Changeset 119 for plone4bio.base/trunk

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Ignore:
Timestamp:
10/19/09 00:34:36 (3 years ago)
Author:
mauro
Message:

fix #14

Location:
plone4bio.base/trunk
Files:
5 modified

Legend:

Unmodified
Added
Removed

  • plone4bio.base/trunk/docs/AUTHORS.txt

    r8 r119  
    1 Mauro Amico - amico (at) biodec.com 
     1Maintainer 
     2---------- 
     3 
     4* Mauro Amico (mauro AT biodec DOT com) is the active maintainer of the *plone4bio.base* package. 
     5 
     6Thanks 
     7------ 
     8 
     9* James Procter 
     10 
     11 

  • plone4bio.base/trunk/docs/CHANGES.txt

    r117 r119  
    1010 
    1111* fix #8 "sequence feature diagram generator does not support feature types containing ' '" 
     12 
     13* fix #14 "off-by one error in feature start for biosql sequence features" 
     14 
    1215 
    1316plone4bio.base 1.0.1 (2009-09-21) 

  • plone4bio.base/trunk/src/plone4bio/base/browser/templates/features.pt

    r45 r119  
    2929                                                <tr 
    3030                                                        tal:define="oddrow repeat/feature/odd; 
    31                                                                     start python:'Start: ' + str(feature.location.start.position); 
     31                                                                    start python:'Start: ' + str(feature.location.start.position + 1); 
    3232                                                                    end python:'End: ' + str(feature.location.end.position);" 
    3333                                                        tal:attributes="class python:(oddrow and 'even' or 'odd')"> 

  • plone4bio.base/trunk/src/plone4bio/base/png/perl/graphics.pm

    r45 r119  
    230230      foreach (@$boxes){ 
    231231        my ($feature,$left,$top,$right,$bottom,$track) = @$_; 
    232         my $start = $feature->start - 1; 
     232        my $start = $feature->start; 
    233233        my $end = $feature->end; 
    234234        my $tag = eval {$feature->method} || $feature->primary_tag; 

  • plone4bio.base/trunk/src/plone4bio/base/png/seqrecord.py

    r117 r119  
    4141    seqrecord = context.seqrecord 
    4242    seqrecord.name = seqrecord.name[:16] 
     43    for f in seqrecord.features: 
     44        f.type = f.type.replace(" ", "_") 
    4345    SeqIO.write([seqrecord, ], genbank, "genbank") 
    4446    (stdoutdata, stderrdata) = graphics.communicate(genbank.getvalue())