line |
count |
pod |
subroutine |
25
|
4 |
n/a |
BEGIN |
27
|
4 |
n/a |
BEGIN |
28
|
4 |
n/a |
BEGIN |
29
|
4 |
n/a |
BEGIN |
30
|
4 |
n/a |
BEGIN |
31
|
4 |
n/a |
BEGIN |
33
|
4 |
n/a |
BEGIN |
35
|
4 |
n/a |
BEGIN |
36
|
4 |
n/a |
BEGIN |
38
|
4 |
n/a |
BEGIN |
57
|
862 |
Yes |
new |
67
|
0 |
No |
getConsensusSpliceOffsets |
71
|
862 |
Yes |
getAnnotation |
86
|
4 |
n/a |
BEGIN |
89
|
639 |
Yes |
addMessage |
94
|
14766 |
n/a |
_debug |
103
|
1 |
Yes |
getMessages |
109
|
862 |
n/a |
_clearMessages |
113
|
862 |
n/a |
_assignBookmarks |
121
|
4 |
n/a |
BEGIN |
124
|
862 |
n/a |
_init |
148
|
852 |
n/a |
_getmRNAPositions |
429
|
441 |
n/a |
_buildProteinAnnotation |
627
|
4 |
n/a |
BEGIN |
629
|
4 |
n/a |
BEGIN |
631
|
4 |
n/a |
BEGIN |
634
|
441 |
n/a |
_buildCDSAnnotation |
709
|
4 |
n/a |
BEGIN |
711
|
4 |
n/a |
BEGIN |
713
|
4 |
n/a |
BEGIN |
715
|
4 |
n/a |
BEGIN |
717
|
4 |
n/a |
BEGIN |
720
|
152 |
n/a |
_buildUnknownCDSAnnotation |
742
|
0 |
n/a |
_buildUnaffectedCDSAnnotation |
763
|
377 |
n/a |
_buildUnknownProteinAnnotation |
785
|
0 |
n/a |
_buildUnaffectedProteinAnnotation |
806
|
3 |
n/a |
_buildRemovedProteinAnnotation |
827
|
308 |
n/a |
_buildUnknownMRNAAnnotation |
849
|
66 |
n/a |
_isOffsetAConsensusSpliceDistance |
859
|
189 |
n/a |
_getConsesnsusSpliceBeforeBoundry |
863
|
194 |
n/a |
_getConsesnsusSpliceAfterBoundry |
867
|
692 |
n/a |
_isIntronicOffsetDistance |
875
|
147 |
n/a |
_isWithin5KBOffsetDistance |
883
|
0 |
No |
getUpDownStream5kbCutoff |
887
|
142 |
n/a |
_isWithin2KBUpstreamOffsetDistance |
895
|
0 |
No |
getUpStream2kbCutoff |
899
|
121 |
n/a |
_isWithin500BPDownstreamOffsetDistance |
907
|
0 |
No |
getDownStream500bpCutoff |
912
|
371 |
n/a |
_coversStartCodon |
948
|
371 |
n/a |
_coversStopCodon |
983
|
862 |
n/a |
_getTranscriptSource |
987
|
441 |
n/a |
_calculateCdsTranslationPadStrings |
1020
|
441 |
n/a |
_canAnnotateToCDS |
1088
|
441 |
n/a |
_canAnnotateToProtein |
1124
|
487 |
n/a |
_revcompSeq |
1134
|
26 |
n/a |
_sequenceStartsWithSequence |
1152
|
26 |
n/a |
_calculateFrameShiftProteinChange |
1202
|
14 |
n/a |
_calculateGenomicCdsPosition |
1235
|
605 |
n/a |
_arrayHasString |
1243
|
0 |
n/a |
_defaultTranscriptSort |
1245
|
0 |
n/a |
__ANON__ |