[Bioperl-guts-l] bioperl-live/doc/howto/xml Feature-Annotation.xml, 1.8, 1.9

[Brian Osborne]

Update of /home/repository/bioperl/bioperl-live/doc/howto/xml
In directory pub.open-bio.org:/tmp/cvs-serv14223/xml

Modified Files:
	Feature-Annotation.xml 
Log Message:
Correct


Index: Feature-Annotation.xml
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/xml/Feature-Annotation.xml,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Feature-Annotation.xml	26 Oct 2005 12:20:10 -0000	1.8
--- Feature-Annotation.xml	6 Nov 2005 17:24:04 -0000	1.9
***************
*** 1169,1187 ****
        addition of data that's not explicitly accounted for by its
        methods, that's what the "-tag" is for, above.
!       If you want to add your own custom data to a feature you could
!       use the "-tag" tag or you could add values after the object has 
!       been created:
      </para>
      <para>
        <programlisting>
! 	$feat->add_tag_value("match1","PF000123 e-7.2");
! 	$feat->add_tag_value("match2","PF002534 e-3.1");
  	
! 	my @arr = $feat->get_all_tags;
! 	for my $tag (@arr) {
! 	  print $tag,":",$feat->get_tag_values($tag),"  ";
! 	}
!         # prints out:
! 	# author:john  match1:PF000123 e-7.2  match2:PF002534 e-3.1  note:TATA box
        </programlisting>
      </para>
--- 1169,1198 ----
        addition of data that's not explicitly accounted for by its
        methods, that's what the "-tag" is for, above.
!       Since the value passed to "-tag" could be any kind of scalar,
!       like a reference, it's clear that this approach should be able
!       handle just about any sort of data. 
! 	 </para>
! 	 <para>
! 		You can build on the Feature as well. 
! 		Here we'll add some Annotations to the newly-created Feature:
      </para>
      <para>
        <programlisting>
! 	$feat->add_Annotation("match1","PF000123 e-7.2");
! 	$feat->add_Annotation("match2","PF002534 e-3.1");
  	
! 	my @tags = $feat->get_all_tags;
!         for my $tag (@tags) {
!            for my $val ( $feat->get_tag_values($tag) ) {
! 		   print $tag,":",$val,"\n";
! 	   }
!    }
! 
! # prints out:
! # match2:PF002534 e-3.1
! # match1:PF000123 e-7.2
! # author:john
! # note:TATA box
! # start: 10 end: 22
        </programlisting>
      </para>
***************
*** 1189,1198 ****
      </para>
      <para>
!       Since the value passed to "-tag" could be any kind of scalar,
!       like a reference, it's clear that this approach should be able
!       handle just about any sort of data.
      </para>
      <para>
!       Once the feature is created it can be associated with our sequence:
      </para>
      <para>
--- 1200,1208 ----
      </para>
      <para>
! 
      </para>
      <para>
!       Once the feature, and its annotations, are created it can be
! 		associated with a sequence:
      </para>
      <para>
***************
*** 1234,1238 ****
      <para>
        Now let's examine what we've created by writing the contents of
!       <varname>$seq_obj</varname> to a Genbank file called "test.gb":
      </para>
      <para>
--- 1244,1251 ----
      <para>
        Now let's examine what we've created by writing the contents of
!       <varname>$seq_obj</varname> to a Genbank file called "test.gb".
! 		We should see a sequence, an Annotation associated with the
!       sequence, a sequence Feature, and Annotations associated with 
! 		the Feature:
      </para>
      <para>