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Commit 3748448d authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Changed from "At Risk (Under Development)" to "Stable":

    cdna_start()
    cdna_end()

    cdna_coding_start()
    cdna_coding_end()

    coding_region_start()
    coding_region_end()

Changed POD from saying "in genomic coordinates" to say "in
slice-relative coordinates":

    coding_region_start()
    coding_region_end()
parent d5d9ef36
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......@@ -371,7 +371,7 @@ sub strand {
Throws if the first part of the exon maps into a gap.
Throws if the exon can not be mapped at all.
Caller : General
Status : At Risk (Under Development)
Status : Stable
=cut
......@@ -423,7 +423,7 @@ sub cdna_start {
Throws if the last part of the exon maps into a gap.
Throws if the exon can not be mapped at all.
Caller : General
Status : At Risk (Under Development)
Status : Stable
=cut
......@@ -473,7 +473,7 @@ sub cdna_end {
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : At Risk (Under Development)
Status : Stable
=cut
......@@ -549,7 +549,7 @@ sub cdna_coding_start {
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : At Risk (Under Development)
Status : Stable
=cut
......@@ -615,16 +615,17 @@ sub cdna_coding_end {
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example : $coding_region_start =
$exon->coding_region_start($transcript);
Description : Returns the start position of the coding region of the
exon in genomic coordinates on the forward strand.
Returns undef if the whole exon is non-coding.
Description : Returns the start position of the coding region
of the exon in slice-relative coordinates on the
forward strand. Returns undef if the whole exon is
non-coding.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : At Risk (Under Development)
Status : Stable
=cut
......@@ -692,16 +693,17 @@ sub coding_region_start {
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example : $coding_region_end =
$exon->coding_region_end($transcript);
Description : Returns the end position of the coding region of the
exon in genomic coordinates on the forward strand.
Returns undef if the whole exon is non-coding.
Description : Returns the end position of the coding region of
the exon in slice-relative coordinates on the
forward strand. Returns undef if the whole exon is
non-coding.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : At Risk (Under Development)
Status : Stable
=cut
......
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