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.\" ========================================================================
.\"
.IX Title "SWISS::Entry 3pm"
.TH SWISS::Entry 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "Name"
.IX Header "Name"
SWISS::Entry
.SH "Description"
.IX Header "Description"
Main module to handle SWISS-PROT entries. One Entry object represents one SWISS-PROT entry and provides an \s-1API\s0 for its modification.
.PP
The basic concept is the idea of lazy parsing. If an Entry object is created from the entry in flat file format, the text is simply stored in the private text attribute of the entry object. The member objects of the entry are only created if they are dereferenced.
.SH "Example"
.IX Header "Example"
This minimum program reads entries from a file in SWISS-PROT format and prints the primary accession number for each of the entries.
.SH "Attributes"
.IX Header "Attributes"
The following attributes represent member objects. They can be accessed like e.g. \f(CW$entry\fR\->IDs
.IP "IDs" 4
.IX Item "IDs"
\&\s-1ID\s0 line object
.IP "ACs" 4
.IX Item "ACs"
.PD 0
.IP "DTs" 4
.IX Item "DTs"
.IP "DEs" 4
.IX Item "DEs"
.IP "GNs" 4
.IX Item "GNs"
.IP "OSs" 4
.IX Item "OSs"
.IP "OCs" 4
.IX Item "OCs"
.IP "Refs" 4
.IX Item "Refs"
.PD
The reference block object
.IP "CCs" 4
.IX Item "CCs"
.PD 0
.IP "KWs" 4
.IX Item "KWs"
.IP "DRs" 4
.IX Item "DRs"
.IP "FTs" 4
.IX Item "FTs"
.IP "Stars" 4
.IX Item "Stars"
.PD
Object for the annotator's section stored in the ** lines.
.IP "SQs" 4
.IX Item "SQs"
The sequence object.
.SH "Methods"
.IX Header "Methods"
.IP "new" 4
.IX Item "new"
Return a new Entry object
.IP "initialize" 4
.IX Item "initialize"
Initialise an Entry object and return it.
.IP "update [force]" 4
.IX Item "update [force]"
Update an
entry. The content of the member objects is written back into the private text
attribute of the entry if necessary. If \f(CW$force\fR is true, an update of all 
member objects is forced.
.IP "reformat" 4
.IX Item "reformat"
Reformat all fields of an entry.
.ie n .IP "fromText $text [, $fullParse[, $removeInternalComments]]" 4
.el .IP "fromText \f(CW$text\fR [, \f(CW$fullParse\fR[, \f(CW$removeInternalComments\fR]]" 4
.IX Item "fromText $text [, $fullParse[, $removeInternalComments]]"
Create an Entry object from the text \f(CW$text\fR. If \f(CW$fullParse\fR is true, the entry is
parsed at creation time. Otherwise the individual line objects are only 
created if they are dereferenced. If \f(CW$removeInternalComments\fR is true, wild comments
and indentation will be removed from the text before the parsing is done. [\s-1NOTE:\s0 
wild comments are lines starting with a double asterisk located outside the Stars
section, and indented lines are lines starting with spaces. Both are used internally
by SWISS-PROT annotators during their work and excluded from internal and external
releases.]
.IP "toText [$insertInternalComments]" 4
.IX Item "toText [$insertInternalComments]"
Return the entry in flat file text format. If internal comments and indentation
have been removed as specified in the parameters to \fBfromText()\fR, you may wish
to reinsert them in the text output by setting \f(CW$insertInternalComments\fR to true.
.IP "toFasta [isoformName]" 4
.IX Item "toFasta [isoformName]"
Return the entry in Fasta format (canonical/displayed sequence if no isoform name provided)
.IP "isoFormNames [all]" 4
.IX Item "isoFormNames [all]"
Return the list of (filtered for not: External|Displayed|Not described|Unknown) isoform names.
If all is true: list all isoform names
.IP "isoIds [isoformName]" 4
.IX Item "isoIds [isoformName]"
Return list of isoform Ids for a particular isoform name (isoIds for canonical/displayed if no isoform name provided)
.IP "isoId [isoformName]" 4
.IX Item "isoId [isoformName]"
Return primary isoform Id for a particular isoform name (primary isoId for canonical/displayed if no isoform name provided)
.IP "isoFormSequence [isoform name]" 4
.IX Item "isoFormSequence [isoform name]"
Return the raw sequence for a specified isoform name (raw canonical sequence if no isoform name provided)
.IP "equal" 4
.IX Item "equal"
Returns True if two entries are equal, False otherwise
.PP
The following methods are provided for your convenience. They are shortcuts for methods of the individual line objects.
.IP "\s-1ID\s0" 4
.IX Item "ID"
Returns the primary \s-1ID\s0 of the entry.
.IP "\s-1AC\s0" 4
.IX Item "AC"
Returns the primary \s-1AC\s0 of the entry.
.IP "\s-1SQ\s0" 4
.IX Item "SQ"
Returns the sequence of the entry.
.IP "\s-1EV\s0" 4
.IX Item "EV"
Returns the \s-1EV\s0 (evidence) object of an entry. SWISS-PROT internal method.
.SS "Data access methods"
.IX Subsection "Data access methods"
.IP "text" 4
.IX Item "text"
Returns the current text of the entry. 
\&\fBQuick and dirty!\fR No update of the text is performed before.
.IP "database_code" 4
.IX Item "database_code"
Is it a SWISS-PROT, \s-1TREMBL\s0 or \s-1TREMBLNEW\s0 entry?
database_code tries to find it out.
Return values are S for SWISS-PROT, 3 for \s-1TREMBL, Q\s0 for \s-1TREMBLNEW,\s0 ? for unknown.
.IP "isFragment" 4
.IX Item "isFragment"
Returns true if the \s-1DE\s0 line indicates a fragment, or of the entry 
contains a \s-1NON_CONS\s0 or \s-1NON_TER\s0 feature.
.IP "isCurated" 4
.IX Item "isCurated"
Returns 1 if the entry is a curated entry, 
0 otherwise.
.Sp
SWISS-PROT internal use only.
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 731:" 4
.IX Item "Around line 731:"
=over without closing =back