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* Version Creation Date: 10/01
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* File Description: SeqAlign indexing, access, and manipulation functions
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* --------------------------------------------------------------------------
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* $Log: alignmgr2.h,v $
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* Revision 6.21 2003/10/09 13:46:39 rsmith
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* Add AlnMgr2GetFirstNForSipList.
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* Revision 6.20 2003/04/23 20:37:06 rsmith
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* Added four functions in section 11 to allow examination of Std-Seg alignments.
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* Revision 6.19 2003/03/31 20:17:11 todorov
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* Added AlnMgr2IndexSeqAlignEx
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* Revision 6.18 2002/08/07 21:57:33 kans
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* added AlignMgr2GetFirstNForStdSeg
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* Revision 6.17 2002/07/11 14:35:51 kans
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* fixed Mac complaints about prototypes
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* Revision 6.16 2002/07/11 12:55:33 wheelan
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* added support for std-seg alignments
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* Revision 6.15 2002/05/21 12:26:25 wheelan
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* added n5 field to AMSmallPtr
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* Revision 6.14 2002/04/09 18:21:55 wheelan
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* changed params for AlnMgr2IndexAsRows
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* Revision 6.13 2002/03/04 17:19:29 wheelan
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* added AlnMgr2FuseSet, changed behavior of RemoveInconsistent
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* Revision 6.12 2002/01/30 19:12:20 wheelan
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* added RemoveInconsistentAlnsFromSet, ExtractPairwiseSeqAlign, changed behavior of GetSubAlign, changed structures and behavior of GetNextAlnBit, added GetInterruptInfo
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* Revision 6.11 2001/12/28 22:53:46 wheelan
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* added AlnMgr2DupAlnAndIndexes, changed amaip struct
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* Revision 6.10 2001/12/14 12:38:35 wheelan
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* added functions for ddv
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NLM_EXTERN Boolean LIBCALLBACK AMAlignIndex2Free2(VoidPtr index);
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typedef struct am_adjacent {
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} AMAdjac, PNTR AMAdjacPtr;
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} AMInterrupt, PNTR AMInterruptPtr;
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typedef struct am_msg2 {
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/* fields filled in by calling function */
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Int4 from_aln; /* from is in alignment coordinates */
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Int4 to_aln; /* to is in alignment coordinates */
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Int4 row_num; /* which row the function wants to retrieve */
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Int4 from_aln; /* from is in alignment coordinates */
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Int4 to_aln; /* to is in alignment coordinates */
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Int4 row_num; /* which row the function wants to retrieve */
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/* fields filled in by AlnMgr2GetNextAlnBit */
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Uint1 type; /* AM_SEQ or AM_GAP */
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AMAdjacPtr left_insert;
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AMAdjacPtr right_insert;
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AMAdjacPtr left_unaligned;
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AMAdjacPtr right_unaligned;
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Uint1 type; /* AM_SEQ or AM_GAP */
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AMInterruptPtr left_interrupt;
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AMInterruptPtr right_interrupt;
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/* fields used internally */
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} AlnMsg2, PNTR AlnMsg2Ptr;
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NLM_EXTERN AlnMsg2Ptr AlnMsgNew2(void);
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* 'from' to 'to' in the row coordinates specified, or if which_row is 0,
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* 'from' and 'to' are assumed to be alignment coordinates. If 'to' is -1,
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* the subalignment will go to the end of the specified row (or to the end
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* of the whole alignment).
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* of the whole alignment). If the alignment is discontinuous and fill_in
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* is FALSE, the alignment will be returned as an SAS_DISC set, each piece
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* represented by a single alignment. If the alignment is discontinuous and
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* fill_in is TRUE, the unaligned regions will be added in to the alignment,
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* with all gaps in all other rows. If the alignment is continuous, it
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* doesn't matter whether fill_in is TRUE or FALSE. (SUBALIGN)
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***************************************************************************/
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NLM_EXTERN SeqAlignPtr AlnMgr2GetSubAlign(SeqAlignPtr sap, Int4 from, Int4 to, Int4 row);
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NLM_EXTERN SeqAlignPtr AlnMgr2GetSubAlign(SeqAlignPtr sap, Int4 from, Int4 to, Int4 which_row, Boolean fill_in);
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/***************************************************************************
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***************************************************************************/
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NLM_EXTERN SeqAlignPtr AlnMgr2PadConservatively(SeqAlignPtr sap);
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/***************************************************************************
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* AlnMgr2ExtractPairwiseSeqAlign takes an indexed alignment (parent or
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* child, but must be fully indexed, not lite) and extracts a pairwise
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* subalignment containing the two requested rows. The subalignment is
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* unindexed and may have internal unaligned regions.
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***************************************************************************/
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NLM_EXTERN SeqAlignPtr AlnMgr2ExtractPairwiseSeqAlign(SeqAlignPtr sap, Int4 n1, Int4 n2);
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/***************************************************************************
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* AlnMgr2RemoveInconsistentAlnsFromSet takes an alignment that is
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* indexed at least at the AM2_LITE level, and prunes the child
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* alignments so that the remaining alignments form a consistent,
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* nonoverlapping set. All alignments must have the same number of rows,
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* and they must be the same rows (although not necessarily in the same
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* order). The function uses a simple greedy algorithm to construct the
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* nonoverlapping set, starting with the highest-scoring alignment.
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* If fuzz is negative, the function creates the best nonoverlapping set
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* by actually truncating alignments.
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***************************************************************************/
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NLM_EXTERN void AlnMgr2RemoveInconsistentAlnsFromSet(SeqAlignPtr sap_head, Int4 fuzz);
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/***************************************************************************
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* AlnMgr2FuseSet takes a set of alignments sharing all their rows and orders
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* the alignments, then fuses together any adjacent alignments. If returnall
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* is TRUE, all pieces are returned; if not, then only the largest piece is
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* returned. This function will work best when called after
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* AlnMgr2RemoveInconsistentAlnsFromSet(sap_head, -1).
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***************************************************************************/
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NLM_EXTERN SeqAlignPtr AlnMgr2FuseSet(SeqAlignPtr sap_head, Boolean returnall);
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/* SECTION 11 -- functions for std-segs */
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NLM_EXTERN Int4 AlignMgr2GetFirstNForStdSeg(SeqAlignPtr sap, SeqIdPtr sip);
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NLM_EXTERN SeqIdPtr AlnMgr2GetNthSeqIdPtrStdSeg(SeqAlignPtr sap, Int4 n);
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NLM_EXTERN void AlnMgr2GetNthSeqRangeInSAStdSeg(SeqAlignPtr sap, Int4 n, Int4Ptr start, Int4Ptr stop);
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/***************************************************************************
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* AlnMgr2GetSeqRangeForSipInSAStdSeg returns the smallest and largest sequence
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* coordinates in in a Std-Seg seqalign for a given Sequence Id. Also return the
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* strand type if it is the same on every segment, else set it to Seq_strand_unknown.
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* Either start, stop or strand can be NULL to only retrieve some of them.
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* If start and stop are -1, there is an error (not a std-seg), the SeqID does not participate in this
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* alignment or the alignment is one big insert on that id. Returns true if the sip was found
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* in the alignment with real coordinates, i.e. *start would not be -1. RANGE
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***************************************************************************/
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NLM_EXTERN Boolean AlnMgr2GetSeqRangeForSipInSAStdSeg(SeqAlignPtr sap, SeqIdPtr sip, Int4Ptr start, Int4Ptr stop, Uint1Ptr strand);
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/***************************************************************************
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* AlnMgr2GetSeqRangeForSipInStdSeg returns the start and stop sequence
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* coordinates in a Std-Segment for a given Sequence Id. Also return the
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* strand type. Either start, stop, strand or segType can be NULL to only retrieve some of them.
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* Returns false if the SeqID was not found in this segment, so no meaningful
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* data was passed back in other arguments.
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* Returns true if the sip was found, even if it is a gap (start, stop = -1).
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* segType is set to AM_SEQ if the SeqID Sequence is not empty and one of
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* the other sequences aligned with it is also not empty. To AM_GAP if
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* the other sequences are all empty, and to AM_INSERT if the main sequence
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***************************************************************************/
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NLM_EXTERN Boolean AlnMgr2GetSeqRangeForSipInStdSeg(
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Uint1Ptr segType); /* AM_SEQ, AM_GAP, AM_INSERT */
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/***************************************************************************
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* AlnMgr2GetNthStdSeg returns the a pointer to the Nth segment of
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* a standard segment alignment.
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* returns NULL if not n segments or is not a std-seg aligment.
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* Useful to pass its return value to AlnMgr2GetSeqRangeForSipInStdSeg()
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***************************************************************************/
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NLM_EXTERN StdSegPtr AlnMgr2GetNthStdSeg(SeqAlignPtr sap, Int2 n);
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/***************************************************************************
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* AlnMgr2GetNumStdSegs returns the number of segments in a standar-seg alignment.
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* returns -1 if sap is null or not a standard-seg alignment.
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* the Std-Seg version of AlnMgr2GetNumSegs
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***************************************************************************/
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NLM_EXTERN Int4 AlnMgr2GetNumStdSegs(SeqAlignPtr sap);
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/***************************************************************************
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* The two mapping functions act a little differently for std-segs. The
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* alignment coordinates are 1:1 linearly correlated with the longest
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* seqloc in the set; the others may be significantly shorter.
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* The mapping functions deal with % lengths, and map those instead of
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* coordinates (which may not be linear);
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***************************************************************************/
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NLM_EXTERN Int4 AlnMgr2MapBioseqToSeqAlignStdSeg(SeqAlignPtr sap, Int4 n, Int4 pos);
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NLM_EXTERN Int4 AlnMgr2MapSeqAlignToBioseqStdSeg(SeqAlignPtr sap, Int4 n, Int4 pos);
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NLM_EXTERN Int4 AlnMgr2GetAlnLengthStdSeg(SeqAlignPtr sap);
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/***************************************************************************/
added
removed
api/alignmgr2.h
