/* Adding features to a RichSequence. */

foisys · andreasprlic · commit d582fa06f262 · 2016-04-09T10:57:22.000-07:00
diff --git a/_wikis/BioJava:BioJavaXDocs.md b/_wikis/BioJava:BioJavaXDocs.md
@@ -1709,24 +1709,24 @@ Features
 
 The best way to create a new feature is like this:
 
-<java> Feature.Template templ = new RichFeature.Template(); // create a
-feature template templ.location = ...; // assign the feature template a
-location, type, and source templ.typeTerm = ...; templ.sourceTerm = ...;
-templ.annotation = new SimpleRichAnnotation(); // assign the rest of the
-necessary stuff templ.featureRelationshipSet = new TreeSet();
-templ.rankedCrossRefs = new TreeSet(); RichSequence rs = ...; // get a
-sequence from somewhere RichFeature feat =
-rs.createFeature(RichFeature.Template()); // make a new feature on that
-sequence </java>
+<java> // create a feature template Feature.Template templ = new
+RichFeature.Template(); // assign the feature template a location, type,
+and source templ.location = ...; templ.typeTerm = ...; templ.sourceTerm
+= ...; // assign the rest of the necessary stuff templ.annotation = new
+SimpleRichAnnotation(); templ.featureRelationshipSet = new TreeSet();
+templ.rankedCrossRefs = new TreeSet(); // get a sequence from somewhere
+RichSequence rs = ...; // make a new feature on that sequence
+RichFeature feat = rs.createFeature(RichFeature.Template()); </java>
 
 Alternatively, you can start with a completely empty dummy feature and
 just customise the bits you need:
 
-<java> RichSequence rs = ...; // get a sequence RichFeature feat =
-RichFeature.Tools.makeEmptyFeature(); // make an empty feature
-feat.setParent(rs): // associate sequence with feature
-rs.getFeatureSet().add(feat); // associate feature with sequence //
-customise the feature here, eg. location, type, source etc. </java>
+<java> // get a sequence RichSequence rs = ...; // make an empty feature
+RichFeature feat = RichFeature.Tools.makeEmptyFeature(); // associate
+sequence with feature feat.setParent(rs): // associate feature with
+sequence rs.getFeatureSet().add(feat);
+
+// customise the feature here, eg. location, type, source etc. </java>
 
 ### Qualifiers as annotations.
 
diff --git a/_wikis/BioJava:BioJavaXDocs.mediawiki b/_wikis/BioJava:BioJavaXDocs.mediawiki
@@ -1669,24 +1669,34 @@ The sequences of locations on the negative strand will be reverse complemented b
 The best way to create a new feature is like this:
 
 <java>
-Feature.Template templ = new RichFeature.Template();           // create a feature template
-templ.location = ...;                                          // assign the feature template a location, type, and source
+// create a feature template
+Feature.Template templ = new RichFeature.Template();           
+// assign the feature template a location, type, and source
+templ.location = ...;                                          
 templ.typeTerm = ...;
 templ.sourceTerm = ...;  
-templ.annotation = new SimpleRichAnnotation();                 // assign the rest of the necessary stuff
+// assign the rest of the necessary stuff
+templ.annotation = new SimpleRichAnnotation();                 
 templ.featureRelationshipSet = new TreeSet();
 templ.rankedCrossRefs = new TreeSet();
-RichSequence rs = ...;                                         // get a sequence from somewhere
-RichFeature feat = rs.createFeature(RichFeature.Template());   // make a new feature on that sequence
+// get a sequence from somewhere
+RichSequence rs = ...;                                         
+// make a new feature on that sequence
+RichFeature feat = rs.createFeature(RichFeature.Template());   
 </java>
 
 Alternatively, you can start with a completely empty dummy feature and just customise the bits you need:
 
 <java>
-RichSequence rs = ...;                                     // get a sequence
-RichFeature feat = RichFeature.Tools.makeEmptyFeature();   // make an empty feature
-feat.setParent(rs):                                        // associate sequence with feature
-rs.getFeatureSet().add(feat);                              // associate feature with sequence
+// get a sequence
+RichSequence rs = ...;                                     
+// make an empty feature
+RichFeature feat = RichFeature.Tools.makeEmptyFeature();   
+// associate sequence with feature
+feat.setParent(rs):                                        
+// associate feature with sequence
+rs.getFeatureSet().add(feat);                              
+
 // customise the feature here, eg. location, type, source etc.
 </java>
 
