[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Mon Jul 14 15:52:14 UTC 2003
mwilkinson
Mon Jul 14 11:52:14 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv763/MOBY
Modified Files:
CommonSubs.html CommonSubs.pm
Log Message:
found documentation errors
moby-live/Perl/MOBY CommonSubs.html,1.1,1.2 CommonSubs.pm,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/07/13 20:09:32 1.1
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html 2003/07/14 15:52:14 1.2
@@ -18,6 +18,7 @@
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#authors">AUTHORS</a></li>
+ <li><a href="#methods">METHODS</a></li>
<ul>
<li><a href="#getsimplearticleids">getSimpleArticleIDs</a></li>
@@ -25,7 +26,7 @@
<li><a href="#simpleresponse">simpleResponse</a></li>
<li><a href="#responseheader">responseHeader</a></li>
<li><a href="#responsefooter">responseFooter</a></li>
- <li><a href="#getsimplearticleobjects">getSimpleArticleObjects</a></li>
+ <li><a href="#getinputarticles">getInputArticles</a></li>
<li><a href="#getnodecontentwitharticle">getNodeContentWithArticle</a></li>
</ul>
@@ -43,9 +44,10 @@
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
-<p>use MOBY::CommonSubs qw(:all);
-my @ids = getSimpleArticleIDs(``NCBI_gi'', \@SimpleArticles);
-my $ns = getSimpleArticleNamespaceURI($SimpleArticle);</p>
+<pre>
+ use MOBY::CommonSubs qw(:all);
+ my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
+ my $ns = getSimpleArticleNamespaceURI($SimpleArticle);</pre>
<p>
</p>
<hr />
@@ -62,6 +64,10 @@
<p>BioMOBY Project: <a href="http://www.biomoby.org">http://www.biomoby.org</a></p>
<p>
</p>
+<hr />
+<h1><a name="methods">METHODS</a></h1>
+<p>
+</p>
<h2><a name="getsimplearticleids">getSimpleArticleIDs</a></h2>
<pre>
name : getSimpleArticleIDs
@@ -131,7 +137,7 @@
</moby:MOBY></pre>
<p>
</p>
-<h2><a name="getsimplearticleobjects">getSimpleArticleObjects</a></h2>
+<h2><a name="getinputarticles">getInputArticles</a></h2>
<pre>
name : getInputArticles
function : get the Simple/Collection articles for each input query, in order
@@ -174,6 +180,8 @@
notes : This was written for the purpose of getting the values of
String, Integer, Float, Date_Time, and other such primitives.
For example, in the following XML:
+ ...
+ ...
<moby:Query>
<queryInput>
<Simple>
@@ -183,14 +191,21 @@
</Sequence>
</Simple>
</queryInput>
- </moby:Query></pre>
-<pre>
+ </moby:Query>
+ ...
+ ...
+
would be analysed as follows:
- use XML::DOM;
- $p = new XML::DOM::Parser;
- $dom = $p->parse($XML);
- @sequence = getNodeContentWithArticle($dom, "String", "SequenceString");
- print "Sequence was $sequence[0]";</pre>
+
+ my ($query) = @_; # get the incoming MOBY query XML
+ my @queries = getInputArticles($query); # returns DOM nodes
+ foreach (@queries){
+ my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
+ foreach my $input(@inputs){
+ @sequence = getNodeContentWithArticle($_, "String", "SequenceString");
+ print "Sequence was ".(join "", @sequence)."\n"; # join all lines of string
+ }
+ }</pre>
</body>
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/07/13 20:10:20 1.2
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm 2003/07/14 15:52:14 1.3
@@ -11,9 +11,9 @@
=head1 SYNOPSIS
-use MOBY::CommonSubs qw(:all);
-my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
-my $ns = getSimpleArticleNamespaceURI($SimpleArticle);
+ use MOBY::CommonSubs qw(:all);
+ my @ids = getSimpleArticleIDs("NCBI_gi", \@SimpleArticles);
+ my $ns = getSimpleArticleNamespaceURI($SimpleArticle);
=head1 DESCRIPTION
@@ -257,7 +257,7 @@
-=head2 getSimpleArticleObjects
+=head2 getInputArticles
name : getInputArticles
function : get the Simple/Collection articles for each input query, in order
@@ -329,6 +329,8 @@
notes : This was written for the purpose of getting the values of
String, Integer, Float, Date_Time, and other such primitives.
For example, in the following XML:
+ ...
+ ...
<moby:Query>
<queryInput>
<Simple>
@@ -339,13 +341,20 @@
</Simple>
</queryInput>
</moby:Query>
-
+ ...
+ ...
+
would be analysed as follows:
- use XML::DOM;
- $p = new XML::DOM::Parser;
- $dom = $p->parse($XML);
- @sequence = getNodeContentWithArticle($dom, "String", "SequenceString");
- print "Sequence was $sequence[0]";
+
+ my ($query) = @_; # get the incoming MOBY query XML
+ my @queries = getInputArticles($query); # returns DOM nodes
+ foreach (@queries){
+ my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
+ foreach my $input(@inputs){
+ @sequence = getNodeContentWithArticle($_, "String", "SequenceString");
+ print "Sequence was ".(join "", @sequence)."\n"; # join all lines of string
+ }
+ }
=cut
More information about the MOBY-guts
mailing list