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.\" ========================================================================
.\"
.IX Title "SWISS::GNs 3pm"
.TH SWISS::GNs 3pm "2006-01-26" "perl v5.10.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "Name"
.IX Header "Name"
SWISS::GNs.pm
.SH "Description"
.IX Header "Description"
\&\fBSWISS::GNs\fR represents the \s-1GN\s0 lines within an SWISS-PROT + TrEMBL
entry as specified in the user manual
 http://www.expasy.org/sprot/userman.html . The GNs object is a 
container object which holds a list of SWISS::GeneGroup objects.
.SH "Inherits from"
.IX Header "Inherits from"
SWISS::ListBase.pm
.SH "Attributes"
.IX Header "Attributes"
.ie n .IP """list""" 4
.el .IP "\f(CWlist\fR" 4
.IX Item "list"
.Vb 1
\&  Each list element is a SWISS::GeneGroup object.
.Ve
.ie n .IP """and"" \fI(deprecated, for old format only)\fR" 4
.el .IP "\f(CWand\fR \fI(deprecated, for old format only)\fR" 4
.IX Item "and (deprecated, for old format only)"
.Vb 1
\&  Delimiter used between genes. Defaults to " AND ".
.Ve
.ie n .IP """or"" \fI(deprecated, for old format only)\fR" 4
.el .IP "\f(CWor\fR \fI(deprecated, for old format only)\fR" 4
.IX Item "or (deprecated, for old format only)"
.Vb 1
\&  Delimiter used between gene names. Defaults to " OR ".
.Ve
.SH "Methods"
.IX Header "Methods"
.SS "Standard methods"
.IX Subsection "Standard methods"
.IP "new" 4
.IX Item "new"
.PD 0
.IP "fromText" 4
.IX Item "fromText"
.IP "toText" 4
.IX Item "toText"
.PD
.SS "Reading/Writing methods"
.IX Subsection "Reading/Writing methods"
.IP "text [($newText)]" 4
.IX Item "text [($newText)]"
Sets the text of the \s-1GN\s0 line to the parameter if it is present, and returns
the (unwrapped) text of the line.  Also sets 'and' and 'or' delimiters to 
the first occurrences of the words \*(L"\s-1OR\s0\*(R" and \*(L"\s-1AND\s0\*(R" in the line, conserving
the case.
.IP "lowercase \fI(deprecated, for old format only)\fR" 4
.IX Item "lowercase (deprecated, for old format only)"
Sets the GNs::and and GNs::or delimiters to their lower case
values.
.IP "uppercase \fI(deprecated, for old format only)\fR" 4
.IX Item "uppercase (deprecated, for old format only)"
Sets the GNs::and and GNs::or delimiters to their upper case
values.
.IP "\fIgetFirst()\fR" 4
.IX Item "getFirst()"
Returns first gene name in gene line
.IP "getTags($target)" 4
.IX Item "getTags($target)"
Returns evidence tags associated with \f(CW$target\fR
.Sp
\&\f(CW$target\fR is a string
.IP "isPresent($target)" 4
.IX Item "isPresent($target)"
Returns 1 if \f(CW$target\fR is present in the \s-1GN\s0 line
.Sp
\&\f(CW$target\fR is a string
.IP "needsReCasing($target)" 4
.IX Item "needsReCasing($target)"
If \f(CW$target\fR is present in the \s-1GN\s0 line, but wrongly cased, method returns the
matching name in its current case
.Sp
\&\f(CW$target\fR is a string
.ie n .IP "replace($newName, $target, $evidenceTag)" 4
.el .IP "replace($newName, \f(CW$target\fR, \f(CW$evidenceTag\fR)" 4
.IX Item "replace($newName, $target, $evidenceTag)"
Replaces the first \s-1GN\s0 object in the \s-1GN\s0 line whose text attribute is \f(CW$target\fR with
a new \s-1GN\s0 object whose text attribute is set to \f(CW$newName\fR and whose evidenceTags
attribute is is set using values set by splitting \f(CW$evidenceTag\fR on /, / (as name
is not being changed, programs should keep old tag and add new tag).  Does 
nothing if \f(CW$target\fR is not found.
.IP "delete($target)" 4
.IX Item "delete($target)"
Removes synonym/single\-member gene group matching \f(CW$target\fR. Note that if a \*(L"Name\*(R" 
is deleted, the first \*(L"Synonym\*(R" will be promoted to \*(L"Name\*(R"
.ie n .IP "addAsNewSynonym($newName, $target, $evidenceTag, $location)" 4
.el .IP "addAsNewSynonym($newName, \f(CW$target\fR, \f(CW$evidenceTag\fR, \f(CW$location\fR)" 4
.IX Item "addAsNewSynonym($newName, $target, $evidenceTag, $location)"
Adds a new \s-1GN\s0 object (with text attribute set to new \f(CW$newName\fR, and evidenceTags
attribute set to ($evidenceTag)), as a synonym to the first gene group in which
\&\f(CW$target\fR is a gene name.  Does nothing if \f(CW$target\fR is not found.  Will not add a
duplicate gene name.  \f(CW$location\fR determines where in gene group new object is
added: if \f(CW$location\fR == 1, 2, 3, ..., new object added in the 1st, 2nd, 3rd, ... 
position; if \f(CW$location\fR == 0, new object added before \f(CW$target\fR; if \f(CW$location\fR
== \-1, new object added after \f(CW$target\fR (default); if \f(CW$location\fR == \-2, new object
added at end of gene group.  Note that if the new synonym is inserted in the 
first postion, it will become the \*(L"Name\*(R" and the previous \*(L"Name\*(R" will be downgraded
to first \*(L"Synonym\*(R"
.ie n .IP "addAsNewGeneGroup($newName, $target, $evidenceTag, $location)" 4
.el .IP "addAsNewGeneGroup($newName, \f(CW$target\fR, \f(CW$evidenceTag\fR, \f(CW$location\fR)" 4
.IX Item "addAsNewGeneGroup($newName, $target, $evidenceTag, $location)"
Adds a new GeneGroup object, comprising 1 \s-1GN\s0 object (with text attribute set to
new \f(CW$newName\fR, and evidenceTags attribute set to ($evidenceTag)). Will not add a
duplicate gene name.  \f(CW$location\fR and \f(CW$target\fR determine where in GNs line new 
group is added: if \f(CW$location\fR == 1, 2, 3, ..., new object added in the 1st, 2nd,
3rd, ... position; if \f(CW$location\fR == 0, new object added before \f(CW$target\fR; if
\&\f(CW$location\fR == \-1, new object added after \f(CW$target\fR (default); if \f(CW$location\fR == \-2,
new object added at end of GNs line.  Does nothing if \f(CW$target\fR is not found, and
\&\f(CW$location\fR == 0 or \-1; otherwise \f(CW$target\fR does not need to be set.
.ie n .IP "replaceGeneGroup($newGeneGroup, $target)" 4
.el .IP "replaceGeneGroup($newGeneGroup, \f(CW$target\fR)" 4
.IX Item "replaceGeneGroup($newGeneGroup, $target)"
Replaces the first gene group containing \f(CW$target\fR with \f(CW$newGeneGroup\fR.  Creating
the \f(CW$newGeneGroup\fR correctly is the user's responsibility
.IP "getGeneGroup($target)" 4
.IX Item "getGeneGroup($target)"
Returns the first gene group that contains \f(CW$target\fR
.IP "\fIsetToOr()\fR" 4
.IX Item "setToOr()"
Retruns a new GNs object, but with all GNs objects in a single gene group.  
Needed when adding 'C' to 'A and B', when the relationship of 'C' to 'A' and 
\&'B' is unknown: the universal use of ' or ' is the default delimeter for TrEMBL 
entries
.SH "TRANSITION"
.IX Header "TRANSITION"
The format of the \s-1GN\s0 line will change in 2004 from:
.PP
.Vb 2
\& GN   (CYSA1 OR CYSA OR RV3117 OR MT3199 OR MTCY164.27) AND (CYSA2 OR
\& GN   RV0815C OR MT0837 OR MTV043.07C).
.Ve
.PP
to:
.PP
.Vb 4
\& GN   Name=CysA1; Synonyms=CysA; OrderedLocusNames=Rv3117, MT3199;
\& GN   ORFNames=MtCY164.27;
\& GN   and
\& GN   Name=CysA2; OrderedLocusNames=Rv0815c, MT0837; ORFNames=MTV043.07c;
.Ve
.PP
This module supports both formats. To convert an entry from the old to
the new format, do:
.PP
.Vb 1
\& $entry\->GNs\->is_old_format(0);
.Ve