ARB
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#include <seq_search.hxx>
Public Member Functions | |
AlignBuffer (long size) | |
~AlignBuffer () | |
const char * | text () const |
const char * | quality () const |
long | length () const |
long | offset () const |
long | free () const |
void | copy (const char *s, char q, long len) |
void | set (char c, char q) |
void | set (char c, char q, long len) |
void | reset (long newOffset=0) |
void | correctUnalignedPositions () |
void | restoreDots (CompactedSubSequence &slaveSequence) |
void | setDotsAtEOSequence () |
Definition at line 300 of file seq_search.hxx.
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Definition at line 337 of file seq_search.hxx.
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Definition at line 345 of file seq_search.hxx.
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Definition at line 350 of file seq_search.hxx.
References fa_assert, and free().
Referenced by alignCompactedTo(), and FastSearchSequence::fast_align().
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Definition at line 351 of file seq_search.hxx.
References fa_assert, and free().
Referenced by alignCompactedTo(), and correctUnalignedPositions().
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Definition at line 352 of file seq_search.hxx.
Referenced by alignCompactedTo().
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Definition at line 354 of file seq_search.hxx.
Referenced by FastSearchSequence::fast_align(), and insertsToNextBase().
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Definition at line 355 of file seq_search.hxx.
Referenced by alignCompactedTo(), copy(), insertAligned(), insertClustalValigned(), quality(), set(), and text().
Definition at line 357 of file seq_search.hxx.
References fa_assert, and free().
Referenced by cannot_fast_align(), and insertSlaveBases().
Definition at line 363 of file seq_search.hxx.
References fa_assert, and free().
Referenced by alignCompactedTo(), insertAligned(), insertBase(), insertClustalValigned(), and insertGap().
Definition at line 369 of file seq_search.hxx.
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Definition at line 375 of file seq_search.hxx.
References fa_assert.
void AlignBuffer::correctUnalignedPositions | ( | ) |
Definition at line 124 of file seq_search.cxx.
References after(), before(), and quality().
Referenced by alignCompactedTo().
void AlignBuffer::restoreDots | ( | CompactedSubSequence & | slaveSequence | ) |
Definition at line 168 of file seq_search.cxx.
References CompactedSubSequence::firstDotPosition(), is_gap(), CompactedSubSequence::name(), and CompactedSubSequence::nextDotPosition().
Referenced by alignCompactedTo().
void AlignBuffer::setDotsAtEOSequence | ( | ) |
Definition at line 197 of file seq_search.cxx.
References is_gap().
Referenced by alignCompactedTo().