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