Bio::Location::Simple or Bio::SeqFeatureI, not [".
815  
-		ref($value). "]")
  815
+                ref($value). "]")
816 816
        unless ref($value) && ($value->isa('Bio::Location::Simple') or
817 817
                               $value->isa('Bio::Location::SplitLocationI') or
818  
-			      $value->isa('Bio::SeqFeatureI'));
  818
+                              $value->isa('Bio::SeqFeatureI'));
819 819
    $self->throw("Input coordinate system not set")
820 820
        unless $self->{'_in'};
821 821
    $self->throw("Output coordinate system not set")
822 822
        unless $self->{'_out'};
823 823
    $self->throw("Do not be silly. Input and output coordinate ".
824  
-		"systems are the same!")
  824
+                "systems are the same!")
825 825
        unless $self->{'_in'} != $self->{'_out'};
826 826
 
827 827
    $self->_check_direction();
828 828
 
829 829
    $value = $value->location if $value->isa('Bio::SeqFeatureI');
830 830
    $self->debug( "=== Start location: ". $value->start. ",".
831  
-		 $value->end. " (". ($value->strand || ''). ")\n");
832  
-	       
  831
+                 $value->end. " (". ($value->strand || ''). ")\n");
  832
+
833 833
    # if nozero coordinate system is used in the input values
834 834
    if ( defined $self->{'_nozero'} &&
835  
-	( $self->{'_nozero'} == 1 || $self->{'_nozero'} == 3 ) ) {
  835
+        ( $self->{'_nozero'} == 1 || $self->{'_nozero'} == 3 ) ) {
836 836
        $value->start($value->start + 1)
837  
-	   if defined $value->start && $value->start < 1;
  837
+           if defined $value->start && $value->start < 1;
838 838
        $value->end($value->end + 1)
839  
-	   if defined $value->end && $value->end < 1;
  839
+           if defined $value->end && $value->end < 1;
840 840
    }
841 841
 
842 842
    my @steps = $self->_get_path();
843 843
    $self->debug( "mapping ". $self->{'_in'}. "->". $self->{'_out'}.
844  
-		 "  Mappers: ". join(", ", @steps). "\n");
845  
-   
  844
+                 "  Mappers: ". join(", ", @steps). "\n");
  845
+
846 846
    foreach my $mapper (@steps) {
847 847
        if ($mapper eq $TRANSLATION) {
848  
-	   if ($self->direction == 1) {
849  
-
850  
-	       $value = $self->_translate($value);
851  
-	       $self->debug( "+   $TRANSLATION cds -> propeptide (translate) \n");
852  
-	   } else {
853  
-	       $value = $self->_reverse_translate($value);
854  
-	       $self->debug("+   $TRANSLATION propeptide -> cds (reverse translate) \n");
855  
-	   }
  848
+           if ($self->direction == 1) {
  849
+
  850
+               $value = $self->_translate($value);
  851
+               $self->debug( "+   $TRANSLATION cds -> propeptide (translate) \n");
  852
+           } else {
  853
+               $value = $self->_reverse_translate($value);
  854
+               $self->debug("+   $TRANSLATION propeptide -> cds (reverse translate) \n");
  855
+           }
856 856
        }
857 857
        # keep the start and end values, and go on to next iteration
858 858
        #  if this mapper is not set
859 859
        elsif ( ! defined $self->{'_mappers'}->{$mapper} ) {
860  
-	   # update mapper name
861  
-	   $mapper =~ /\d+-(\d+)/;   my ($counter) = $1;
862  
-	   $value->seq_id($COORDINATE_INTS{$counter});
863  
-	   $self->debug( "-   $mapper\n");
  860
+           # update mapper name
  861
+           $mapper =~ /\d+-(\d+)/;   my ($counter) = $1;
  862
+           $value->seq_id($COORDINATE_INTS{$counter});
  863
+           $self->debug( "-   $mapper\n");
864 864
        } else {
865 865
            #
866  
-	   # the DEFAULT : generic mapping
  866
+           # the DEFAULT : generic mapping
867 867
            #
868  
-	   
869  
-	   $value = $self->{'_mappers'}->{$mapper}->map($value);
870  
-           
871  
-	   $value->purge_gaps
872  
-	       if ($value && $value->isa('Bio::Location::SplitLocationI') && 
873  
-		   $value->can('gap'));
874  
-	   
875  
-	   $self->debug( "+  $mapper (". $self->direction. "):  start ".
876  
-			 $value->start. " end ". $value->end. "\n")
877  
-	       if $value && $self->verbose > 0;
  868
+
  869
+           $value = $self->{'_mappers'}->{$mapper}->map($value);
  870
+
  871
+           $value->purge_gaps
  872
+               if ($value && $value->isa('Bio::Location::SplitLocationI') &&
  873
+                   $value->can('gap'));
  874
+
  875
+           $self->debug( "+  $mapper (". $self->direction. "):  start ".
  876
+                         $value->start. " end ". $value->end. "\n")
  877
+               if $value && $self->verbose > 0;
878 878
        }
879 879
    }
880 880
 
881 881
    # if nozero coordinate system is asked to be used in the output values
882 882
    if ( defined $value && defined $self->{'_nozero'} &&
883  
-	( $self->{'_nozero'} == 2 || $self->{'_nozero'} == 3 ) ) {
  883
+        ( $self->{'_nozero'} == 2 || $self->{'_nozero'} == 3 ) ) {
884 884
 
885 885
        $value->start($value->start - 1)
886  
-	   if defined $value->start && $value->start < 1;
  886
+           if defined $value->start && $value->start < 1;
887 887
        $value->end($value->end - 1)
888  
-	   if defined $value->end && $value->end < 1;
  888
+           if defined $value->end && $value->end < 1;
889 889
    }
890 890
 
891 891
    # handle merging of adjacent split locations!
@@ -901,8 +901,8 @@ sub map {
901 901
                push @matches, $prevloc;
902 902
                next;
903 903
            }
904  
-           if ($prevloc->end == ($loc->start - 1) && 
905  
-	       $prevloc->seq_id eq $loc->seq_id) {
  904
+           if ($prevloc->end == ($loc->start - 1) &&
  905
+               $prevloc->seq_id eq $loc->seq_id) {
906 906
                $prevloc->end($loc->end);
907 907
                $merging = 1;
908 908
            } else {
@@ -920,13 +920,13 @@ sub map {
920 920
                     -start    => $matches[0]->start,
921 921
                     -end      => $matches[0]->end,
922 922
                     -strand   => $matches[0]->strand,
923  
-		    -verbose  => $self->verbose,);
  923
+                    -verbose  => $self->verbose,);
924 924
            }
925 925
            $value = $newvalue;
926 926
        }
927  
-   } 
928  
-   elsif (ref $value eq "Bio::Coordinate::Result" && 
929  
-	  $value->each_match == 1 ){
  927
+   }
  928
+   elsif (ref $value eq "Bio::Coordinate::Result" &&
  929
+          $value->each_match == 1 ){
930 930
        $value = $value->match;
931 931
    }
932 932
 
@@ -1116,23 +1116,23 @@ sub _create_pair {
1116 1116
 
1117 1117
    my $match1 = Bio::Location::Simple->new
1118 1118
        (-seq_id  => $in,
1119  
-	-start   => $offset+1,
1120  
-	-end     => $offset+$length, 
1121  
-	-strand  => 1,
1122  
-	-verbose => $self->verbose);
  1119
+        -start   => $offset+1,
  1120
+        -end     => $offset+$length,
  1121
+        -strand  => 1,
  1122
+        -verbose => $self->verbose);
1123 1123
 
1124 1124
    my $match2 = Bio::Location::Simple->new
1125 1125
        (-seq_id  => $out,
1126  
-	-start   => 1,
1127  
-	-end     => $length, 
1128  
-	-strand  => $strand,
1129  
-	-verbose => $self->verbose);
  1126
+        -start   => 1,
  1127
+        -end     => $length,
  1128
+        -strand  => $strand,
  1129
+        -verbose => $self->verbose);
1130 1130
 
1131 1131
    my $pair = Bio::Coordinate::ExtrapolatingPair->new
1132 1132
        (-in      => $match1,
1133 1133
         -out     => $match2,
1134 1134
         -strict  => $strict,
1135  
-	-verbose => $self->verbose,
  1135
+        -verbose => $self->verbose,
1136 1136
        );
1137 1137
 
1138 1138
    return $pair;
@@ -1161,17 +1161,17 @@ sub _translate {
1161 1161
            ($value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI'));
1162 1162
 
1163 1163
    my $seqid = 'propeptide';
1164  
-   
  1164
+
1165 1165
    if ($value->isa("Bio::Location::SplitLocationI") ) {
1166 1166
        my $split = Bio::Location::Split->new(-seq_id=>$seqid);
1167 1167
        foreach my $loc ( $value->each_Location(1) ) {
1168 1168
            my $match = Bio::Location::Simple->new
1169  
-	       (-start   => int ($loc->start / 3 ) +1,
1170  
-		-end     => int ($loc->end / 3 ) +1,
1171  
-		-seq_id  => $seqid,
1172  
-		-strand  => 1,
1173  
-		-verbose => $self->verbose,
1174  
-		);
  1169
+               (-start   => int ($loc->start / 3 ) +1,
  1170
+                -end     => int ($loc->end / 3 ) +1,
  1171
+                -seq_id  => $seqid,
  1172
+                -strand  => 1,
  1173
+                -verbose => $self->verbose,
  1174
+                );