void StringTotString(tString& tstrDest, const std::string& strSrc)
{
TCHAR* pwszStr = NULL;
C2T(&pwszStr, strSrc.c_str());
tstrDest = pwszStr;
SAFE_ARRYDELETE(pwszStr);
}
void StringTotString(tString& tstrDest, LPCSTR lpcSrc)
{
TCHAR* pwszStr = NULL;
C2T(&pwszStr, lpcSrc);
tstrDest = pwszStr;
SAFE_ARRYDELETE(pwszStr);
}
BOOL CPicDowloadThread::Run()
{
//tString tstrUrl;
//tString tstrFriendId;
PicInfo* pInfo = (PicInfo*)m_pPara;
//TCHAR tszPicPath[MAX_PATH] = {0x0};
GetDownloadUrl();
// 向 界面发送消息将已经有的头像图片贴上去
PostMessage(pInfo->m_hWnd, WM_SETHEADPICTURE, MAKELPARAM(m_downloadType, 0), (LPARAM)this);
HINSTANCE hDll = NULL;
#ifdef USE_WININET_DOWNLOAD
#ifdef _DEBUG
hDll = LoadLibrary(_T("HtttpDownload_d.dll"));
#else
hDll = LoadLibrary(_T("HtttpDownload.dll"));
#endif
#endif
for (map<std::string, tString>::iterator it = pInfo->m_mapIdNotHadPic.begin(); it != pInfo->m_mapIdNotHadPic.end(); it++)
{
TCHAR tszPicPath[MAX_PATH] = {0x0};
LPTSTR lptId = NULL;
C2T(&lptId, it->first.c_str());
GetLinkmanPicPath(tszPicPath, MAX_PATH,it->second.c_str(), lptId);
if (URLDownloadPicture(it->second.c_str(), tszPicPath, hDll))
it->second = tszPicPath;
else
//下载失败
it->second = _T("");
SAFE_ARRYDELETE(lptId);
}
#ifdef USE_WININET_DOWNLOAD
FreeLibrary(hDll);
#endif
//下载的图片
PostMessage(pInfo->m_hWnd, WM_SETHEADPICTURE, MAKELPARAM(m_downloadType, 1), (LPARAM)this);
return FALSE;
}
void BuildIndex(const vector<string>& chrom_files, const int& indicator,
const string& output_file, uint32_t& size_of_index) {
switch (indicator) {
case 0:
fprintf(stderr, "[BIULD INDEX FOR FORWARD STRAND (C->T)]\n");
break;
case 1:
fprintf(stderr, "[BIULD INDEX FOR REVERSE STRAND (C->T)]\n");
break;
case 2:
fprintf(stderr, "[BIULD INDEX FOR FORWARD STRAND (G->A)]\n");
break;
case 3:
fprintf(stderr, "[BIULD INDEX FOR REVERSE STRAND (G->A)]\n");
}
Genome genome;
HashTable hash_table;
ReadGenome(chrom_files, genome);
if (indicator % 2) {
ReverseComplementGenome(genome);
}
if (indicator == 0 || indicator == 1) {
C2T(genome.sequence);
} else {
G2A(genome.sequence);
}
set<uint32_t> extremal_large_bucket;
CountBucketSize(genome, hash_table, extremal_large_bucket);
HashToBucket(genome, hash_table, extremal_large_bucket);
SortHashTableBucket(genome, hash_table);
WriteIndex(output_file, genome, hash_table);
size_of_index =
hash_table.index_size > size_of_index ?
hash_table.index_size : size_of_index;
}
term hlist(register term H, register term regs, stack wam)
{ no i; cell xval; bp_long ival; byte stamp;
#if TRACE>0
fprintf(STD_err,"entering hlist, wam=%d, bboard=%d H=%d\n",
wam,g.shared[BBoardStk].base,H);
bbcheck(wam);
#endif
if(!INTEGER(X(1))) return NULL; /* first arg: stamp */
stamp=(byte)(OUTPUT_INT(X(1)));
xval=X(2); /* second arg: starting arity of listed terms */
if(!INTEGER(xval)) return NULL;
ival=OUTPUT_INT(xval);
for(i=0; i<HMAX; i++)
if(hstamp[i]>=stamp && HUSED())
{ term xref=C2T(g.predmark);
if(hstamp[i]<=RUNTIME)
{ /* gets preds of arity < ival `represented' as g.predmark*/
if(g.predmark!=htable[i].pred
|| GETARITY(htable[i].fun)<(no)ival)
continue;
xval=g.predmark;
}
else
{ /* gets RUNTIME data of arity > ival */
cell v=htable[i].val;
if(NULL==(term)v)
continue;
if(VAR(v) &&
!(
ONSTACK(g.shared[BBoardStk],v) ||
ONSTACK(g.shared[InstrStk],v) /*|| ON(HeapStk,v) */
)) {
#if TRACE>0
fprintf(STD_err,
"unexpected data in htable[%d]=>\n<%s,%s>->%s\n",i,
smartref(htable[i].pred,wam),
smartref(htable[i].fun,wam),
smartref(v,wam));
#endif
/* continue; */
}
FDEREF(v);
if((INTEGER(xval) && ival>0)
|| VAR(xval)
|| (GETARITY(xval) < (no)ival)
|| xval==g.empty
)
continue;
if(COMPOUND(xval))
xval=T2C(xref);
}
IF_OVER("COPY_KEYS",(term *)H,HeapStk,bp_halt(9));
SAVE_FUN(htable[i].pred);
SAVE_FUN(htable[i].fun);
#if 0
ASSERT2(( ATOMIC(xval)
|| ONSTACK(g.shared[BBoardStk],xval)
|| ON(HeapStk,xval)), /* will fail with multiple engines */
xval);
#endif
PUSH_LIST(xval);
}
PUSH_NIL();
return H;
}
void PairEndMapping(const string& org_read, const Genome& genome,
const HashTable& hash_table, const char& strand,
const bool& AG_WILDCARD, const uint32_t& max_mismatches,
TopCandidates& top_match) {
uint32_t read_len = org_read.size();
if (read_len < MINIMALREADLEN) {
return;
}
/* return the maximal seed length for a particular read length */
uint32_t seed_pattern_repeats = (read_len - SEEPATTERNLEN + 1)
/ SEEPATTERNLEN;
uint32_t seed_len = seed_pattern_repeats * SEEPATTERNCAREDWEIGHT;
string read;
if (AG_WILDCARD) {
G2A(org_read, read_len, read);
} else {
C2T(org_read, read_len, read);
}
uint32_t cur_max_mismatches = max_mismatches;
for (uint32_t seed_i = 0; seed_i < SEEPATTERNLEN; ++seed_i) {
/* all exact matches are covered by the first seed */
if (!top_match.Empty() && top_match.Full() && top_match.Top().mismatch == 0
&& seed_i)
break;
#if defined SEEDPATTERN3 || SEEDPATTERN5
/* all matches with 1 mismatch are covered by the first two seeds */
if (!top_match.Empty() && top_match.Full() && top_match.Top().mismatch == 1
&& seed_i >= 2)
break;
#endif
#ifdef SEEDPATTERN7
/* all matches with 1 mismatch are covered by the first two seeds */
if (!top_match.Empty() && top_match.Full() && top_match.Top().mismatch == 1
&& seed_i >= 4)
break;
#endif
string read_seed = read.substr(seed_i);
uint32_t hash_value = getHashValue(read_seed.c_str());
pair<uint32_t, uint32_t> region;
region.first = hash_table.counter[hash_value];
region.second = hash_table.counter[hash_value + 1];
if (region.first == region.second)
continue;
IndexRegion(read_seed, genome, hash_table, seed_len, region);
if (region.second - region.first + 1 > 5000) {
continue;
}
for (uint32_t j = region.first; j <= region.second; ++j) {
uint32_t genome_pos = hash_table.index[j];
uint32_t chr_id = getChromID(genome.start_index, genome_pos);
if (genome_pos - genome.start_index[chr_id] < seed_i)
continue;
genome_pos = genome_pos - seed_i;
if (genome_pos + read_len >= genome.start_index[chr_id + 1])
continue;
/* check the position */
uint32_t num_of_mismatch = 0;
uint32_t num_of_nocared = seed_pattern_repeats * SEEPATTERNNOCAREDWEIGHT
+ seed_i;
for (uint32_t p = 0;
p < num_of_nocared && num_of_mismatch <= cur_max_mismatches; ++p) {
if (genome.sequence[genome_pos + F2NOCAREDPOSITION[seed_i][p]]
!= read[F2NOCAREDPOSITION[seed_i][p]]) {
num_of_mismatch++;
}
}
for (uint32_t p = seed_pattern_repeats * SEEPATTERNLEN + seed_i;
p < read_len && num_of_mismatch <= cur_max_mismatches; ++p) {
if (genome.sequence[genome_pos + p] != read[p]) {
num_of_mismatch++;
}
}
if (num_of_mismatch > max_mismatches) {
continue;
}
top_match.Push(CandidatePosition(genome_pos, strand, num_of_mismatch));
if (top_match.Full()) {
cur_max_mismatches = top_match.Top().mismatch;
}
}
}
}
Node TarjanHD::hd(const Digraph& g,
const DoubleArcMap& w,
SubDigraph& subG,
NodeNodeMap& mapToOrgG,
NodeNodeMap& G2T,
const ArcList& sortedArcs,
int i)
{
assert(i >= 0);
int m = static_cast<int>(sortedArcs.size());
assert(m == lemon::countArcs(subG));
int r = m - i;
if (r == 0 || r == 1)
{
// add to _T a subtree rooted at node r,
// labeled with w(e_m) and having n children labeled with
// the vertices of subG
Node root = _T.addNode();
_label[root] = w[sortedArcs.back()];
_T2OrgG[root] = lemon::INVALID;
for (SubNodeIt v(subG); v != lemon::INVALID; ++v)
{
Node vv = G2T[v];
if (vv == lemon::INVALID)
{
vv = _T.addNode();
_label[vv] = -1;
if (mapToOrgG[v] != lemon::INVALID)
{
_orgG2T[mapToOrgG[v]] = vv;
_T2OrgG[vv] = mapToOrgG[v];
}
}
_T.addArc(vv, root);
}
return root;
}
else
{
int j = (i + m) % 2 == 0 ? (i + m) / 2 : (i + m) / 2 + 1;
// remove arcs j+1 .. m
ArcListIt arcEndIt, arcIt = sortedArcs.begin();
for (int k = 1; k <= m; ++k)
{
if (k == j + 1)
{
arcEndIt = arcIt;
}
if (k > j)
{
subG.disable(*arcIt);
}
++arcIt;
}
// compute SCCs
IntNodeMap comp(g, -1);
int numSCC = lemon::stronglyConnectedComponents(subG, comp);
if (numSCC == 1)
{
ArcList newSortedArcs(sortedArcs.begin(), arcEndIt);
// _subG is strongly connected
return hd(g, w, subG, mapToOrgG, G2T, newSortedArcs, i);
}
else
{
// determine strongly connected components
NodeHasher<Digraph> hasher(g);
NodeSetVector components(numSCC, NodeSet(42, hasher));
for (SubNodeIt v(subG); v != lemon::INVALID; ++v)
{
components[comp[v]].insert(v);
}
NodeVector roots(numSCC, lemon::INVALID);
double w_i = i > 0 ? w[getArcByRank(sortedArcs, i)] : -std::numeric_limits<double>::max();
for (int k = 0; k < numSCC; ++k)
{
const NodeSet& component = components[k];
if (component.size() > 1)
{
// construct new sorted arc list for component: O(m) time
ArcList newSortedArcs;
for (ArcListIt arcIt = sortedArcs.begin(); arcIt != arcEndIt; ++arcIt)
{
Node u = g.source(*arcIt);
Node v = g.target(*arcIt);
bool u_in_comp = component.find(u) != component.end();
bool v_in_comp = component.find(v) != component.end();
if (u_in_comp && v_in_comp)
{
newSortedArcs.push_back(*arcIt);
}
}
// remove nodes not in component from the graph
for (NodeIt v(g); v != lemon::INVALID; ++v)
{
subG.status(v, component.find(v) != component.end());
}
// find new_i, i.e. largest k such that w(e'_k) <= w(e_i)
// if i == 0 or i > 0 but no such k exists => new_i := 0
int new_i = get_i(newSortedArcs, w, w_i);
// recurse on strongly connected component
roots[k] = hd(g, w, subG, mapToOrgG, G2T, newSortedArcs, new_i);
}
// enable all nodes again
for (int k = 0; k < numSCC; ++k)
{
const NodeSet& component = components[k];
for (NodeSetIt nodeIt = component.begin(); nodeIt != component.end(); ++nodeIt)
{
subG.enable(*nodeIt);
}
}
}
// construct the condensed graph:
// each strongly connected component is collapsed into a single node, and
// from the resulting sets of multiple arcs retain only those with minimum weight
Digraph c;
DoubleArcMap ww(c);
NodeNodeMap mapCToOrgG(c);
NodeNodeMap C2T(c);
ArcList newSortedArcs;
int new_i = constructCondensedGraph(g, w, mapToOrgG, G2T, sortedArcs,
comp, components, roots, j,
c, ww, mapCToOrgG, C2T, newSortedArcs);
BoolArcMap newArcFilter(c, true);
BoolNodeMap newNodeFilter(c, true);
SubDigraph subC(c, newNodeFilter, newArcFilter);
Node root = hd(c, ww, subC, mapCToOrgG, C2T, newSortedArcs, new_i);
return root;
}
}
return lemon::INVALID;
}
