This file is indexed.

/usr/share/perl5/SWISS/DEs.pm is in libswiss-perl 1.67-1.1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
package SWISS::DEs;

use vars qw($AUTOLOAD @ISA @EXPORT_OK %fields);

use Exporter;
use Carp;
use strict;

use SWISS::TextFunc;
use SWISS::ListBase;
use SWISS::DE;

BEGIN {
  @EXPORT_OK = qw();
  
  @ISA = ( 'Exporter', 'SWISS::ListBase');
  
  %fields = ('text' => undef,
             'hasFragment' => undef,
             'isPrecursor' => undef,
             'version' => undef,
             'Contains' => undef,
             'Includes' => undef,
             'is_old_format' => undef,
            );
}

sub new {
  my $ref = shift;
  my $class = ref($ref) || $ref;
  my $self = new SWISS::ListBase;
  $self->rebless($class);
  $self->Contains (new SWISS::ListBase);
  $self->Includes (new SWISS::ListBase);
  $self->{is_old_format} = 0;# now the default is new format
  return $self;
}

sub fromText {
  my $class = shift;
  my $textRef = shift;
  my $self = new SWISS::DEs;

  my $line = '';
  my $evidence = '';
 
  if ($$textRef =~ /($SWISS::TextFunc::linePattern{'DE'})/m) {
    $line = $1;  
    $self->{indentation} = $line =~ s/^ //mg;
    
    # if not new DE format
    unless($line =~ / RecName:| AltName:| SubName:/) {
        # is old format
        $self->{is_old_format} = 1;
        $line = SWISS::TextFunc->joinWith('', ' ', '(?<! )-', 'and ',
                                          map {SWISS::TextFunc->cleanLine($_)}
                                              (split "\n", $line));
        # Drop trailing spaces and dots
        $line =~ s/[\. ]*$//;
    }
    else {
        $self->{is_old_format} = 0;
    }

  };
  if ($self->{is_old_format}) {
  # Parse for evidence tags
      if (($evidence) = $line =~ /($SWISS::TextFunc::evidencePattern)/m) {
        $line =~ s/$evidence//m;
        $self->evidenceTags($evidence);
      }
  }

  $self->{text} = $line;
  $self->{is_old_format} = 1 unless $line;
  $self->advancedParse();

  $self->{_dirty} = 0;
  
  return $self;
}

sub fromString {
  my $class = shift;
  my $string = shift;
  my $is_old_format = shift;
  my $self = new SWISS::DEs;
  $self->{text} = $string;
  $self->{is_old_format} = $is_old_format;
  $self->advancedParse;
  $self->{_dirty} = 0;
  return $self;
} 

sub text {
  my $self = shift;
  my $text = shift;
  if ($text) {
    $self->{_dirty} = 1;
    $self->{text} = $text;
    $self->{is_old_format} = 
        ($text =~ /RecName:|AltName:|SubName:/ ? 0 : 1);
    $self->advancedParse;
  }
  else {
    $text = $self->toString();
  }
  return $text;
}

sub to_old_format {
    my $self = shift; 
    $self->{is_old_format} = 1;
    $self->{_dirty} = 1;
    
    # stupid: in old format we want EC before short, in new they are after
    sub move_back_ec {
        my $de = shift or return;
        my $j=0;
        for (my $i=0;$i<scalar(@$de);$i++) {
            $de->[$i]->{is_old_format} = 1;
            if ($de->[$i]->{type} eq 'Short') {
                $j++;
            }
            elsif ($de->[$i]->{type} eq 'EC' && $j) {
                my $tmp = $de->[$i];
                for (my $k=0;$k<$j;$k++) {
                    next if $i-$k <2;
                    $de->[$i-$k] = $de->[$i-$k-1]
                }
                $de->[$i-$j] = $tmp;# put EC at beginning
            }
            else {
                $j=0;
            }
        }        
    }
    
    foreach my $de ($self->{list}) {
        move_back_ec($de);
    }
    foreach my $dess ($self->Contains->{list}) {
        foreach my $des (@$dess) {
            foreach my $de ($des->{list}) {
                move_back_ec($de);
            }
        }
    }
    foreach my $dess ($self->Includes->{list}) {
        foreach my $des (@$dess) {
            foreach my $de ($des->{list}) {
                move_back_ec($de);
            }
        }
    }
    
    # FIXME: evtags (are flag evt!) remove them?
}

sub advancedParse {
  my $self = shift;
  # if is new format
  return $self->advancedParseNew() unless $self->{is_old_format};
  
  # parse old format
  
  my $t = $self->{text};     
  $self->initialize;
  my($hasFragment, $version);
                                                              
  #1)version
  if ($t =~ s/\s*\((Version \S+)\)//i) {
    $version = $1;
  }
  $self->version($version);
   
  #2)fragment                                                              
  if ($t =~ s/\s*\((Fragments?)\)//i) {
    $hasFragment = $1;
  }
  $self->hasFragment($hasFragment);
   
  #3)children
  $self->Contains->set();
  $self->Includes->set();

  #protect internal [] by converting to {- -}
  1 while $t =~  s/(\[[^\[\]]*)\[(.*?)\]/$1\{-$2-\}/;
  #parse Contains/Includes
  while ($t =~ s/\s*\[((?:Contains)|(?:Includes)):\s*(.*?)\]//i) {  
    my $type = lc $1 eq "contains" ? $self->Contains : $self->Includes;
    $type->push(
        map {
            s/\{-/[/g; s/-\}/]/g;
            SWISS::DEs->fromString($_,1);
        } split /;\s*/, $2);
  }
  # convert protected brackets back to original form
  $t =~ s/\{-/[/g; $t =~ s/-\}/]/g;

  #4)list
  #protect internal () by converting to {- -}
  1 while $t =~  s/(\([^\(\)]*)\((.*?)\)/$1\{-$2-\}/;
  #must reverse before parsing to match successively all exprs between ()
  $t = reverse $t;
  my $ev = $SWISS::TextFunc::evidencePatternReversed;
  while ($t =~  s/^($ev)?\)(.*?)\(\s+//) {
    my $a = $3; #$2 is set by the evidence pattern
    $a = $1.$a if $1; #evidence tag
    $a =~ s/-\{/\(/g;
    $a =~ s/\}-/\)/g;
    $self->unshift(SWISS::DE->fromText(scalar reverse $a));
  }
  # convert protected brackets back to original form, 
  # then add remaining text
  $t =~ s/-\{/\(/g;
  $t =~ s/\}-/\)/g;
  $self->unshift(SWISS::DE->fromText(scalar reverse $t));
    # note: even if {text} is empty (no DE line) there will be a DE obj
    # so head method will work
}


sub advancedParseNew {
# advance parsing for new format
# Note: the new format is saved into the old simple structure !...
# Code will work ~ the same with both format.
# Adding a DE in the new format will just require specifying 
# category (RecName, AltName, SubName) and type (Full, Short, EC, Allergen, 
# CD_antigen) in DE stored in DEs
    my $self = shift;
  
    $self->Contains->set();
    $self->Includes->set();
  
    $self->initialize;
    
    my $by_mode = {# dispatch table to save new data into old structure
       'Main' => sub {  
                        my ($str,$is_new_list,$cat,$type,$hide_in_old) = @_;
                        my $de = SWISS::DE->fromText($str);
                        $de->category($cat);
                        $de->type($type);
                        $de->hide_in_old($hide_in_old);                        
                        $self->push($de);
                    },
       'Contains' => sub {   
                        my ($str,$is_new_list,$cat,$type,$hide_in_old) = @_;
                        my $obj = $self->Contains;
                        if ($is_new_list) {
                        # is new contains: create new DEs to add names
                            my $contains = new SWISS::DEs;
                            $obj->push($contains);
                        }
                        # add DE (from str) to DEs(listbase)
                        my $de = SWISS::DE->fromText($str);
                        $de->category($cat);
                        $de->type($type);
                        $de->hide_in_old($hide_in_old); 
                        $obj->item(-1)->push($de);
                    },
       'Includes' => sub{
                        my ($str,$is_new_list,$cat,$type,$hide_in_old) = @_;
                        my $obj = $self->Includes;
                        if ($is_new_list) {
                            my $inludes = new SWISS::DEs;
                            $obj->push($inludes);
                        }
                        my $de = SWISS::DE->fromText($str);
                        $de->category($cat);
                        $de->type($type);
                        $de->hide_in_old($hide_in_old); 
                        $obj->item(-1)->push($de);
                    }
    };
    
    my $process_txt_by_type = {
    # transform name string into the old format (so that new format could be 
    # converted into old one, if needed [transitory period])
        'EC'        =>  sub {
                            my $str = shift or return;
                            return "EC $str";
                        },
        'Allergen'  =>  sub {
                            my $str = shift or return;
                            return "Allergen $str";
                        },
        'CD_antigen'  =>  sub {
                            my $str = shift or return;
                            return "$str antigen";
                        }
    };

    my $raw = $self->{text};
    my $mode = 'Main';
    my $is_new_list;
    my $cat = '';
    my @flags;
    my $cd_antigen_outside = {};

    foreach my $line (map {s/^DE   //;$_} split '\r?\n',$raw) {
        if ($line =~ /^(Contains|Includes)/) {# Contains: | Includes:
            $mode = $1;
            $is_new_list = 1;
            next;
        }
        if ($line =~ /^Flags:\s+(.+)/) {# flags (Precursor, Fragment, Fragments)
            my $flags = $1;
            @flags = map {
                if (/($SWISS::TextFunc::evidencePattern)/m) {
                # store flag evtag as evtag for DEs self obj itself! (hack)
                    my $ev = $1;
                    $self->addEvidenceTag($ev);
                    s/\Q$ev//;# strip evtag
                }
                if (/(Fragments?)/) {
                    $self->hasFragment(my $flag = $1);# !($1) doesn't work
                }
                $_;
            } sort {$b cmp $a} split '; *', $flags;
            next;
        }

        $cat = $1 if $line =~ s/^ *(\w+): *//;# category: RecName: | AltName:
        my ($type,$val) = split '= *', $line;
        $type =~ s/\s+//g;# type: Full | Short | EC | Allergen | CD_antigen
        $val =~ s/;\s*$//g;# value: name/descriptor
        $cd_antigen_outside->{$1} = 1
            if $type ne 'CD_antigen' && $val =~ /^(CDw?\d+) antigen/;
        my $hide_in_old = 
            $type eq 'CD_antigen' && $cd_antigen_outside->{$val} ?
                1 : 0;
        # put data into old structure, so that new format could be converted 
        # into old one
        $val = $process_txt_by_type->{$type}->($val) 
            if $process_txt_by_type->{$type};
        $by_mode->{$mode}->($val,$is_new_list,$cat,$type,$hide_in_old) 
            if $by_mode->{$mode};
        
        $is_new_list = 0;
    }

    foreach my $f (grep {/^precursor/i} @flags) {
    # to be compatible with old format!:
    # if there are flags to be added to main name:
    # Note: DE text method will show 'precursor', toText will hide it
    # this was due to the constraint of using sk to convert new format back
    # into old one during a transitory period!
        my $str = $self->head->text . ' '.lc($f);
        $self->head->text($str);
        # at the same time store precursor flag
        $self->{isPrecursor} = 1;
    }

}


sub toString {
  my $self = shift;

  # if is new format
  return $self->toStringNew() unless $self->{is_old_format};

  # rebuild old format
  
  my $newText = '';
  
  if ($self->size > 0) {# Main names
    map {$_->{is_old_format} = 1} $self->elements;
    $newText = join(' ', $self->head->toText, 
                    grep {$_} map {$_->toText(1)} $self->tail);
  }
  # Includes/Contains
  for my $p (["Includes", $self->Includes], ["Contains", $self->Contains]) {
    my ($type, $obj) = @$p;
    next unless $obj->size;
    $newText .= ' ' if $newText;
    my $text = join '; ', grep {$_} 
            map {$_->{is_old_format} = 1;            
            $_->toString} $obj->elements;
    $newText .= "[$type: $text]";
  }
  for ($self->hasFragment, $self->version) {
    next unless $_;
    $newText .= ' ' if $newText;
    $newText .= '(' . $_ . ')';
  }
  return $newText;
}


sub toStringNew {
  my $self = shift;
 
    my $str_out = '';
    my @flags;

    my $process_txt_by_type = {
    # transform stored name string (old format) into clean new names
    # Note: in old format name and their type were mixed
        'Full'          => sub {
                            my $str = shift or return;
                            my $i = shift;# position 
                            push @flags, 'Precursor' 
                                if defined($i) && !$i 
                                    && $str =~ s/ precursor$//;
                            return $str;
                        },
        'EC'        =>  sub {
                            my $str = shift or return;
                            $str =~ /^EC (\d.*)/;
                            return $1;
                        },
        'Allergen'  =>  sub {
                            my $str = shift or return;
                            $str =~ /^Allergen (.*)/;
                            return $1;
                        },
        'CD_antigen'  =>  sub {
                            my $str = shift or return;
                            $str =~ /^(.+) antigen$/;
                            return $1;
                        }
    };
    
    my $main = new SWISS::DEs;
    # build main, includes, contains
    foreach my $d (
        ['', ($main->push($self) and $main)],
        ['Includes', $self->Includes],
        ['Contains', $self->Contains]) {
            
        my ($mode, $obj) = @$d;
        next unless $obj->size;

        my $indent = $mode ? '  ' : '';

        foreach my $grp ($obj->elements) {
            $str_out .= "$mode:\n" if $mode;
            my $last_cat = '';
            my $i=0;
            foreach my $de ($grp->elements) {
                my $txt = $de->text() or next;
                my $ev = $de->getEvidenceTagsString() || '';
                my $cat = $de->category() || ($i ? '???????' : 'RecName');
                my $type = $de->type() || ($i ? '????' : 'Full');
                $str_out .= 
                    (($type ne 'Short' && $type ne 'EC') || $cat ne $last_cat  
                        ? "$indent$cat: " : "$indent         " ); 
                $txt = $process_txt_by_type->{$type}->($txt,$i)
                    if $process_txt_by_type->{$type};
                $str_out .= "$type=$txt$ev;\n";
                $i++;
                $last_cat = $cat;
            }
        }

    }
    # build flags
    push @flags, $self->hasFragment if $self->hasFragment;
    # add flag evtag (stored as DEs self evtags!
    if (my @flag_evtag = $self->getEvidenceTags()) {
        my $i = 0;
        @flags = map {
                my $ev = $flag_evtag[$i++] || '';
                $ev = "{$ev}" if $ev;
                $_.$ev;
            } @flags;
    }
    
    $str_out .= 'Flags: '.join('; ',@flags).";\n" if @flags;
    chomp $str_out;

    return $str_out;

}


sub toText {
  my $self = shift;
  my $textRef = shift;

  unless ($self->{_dirty}) {
    return;
  }

    unless ($self->{is_old_format}) {
    # new format
        my $out_str = '';
        my $prefix = "DE   ";$prefix=' '.$prefix if $self->{indentation};
        # FIXME: evtag in new format?
        foreach my $line (split '\r?\n',$self->toString) {
            $out_str .= $prefix.$line."\n";
        }
        $self->{_dirty} = 0;
        
        return SWISS::TextFunc->insertLineGroup($textRef, $out_str, 
                                          $SWISS::TextFunc::linePattern{'DE'});
    }
    
    
  my $newText = $self->toString . $self->getEvidenceTagsString;
  $newText .= "." if $newText;
  my $prefix = "DE   ";
  my $col = $SWISS::TextFunc::lineLength;
  $col++, $prefix=" $prefix" if $self->{indentation};
  $newText = SWISS::TextFunc->wrapOn($prefix, $prefix, $col, $newText);
  $self->{_dirty} = 0;
  
  return SWISS::TextFunc->insertLineGroup($textRef, $newText, 
                                          $SWISS::TextFunc::linePattern{'DE'});

};

sub sort {
  return 1;
}

# for old DE format
# methods acting on evidence tag can be applied either to the entire DE line
# (pass a string) or to each element (passing an ARRAY reference).
# with new DE format: used to store Flags ev tag!, DE element ev tag are stored
# in corresponding DE object itself

sub addEvidenceTag { return ref $_[1] eq 'ARRAY' ? 
	 SWISS::ListBase::addEvidenceTag (@_) :
	SWISS::BaseClass::addEvidenceTag (@_)
}
sub deleteEvidenceTags { return ref $_[1] eq 'ARRAY' ? 
	 SWISS::ListBase::deleteEvidenceTags  (@_) :
	SWISS::BaseClass::deleteEvidenceTags  (@_)
}
sub getEvidenceTags { return ref $_[1] eq 'ARRAY' ? 
	 SWISS::ListBase::getEvidenceTags  (@_) :
	SWISS::BaseClass::getEvidenceTags  (@_)
}
sub getEvidenceTagsString { return ref $_[1] eq 'ARRAY' ? 
	 SWISS::ListBase::getEvidenceTagsString  (@_) :
	SWISS::BaseClass::getEvidenceTagsString  (@_)
}
sub hasEvidenceTag { return ref $_[1] eq 'ARRAY' ? 
	 SWISS::ListBase::hasEvidenceTag  (@_) :
	SWISS::BaseClass::hasEvidenceTag  (@_)
}
sub setEvidenceTags { return ref $_[1] eq 'ARRAY' ? 
	 SWISS::ListBase::setEvidenceTags  (@_) :
	SWISS::BaseClass::setEvidenceTags  (@_)
}

1;

__END__

=head1 Name

SWISS::DEs.pm

=head1 Description

B<SWISS::DEs> represents the DE lines of a UniProt Knowledgebase (Swiss-Prot 
+ TrEMBL) entry as specified in the user manual
http://www.expasy.org/sprot/userman.html.

The DEs object basically holds lists of DE objects, each of them representing a 
protein name element.
The C<elements>, C<hasFragment>, C<Includes> and C<Contains> attributes/methods 
work as follows :

 DE   RecName: Full=CAD protein;
 DE            Short=CAD;
 DE   AltName: Full=Protein rudimentary;
 DE   Includes:
 DE     RecName: Full=Glutamine-dependent carbamoyl-phosphate synthase;
 DE              EC=6.3.5.5;
 DE   Includes:
 DE     RecName: Full=Aspartate carbamoyltransferase;
 DE              EC=2.1.3.2;
 DE   Flags: Fragment;

 -= Entry::DEs =-
 elements (for each DE object, see SWISS::DE.pm documentation) :
    toText:    "CAD protein",  "CAD",       "Protein rudimentary"
    category:  "RecName",      "RecName",   "AltName"
    type:      "Full",         "Short"      "Full"    
 hasFragment : "Fragment"
 Includes : ListBase of DEs (child1, child2)
 Contains : empty ListBase

 -= child1 =-    
 elements (for each DE object) :
    toText:    "Glutamine-dependent carbamoyl-
                phosphate synthase",            "6.3.5.5"
    category:  "RecName",                       "RecName",
    type:      "Full",                          "EC"   
 hasFragment : undef

 -= child2 =-    
 elements (for each DE object) :
    toText:    "Aspartate carbamoyltransferase",  "2.1.3.2"
    category:  "RecName",                         "RecName",
    type:      "Full",                            "EC"  
 hasFragment : undef

Note: the old unstructured DE format can still be used, and will be parsed the 
same way into DE objects (but without setting their attributes 'category' and 
'type'.

 DE   CAD protein (Protein rudimentary) [Includes: Glutamine-dependent
 DE   carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate
 DE   carbamoyltransferase (EC 2.1.3.2)] (Fragment). 

 

=head1 Inherits from

SWISS::ListBase.pm

=head1 Attributes

=over

=item C<text>

The (raw) text of the DE line (without the 'DE   ' line type prefixes)

=item C<list>

Array reference to the SWISS::DE objects containing the different names for 
the entry. The first element of the list is the recommended name.
Note: use C<elements> method (inherited from ListBase) to get (and loop through)
the array of DE objetcs.

=item C<Includes>

=item C<Contains>

Each of these is a SWISS::ListBase object whose list contains a
SWISS::DEs object for each 'child' of the protein (i.e. peptide or functional
domain). See the UniProtKB user manual for an explanation. It is possible
to have both Includes and Contains in a single entry:

 DE   RecName: Full=Arginine biosynthesis bifunctional protein argJ;
 DE   Includes:
 DE     RecName: Full=Glutamate N-acetyltransferase;
 DE              EC=2.3.1.35;
 DE     AltName: Full=Ornithine acetyltransferase;
 DE              Short=OATase;
 DE     AltName: Full=Ornithine transacetylase;
 DE   Includes:
 DE     RecName: Full=Amino-acid acetyltransferase;
 DE              EC=2.3.1.1;
 DE     AltName: Full=N-acetylglutamate synthase;
 DE              Short=AGS;
 DE     RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain;
 DE   Contains:
 DE     RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain;

=item C<hasFragment>

Contains 'Fragment' or 'Fragments' (evaluates to true) if the DE lines contain 
the 'Fragment(s)' indication (in 'Flags:' line with the new DE line format), 
otherwise evaluates to false. Compare to the more robust Entry::isFragment 
which also checks the FT lines for a NON_CONS or NON_TER.

=item C<isPrecursor>

Returns 1 if the flag 'Precursor' is present (undef if not). Note: only with new
DE line format.

=back

=head1 Methods

=head2 Standard methods

=over

=item new

=item fromText

=item toText

=back

=head1 Evidence Tags

With the new DE line format, each DE element can have distinct evidence tags, 
which are stored in the DE object themself (see SWISS::DE.pm documentation). 
The evidence tags for the 'Flags' line are stored in the parent DEs object 
itself.
With the old DE line format, since the DE line did not have a fixed syntax in 
TrEMBL, it is impossible to reliably assign evidence tags separately to the 
different elements of the DE lines. Therefore, the DE line can only be evidence 
tagged as a whole, and the following methods have their prototype defined in 
SWISS::BaseClass instead of the direct parent of SWISS::DEs, SWISS::ListBase :

 addEvidenceTag
 deleteEvidenceTags
 getEvidenceTags
 getEvidenceTagsString
 hasEvidenceTag
 setEvidenceTags

example :

 $evidenceTag = $entry->Stars->EV->addEvidence('P', 'DEfix', '-', 'v1.3');
 # add global DE evtag if old DE line format, 'Flags' evtag if new format
 $entry -> DEs -> addEvidenceTag($evidenceTag);