Source Code for Module Bio.Graphics.GenomeDiagram._CrossLink

 1  # Copyright 2011 by Peter Cock.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5  ################################################################################ 
 6   
 7  """Genome Diagram Feature cross-link module 
 8  """ 
 9   
10  from reportlab.lib import colors 
11   
12   
13 -class CrossLink(object): 
14      """Hold information for drawing a cross link between features. 
15      """ 
16 -    def __init__(self, featureA, featureB, 
17                   color=colors.lightgreen, border=None, flip=False): 
18          """Create a new cross link. 
19   
20          Arguments featureA and featureB should GenomeDiagram feature objects, 
21          or 3-tuples (track object, start, end), and currently must be on 
22          different tracks. 
23   
24          The color and border arguments should be ReportLab colour objects, or 
25          for border use a boolean False for no border, otherwise it defaults to 
26          the same as the main colour. 
27   
28          The flip argument draws an inverted cross link, useful for showing a 
29          mapping where one sequence has been reversed. It is conventional to 
30          also use a different colour (e.g. red for simple links, blue for any 
31          flipped links). 
32          """ 
33          # Initialise attributes 
34          self.featureA = featureA 
35          self.featureB = featureB 
36          self.color = color            # default color to draw the feature 
37          self.border = border 
38          self.flip = flip 
39   
40      @property 
41 -    def startA(self): 
42          try: 
43              return self.featureA.start 
44          except AttributeError: 
45              track, start, end = self.featureA 
46              return start 
47   
48      @property 
49 -    def endA(self): 
50          try: 
51              return self.featureA.end 
52          except AttributeError: 
53              track, start, end = self.featureA 
54              return end 
55   
56 -    def _trackA(self, tracks): 
57          try: 
58              track, start, end = self.featureA 
59              assert track in tracks 
60              return track 
61          except: 
62              for track in tracks: 
63                  for feature_set in track.get_sets(): 
64                      if hasattr(feature_set, "features"): 
65                          if self.featureA in feature_set.features.values(): 
66                              return track 
67              return None 
68   
69      @property 
70 -    def startB(self): 
71          try: 
72              return self.featureB.start 
73          except AttributeError: 
74              track, start, end = self.featureB 
75              return start 
76   
77      @property 
78 -    def endB(self): 
79          try: 
80              return self.featureB.end 
81          except AttributeError: 
82              track, start, end = self.featureB 
83              return end 
84   
85 -    def _trackB(self, tracks): 
86          try: 
87              track, start, end = self.featureB 
88              assert track in tracks 
89              return track 
90          except: 
91              for track in tracks: 
92                  for feature_set in track.get_sets(): 
93                      if hasattr(feature_set, "features"): 
94                          if self.featureB in feature_set.features.values(): 
95                              return track 
96              return None 
97