[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Sat Dec 27 15:24:52 EST 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv30103/Perl/MOBY

Modified Files:
	CommonSubs.html CommonSubs.pm 
Log Message:
changed my mind and decided to return both the object name as well as its LSID, since the latter is a bit arcane sometimes.

moby-live/Perl/MOBY CommonSubs.html,1.7,1.8 CommonSubs.pm,1.37,1.38
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2003/12/27 20:15:45	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2003/12/27 20:24:52	1.8
@@ -492,10 +492,10 @@
  name     : whichDeepestParentObject
  function : select the parent node from nodeList that is
             closest to the querynode
- usage    : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList)
+ usage    : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList)
  args     : $CENTRAL - your MOBY::Client::Central object
-            $queryNode - the node I am interested in
-            \@nodelist - the list of nodes that I know about
+            $queryTerm - the object type I am interested in
+            \@termlist - the list of object types that I know about
  returns  : an ontology term as a scalar, or undef if there
             is no parent of this node in the nodelist</pre>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -u -r1.37 -r1.38
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2003/12/27 20:15:45	1.37
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2003/12/27 20:24:52	1.38
@@ -1080,10 +1080,10 @@
  name     : whichDeepestParentObject
  function : select the parent node from nodeList that is
             closest to the querynode
- usage    : whichDeepestParentObject($CENTRAL, $queryNode, \@nodeList)
+ usage    : ($term, $lsid) = whichDeepestParentObject($CENTRAL, $queryTerm, \@termList)
  args     : $CENTRAL - your MOBY::Client::Central object
-            $queryNode - the node I am interested in
-            \@nodelist - the list of nodes that I know about
+            $queryTerm - the object type I am interested in
+            \@termlist - the list of object types that I know about
  returns  : an ontology term as a scalar, or undef if there
             is no parent of this node in the nodelist
 
@@ -1093,21 +1093,21 @@
 sub whichDeepestParentObject {
     use MOBY::Client::OntologyServer;
     my ($CENTRAL, $queryTerm, $termlist) = @_;
-    return undef unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/));
+    return (undef,undef) unless ($CENTRAL && $queryTerm && $termlist && (ref($termlist) =~ /ARRAY/));
     my %nodeLSIDs;
     foreach (@$termlist){ # get list of known LSIDs
         my $lsid = $CENTRAL->ObjLSID($_);
-        $nodeLSIDs{$lsid}=1;
+        $nodeLSIDs{$lsid}=$_;
     }
     my $queryLSID = $CENTRAL->ObjLSID($queryTerm);
-    return undef unless keys(%nodeLSIDs);
+    return (undef, undef) unless keys(%nodeLSIDs);
     my $isa = $CENTRAL->ISA($queryTerm, 'Object'); # set the complete parentage in the cache if it isn't already
-    return undef unless $isa; # this should return true or we are in BIIIG trouble!
-    my @lsids = $CENTRAL->ISA_CACHE($queryTerm);  # returns **LSIDs** in order, so we can shift our way back to root
-    while (my $thisnode = shift @lsids){  # @isas are lsid's
-        return $thisnode if $nodeLSIDs{$thisnode};
+    return (undef, undef) unless $isa; # this should return true or we are in BIIIG trouble!
+    my @ISAlsids = $CENTRAL->ISA_CACHE($queryTerm);  # returns **LSIDs** in order, so we can shift our way back to root
+    while (my $thislsid = shift @ISAlsids){  # @isas are lsid's
+        return ($nodeLSIDs{$thislsid},$thislsid) if $nodeLSIDs{$thislsid};
     }
-    return undef
+    return (undef, undef);
 }
 
 sub _makeXrefType {