cmProc5.h/c : Added cmSeqAlign.
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kevin
parent
1b6ce35176
commit
5208cfae60
204
cmProc5.c
204
cmProc5.c
@ -1098,3 +1098,207 @@ void cmNlmsEcSetIrN( cmNlmsEc_t* p, unsigned hN )
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p->hN = hN;
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p->hN = hN;
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}
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}
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//=======================================================================================================================
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//
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//
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cmSeqAlign_t* cmSeqAlignAlloc( cmCtx* ctx, cmSeqAlign_t* ap )
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{
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cmSeqAlign_t* p = cmObjAlloc(cmSeqAlign_t,ctx,ap);
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if( cmSeqAlignInit(p) != cmOkRC )
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cmSeqAlignFree(&p);
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return p;
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}
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cmRC_t cmSeqAlignFree( cmSeqAlign_t** pp )
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{
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cmRC_t rc = cmOkRC;
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if( pp == NULL || *pp == NULL )
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return rc;
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cmSeqAlign_t* p = *pp;
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if((rc = cmSeqAlignFinal(p)) != cmOkRC )
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return rc;
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while( p->seqL != NULL )
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{
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while( p->seqL->locL != NULL )
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{
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cmSeqAlignLoc_t* lp = p->seqL->locL->link;
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cmMemFree(p->seqL->locL->vV);
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cmMemFree(p->seqL->locL);
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p->seqL->locL = lp;
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}
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cmSeqAlignSeq_t* sp = p->seqL->link;
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cmMemFree(p->seqL);
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p->seqL = sp;
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}
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cmObjFree(pp);
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return rc;
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}
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cmRC_t cmSeqAlignInit( cmSeqAlign_t* p )
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{ return cmOkRC; }
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cmRC_t cmSeqAlignFinal( cmSeqAlign_t* p )
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{ return cmOkRC; }
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cmSeqAlignSeq_t* _cmSeqAlignIdToSeq( cmSeqAlign_t* p, unsigned seqId )
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{
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cmSeqAlignSeq_t* sp = p->seqL;
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for(; sp!=NULL; sp=sp->link)
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if( sp->id == seqId )
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return sp;
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return NULL;
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}
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cmSeqAlignLoc_t* _cmSeqAlignIdToLoc( cmSeqAlignSeq_t* sp, unsigned locId )
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{
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cmSeqAlignLoc_t* lp = sp->locL;
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for(; lp!=NULL; lp=lp->link)
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{
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// if the locId's match
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if( lp->id == locId )
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return lp;
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if( (lp->link != NULL && lp->link->id > locId) || lp->link==NULL )
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return lp; // return record previous to locId
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}
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// return NULL: locId is less than all other locations id's in the list
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return lp;
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}
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cmRC_t cmSeqAlignInsert( cmSeqAlign_t* p, unsigned seqId, unsigned locId, unsigned value )
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{
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cmSeqAlignSeq_t* sp;
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// if the requested sequence does not already exist ...
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if((sp = _cmSeqAlignIdToSeq(p,seqId)) == NULL )
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{
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// ... then create it
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sp = cmMemAllocZ(cmSeqAlignSeq_t,1);
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sp->id = seqId;
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if( p->seqL == NULL )
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p->seqL = sp;
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else
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{
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cmSeqAlignSeq_t* s0 = p->seqL;
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while( s0->link != NULL )
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s0 = s0->link;
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s0->link = sp;
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}
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}
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assert(sp != NULL);
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cmSeqAlignLoc_t* lp;
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// if the requested location does not exist in the requested sequence ...
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if((lp = _cmSeqAlignIdToLoc(sp,locId)) == NULL || lp->id != locId)
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{
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// ... then create it
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cmSeqAlignLoc_t* nlp = cmMemAllocZ(cmSeqAlignLoc_t,1);
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nlp->id = locId;
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// if lp is NULL then link nlp as first record in sequence
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if( lp == NULL )
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{
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// make new loc recd first on the list
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nlp->link = sp->locL;
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sp->locL = nlp;
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}
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else // otherwise link nlp after lp
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{
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nlp->link = lp->link;
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lp->link = nlp;
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}
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lp = nlp;
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}
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assert( lp!=NULL );
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// insert the new value
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lp->vV = cmMemResizeP(unsigned,lp->vV,lp->vN+1);
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lp->vV[ lp->vN ] = value;
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lp->vN += 1;
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return cmOkRC;
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}
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double _cmSeqAlignCompare( const cmSeqAlignLoc_t* l0, const cmSeqAlignLoc_t* l1)
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{
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double dist = 0;
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unsigned i=0;
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for(i=0; i<l0->vN; ++i)
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{
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unsigned j=0;
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for(j=0; j<l1->vN; ++j)
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if( l0->vV[i] == l1->vV[j] )
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break;
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if( l0->vV[i] != l1->vV[j] )
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dist += 1.0;
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}
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return dist;
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}
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cmRC_t cmSeqAlignExec( cmSeqAlign_t* p )
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{
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return cmOkRC;
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}
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void _cmSeqAlignReportLoc( cmRpt_t* rpt, const cmSeqAlignLoc_t* lp )
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{
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//cmRptPrintf(rpt,"%5i : ",lp->id);
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unsigned i;
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for(i=0; i<lp->vN; ++i)
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{
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//cmRptPrintf(rpt,"%3i ",lp->vV[i]);
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cmRptPrintf(rpt,"%4s ",cmMidiToSciPitch(lp->vV[i],NULL,0));
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}
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cmRptPrintf(rpt," | ");
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}
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void cmSeqAlignReport( cmSeqAlign_t* p, cmRpt_t* rpt )
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{
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cmSeqAlignLoc_t* slp = p->seqL->locL;
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for(; slp!=NULL; slp=slp->link)
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{
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cmRptPrintf(rpt,"%5i : ",slp->id);
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// report the next location on the first sequence as the reference location
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_cmSeqAlignReportLoc( rpt, slp );
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// for each remaining sequence
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cmSeqAlignSeq_t* sp = p->seqL->link;
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for(; sp!=NULL; sp=sp->link)
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{
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// locate the location with the same id as the reference location ...
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cmSeqAlignLoc_t* lp;
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if((lp = _cmSeqAlignIdToLoc(sp,slp->id)) != NULL && lp->id == slp->id)
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{
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_cmSeqAlignReportLoc(rpt,lp); // ... and report it
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}
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}
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cmRptPrintf(rpt,"\n");
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}
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}
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37
cmProc5.h
37
cmProc5.h
@ -265,8 +265,45 @@ extern "C" {
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void cmNlmsEcSetMu( cmNlmsEc_t* p, float mu );
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void cmNlmsEcSetMu( cmNlmsEc_t* p, float mu );
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void cmNlmsEcSetDelayN( cmNlmsEc_t* p, unsigned delayN );
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void cmNlmsEcSetDelayN( cmNlmsEc_t* p, unsigned delayN );
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void cmNlmsEcSetIrN( cmNlmsEc_t* p, unsigned irN );
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void cmNlmsEcSetIrN( cmNlmsEc_t* p, unsigned irN );
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//------------------------------------------------------------------------------------------------------------
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//)
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//)
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//( { label:cmSeqAlign file_desc:"Align two sequences where each sequence is composed of records with varying numbers of features." kw:[proc]}
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typedef struct cmSeqAlignLoc_str
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{
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unsigned id; // location id
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unsigned vN; //
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unsigned* vV; // vV[vN]
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struct cmSeqAlignLoc_str* link;
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} cmSeqAlignLoc_t;
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typedef struct cmSeqAlignSeq_str
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{
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unsigned id;
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cmSeqAlignLoc_t* locL;
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struct cmSeqAlignSeq_str* link;
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} cmSeqAlignSeq_t;
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typedef struct
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{
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cmObj obj;
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cmSeqAlignSeq_t* seqL;
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} cmSeqAlign_t;
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cmSeqAlign_t* cmSeqAlignAlloc( cmCtx* ctx, cmSeqAlign_t* p );
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cmRC_t cmSeqAlignFree( cmSeqAlign_t** p );
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cmRC_t cmSeqAlignInit( cmSeqAlign_t* p );
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cmRC_t cmSeqAlignFinal( cmSeqAlign_t* p );
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cmRC_t cmSeqAlignInsert( cmSeqAlign_t* p, unsigned seqId, unsigned locId, unsigned value );
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cmRC_t cmSeqAlignExec( cmSeqAlign_t* p );
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void cmSeqAlignReport( cmSeqAlign_t* p, cmRpt_t* rpt );
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//------------------------------------------------------------------------------------------------------------
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//)
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#ifdef __cplusplus
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#ifdef __cplusplus
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}
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}
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