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Add the exonManager, that does garbage collection of exons. Improve
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general garbage collection.  Claim that there are no leaks left ('cause
everything is garbage collected now).
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@brianwalenz
brianwalenz committed Jul 13, 2005
1 parent 89404ca commit 794f606
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Showing 14 changed files with 322 additions and 231 deletions.
155 changes: 107 additions & 48 deletions kmer/libsim4/sim4core/exon.H
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Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,62 @@
// Define this only if Liliana is watching you.
//#define SPLSCORE


class Exon {
public:
Exon(int f1, int f2, int t1, int t2, int len, int edist, int flag, Exon *next);
~Exon();
private:
Exon() {
next_exon = 0L;
frGEN = 0;
frEST = 0;
toGEN = 0;
toEST = 0;
ori = 'U';
length = 0;

edist = 0;
flag = 0;

percentID = 0;
alignmentLength = 0;
numMatches = 0;
numNs = 0;
numInDel = 0;
numEdits = 0;

#ifdef SPLSCORE
splScore = -999999;
#endif
};
~Exon() {};

void init(int f1, int f2, int t1, int t2, int len, int edist, int flag, Exon *next) {
next_exon = next;

frGEN = f1;
frEST = f2;
toGEN = t1;
toEST = t2;

ori = 'U';
length = (len < 0) ? (t2-f2+1) : len;

edist = edost;
flag = flog;

percentID = 0;
alignmentLength = 0;
numMatches = 0;
numNs = 0;
numInDel = 0;
numEdits = 0;

#ifdef SPLSCORE
splScore = -999999;
#endif
};

friend class exonManager;

public:
void printList(char *label) {
Exon *l = this;

Expand Down Expand Up @@ -56,59 +106,68 @@ public:
#endif
};

inline
Exon::Exon(int f1, int f2, int t1, int t2, int len, int edost, int flog, Exon *next) {
next_exon = next;

frGEN = f1;
frEST = f2;
toGEN = t1;
toEST = t2;

ori = 'U';
length = (len < 0) ? (t2-f2+1) : len;

edist = edost;
flag = flog;

percentID = 0;
alignmentLength = 0;
numMatches = 0;
numNs = 0;
numInDel = 0;
numEdits = 0;

#ifdef SPLSCORE
splScore = -999999;
#endif
}

inline
Exon::~Exon() {
}


inline
void
freeExon(Exon *&l) {
delete l;
l = 0L;
}
// Just for allocating exons. It takes care of deleting exons. You
// are not allowed to delete them.
//
class exonManager {

public:
exonManager() {
_listLen = 1;
_listMax = 8;
_list = new Exon* [_listMax];

_curLen = 0;
_curMax = 256;
_list[0] = new Exon [_curMax];
};
~exonManager() {
for (u32bit i=0; i<_listLen; i++)
delete [] _list[i];
delete [] _list;
};

inline
void
freeExonList(Exon *&l) {
Exon *t;
Exon *newExon(int f1, int f2, int t1, int t2, int len, int edist, int flag, Exon *next) {

// If the current list is full, move to the next one, or allocate
// more space.
//
if (_curLen >= _curMax) {
if (_listLen >= _listMax) {
_listMax *= 2;
Exon **l = new Exon* [_listMax];
memcpy(l, _list, sizeof(Exon**) * _listLen);
delete [] _list;
_list = l;
}

_list[_listLen++] = new Exon [_curMax];
_curLen = 0;
}

while (l) {
t = l->next_exon;
freeExon(l);
l = t;
}
Exon *e = _list[_listLen - 1] + _curLen;
_curLen++;
e->init(f1, f2, t1, t2, len, edist, flag, next);
return(e);;
};

l = 0L;
}
private:
// Exon pointers are valid throughout the lifetime of execution,
// so we can't use realloc here. Instead, we keep a list of arrays
// of exons.
//
u32bit _listLen;
u32bit _listMax;
Exon **_list;

u32bit _curLen;
u32bit _curMax;
};


#endif // EXON_H
68 changes: 34 additions & 34 deletions kmer/libsim4/sim4core/greedy.C
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@ Sim4::greedy(char *s1, char *s2, int m, int n0, int OFFSET1, int OFFSET2, Exon *

if (n0 < m) {
if (m < (int)min(wordSize, (1 + globalParams->_percentError) * n0)) {
*lblock = *rblock = new Exon(OFFSET2+1,OFFSET1+1,OFFSET2+n0,OFFSET1+m,
m,n0-m+(int)(globalParams->_percentError * m + 1),0,NULL);
*lblock = *rblock = _exonManager.newExon(OFFSET2+1,OFFSET1+1,OFFSET2+n0,OFFSET1+m,
m,n0-m+(int)(globalParams->_percentError * m + 1),0,NULL);
ANNOUNCEEXIT("greedy-1\n");
return(m-n0+(int)(globalParams->_percentError * n0 + 1));
} else if (m > (int)min(wordSize, (1 + globalParams->_percentError) * n0)) {
Expand Down Expand Up @@ -59,8 +59,8 @@ Sim4::greedy(char *s1, char *s2, int m, int n0, int OFFSET1, int OFFSET2, Exon *

if (row == 0) {
/* hit last row; stop search */
*lblock = *rblock = new Exon(r_offset2-m+n2+1,r_offset1+1,r_offset2+n2,
r_offset1+m,m,0,0,NULL);
*lblock = *rblock = _exonManager.newExon(r_offset2-m+n2+1,r_offset1+1,r_offset2+n2,
r_offset1+m,m,0,0,NULL);
ANNOUNCEEXIT("greedy-3\n");
return 0;
}
Expand Down Expand Up @@ -98,8 +98,8 @@ Sim4::greedy(char *s1, char *s2, int m, int n0, int OFFSET1, int OFFSET2, Exon *

if (row == m) {
/* hit last row; stop search */
*lblock = *rblock = new Exon(l_offset2+1,l_offset1+1,l_offset2+m,
l_offset1+m,m,0,0,NULL);
*lblock = *rblock = _exonManager.newExon(l_offset2+1,l_offset1+1,l_offset2+m,
l_offset1+m,m,0,0,NULL);
ckfree(allocdSpace);

ANNOUNCEEXIT("greedy-4\n");
Expand Down Expand Up @@ -289,35 +289,35 @@ Sim4::greedy(char *s1, char *s2, int m, int n0, int OFFSET1, int OFFSET2, Exon *

if (m-min_row[back]>=max_row[forth]) {

if ((r_offset2+1+min_diag[back]-R_ORIGIN) <
(l_offset2+max_diag[forth]-L_ORIGIN)) {
*rblock = *lblock = new Exon(l_offset2+1,l_offset1+1,
l_offset2+n0,l_offset1+m,
m,back+forth,0,NULL);
} else {
*rblock = new Exon(r_offset2+1+min_row[back]+min_diag[back]-R_ORIGIN,
r_offset1+1+min_row[back],
r_offset2+n2,r_offset1+m,
m-min_row[back],back,0,NULL);
*lblock = new Exon(l_offset2+1,l_offset1+1,
l_offset2+min_row[back]+max_diag[forth]-L_ORIGIN,
l_offset1+min_row[back],
min_row[back],forth,0,*rblock);
}
if ((r_offset2+1+min_diag[back]-R_ORIGIN) <
(l_offset2+max_diag[forth]-L_ORIGIN)) {
*rblock = *lblock = _exonManager.newExon(l_offset2+1,l_offset1+1,
l_offset2+n0,l_offset1+m,
m,back+forth,0,NULL);
} else {
*rblock = _exonManager.newExon(r_offset2+1+min_row[back]+min_diag[back]-R_ORIGIN,
r_offset1+1+min_row[back],
r_offset2+n2,r_offset1+m,
m-min_row[back],back,0,NULL);
*lblock = _exonManager.newExon(l_offset2+1,l_offset1+1,
l_offset2+min_row[back]+max_diag[forth]-L_ORIGIN,
l_offset1+min_row[back],
min_row[back],forth,0,*rblock);
}
} else {
if ((r_offset2+1+min_diag[back]-R_ORIGIN) <
(l_offset2+max_diag[forth]-L_ORIGIN)) {
*rblock = *lblock = new Exon(l_offset2+1,l_offset1+1,
l_offset2+n0,l_offset1+m,
m,back+forth,0,NULL);
} else {
*rblock = new Exon(r_offset2+1+max_row[forth]+min_diag[back]-R_ORIGIN,
r_offset1+1+max_row[forth],
r_offset2+n2,r_offset1+m,m-max_row[forth],back,0,NULL);
*lblock = new Exon(l_offset2+1,l_offset1+1,
l_offset2+max_row[forth]+max_diag[forth]-L_ORIGIN,
l_offset1+max_row[forth],max_row[forth],forth,0,*rblock);
}
if ((r_offset2+1+min_diag[back]-R_ORIGIN) <
(l_offset2+max_diag[forth]-L_ORIGIN)) {
*rblock = *lblock = _exonManager.newExon(l_offset2+1,l_offset1+1,
l_offset2+n0,l_offset1+m,
m,back+forth,0,NULL);
} else {
*rblock = _exonManager.newExon(r_offset2+1+max_row[forth]+min_diag[back]-R_ORIGIN,
r_offset1+1+max_row[forth],
r_offset2+n2,r_offset1+m,m-max_row[forth],back,0,NULL);
*lblock = _exonManager.newExon(l_offset2+1,l_offset1+1,
l_offset2+max_row[forth]+max_diag[forth]-L_ORIGIN,
l_offset1+max_row[forth],max_row[forth],forth,0,*rblock);
}
}

ckfree(allocdSpace);
Expand Down
65 changes: 32 additions & 33 deletions kmer/libsim4/sim4core/mspManager.C
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@
mspManager::mspManager() {
_sorted = true;

_ESTlen = 0;
_GENlen = 0;

_allocMSPs = 16384;
_numMSPs = 0;
_allMSPs = new msp [_allocMSPs];
Expand All @@ -24,15 +27,20 @@ mspManager::mspManager() {
//
_tooManyMSPs = false;
_cDNALength = 0;
_mspLimitPercent = 0.0;
_mspLimitAbsolute = 0;
_mspLimitPercent = 0;

// These need to be reset with setParameters. The code will die
// during link() if they are not set.
//
_match = 0;
_matchdiff = 0;
_percentError = 0.0;
_wordExtAllow = 0;

_exonManager = 0L;

_minMSPScore = 0;

_diagMax = 0;
_diagExt = 0L;
Expand Down Expand Up @@ -190,31 +198,22 @@ mspManager::doLinking(int weight,
}
}

if (best < 0)
return(0L);




// In the code below, last_msp = best.
//
int last_msp = best;
int diag_dist;
int diff;

Exon *elist = 0L;

if (last_msp < 0)
return(elist);

msp *mp = _allMSPs + last_msp;

elist = new Exon(mp->pos1,
mp->pos2,
mp->pos1+mp->len-1,
mp->pos2+mp->len-1,
-1,
(mp->len * _match - mp->score) / _matchdiff,
0,
elist);
int diag_dist;
int diff;

msp *mp = _allMSPs + last_msp;
Exon *elist = _exonManager->newExon(mp->pos1,
mp->pos2,
mp->pos1+mp->len-1,
mp->pos2+mp->len-1,
-1,
(mp->len * _match - mp->score) / _matchdiff,
0,
0L);

last_msp = mp->prev;

Expand All @@ -223,7 +222,7 @@ mspManager::doLinking(int weight,

int l1 = elist->frEST - elist->frGEN;
int l2 = mp->pos2 - mp->pos1;

if (l1 > l2)
diag_dist = l1 - l2;
else
Expand All @@ -249,14 +248,14 @@ mspManager::doLinking(int weight,
elist->frGEN = min(elist->frGEN,mp->pos1);
elist->frEST = min(elist->frEST,mp->pos2);
} else {
elist = new Exon(mp->pos1,
mp->pos2,
mp->pos1+mp->len-1,
mp->pos2+mp->len-1,
-1,
(mp->len * _match - mp->score) / _matchdiff,
0,
elist);
elist = _exonManager->newExon(mp->pos1,
mp->pos2,
mp->pos1+mp->len-1,
mp->pos2+mp->len-1,
-1,
(mp->len * _match - mp->score) / _matchdiff,
0,
elist);
}

last_msp = mp->prev;
Expand Down
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