// 从配置文件重新生成插件列表
int CPluginManager::ReloadPlugin(DWORD dwFlag)
{
LOG((LEVEL_FUNC_IN_OUT,"CPluginManager::ReloadPlugin,flag = %d\n",dwFlag));
// 卸载所有插件
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::UnLoadPlug),0));
// 清除链表
m_PluginList.clear();
// 重新从配置文件读
std::string strPluginConfigFile(m_szPluginConfigPath);
strPluginConfigFile += TSP_PLUGIN_S_CONFIG_NAME;
// 如果配置文件不正确，由于下载模块很可能调用此函数，所以不返回错，这样可以通过升级更新到新的
if( !ReadPluginIniFile<CPluginInfo>(m_PluginList,strPluginConfigFile,true) )
{
LOG((LEVEL_ERROR,"读取插件配置文件错\n"));
return DDCE_CALL_FAIL;
}
// 去除不属于此部分管理的插件,不用判断返回值
ExceptPluginFile(m_PluginList);
// 设置所有插件状态为未加载
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::Status),CPluginInfo::STATUS_UNLOAD));
return 0;
}
//改变所有插件状态
int CPluginManager::StatusAll(int flag)
{
if( flag == CPluginInfo::STATUS_RUNNING )
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::StartPlug),&m_plugParam));
else if( flag == CPluginInfo::STATUS_UNLOAD )
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::UnLoadPlug),0));
else if( flag == CPluginInfo::STATUS_LOAD )
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::LoadPlug),0));
else if( flag == CPluginInfo::STATUS_STOP )
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::StopPlug),0));
else if( flag == CPluginInfo::STATUS_DELETE )
{
// 需要删除链表中记录
for_each(m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::RemovePlug),0));
m_PluginList.clear();
// 除了测试，其他情况只有卸载会调这个，把自己的配置文件也删了
std::string strPluginConfigFile(m_szPluginConfigPath);
strPluginConfigFile += TSP_PLUGIN_S_CONFIG_NAME;
if( !DeleteFile(strPluginConfigFile.c_str()) )
{
LOG((LEVEL_ERROR,"删除插件失败(%s):%d \n",strPluginConfigFile.c_str(),GetLastError()));
}
}
else
{
LOG((LEVEL_WARNNING,"插件状态未找到:%d\n",flag));
}
return 0;
}
int main()
{
Klasse obj;
const Klasse& objc = obj;
mem_fun(&Klasse::vf0c)(&objc);
mem_fun(&Klasse::vf1c)(&objc, 1);
mem_fun_ref(&Klasse::vf0c)(objc);
mem_fun_ref(&Klasse::vf1c)(objc, 1);
return 0;
}
void CLatticeFrame::print (std::string prefix)
{
if (m_bwType & BESTWORD) printf ("B");
if (m_bwType & USER_SELECTED) printf ("U");
printf ("\n");
prefix += " ";
printf (" Lexicon States:\n");
for_each (m_lexiconStates.begin (), m_lexiconStates.end (),
bind2nd (mem_fun_ref (&TLexiconState::print), prefix));
printf (" Lattice States:\n");
for_each (m_latticeStates.begin (), m_latticeStates.end (),
bind2nd (mem_fun_ref (&TLatticeState::print), prefix));
printf ("\n");
}
TTErr TTAudioGraphObject::resetAudio()
{
sSharedMutex->lock();
for_each(mAudioInlets.begin(), mAudioInlets.end(), mem_fun_ref(&TTAudioGraphInlet::reset));
sSharedMutex->unlock();
return kTTErrNone;
}
result_type operator()(ast::score& score)
{
if (!score.time_sigs.empty()) global_time_signature = score.time_sigs.front();
{
std::vector<std::future<bool>> staves;
for (ast::part &part: score.parts) {
if (!part.empty()) {
std::size_t const staff_count{part.front().paragraphs.size()};
for (std::size_t staff_index = 0; staff_index < staff_count;
++staff_index) {
staves.emplace_back
( async( std::launch::async
, std::move(annotate_staff<ErrorHandler>( error_handler
, report_error
, global_time_signature
, score.key_sig
))
, staff_index, std::ref(part))
);
}
}
}
if (!all_of( begin(staves), end(staves)
, mem_fun_ref(&std::future<bool>::get)))
return false;
}
return unfold(score);
}
void reads::estimateFragLengthMean()
{
int i;
int totalRC = readsClusterVec.size();
int topNo = (int) (param.topPercent * totalRC / 100.0);
vector<readsCluster> sub_rcv;
sort(readsClusterVec.begin(), readsClusterVec.end(), mem_fun_ref(&readsCluster::sortByDense));
sort(readsClusterVec.begin(), readsClusterVec.begin()+topNo, mem_fun_ref(&readsCluster::sortByPos));
for (i=0; i<(topNo-1); i++)
{
if (readsClusterVec[i].r_chrIdx == readsClusterVec[i+1].r_chrIdx && readsClusterVec[i].r_end > readsClusterVec[i+1].r_start)
{
sub_rcv.push_back(readsClusterVec[i++]);
sub_rcv.push_back(readsClusterVec[i]);
}
}
totalRC = sub_rcv.size();
double avgPos, lastAvgPos = 0;
vector<double> fragLengthSample;
for (i=0; i<totalRC; i++)
{
avgPos = sub_rcv[i].r_avgPos;
if (i%2==0)
lastAvgPos = avgPos;
else
fragLengthSample.push_back(avgPos - lastAvgPos);
//printf("%d\t%d\t%d\t%d\t%d\t%.1f\t%d\t%d\t%d\t%.1f\t%.lf\t%c\n",
// sub_rcv[i].r_chrIdx, sub_rcv[i].r_start, sub_rcv[i].r_end, sub_rcv[i].r_length, sub_rcv[i].r_count, sub_rcv[i].r_dense, sub_rcv[i].r_thickStart, sub_rcv[i].r_thickEnd, sub_rcv[i].r_summit, sub_rcv[i].r_summitVal, avgPos, sub_rcv[i].r_strand);
}
if (fragLengthSample.size() == 0)
{
fprintf(stderr, "WARNING: not enough binding regions to estimate the everage fragment length.\n");
param.fragLengthMean = -1;
return;
}
//printVec(fragLengthSample);
//printf("%f\t%f\n", avg(fragLengthSample), var(fragLengthSample));
param.fragLengthMean = avg(fragLengthSample); // avg(fragLengthSample) under estimates the fragment length mean, because of the truncation at the tail and overlap bindings.
}
TTErr TTAudioGraphObject::process(TTAudioSignalPtr& returnedSignal, TTUInt16 forOutletNumber)
{
lock();
switch (mStatus) {
// we have not processed anything yet, so let's get started
case kTTAudioGraphProcessNotStarted:
mStatus = kTTAudioGraphProcessingCurrently;
if (mAudioFlags & kTTAudioGraphGenerator) { // a generator (or no input)
getUnitGenerator()->process(mInputSignals, mOutputSignals);
}
else { // a processor
// zero our collected input samples
mInputSignals->clearAll();
// pull (process, sum, and collect) all of our source audio
for_each(mAudioInlets.begin(), mAudioInlets.end(), mem_fun_ref(&TTAudioGraphInlet::process));
if (!(mAudioFlags & kTTAudioGraphNonAdapting)) {
// examples of non-adapting objects are join≈ and matrix≈
// non-adapting in this case means channel numbers -- vector sizes still adapt
mOutputSignals->matchNumChannels(mInputSignals);
}
mOutputSignals->allocAllWithVectorSize(mInputSignals->getVectorSize());
getUnitGenerator()->process(mInputSignals, mOutputSignals);
}
// TODO: we're doing a copy below -- is that what we really want? Or can we just return the pointer?
returnedSignal = mAudioOutlets[forOutletNumber].mBufferedOutput;
mStatus = kTTAudioGraphProcessComplete;
break;
// we already processed everything that needs to be processed, so just set the pointer
case kTTAudioGraphProcessComplete:
returnedSignal = mAudioOutlets[forOutletNumber].mBufferedOutput;
break;
// to prevent feedback / infinite loops, we just hand back the last calculated output here
case kTTAudioGraphProcessingCurrently:
returnedSignal = mAudioOutlets[forOutletNumber].mBufferedOutput;
break;
// we should never get here
default:
unlock();
return kTTErrGeneric;
}
unlock();
return kTTErrNone;
}
/// free all memory allocations for database
/// \param dbInfo - pointer to database information
void CDatabaseManager::ReleaseDatabase(DATABASEINFO *dbInfo)
{
DATABASEDATA *data = dbInfo->m_DatabaseData;
if (data != NULL)
{
for_each(data, data + dbInfo->m_nItems, mem_fun_ref(&DATABASEDATA::Release));
GLOBALFREE(data);
}
// free up the alloc CHashString*
delete dbInfo->m_SchemaName;
delete dbInfo->m_FileName;
// TODO: Check that name is owned by DATABASEINFO structure also
//delete dbInfo->m_DatabaseName;
//delete dbInfo->m_SchemaFile;
}
//---------------------------------------------------------
int main()
{
int a[3]={ 4, 6, 2 };
std::vector<int> v(a, a+3);
std::vector<base*> u;
u.push_back(new A());
u.push_back(new B());
Fct Fct_obj;
///////////////////////////////////////////////////
std::for_each(a, a+3, fct);
std::cout<<std::endl;
///////////////////////////////////////////////////
std::for_each(v.begin(), v.end(), fct);
std::cout<<std::endl;
// or:
std::for_each(v.begin(), v.end(), Fct_obj);
std::cout<<std::endl;
///////////////////////////////////////////////////
std::for_each(u.begin(), u.end(), std::mem_fun(&base::f));
///////////////////////////////////////////////////
/*std::vector<base> t;
t.push_back(A());
t.push_back(B());
std::std::for_each(u.begin(), u.end(), mem_fun(&base::f));*/
///////////////////////// http://www.java2s.com/Code/Cpp/Vector/Callmemberfunctionforeachelementinvector.htm
///////////////////////////////////////////////////
std::vector<myClass> z(5);
std::for_each(z.begin(), z.end(), std::mem_fun_ref(&myClass::print));
std::for_each(z.begin(), z.end(), std::bind2nd(mem_fun_ref(&myClass::printString), "some text"));
///////////////////////////////////////////////////
std::vector<myClass*> y;
y.push_back(new myClass(5));
std::for_each(y.begin(), y.end(), std::mem_fun(&myClass::print));
std::for_each(y.begin(), y.end(), std::bind2nd(mem_fun(&myClass::printString), "some text"));
///////////////////////////////////////////////////
myClass c;
c.print_();
///////////////////////////////////////////////////
return 0;
}
// Remove trailing whitespace
void
Macro::value_rtrim()
{
// Took me three hours to arrive at
value.erase((find_if(value.rbegin(), value.rend(), not1(mem_fun_ref(&Ptoken::is_space)))).base(), value.end());
}
void h ()
{
mem_fun_ref(&A::f);
}
/*! Check if this Wall still belongs to Cell a, otherwise gives it to Cell b.
\return true: Wall was corrected
\return false: Wall was still correct
*/
bool Wall::CorrectWall( void ) {
// collect all cells to which my nodes are connected on one list
list<CellBase *> owners;
transform(n1->owners.begin(),n1->owners.end(), back_inserter(owners), mem_fun_ref(&Neighbor::getCell));
transform(n2->owners.begin(),n2->owners.end(), back_inserter(owners), mem_fun_ref(&Neighbor::getCell));
// get the list of duplicates
list<CellBase *> wall_owners;
owners.sort();
//transform(owners.begin(), owners.end(), ostream_iterator<int>(cerr, ", "), mem_fun(&Cell::Index));
duplicates_copy( owners.begin(), owners.end(), back_inserter(wall_owners) );
// duplicates are the cells to which the Wall belongs
// For the first division, wall finds three "owners", including the boundary_polygon.
// Remove that one from the list.
//cerr << "wall_owners.size() = " << wall_owners.size() << endl;
if (wall_owners.size() == 3 && nwalls==1 /* bug-fix 22/10/2007; confine this condition to first division only */) {
#ifdef QDEBUG
qDebug() << "nwalls = " << nwalls << endl;
#endif
// special case for first cleavage
// find boundary polygon in the wall owners list
list<CellBase *>::iterator bpit = find_if (
wall_owners.begin(), wall_owners.end(),
mem_fun( &CellBase::BoundaryPolP )
);
if (bpit!=wall_owners.end()) {
// add a Wall with the boundary_polygon to each cell
Wall *bp_wall1 = new Wall( n2, n1, c1, (*bpit) );
bp_wall1->CopyWallContents(*this);
((Cell *)c1)->AddWall( bp_wall1);
((Cell *)(*bpit))->AddWall(bp_wall1);
Wall *bp_wall2 = new Wall( n1, n2, c2, (*bpit) );
bp_wall2->CopyWallContents(*this);
((Cell *)c2)->AddWall( bp_wall2);
((Cell *)(*bpit))->AddWall(bp_wall2);
wall_owners.erase(bpit);
}else {
#ifdef QDEBUG
qDebug() << "Wall::CorrectWall says: Wall has three owners, but none of them is the BoundaryPolygon. I have no clue what to do with this case... Sorry!" << endl;
cerr << "Wall: " << *this << endl;
qDebug() << "Owners are: ";
transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(cerr, " "), mem_fun (&CellBase::Index) );
qDebug() << endl;
qDebug() << "Owners node " << n1->Index() << ": ";
for (list<Neighbor>::iterator i = n1->owners.begin(); i!=n1->owners.end(); i++) {
qDebug() << i->getCell()->Index() << " ";
}
qDebug() << endl;
qDebug() << "Owners node " << n2->Index() << ": ";
for (list<Neighbor>::iterator i = n2->owners.begin(); i!=n2->owners.end(); i++) {
qDebug() << i->getCell()->Index() << " ";
}
qDebug() << endl;
#endif
std::exit(1);
}
}
#ifdef QDEBUG
if (wall_owners.size() == 1) {
qDebug() << "Corner point. Special case." << endl;
}
#endif
CellBase *cell1 = wall_owners.front();
CellBase *cell2 = wall_owners.back();
if ( (c1 == cell1 && c2==cell2) || (c1 == cell2 && c2 == cell1) ) {
return false;
}
if ( c1 == cell1 ) {
//cerr << "Block 1\n";
((Cell *)c2) -> RemoveWall(this);
c2 = cell2;
((Cell *)c2) -> AddWall(this);
} else {
if ( c1 == cell2 ) {
// cerr << "Block 2\n";
((Cell *)c2) -> RemoveWall(this);
c2 = cell1;
((Cell *)c2) -> AddWall(this);
} else {
if ( c2 == cell1) {
((Cell *)c1)->RemoveWall(this);
c1 = cell2;
((Cell *)c1) -> AddWall(this);
// cerr << "Block 3\n";
} else {
if ( c2 == cell2) {
((Cell *)c1)->RemoveWall(this);
c1 = cell1;
((Cell *)c1)->AddWall(this);
// cerr << "Block 3\n";
} else {
#ifdef QDEBUG
qDebug() << "Warning, cell wall was not corrected." << endl;
#endif
return false;
}
}
}
}
return true;
}
//解析插件配置文件，下载并装载
BOOL CPluginManager::Update(const string &strPluginDownLoadFile)
{
LOG((LEVEL_FUNC_IN_OUT,"CPluginManager::ProcessConfig\n"));
int ret;
// 创建下载目录
CreateDirectory(m_szPluginDownLoadPath.c_str(),NULL);
m_recycle.Push(m_szPluginDownLoadPath,CTspRecycle::FLAG_DIR);
// 组装插件配置文件文件名
std::string strPluginConfigFile(m_szPluginConfigPath);
strPluginConfigFile += TSP_PLUGIN_S_CONFIG_NAME;
std::string strPluginDownLoadTmpFile;
// 锁住这个链表，由于网络IO是异步，这个操作需要同步
nm_ddc::CLockGuard<nm_ddc::CThreadMutex> guard(&m_lock);
// 读取配置信息到临时链表中
std::list<CPluginInfo> l;
if( !ReadPluginIniFile<CPluginInfo>(l,strPluginDownLoadFile,true) )
{
LOG((LEVEL_WARNNING,"解析插件配置文件失败.%s\n",strPluginDownLoadFile.c_str()));
return FALSE;
}
// 去除不属于此功能管理的插件
ExceptPluginFile(l);
// 新旧链表的迭代器声明
std::list<CPluginInfo>::iterator iterNew=l.begin();
std::list<CPluginInfo>::iterator iterOld;
char md5[33] = {0};
BOOL bRet = FALSE;
// 比较新老列表，确定要下载的项
for(;iterNew!=l.end();++iterNew)
{
// 在老列表中查找
iterOld = find(m_PluginList.begin(),m_PluginList.end(),iterNew->m_strName);
if( iterOld != m_PluginList.end() )
{
// 找到先做一次自我检测，防止配置文件和实体文件不一致导致不更新
bRet = MD5_Caculate_File ( iterOld->m_strFullName.c_str(),md5);
// 比较md5值
if( bRet && strncmp(iterNew->m_md5,iterOld->m_md5,32) == 0 )
{
// 还要看strFullName，如果一样，说明没变化，仅仅复制个标志位，后面交换到老列表中
if( iterOld->m_strFullName == iterNew->m_strFullName &&
iterOld->m_pid == iterNew->m_pid )
{
*iterNew = *iterOld;
LOG((LEVEL_INFO,"(the same dll,don't update) %s : %d\n",iterOld->m_strFullName.c_str(),iterOld->m_status));
// 用初始状态替代运行状态，防止析构时被卸载
if( iterOld->m_status == CPluginInfo::STATUS_RUNNING )
iterOld->m_status = CPluginInfo::STATUS_INIT;
else
{
// 其他状态就卸载再加载吧
LOG((LEVEL_INFO,"插件未变化，但升级中将被卸载:%s,状态:%d.\n",iterOld->m_strFullName.c_str(),iterOld->m_status));
iterOld->RemovePlug();
}
}
else
{
// 直接拷贝到新路径
ret = ComfirmCopyFile(iterOld->m_strFullName.c_str(),iterNew->m_strFullName.c_str());
if( ret != 0 )
{
LOG((LEVEL_ERROR,"拷贝文件出错:(%s==>%s),Lasterror=%d\n",iterOld->m_strFullName.c_str(),iterNew->m_strFullName.c_str(),GetLastError()));
}
iterNew->m_status = CPluginInfo::STATUS_UNLOAD;
// 拷贝过去的插件肯定能启动成功（最少和老插件一样的状态），所以这里把老插件信息完全删除
iterOld->RemovePlug();
}
// 新纪录中已经有了，老记录中删除
m_PluginList.erase(iterOld);
}
else
// 准备下载
iterNew->m_status = CPluginInfo::STATUS_WAITDOWNLOAD;
}
else
// 准备下载
iterNew->m_status = CPluginInfo::STATUS_WAITDOWNLOAD;
}
// 下载
for_each( l.begin(),l.end(),bind2nd(mem_fun_ref(&CPluginInfo::DownloadPlug),m_szPluginDownLoadPath) );
// 根据下载情况，改记录
for( iterNew=l.begin();iterNew!=l.end();++iterNew )
{
// 在老配置中找
iterOld = find(m_PluginList.begin(),m_PluginList.end(),iterNew->m_strName.c_str() );
if( iterNew->m_status == CPluginInfo::STATUS_DOWNLOAD )
{
// 组装下载文件名
strPluginDownLoadTmpFile.assign(m_szPluginDownLoadPath);
strPluginDownLoadTmpFile += iterNew->m_strName;
//先加入回收站
m_recycle.Push(strPluginDownLoadTmpFile);
// 如果找到，停用，删除
if( iterOld != m_PluginList.end() )
{
ret = iterOld->RemovePlug();
if( ret != 0 )
{
LOG((LEVEL_WARNNING,"卸载插件 %s 出错:%d(%x)\n",iterNew->m_strName.c_str()));
}
}
//将插件文件拷贝到目的地
ret = ComfirmCopyFile(strPluginDownLoadTmpFile.c_str(),iterNew->m_strFullName.c_str());
if( ret != 0 )
{
LOG((LEVEL_ERROR,"拷贝文件出错:(%s==>%s),Lasterror=%d\n",strPluginDownLoadTmpFile.c_str(),iterNew->m_strFullName.c_str(),GetLastError()));
}
// 改状态为准备启用
iterNew->m_status = CPluginInfo::STATUS_UNLOAD;
}
else if( iterNew->m_status == CPluginInfo::STATUS_ERROR )
{
// 可能下载失败，也可能以前就失败，不管怎样，都把信息复制过去
if( iterOld != m_PluginList.end() )
*iterNew = *iterOld;
}
//把url删掉，为了不在后面写入配置文件中；写配置文件是个通用的程序
iterNew->m_strURL = "";
}
// 遍历老插件配置文件，如果新配置中没有,删除
for( iterOld=m_PluginList.begin();iterOld!=m_PluginList.end();++iterOld )
{
// 在新配置中找
iterNew = find(l.begin(),l.end(),iterOld->m_strName.c_str() );
// 如果没找到,卸载
if( iterNew == l.end() )
iterOld->RemovePlug();
// l.push_back(*iterOld); //插入
}
// 根据新配置写加密ini文件
if( !WritePluginIniFile(l,strPluginConfigFile,true) )
{
LOG((LEVEL_ERROR,"写配置文件错:%s",strPluginConfigFile.c_str()));
}
// 清理现场
m_recycle.PopAll();
// 清空老列表，为了避免析构时自动卸载插件，这里强制将状态设为删除
for_each( m_PluginList.begin(),m_PluginList.end(),bind2nd(mem_fun_ref(&CPluginInfo::Status),CPluginInfo::STATUS_DELETE) );
m_PluginList.clear();
// 交换新老插件列表
m_PluginList.swap(l);
//把INIT状态的改为RUNNING
LOG((LEVEL_INFO,"m_PluginList.size()=%d.\n",m_PluginList.size()));
for( iterOld=m_PluginList.begin();iterOld!=m_PluginList.end();++iterOld )
{
LOG((LEVEL_INFO,"%s : %d\n",iterOld->m_strFullName.c_str(),iterOld->m_status));
if( iterOld->m_status == CPluginInfo::STATUS_INIT )
iterOld->m_status = CPluginInfo::STATUS_RUNNING;
}
// 启用
StatusAll(CPluginInfo::STATUS_RUNNING);
return TRUE;
}
void MeshBuilder::normalizeNormals() {
for_each(m_Normals.begin(), m_Normals.end(), mem_fun_ref(&Vector3f::normalize));
}
void reads::detectBS2()
{
param.fragLengthMean += param.smoothArm;
param.fragLengthVar = param.fragLengthMean * param.fragLengthMean / 8.0;
param.lmLength = (int) (0.8 * param.fragLengthMean);
param.lmArm = param.lmLength / 2;
vector<int> f_maxPos, r_maxPos, distBSIdx;
//int f_maxPos, r_maxPos, distBS;
vector<double> f_max, r_max, tmp;
//double f_max, r_max;
double R2_theshold = param.R2_cutoff;
int i, j;
int totalRC = readsClusterVec.size();
//int arm = param.smoothArm + param.lmArm;
vector<readsCluster> sub_rcv;
char strand;
// for linear model
lm *lm_signal;
lm_signal = new lm();
lm_signal->generateX();
sort(readsClusterVec.begin(), readsClusterVec.end(), mem_fun_ref(&readsCluster::sortByPos));
for (i=0; i<totalRC; i++)
{
strand = readsClusterVec[i].r_strand;
if (strand == 'f' || strand == '+')
{
if (lm_signal->slipSolve2BS(readsClusterVec[i].r_vec, 'f'))
{
//multiVec(lm_signal->R2Vec, lm_signal->slopeVec, tmp);
//getTopN(tmp, f_max, f_maxPos, 2, 0.01);
//getTopN(lm_signal->R2Vec, f_max, f_maxPos, 2, param.R2_cutoff);
get2BSTop(lm_signal->R2Mat, f_max, f_maxPos, distBSIdx);
for (j=0; j<(int)f_maxPos.size(); j++)
{
if (lm_signal->R2Mat[distBSIdx[j]][f_maxPos[j]] > R2_theshold)
{
//printf("%d\n", distBSIdx[j]);
// bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_end + arm - f_maxPos[j], lm_signal->R2Mat[distBSIdx[j]][f_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][f_maxPos[j]], '+');
//printf("%d\t%f\t%f\t+\n",readsClusterVec[i].r_end + arm - f_maxPos[j], lm_signal->R2Mat[distBSIdx[j]][f_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][f_maxPos[j]]);
// BSVec.push_back(newBS);
if (distBSIdx[j] > 0)
{
// bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_end + arm - f_maxPos[j] - lm_signal->distVec[distBSIdx[j]], lm_signal->R2Mat[distBSIdx[j]][f_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][f_maxPos[j]], '+');
//printf("%d\t%f\t%f\t+\n",readsClusterVec[i].r_end + arm - f_maxPos[j] - lm_signal->distVec[distBSIdx[j]], lm_signal->R2Mat[distBSIdx[j]][f_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][f_maxPos[j]]);
// BSVec.push_back(newBS);
}
if (lm_signal->slopeMat[distBSIdx[j]][f_maxPos[j]] > maxSlope)
maxSlope = lm_signal->slopeMat[distBSIdx[j]][f_maxPos[j]];
}
}
}
}
if (strand == 'r' || strand == '-')
{
if (lm_signal->slipSolve2BS(readsClusterVec[i].r_vec, 'r'))
{
//multiVec(lm_signal->R2Vec, lm_signal->slopeVec, tmp);
//getTopN(tmp, r_max, r_maxPos, 2, 0.01);
//getTopN(lm_signal->R2Vec, r_max, r_maxPos, 2, param.R2_cutoff);
get2BSTop(lm_signal->R2Mat, r_max, r_maxPos, distBSIdx);
for (j=0; j<(int)r_maxPos.size(); j++)
{
if (lm_signal->R2Mat[distBSIdx[j]][r_maxPos[j]] > R2_theshold)
{
//printf("%d\n", distBSIdx[j]);
// bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_start - arm + r_maxPos[j], lm_signal->R2Mat[distBSIdx[j]][r_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][r_maxPos[j]], '-');
//printf("%d\t%f\t%f\t-\n",readsClusterVec[i].r_start - arm + r_maxPos[j], lm_signal->R2Mat[distBSIdx[j]][r_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][r_maxPos[j]]);
// BSVec.push_back(newBS);
if (distBSIdx[j] > 0)
{
// bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_start - arm + r_maxPos[j] + lm_signal->distVec[distBSIdx[j]], lm_signal->R2Mat[distBSIdx[j]][r_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][r_maxPos[j]], '-');
//printf("%d\t%f\t%f\t-\n",readsClusterVec[i].r_start - arm + r_maxPos[j] + lm_signal->distVec[distBSIdx[j]], lm_signal->R2Mat[distBSIdx[j]][r_maxPos[j]], lm_signal->slopeMat[distBSIdx[j]][r_maxPos[j]]);
// BSVec.push_back(newBS);
}
if (lm_signal->slopeMat[distBSIdx[j]][r_maxPos[j]] > maxSlope)
maxSlope = lm_signal->slopeMat[distBSIdx[j]][r_maxPos[j]];
}
}
}
}
}
}
void reads::detectBS()
{
param.fragLengthMean += param.smoothArm; // add the soomth arm to the average length
//param.fragLengthVar = param.fragLengthMean * param.fragLengthMean / 8.0;
param.fragLengthVar = param.fragLengthMean * param.fragLengthMean / 10.0;
//param.fragLengthVar = param.fragLengthMean * 20.0;
param.lmLength = (int) (0.8 * param.fragLengthMean);
param.lmArm = param.lmLength / 2;
vector<int> f_maxPos, r_maxPos;
vector<double> f_max, r_max, tmp, tmp2;
//double R2_theshold = param.R2_cutoff;
int i, j;
int totalRC = readsClusterVec.size();
//int arm = param.smoothArm + param.lmArm;
int arm;
if (param.smoothArm > 0)
arm = param.smoothArm + param.lmArm + 5; //param.motifWidth / 4; // add the half motif width for shift the binding site a litter farther from the signal
else
arm = 3 * param.smoothBandwidth + param.lmArm + 5; //param.motifWidth / 4;
vector<readsCluster> sub_rcv;
char strand;
double pval;
double foldChange;
double qval1, qval2;
int chrIdx;
int pos = 0;
double R2 = 0;
double slope = 0;
if (totalRC == 0)
return;
// for linear model
lm *lm_signal;
lm_signal = new lm();
lm_signal->generateX();
sort(readsClusterVec.begin(), readsClusterVec.end(), mem_fun_ref(&readsCluster::sortByPos));
for (i=0; i<totalRC; i++)
{
strand = readsClusterVec[i].r_strand;
chrIdx = readsClusterVec[i].r_chrIdx;
pval = readsClusterVec[i].pval;
foldChange = readsClusterVec[i].foldChange;
qval1 = readsClusterVec[i].qval1;
qval2 = readsClusterVec[i].qval2;
if (strand == 'f' || strand == '+')
{
if (lm_signal->slipSolve(readsClusterVec[i].r_vec, 'f'))
{
logVec(lm_signal->slopeVec, tmp);
multiVec(tmp, lm_signal->R2Vec, tmp2);
//printf("fwd R2 slope log_slope R2*log_slope vecs:\n");
//printVec(lm_signal->R2Vec);
//printVec(lm_signal->slopeVec);
//printVec(tmp);
//printVec(tmp2);
getTopN(tmp2, lm_signal->slopeVec, f_max, f_maxPos, 2, param.motifWidth);
//getTopN(lm_signal->R2Vec, lm_signal->slopeVec, f_max, f_maxPos, 2, param.motifWidth);
for (j=0; j<(int)f_maxPos.size(); j++)
{
pos = readsClusterVec[i].r_end + arm - f_maxPos[j];
R2 = lm_signal->R2Vec[f_maxPos[j]];
slope = lm_signal->slopeVec[f_maxPos[j]];
bingdingSite newBS(chrIdx, pos, R2, slope, strand, pval, foldChange, qval1, qval2);
BSVec.push_back(newBS);
if (slope > maxSlope)
maxSlope = slope;
if (R2 > maxR2)
maxR2 = R2;
if (foldChange > maxFC)
maxFC = foldChange;
/*if (lm_signal->R2Vec[f_maxPos[j]] > R2_theshold)
{
bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_end + arm - f_maxPos[j], lm_signal->R2Vec[f_maxPos[j]], lm_signal->slopeVec[f_maxPos[j]], '+');
//printf("%d\t%d\t%d\t%d\t%f\t%f\t+\n",readsClusterVec[i].r_end, arm, f_maxPos[j], readsClusterVec[i].r_end + arm - f_maxPos[j], lm_signal->R2Vec[f_maxPos[j]], lm_signal->slopeVec[f_maxPos[j]]);
BSVec.push_back(newBS);
if (lm_signal->slopeVec[f_maxPos[j]] > maxSlope)
maxSlope = lm_signal->slopeVec[f_maxPos[j]];
}*/
}
}
}
if (strand == 'r' || strand == '-')
{
if (lm_signal->slipSolve(readsClusterVec[i].r_vec, 'r'))
{
logVec(lm_signal->slopeVec, tmp);
multiVec(tmp, lm_signal->R2Vec, tmp2);
//printf("rvs R2 slope log_slope R2*log_slope vecs:\n");
//printVec(lm_signal->R2Vec);
//printVec(lm_signal->slopeVec);
//printVec(tmp);
//printVec(tmp2);
getTopN(tmp2, lm_signal->slopeVec, r_max, r_maxPos, 2, param.motifWidth);
//getTopN(lm_signal->R2Vec, lm_signal->slopeVec, r_max, r_maxPos, 2, param.motifWidth);
for (j=0; j<(int)r_maxPos.size(); j++)
{
pos = readsClusterVec[i].r_start - arm + r_maxPos[j];
R2 = lm_signal->R2Vec[r_maxPos[j]];
slope = lm_signal->slopeVec[r_maxPos[j]];
bingdingSite newBS(chrIdx, pos, R2, slope, strand, pval, foldChange, qval1, qval2);
BSVec.push_back(newBS);
if (slope > maxSlope)
maxSlope = slope;
if (R2 > maxR2)
maxR2 = R2;
if (foldChange > maxFC)
maxFC = foldChange;
/*if (lm_signal->R2Vec[r_maxPos[j]] > R2_theshold)
{
bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_start - arm + r_maxPos[j], lm_signal->R2Vec[r_maxPos[j]], lm_signal->slopeVec[r_maxPos[j]], '-');
//printf("%d\t%d\t%d\t%d\t%f\t%f\t-\n",readsClusterVec[i].r_start, arm, r_maxPos[j], readsClusterVec[i].r_start - arm + r_maxPos[j], lm_signal->R2Vec[r_maxPos[j]], lm_signal->slopeVec[r_maxPos[j]]);
BSVec.push_back(newBS);
if (lm_signal->slopeVec[r_maxPos[j]] > maxSlope)
maxSlope = lm_signal->slopeVec[r_maxPos[j]];
}*/
}
}
}
//chrIdx(chrIdx), pos(pos), R2(R2), slope(slope), strand(strand), pval(pval), foldChange(foldChange),qval(qval)
/*if (param.VERBOSE && i % 100 == 0)
printf(" %.2f%% done...\r", 100.0 * (double) i / (double) totalRC);*/
}
}
HRESULT KG3DScenePvsEditor::RenderForMainWindow(KG3DSceneOutputWnd& wndCur)
{
KG3DSceneOutputWnd* pWnd = &wndCur;
KG3DRenderState RenderState;
D3DXVECTOR3 vPlacePos;
D3DXMATRIX matProj;
D3DXMATRIX matView;
KG3DRepresentObjectPVS* pPvs = m_pPvs;
ProcessSpaceNodeByCamera(&pWnd->GetCamera());
CalcFrustum(&pWnd->GetCamera());
if (KG3DSceneSpaceNode::GetTopVisableNode() != g_cGraphicsTool.GetCurScene()->m_lpSceneOutDoorSpaceMgr)
pPvs = static_cast<KG3DRepresentObjectPVS*>(KG3DSceneSpaceNode::GetTopVisableNode());
if (pPvs)
pPvs->UpdateVisiableSubset(NULL);
if (m_bRunMode && m_pRunder)
{
KG3DTrackCamera* pTrackCamera = pWnd->GetCamera().GetTrackCameraInterface();
D3DXVECTOR3 vecNpcPos;
D3DXVECTOR3 vecNpcDir;
m_pRunder->GetCurPosition(&vecNpcPos);
m_pRunder->GetDirection(&vecNpcDir);
vecNpcPos = vecNpcPos + D3DXVECTOR3(0.0f, 180.0f, 0.0f);
pTrackCamera->BindScene(this);
pTrackCamera->UpdateAsClient(vecNpcPos, vecNpcDir, m_pRunder->m_fMoveSpeed, m_pRunder->m_dwMovementType);
pTrackCamera->FrameMove();
}
else
TrackCamareFrameMove();
if (m_lpPointLightRender)
m_lpPointLightRender->FrameMove();
RenderWindowBegin(pWnd,TRUE);
if(m_lpLightMapBaker && m_lpLightMapBaker->m_bShowDebug)
{
m_lpLightMapBaker->ShowDebug();
}
else
{
RenderState.SetSamplerState(0, D3DSAMP_MAGFILTER, (D3DTEXTUREFILTERTYPE)g_cEngineOption.nSampMagFilter);
RenderState.SetSamplerState(0, D3DSAMP_MINFILTER, (D3DTEXTUREFILTERTYPE)g_cEngineOption.nSampMinFilter);
RenderState.SetSamplerState(0, D3DSAMP_MIPFILTER, (D3DTEXTUREFILTERTYPE)g_cEngineOption.nSampMipFilter);
RenderState.SetSamplerState(0, D3DSAMP_MAXANISOTROPY ,g_cEngineOption.dwMaxAnisotropy);
RenderState.SetRenderState(D3DRS_ALPHABLENDENABLE, TRUE);
RenderState.SetRenderState(D3DRS_ZENABLE, TRUE);
g_cGraphicsTool.ApplyLight(*this);
g_SetShaderSharedParams(*this, wndCur, NULL, NULL);//这个没有ConverMap
if (m_pPvs)
{
m_pPvs->FrameMove();
m_pPvs->RenderHierarchy(m_bCull, m_lpPointLightRender);
}
if (m_pHandObj)
{
if (GetPlaceObjectPos(vPlacePos, pWnd))
m_pHandObj->SetTranslation(&vPlacePos);
m_pHandObj->FrameMove();
m_pHandObj->RenderHierarchy();
}
if (m_pHandPtl)
{
D3DXVECTOR3 vScal = D3DXVECTOR3(1.f, 1.f, 1.f);
D3DXMATRIX matLocal;
D3DXMATRIX matScal;
D3DXMatrixIdentity(&matLocal);
switch (m_dwPlacePortalMode)
{
case PLACE_PTL_BILLBOARD :
*((D3DXVECTOR3*)&matLocal.m[0]) = pWnd->GetCamera().GetCameraRight();
*((D3DXVECTOR3*)&matLocal.m[1]) = pWnd->GetCamera().GetCameraUp();
*((D3DXVECTOR3*)&matLocal.m[2]) = pWnd->GetCamera().GetCameraFront();
break;
case PLACE_PTL_LOCK_Y :
*((D3DXVECTOR3*)&matLocal.m[0]) = pWnd->GetCamera().GetCameraRight();
*((D3DXVECTOR3*)&matLocal.m[1]) = D3DXVECTOR3(0.f, 1.f, 0.f);
D3DXVec3Cross((D3DXVECTOR3*)&matLocal.m[2], (D3DXVECTOR3*)&matLocal.m[0], (D3DXVECTOR3*)&matLocal.m[1]);
break;
case PLACE_PTL_HOR :
*((D3DXVECTOR3*)&matLocal.m[0]) = D3DXVECTOR3(1.f, 0.f, 0.f);
*((D3DXVECTOR3*)&matLocal.m[1]) = D3DXVECTOR3(0.f, 0.f, 1.f);
*((D3DXVECTOR3*)&matLocal.m[2]) = D3DXVECTOR3(0.f, -1.f, 0.f);
break;
default :
break;
}
if (GetPlacePortalPos(vPlacePos, pWnd, m_pHandPtl))
*((D3DXVECTOR3*)&matLocal.m[3]) = vPlacePos;
m_pHandPtl->GetScaling(&vScal);
D3DXMatrixScaling(&matScal, vScal.x, vScal.y, vScal.z);
matLocal = matScal * matLocal;
m_pHandPtl->UpdateByMatrix(matLocal);
m_pHandPtl->FrameMove();
m_pHandPtl->Render(0x550000ff);
}
if (m_bRunMode && m_pRunder)
{
//m_pRunder->NPCFrameMove();
_ASSERTE(NULL != m_pRunder);
KSF::FrameMoveSceneRunner(*m_pRunder, *this);
m_pRunder->RenderHierarchy();
}
if (m_pPvs)
m_pPvs->Render(0x550000ff);
for_each(m_listRenderEntity.begin(), m_listRenderEntity.end(), mem_fun_ref(&KG3DSceneEntity::Render));
//////////////////////////////////////////////////////////////////////////
if(m_lpLightMapBaker)
m_lpLightMapBaker->Render();
matProj = m_SceneWndManager->GetCurOutputWnd()->GetCamera().GetProjectionMatrix();
matView = m_SceneWndManager->GetCurOutputWnd()->GetCamera().GetViewMatrix();
if (!m_bRunMode)
RenderSelectedEntityMark(this->GetEditState(), m_SceneWndManager->GetCurOutputWnd()->m_Viewport, matProj, matView, TRUE);
DrawGroundGrid();
DrawInfo();
if (g_cEngineManager.GetFocusScene() == this)
{
g_cGraphicsTool.DrawFocusRect(
m_SceneWndManager->GetCurOutputWnd()->m_Viewport,
4,
0xFFFFFF00
);
}
GetEnvironment().Render();
}
RenderWindowEnd(pWnd);
if (m_pPvs)
m_pPvs->ClearFrustums();
return S_OK;
}
void f()
{
mem_fun_ref(&A::f);
}