Add support for giving GenomeDiagram features a URL, useful with SVG …

…output from ReportLab 2.4

Bio/Graphics/GenomeDiagram/_AbstractDrawer.py

@@ -118,7 +118,9 @@ def draw_box((x1, y1), (x2, y2),
     return Polygon([x1, y1, x2, y1, x2, y2, x1, y2],
                    strokeColor=strokecolor,
                    fillColor=color,
-                   strokewidth=0)
+                   strokewidth=0,
+                   **kwargs)
+
 
 def draw_polygon(list_of_points,
                  color=colors.lightgreen, border=None, colour=None,
@@ -153,7 +155,8 @@ def draw_polygon(list_of_points,
     return Polygon(xy_list,
                    strokeColor=strokecolor,
                    fillColor=color,
-                   strokewidth=0)
+                   strokewidth=0,
+                   **kwargs)
 
 
 def draw_arrow((x1, y1), (x2, y2), color=colors.lightgreen, border=None,
@@ -222,7 +225,8 @@ def draw_arrow((x1, y1), (x2, y2), color=colors.lightgreen, border=None,
                    strokeWidth=1,
                    #default is mitre/miter which can stick out too much:
                    strokeLineJoin=1, #1=round
-                   fillColor=color)
+                   fillColor=color,
+                   **kwargs)
 
 def angle2trig(theta):
     """ angle2trig(angle)

Bio/Graphics/GenomeDiagram/_CircularDrawer.py

@@ -408,15 +408,23 @@ def get_feature_sigil(self, feature, locstart, locend, **kwargs):
         draw_methods = {'BOX': self._draw_arc,
                         'ARROW': self._draw_arc_arrow,
                         }
+
+        # Get sigil for the feature, location dependent on the feature strand        
+        method = draw_methods[feature.sigil]
         kwargs['head_length_ratio'] = feature.arrowhead_length
         kwargs['shaft_height_ratio'] = feature.arrowshaft_height
 
-        # Get sigil for the feature, location dependent on the feature strand        
-        method = draw_methods[feature.sigil]
+        #Support for clickable links... needs ReportLab 2.4 or later
+        #which added support for links in SVG output.
+        if hasattr(feature, "url") :
+            kwargs["hrefURL"] = feature.url
+            kwargs["hrefTitle"] = feature.name
+
         if feature.color == colors.white:
             border = colors.black
         else:
             border = feature.color
+
         if feature.strand == 1:
             sigil = method(ctr, top, startangle, endangle, feature.color,
                            border, orientation='right', **kwargs)
@@ -426,6 +434,7 @@ def get_feature_sigil(self, feature, locstart, locend, **kwargs):
         else:
             sigil = method(btm, top, startangle, endangle, feature.color,
                            border, **kwargs)
+
         if feature.label:   # Feature needs a label
             label = String(0, 0, feature.name.strip(),
                            fontName=feature.label_font,
@@ -1043,7 +1052,6 @@ def _draw_arc_arrow(self, inner_radius, outer_radius, startangle, endangle,
                 x1,y1 = (x0+inner_radius*endsin, y0+inner_radius*endcos)
                 x2,y2 = (x0+outer_radius*endsin, y0+outer_radius*endcos)
                 x3,y3 = (x0+middle_radius*startsin, y0+middle_radius*startcos)
-
             #return draw_polygon([(x1,y1),(x2,y2),(x3,y3)], color, border,
             #                    stroke_line_join=1)
             return Polygon([x1,y1,x2,y2,x3,y3],
@@ -1056,7 +1064,8 @@ def _draw_arc_arrow(self, inner_radius, outer_radius, startangle, endangle,
                         fillColor=color,
                         #default is mitre/miter which can stick out too much:
                         strokeLineJoin=1, #1=round
-                        strokewidth=0)
+                        strokewidth=0,
+                        **kwargs)
             #Note reportlab counts angles anti-clockwise from the horizontal
             #(as in mathematics, e.g. complex numbers and polar coordinates)
             #but we use clockwise from the vertical.  Also reportlab uses
@@ -1094,7 +1103,8 @@ def _draw_arc_arrow(self, inner_radius, outer_radius, startangle, endangle,
                         fillColor=color,
                         #default is mitre/miter which can stick out too much:
                         strokeLineJoin=1, #1=round
-                        strokewidth=0)
+                        strokewidth=0,
+                        **kwargs)
             #Note reportlab counts angles anti-clockwise from the horizontal
             #(as in mathematics, e.g. complex numbers and polar coordinates)
             #but we use clockwise from the vertical.  Also reportlab uses

Bio/Graphics/GenomeDiagram/_LinearDrawer.py

@@ -779,7 +779,14 @@ def get_feature_sigil(self, feature, x0, x1, fragment, **kwargs):
         kwargs['head_length_ratio'] = feature.arrowhead_length
         kwargs['shaft_height_ratio'] = feature.arrowshaft_height
 
+        #Support for clickable links... needs ReportLab 2.4 or later
+        #which added support for links in SVG output.
+        if hasattr(feature, "url") :
+            kwargs["hrefURL"] = feature.url
+            kwargs["hrefTitle"] = feature.name
+
         strand = feature.strand
+
         # Get sigil for the feature, location dependent on the feature strand
         if strand == 1:
             sigil = method((x0, ctr), (x1, top), color=feature.color,

Tests/test_GenomeDiagram.py

@@ -491,6 +491,14 @@ def test_partial_diagram(self):
                 #Out of frame (too far right)
                 continue
 
+            #This URL should work in SVG output from recent versions
+            #of ReportLab.  You need ReportLab 2.4 or later
+            try :
+                url = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"+\
+                      "?db=protein&id=%s" % feature.qualifiers["protein_id"][0]
+            except KeyError :
+                url = None
+
             #Note that I am using strings for color names, instead
             #of passing in color objects.  This should also work!
             if len(gds_features) % 2 == 0:
@@ -500,6 +508,7 @@ def test_partial_diagram(self):
             #Checking it can cope with the old UK spelling colour.
             #Also show the labels perpendicular to the track.
             gds_features.add_feature(feature, colour=color,
+                                     url = url,
                                      sigil="ARROW",
                                      label_position = "start",
                                      label_size = 8,
@@ -568,13 +577,23 @@ def test_diagram_via_methods_pdf(self):
                 index  = genbank_entry.seq.find(site, start=index)
                 if index == -1 : break
                 feature = SeqFeature(FeatureLocation(index, index+6), strand=None)
-                gds_features.add_feature(feature, color=color,
-                                            #label_position = "middle",
-                                            label_size = 10,
-                                            label_color=color,
-                                            #label_angle = 90,
-                                            name=name,
-                                            label=True)
+
+                #This URL should work in SVG output from recent versions
+                #of ReportLab.  You need ReportLab 2.4 or later
+                try :
+                    url = "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi"+\
+                          "?db=protein&id=%s" % feature.qualifiers["protein_id"][0]
+                except KeyError :
+                    url = None
+
+                gds_features.add_feature(feature, color = color,
+                                         url = url,
+                                         #label_position = "middle",
+                                         label_size = 10,
+                                         label_color = color,
+                                         #label_angle = 90,
+                                         name = name,
+                                         label = True)
                 index += len(site)
             del index