Word GMSDS(Word *A, Word m, Word (*C)(Word,Word))
{
Word *T,*T1,*T2,*A1,*A2,m1,m1p,m2,m2p,mp,k,l;
Step1: /* Split. */
m1 = m >> 1;
m2 = m1 + ODD(m);
A1 = A;
A2 = A + m1;
Step2: /* Sort sublists. */
if (m1 < 4) {
m1p = G23VSDS(A1,m1,C); }
else m1p = GMSDS(A1,m1,C);
if (m2 < 4) {
m2p = G23VSDS(A2,m2,C); }
else m2p = GMSDS(A2,m2,C);
Step3: /* Copy A1 into a temporary array. */
T1 = GETARRAY(m1);
for(k = 0; k < m1; k++) T1[k] = A1[k];
A1 = T1;
Step4: /* Copy A2 into a temporary array. */
T2 = GETARRAY(m2);
for(k = 0; k < m2; k++) T2[k] = A2[k];
A2 = T2;
Step5: /* Merge A1 and A2 until one or both is exhausted. */
mp = m;
for(k = 0; (m1p > 0) && (m2p > 0); k++) {
switch(C(A1[0],A2[0])) {
case (1) : A[k] = A2[0]; A2++; m2p--; break;
case (0) : A[k] = A1[0]; A1++; m1p--;
A[--mp] = A2[0];A2++; m2p--; break;
case (-1): A[k] = A1[0]; A1++; m1p--; break; } }
Step6: /* Complete merge. */
while (m1p > 0) {
A[k++] = A1[0]; A1++; m1p--; }
while (m2p > 0) {
A[k++] = A2[0]; A2++; m2p--; }
Step7: /* Write suppressed duplicates to end. */
for(T = T1 + m1 -1; T >= A1; T--) {
A[--mp] = T[0]; }
for(T = T2 + m2 -1; T >= A2; T--) {
A[--mp] = T[0]; }
Return: /* Prepare to return. */
FREEARRAY(T1);
FREEARRAY(T2);
return (mp);
}
Word MINHITSETSRDR(Word A, Word B)
{
Word n,*N,i,L,Ap;
Step1: /* Quick decisions. */
if (A == NIL) return (NIL);
if ((B == 0) || (FIRST(A) == NIL)) return (MC_FAIL);
Step2: /* Sort Rows. */
n = LENGTH(A);
N = GETARRAY(n);
i = 0;
for(L = A; L != NIL; L = RED(L))
N[i++] = FIRST(L);
n = GMSDS(N,n,comp);
Step3: /* Reconstruct list. */
Ap = NIL;
for(i = n - 1; i >= 0; i--)
Ap = COMP(N[i],Ap);
Return: /* Return. */
FREEARRAY(N);
return (MINHITSET(Ap,B));
}
Word LDCOEFMASK(Word c, Word P, Word J)
{
Word *A,P_2,n,i,M,P_1,L,m,j,p,Lp,h,q,v,l;
Step1: /* Set up A to be a characteristic vector for the set of
level 2 proj fac's whose leading coefficients vanish in c. */
P_2 = LELTI(P,2);
n = THIRD(LELTI(LAST(P_2),PO_LABEL));
A = GETARRAY(n + 1);
for(i = 1; i <= n; i++)
A[i] = 0;
Step2: /* Set L to be the list of projection factors which vanish in c. */
M = LELTI(c,MULSUB);
P_1 = LELTI(P,1);
L = NIL;
while(M != NIL) {
ADV(M,&m,&M);
j = FIRST(m);
do
ADV(P_1,&p,&P_1);
while(j != THIRD(LELTI(p,PO_LABEL)));
L = COMP(p,L); }
Step3: /* Set Lp to the list of projection polynomials with factors in L. */
Lp = NIL;
while(L != NIL) {
ADV(L,&p,&L);
for(h = LELTI(p,PO_PARENT); h != NIL; h = RED(h))
Lp = COMP(THIRD(FIRST(h)),Lp); }
Step4: /* Run through the histories of each polynomial in Lp. If the
polynomial is the leading coefficient of some bivariate projection factor,
set A at the index for that projection factor to 1. */
while(Lp != NIL) {
ADV(Lp,&p,&Lp);
for(h = LELTI(p,PO_PARENT); h != NIL; h = RED(h)) {
q = FIRST(h);
if (FIRST(q) == PO_LCO) {
l = LELTI(THIRD(q),PO_LABEL);
if (SECOND(l) == 2)
A[ THIRD(l) ] = 1; } } }
Step5: /* Create the vector itself! */
v = NIL;
while(P_2 != NIL) {
ADV(P_2,&p,&P_2);
j = THIRD(LELTI(p,PO_LABEL));
v = COMP(A[j],v); }
v = INV(v);
Return: /* Prepare to return. */
FREEARRAY(A);
return v;
}
void setDMSFriendlyName(JNIEnv* env,jobject jthiz,jstring jstrFriendlyName)
{
icstring strName = env->GetStringUTFChars(jstrFriendlyName,NULL);
if(!strName)
return;
FREEARRAY(CESDMServer_Android::m_ServerName);
CESDMServer_Android::m_ServerName = strdup(strName);
env->ReleaseStringUTFChars(jstrFriendlyName,strName);
return;
}
CESContentDirectory_Device_Android::~CESContentDirectory_Device_Android()
{
FREEARRAY(m_thizUDN);
CFileHandleList::iterator itbegin = m_fileHandleList.begin();
CFileHandleList::iterator itend = m_fileHandleList.end();
for (itbegin; itbegin != itend; ++itbegin)
{
int fn = (int)(*itbegin);
if(fn!=-1)
close(fn);
}
m_fileHandleList.clear();
//DELETE(m_pSpecialDevice);
}
bool vFile::Read(void)
{
if(!m_fp) {
return false;
}
if(!(m_iFlags & modeRead)) {
return false;
}
long size = Length();
FREEARRAY(m_pDataBuf)
m_pDataBuf = new unsigned char[size + 1];
memset(m_pDataBuf, NULL, size + 1);
Seek(0, SEEK_SET);
size_t readSize = fread(m_pDataBuf, size, 1, m_fp);
if(readSize < 1) {
return false;
}
return true;
}
void vFile::Close(void)
{
F_FREE(m_fp);
FREEARRAY(m_pDataBuf);
}
Sint depthfirststree(Suffixtree *stree,Reference *startnode,
Sint (*processleaf)(Uint,Bref,void *),
bool (*processbranch1)(Bref,void *),
Sint (*processbranch2)(Bref,void *),
bool (*stoptraversal)(void *),void *stopinfo,void *info)
{
bool godown = true, readyforpop = false;
Uint child, brotherval;
Bref lcpnode = NULL;
Reference currentnode;
ArrayBref stack;
if(startnode->toleaf)
{
if(processleaf((Uint) (startnode->address - stree->leaftab),NULL,info) != 0)
{
return -1;
}
return 0;
}
if(stoptraversal != NULL && stoptraversal(stopinfo))
{
return 0;
}
currentnode.toleaf = false;
currentnode.address = startnode->address;
INITARRAY(&stack,Bref);
STOREINARRAY(&stack,Bref,128,currentnode.address);
SETCURRENT(GETCHILD(currentnode.address));
if(processbranch1 == NULL)
{
#define PROCESSBRANCH1(A,B) /* Nothing */
#define PROCESSBRANCH2(A,B) godown = true
while(true)
{
if(stoptraversal != NULL && stoptraversal(stopinfo))
{
return 0;
}
if(currentnode.toleaf)
{
/*fprintf(stderr,"visit leaf %lu ",
(long unsigned int) LEAFADDR2NUM(stree,currentnode.address));
fprintf(stderr,"below %lu ",(long unsigned int) BRADDR2NUM(stree,startnode->address));
fprintf(stderr,"depth %lu\n",stree->currentdepth);*/
if(processleaf(LEAFADDR2NUM(stree,currentnode.address),lcpnode,info) != 0)
{
return -1;
}
brotherval = LEAFBROTHERVAL(*(currentnode.address));
if(NILPTR(brotherval))
{
readyforpop = true;
currentnode.toleaf = false;
} else
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
}
} else
{
if(readyforpop)
{
if(stack.nextfreeBref == UintConst(1))
{
break;
}
(stack.nextfreeBref)--;
/*fprintf(stderr,"#pop[%lu]=",(long unsigned int) stack.nextfreeBref);
fprintf(stderr,"%lu\n",
(long unsigned int) BRADDR2NUM(stree,stack.spaceBref[stack.nextfreeBref]));*/
PROCESSBRANCH2(stack.spaceBref[stack.nextfreeBref],info);
brotherval = GETBROTHER(stack.spaceBref[stack.nextfreeBref]);
if(!NILPTR(brotherval))
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
readyforpop = false;
}
} else
{
/*fprintf(stderr,"#process1 %lu\n",
(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
PROCESSBRANCH1(currentnode.address,info);
if(godown)
{
STOREINARRAY(&stack,Bref,128,currentnode.address);
/*fprintf(stderr,"#push[%lu]=",(long unsigned int) (stack.nextfreeBref-1));
fprintf(stderr,"%lu\n",(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
child = GETCHILD(currentnode.address);
SETCURRENT(child); // current comes from child
} else
{
brotherval = GETBROTHER(currentnode.address);
if(NILPTR(brotherval))
{
readyforpop = true;
} else
{
SETCURRENT(brotherval); // current comes brother
}
}
}
}
}
} else
{
#undef PROCESSBRANCH1
#undef PROCESSBRANCH2
#define PROCESSBRANCH1(A,B) godown = processbranch1(A,B)
#define PROCESSBRANCH2(A,B) if(processbranch2(A,B) != 0)\
{\
return -2;\
}
while(true)
{
if(stoptraversal != NULL && stoptraversal(stopinfo))
{
return 0;
}
if(currentnode.toleaf)
{
/*fprintf(stderr,"visit leaf %lu ",
(long unsigned int) LEAFADDR2NUM(stree,currentnode.address));
fprintf(stderr,"below %lu ",(long unsigned int) BRADDR2NUM(stree,startnode->address));
fprintf(stderr,"depth %lu\n",stree->currentdepth);*/
if(processleaf(LEAFADDR2NUM(stree,currentnode.address),lcpnode,info) != 0)
{
return -1;
}
brotherval = LEAFBROTHERVAL(*(currentnode.address));
if(NILPTR(brotherval))
{
readyforpop = true;
currentnode.toleaf = false;
} else
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
}
} else
{
if(readyforpop)
{
if(stack.nextfreeBref == UintConst(1))
{
break;
}
(stack.nextfreeBref)--;
/*fprintf(stderr,"#pop[%lu]=",(long unsigned int) stack.nextfreeBref);
fprintf(stderr,"%lu\n",
(long unsigned int) BRADDR2NUM(stree,stack.spaceBref[stack.nextfreeBref]));*/
PROCESSBRANCH2(stack.spaceBref[stack.nextfreeBref],info);
brotherval = GETBROTHER(stack.spaceBref[stack.nextfreeBref]);
if(!NILPTR(brotherval))
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
readyforpop = false;
}
} else
{
/*fprintf(stderr,"#process1 %lu\n",
(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
PROCESSBRANCH1(currentnode.address,info);
if(godown)
{
STOREINARRAY(&stack,Bref,128,currentnode.address);
/*fprintf(stderr,"#push[%lu]=",(long unsigned int) (stack.nextfreeBref-1));
fprintf(stderr,"%lu\n",(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
child = GETCHILD(currentnode.address);
SETCURRENT(child); // current comes from child
} else
{
brotherval = GETBROTHER(currentnode.address);
if(NILPTR(brotherval))
{
readyforpop = true;
} else
{
SETCURRENT(brotherval); // current comes brother
}
}
}
}
}
}
FREEARRAY(&stack,Bref);
return 0;
}
Word MINPFSETNSC(Word P,Word S,Word D,Word K)
{
Word C,Sltr,Pltr,r,L_r,Ls_r,L,l,l_t,l_s,ls,Kp,Js,x,Jsp,s_k,sk;
Word x_s,js,Ls,O,Q,Q_i,Sp,Pp,i,Cp,*V,*Vp,**A,a,N,k,S_r,I,j,p;
Step1: /* Initialization. */
C = NIL; Sltr = NIL; Pltr = NIL; N = LENGTH(K);
Step2: /* Loop over each level in D. */
for(r = 1; r <= N; r++) {
Step3: /* Get signiture and truth value for each cell. */
L_r = CADCL(D,r);
for(Ls_r = NIL; L_r != NIL; L_r = RED(L_r)) {
l = FIRST(L_r);
l_t = LELTI(l,TRUTH); l_s = LELTI(l,SIGNPF);
for(ls = NIL; l_s != NIL; l_s = RED(l_s)) {
ls = CCONC(FIRST(l_s),ls); }
ls = COMP(l_t,ls);
Ls_r = COMP(ls,Ls_r); }
Step4: /* Get conflict cell signitures. */
Jsp = NIL;
for(Kp = LELTI(K,r); Kp != NIL; Kp = RED(Kp)) {
k = FIRST(FIRST(Kp));
s_k = LELTI(k,SIGNPF);
for(sk = NIL; s_k != NIL; s_k = RED(s_k)) {
sk = CCONC(FIRST(s_k),sk); }
if (! MEMBER(sk,Jsp) )
Jsp = COMP(sk,Jsp); }
for(Js = NIL; Jsp != NIL; Jsp = RED(Jsp)) {
Js = COMP(COMP(CFLCT,FIRST(Jsp)),Js); }
Step5: /* Put lists together, and sort with duplicate removal. */
Ls = CCONC(Js,Ls_r);
Ls = GMSDSL(Ls,comp1);
Step6: /* Put this all into array representation. */
a = LENGTH(Ls);
k = LENGTH(FIRST(Ls)) - 1;
V = (Word*)GETARRAY(a*(k + 1)); Vp = V;
A = (Word**)GETARRAY(a*(sizeof(Word*)/sizeof(Word))); /* ASSUMES THIS / IS EXACT! */
for(i = 0; i < a; i++) {
A[i] = V + 1;
for(ADV(Ls,&ls,&Ls); ls != NIL; ls = RED(ls))
*(V++) = FIRST(ls); }
Step7: /* Build S_r. */
Sltr = CCONC(Sltr,LELTI(S,r));
Pltr = CCONC(Pltr,LELTI(P,r));
Sp = CINV(Sltr);
for(S_r = NIL; Sp != NIL; Sp = RED(Sp)) {
i = PFPIPFL(FIRST(Sp),Pltr);
S_r = COMP(i - 1,S_r); }
Step8: /* Sort cell signitures on S_r, and list conflict resolving
polynomials for each pair of conflicting cells in the same
class. */
CSORTSS(A,a,S_r);
for(i = 0;i < a; i = j) {
for(j = i + 1; (j < a) && ( SIGEQUALOL(A[i],A[j],S_r));j++);
Cp = ICSIGDIFFLNSC(A+i,j-i,k);
C = CCONC(C,Cp); }
Step9: /* Deallocate memory. */
FREEARRAY(Vp);
FREEARRAY(A); }
Step10:/* Get a min-hit-set */
O = MINHITSETSR(C,-1);
O = LMERGE(O,S_r);
O = LBIBMS(O); Q = NIL;
for(r = N; r > 0; r--) Q = COMP(NIL,Q);
while (O != NIL) {
ADV(O,&k,&O);
p = LELTI(Pltr,k+1);
i = LELTI(LELTI(p,PO_LABEL),2);
Q_i = SUFFIX(LELTI(Q,i),p);
SLELTI(Q,i,Q_i); }
Return: /* Prepare to return. */
return (Q);
}
Sint procmaxmatches(MMcallinfo *mmcallinfo,Multiseq *subjectmultiseq)
{
Matchprocessinfo matchprocessinfo;
Uint filenum, filelen;
Sint retcode;
Uchar *filecontent;
double start, finish;
/*fprintf(stderr,"# construct suffix tree for sequence of length %lu\n",
(Showuint) subjectmultiseq->totallength);
fprintf(stderr,"# (maximum reference length is %lu)\n",
(Showuint) getmaxtextlenstree());
fprintf(stderr,"# (maximum query length is %lu)\n",
(Showuint) ~((Uint)0));*/
start = omp_get_wtime();
if(constructprogressstree (&matchprocessinfo.stree,
subjectmultiseq->sequence,
subjectmultiseq->totallength,
NULL,
NULL,
NULL) != 0)
{
return -1;
}
finish = omp_get_wtime();
/*fprintf(stderr,"# CONSTRUCTIONTIME %s %s %.2f\n",
&mmcallinfo->program[0],&mmcallinfo->subjectfile[0],
getruntime());*/
matchprocessinfo.subjectmultiseq = subjectmultiseq;
matchprocessinfo.minmatchlength = mmcallinfo->minmatchlength;
matchprocessinfo.showstring = mmcallinfo->showstring;
matchprocessinfo.showsequencelengths = mmcallinfo->showsequencelengths;
matchprocessinfo.showreversepositions = mmcallinfo->showreversepositions;
matchprocessinfo.forward = mmcallinfo->forward;
matchprocessinfo.fourcolumn = mmcallinfo->fourcolumn;
matchprocessinfo.cmum = mmcallinfo->cmum;
matchprocessinfo.cmumcand = mmcallinfo->cmumcand;
matchprocessinfo.reversecomplement = mmcallinfo->reversecomplement;
matchprocessinfo.chunks = mmcallinfo->chunks;
if(mmcallinfo->cmum)
{
INITARRAY(&matchprocessinfo.mumcandtab,MUMcandidate);
}
retcode = getmaxdesclen(subjectmultiseq);
if(retcode < 0)
{
return -2;
}
matchprocessinfo.maxdesclength = (Uint) retcode;
for(filenum=0; filenum < mmcallinfo->numofqueryfiles; filenum++)
{
filecontent = CREATEMEMORYMAP (mmcallinfo->queryfilelist[filenum],
True,
&filelen);
if (filecontent == NULL || filelen == 0)
{
ERROR2("cannot open file \"%s\" or file \"%s\" is empty",
mmcallinfo->queryfilelist[filenum],
mmcallinfo->queryfilelist[filenum]);
return -3;
}
if (scanmultiplefastafile (&matchprocessinfo.querymultiseq,
mmcallinfo->queryfilelist[filenum],
mmcallinfo->matchnucleotidesonly
? MMREPLACEMENTCHARQUERY
: 0,
filecontent, filelen) != 0)
{
return -4;
}
/*fprintf(stderr,
"# matching query-file \"%s\"\n# against subject-file \"%s\"\n",
mmcallinfo->queryfilelist[filenum],
mmcallinfo->subjectfile);*/
if (overallsequences (False,
&matchprocessinfo.querymultiseq,
(void *) &matchprocessinfo,
findmaxmatchesonbothstrands) != 0)
{
return -5;
}
freemultiseq(&matchprocessinfo.querymultiseq);
}
if(mmcallinfo->cmum)
{
FREEARRAY(&matchprocessinfo.mumcandtab,MUMcandidate);
}
freestree (&matchprocessinfo.stree);
fprintf(stdout,"ST=%f,",(double) (finish-start));
return 0;
}
void IBPRRIOAPSF(Word M, Word I, Word B, BDigit p, BDigit k, Word *J_, Word *L_)
{
BDigit *Mp,*bp,*c,i,m,n,q1,q2,S,s,t;
Word b,Bp,I1,I2,J,K,L,Ls,Lp,T,Jp;
Step1: /* Convert the minimal polynomial to a software interval
polynomial. */
n = PDEG(M);
q1 = p + 3;
q2 = q1 + q1;
S = (n + 1) * q2 + 1;
Mp = GETARRAY(S);
IPSIP(M,p,Mp);
Step2: /* Compute the trend of \alpha. */
b = SECOND(I);
bp = GETARRAY(q1);
t = LBRNFEC(b,p,bp);
J = I;
L = 0;
if (t == 0) {
FREEARRAY(bp);
goto Return; }
t = SIPES(Mp,bp);
FREEARRAY(bp);
if (t == NIL)
goto Return;
Step3: /* Refine the isolating interval for \alpha. */
J = SIPIR(Mp,I,t,- (p * ZETA));
FREEARRAY(Mp);
Step4: /* Isolate the real roots of B(J)[Y]. */
L = NIL;
m = PDEG(B);
s = (m + 1) * q2 + 1;
c = GETARRAY(s);
IBPELBRISIPR(B,J,p,c);
L = SIPRRID(c);
if (L == 0)
goto Step8;
t = c[s - q2 + 1];
if (EVEN(m))
t = -t;
Step5: /* Refine the intervals. */
if (k == NIL)
goto Return;
Ls = NIL;
for(Lp = L; Lp != NIL; Lp = RED(Lp))
{
Jp = SIPIR(c,FIRST(Lp),t,-k);
Ls = COMP(Jp,Ls);
t = -t;
}
L = CINV(Ls);
Step8: /* Free arrays. */
FREEARRAY(c);
Return: /* Return J and L. */
*J_ = J;
*L_ = L;
return;
}
void CDlnaFrame::LoadAllPlugins()
{
struct dirent **pDirNameList = NULL;
#if defined(OS_ANDROID) || defined(PLATFORM_64)
int nret = scandir(m_dirName,&pDirNameList,dllFilter,(int (*)(const dirent**, const dirent**))dllComapre);
#else
int nret = scandir(m_dirName,&pDirNameList,dllFilter,(int (*)(const void*, const void*))dllComapre);
#endif
if(nret > 0)
{
int prefixlen = strlen(m_dirName);
BOOL bNeedAppendSlash = (m_dirName[strlen(m_dirName)-1] != '/');
for (int i = 0; i < nret; i++)
{
char* pFullPath = NULL;
if(bNeedAppendSlash)
pFullPath = new char[prefixlen + 1 + strlen(pDirNameList[i]->d_name) + 1];
else
pFullPath = new char[prefixlen + strlen(pDirNameList[i]->d_name) + 1];
memset(pFullPath,0,sizeof(pFullPath));
strcat(pFullPath,m_dirName);
if(bNeedAppendSlash)
strcat(pFullPath,"/");
strcat(pFullPath,pDirNameList[i]->d_name);
void *pHandle = dlopen(pFullPath,/*RTLD_LAZY*/RTLD_NOW|RTLD_GLOBAL);
if(!pHandle)
{
Trace(
"fail to load %s\n",pDirNameList[i]->d_name);
}
else
{
CPlugIn* pPlugin = new CPlugIn;
pPlugin->pHandle = pHandle;
if(LoadAllFunctions(pPlugin) != 0)
{
Trace(
"fail to load functions from %s\n",pDirNameList[i]->d_name);
DELETE(pPlugin);
}
else
{
Trace(
"succeed to load %s\n",pDirNameList[i]->d_name);
pPlugin->pName = strdup(pDirNameList[i]->d_name);
m_ListPlugin.push_back(pPlugin);
}
}
FREE(pDirNameList[i]);
DELETEARRAY(pFullPath);
}
FREEARRAY(pDirNameList);
}
else
Trace("fail to load plugin from %s\n",m_dirName);
}
