[Bioperl-guts-l] bioperl commit

Brian Osborne bosborne at pub.open-bio.org
Thu Jan 15 07:35:28 EST 2004


bosborne
Thu Jan 15 07:35:28 EST 2004
Update of /home/repository/bioperl/bioperl-live/doc/howto/sgml
In directory pub.open-bio.org:/tmp/cvs-serv25234

Modified Files:
	Feature-Annotation.sgml 
Log Message:
Edits

bioperl-live/doc/howto/sgml Feature-Annotation.sgml,1.8,1.9
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/sgml/Feature-Annotation.sgml,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/bioperl/bioperl-live/doc/howto/sgml/Feature-Annotation.sgml	2004/01/15 12:28:32	1.8
+++ /home/repository/bioperl/bioperl-live/doc/howto/sgml/Feature-Annotation.sgml	2004/01/15 12:35:28	1.9
@@ -329,6 +329,8 @@
      tRNA            join(103..111,121..157)
                      /gene="Phe-tRNA"
       </programlisting>
+    </para>
+    <para>
       To get the sequence string from the start to the end of the tRNA
       feature use <function>seq()</function>. To get the spliced
       sequence string, accounting for the start and end locations of 
@@ -463,6 +465,8 @@
 	my $start = $feat_object->location->start;
 	my $end = $feat_object->location->end;
          </programlisting>
+    </para>
+    <para>
       By now you know that the <function>location()</function> method returns
       an object, in this case a Location object, with an <function>
 	end()</function> method.
@@ -652,6 +656,8 @@
 	  print "author: ",$value->authors(), "\n";
 	}
       </programlisting>
+    </para>
+    <para>
       There's also title(), publisher(), medline(), editors(),
       database(), pubmed() and a number of other methods.
     </para>
@@ -755,6 +761,8 @@
 	# then add the feature to the sequence
 	$seq_obj->add_SeqFeature($feat_object);
       </programlisting>
+      </para>
+    <para>
     The <function>add_SeqFeature()</function> method will also accept an array
     of SeqFeature objects.
     </para>
@@ -767,6 +775,8 @@
 	$db_link->primary_id('2367');
 	$feat->annotation->add_Annotation('dblink',$db_link);
 	</programlisting>
+    </para>
+    <para>
       Note that the first argument to <function>add_Annotation()</function>
       is the tag name, 'dblink', this is the general idiom for adding
       Annotations.



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