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.\" ========================================================================
.\"
.IX Title "SWISS::DRs 3pm"
.TH SWISS::DRs 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.
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.SH "Name"
.IX Header "Name"
SWISS::DRs
.SH "Description"
.IX Header "Description"
\&\fBSWISS::DRs\fR represents the \s-1DR\s0 (database crossreference) lines within an SWISS-PROT + TrEMBL
entry as specified in the user manual
http://www.expasy.org/sprot/userman.html .
.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"
An array of arrays. Each element is an array (Database_identifier, primary_key, secondary_key[,further elements]).
.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"
.IP "sort" 4
.IX Item "sort"
.PD
.SS "Reading methods"
.IX Subsection "Reading methods"
.IP "emblacs" 4
.IX Item "emblacs"
Returns a list of all \s-1EMBL\s0 accession numbers. These are the primary keys of \s-1EMBL\s0 crossreferences.
.IP "pids [$dropVersion]" 4
.IX Item "pids [$dropVersion]"
Returns a list of all PIDs. These are the secondary keys of \s-1EMBL\s0 crossreferences.
.Sp
\&\fB\s-1ATTENTION:\s0\fR 
The \s-1EMBL\s0 protein identifiers introduced in 1999 are of the form
xxxxx.yy, e.g. \s-1CAA33128\s0.1
If \f(CW$dropVersion\fR is set, the version number (.yy) will be dropped from
each \s-1PID\s0.
.Sp
Example:
.Sp
If the \s-1EMBL\s0 \s-1DR\s0 line is
.Sp
\&\s-1DR\s0   \s-1EMBL\s0; L37685; \s-1AAC41668\s0.1; \-.
.Sp
\&\fIpids\fR\|(1) will only return \s-1AAC41668\s0, \s-1NOT\s0 \s-1AAC41668\s0.1
.SS "Writing methods"
.IX Subsection "Writing methods"
.ie n .IP "deleteUnlessEvidenceCategories $evidenceCategories, @patterns" 4
.el .IP "deleteUnlessEvidenceCategories \f(CW$evidenceCategories\fR, \f(CW@patterns\fR" 4
.IX Item "deleteUnlessEvidenceCategories $evidenceCategories, @patterns"
Like del, but deletes an item only if the item has no evidence tags, or if the evidence tags are not in one of the categories given in \f(CW$evidenceCategories\fR.
.Sp
Example:
.Sp
\&\f(CW$entry\fR\->DRs\->deleteUnlessEvidenceCategories('\s-1CA\s0', 'FlyBase')
.Sp
will only delete Flybase \s-1DR\s0 lines which do not have the evidence category 'A' or 'C'.
.SS "Filter functions"
.IX Subsection "Filter functions"
.IP "dbName($dbTargetName)" 4
.IX Item "dbName($dbTargetName)"
True if the first element of a \s-1DR\s0 line (the \s-1DB\s0 name) matches \f(CW$dbTargetName\fR.
\&\f(CW$dbTargetName\fR has to match in full, not only a partial match.
.IP "notDbName($dbTargetName)" 4
.IX Item "notDbName($dbTargetName)"
True if the first element of a \s-1DR\s0 line (the \s-1DB\s0 name) does \s-1NOT\s0 macht \f(CW$dbTargetName\fR.
.SS "** lines (SWISS-PROT internal format)"
.IX Subsection "** lines (SWISS-PROT internal format)"
Each \s-1DR\s0 line may be followed by a ** line like
.PP
.Vb 1
\& **   DR   PROSITE; PS12345; XXX_PAT; FALSE_POS_1
\&
\& These will be stored internally as DR lines with the DB identifier 
\& \*(Aq_HIDDEN_\*(Aq. Therefore adding a ** PROSITE line is done as:
\&
\& $entry\->DRs\->add([\*(Aq_HIDDEN_\*(Aq, \*(AqPS12345\*(Aq, \*(AqXXX_PAT\*(Aq, \*(AqFALSE_POS_1\*(Aq]);
.Ve