void ProcEditor::setCurrentProc( const QString &name )
{
actionList->clear();
currentProc = name;
IParser *parser = CWidgetManager::getInstance()->getParser();
CProcedure *proc = parser->getProc( name.toUtf8().constData() );
std::vector< CProcAction >::const_iterator itr;
for( itr = proc->Actions.begin(); itr != proc->Actions.end(); ++itr )
{
actionList->addItem( itr->Action.c_str() );
}
setWindowTitle( QString( "Procedure Editor - %1" ).arg( currentProc ) );
}
bool ProxySession::Transfer(FileDesc& src, FileDesc& dest, IParser& parser, std::error_code &ec)
{
// until we're using an actual plugin, just read and write to a local buffer
auto inBuff = parser.GetWriteSlice();
auto numRead = read(src, inBuff, inBuff.Size());
if(numRead < 0) {
ec = std::error_code(errno, std::system_category());
return false;
}
if(numRead == 0) {
ec = Error::END_OF_FILE;
return false;
}
if(m_config.observeOnly)
{
// in observe only mode we just write the data we read immediately
// there is no guarantee that the parser doesn't modify the buffer
this->WriteAll(dest, RSlice(inBuff, numRead), ec);
// regardless of if there is any error or not, we feed the parser
// but ignore whatever it outputs
parser.Parse(numRead);
}
else
{
// now notify the parser that we wrote some data into its input buffer
if(parser.Parse(numRead))
{
// if the parser didn't reject it, pass output anything the parser kicked back
this->WriteOutputTo(dest, ec);
}
else
{
ec = Error::PARSER_REJECT;
}
}
// always clear any unwritten slices due to error or explicit parser rejection
this->m_output_vec.clear();
return ec.value();
}
void LinkEditor::setLinkId( uint32 linkId )
{
setup();
currentLinkId = linkId;
IParser *parser = CWidgetManager::getInstance()->getParser();
SLinkData data;
if( !parser->getLinkData( currentLinkId, data ) )
return;
expressionEdit->setPlainText( data.expr.c_str() );
targetEdit->setText( data.target.c_str() );
ahEdit->setText( data.action.c_str() );
ahParamEdit->setText( data.params.c_str() );
condEdit->setText( data.cond.c_str() );
}
void LinkEditor::onOKButtonClicked()
{
IParser *parser = CWidgetManager::getInstance()->getParser();
SLinkData data;
if( !parser->getLinkData( currentLinkId, data ) )
return;
data.expr = expressionEdit->toPlainText().toUtf8().constData();
data.target = targetEdit->text().toUtf8().constData();
data.action = ahEdit->text().toUtf8().constData();
data.params = ahParamEdit->text().toUtf8().constData();
data.cond = condEdit->text().toUtf8().constData();
parser->updateLinkData( data.id, data );
Q_EMIT okClicked();
hide();
}
virtual unsigned int output_partitioned_file(const std::string infilename,
const std::string outputfilename,
CallbackFn callback=0,
void * callback_data=0)
{
IParser* parser = IParser::get_parser(infilename);
ofstream outfile(outputfilename.c_str());
unsigned int total_reads = 0;
unsigned int reads_kept = 0;
Read read;
string seq;
std::string first_kmer;
HashIntoType forward_hash = 0, reverse_hash = 0;
map<SetID, unsigned int> lReadCounts;
while(!parser->is_complete()) {
read = parser->get_next_read();
seq = read.seq;
if (check_read(seq)) {
first_kmer = seq.substr(0, _ksize);
// generate the hash for the first kmer in the read (fair amount of work)
HashIntoType bin = _hash(first_kmer.c_str(), _ksize, forward_hash, reverse_hash);
SetID lActualFinalSetID = _sets[ _set_IDs[ bin ] ]->getCurrentPrimarySetID();
lReadCounts[lActualFinalSetID]++;
outfile << ">" << read.name << "\t" << lActualFinalSetID
<< " " << "\n"
<< seq << "\n";
// reset the sequence info, increment read number
total_reads++;
// run callback, if specified
if (total_reads % CALLBACK_PERIOD == 0 && callback) {
try {
callback("do_truncated_partition/output", callback_data,
total_reads, reads_kept);
} catch (...) {
delete parser; parser = NULL;
outfile.close();
throw;
}
}
}
}
for ( map<SetID, unsigned int>::iterator lIt = lReadCounts.begin(); lIt != lReadCounts.end(); ++lIt )
{
cout << setw(10) << lIt->first;
cout << setw(10) << lIt->second << endl;
}
cout << setw(6) << "unique set count: "<< lReadCounts.size() << endl;
cout << endl;
delete parser; parser = NULL;
return lReadCounts.size();
}
//////////////////////////////////////////////////////////////////////////
//
// Class MemoryViewDebugger
//
// 罗嘉飞 2011、5、26 内存显示
//
void MemoryViewDebugger::Debug( VCPU* pCPU, LPVOID param )
{
auto IR = pCPU->GetIR();
if ( IR->m_elements[ 0 ] == "leave" ) {flag = 0; m_funcId.pop();}
else if ( IR->m_elements[ 0 ] == "mov" && IR->m_elements[ 1 ] == "d1" ) {flag = 1;m_funcId.push( pCPU->Getdreg()[ 1 ] );}
if ( !m_funcId.empty() )
{
if ( m_funcId.top() != pCPU->Getdreg()[ 1 ] )
flag = 1;
}
if ( flag == 1 )
{
// 获取语法器
IParser* pParser = (IParser*)m_callBack( NULL );
// 获取符号表
Environment& env = (Environment)pParser->GetTables();
MemorySpy* pProWnd = *(MemorySpy**)( m_callBack( (LPVOID)1 ) );
dword_pointer pebp = pCPU->Getebp();
dword_pointer pesp = pCPU->Getesp();
dword eip = pCPU->Geteip();
//dword c=*(pebp+8);
//dword d=*(pesp+8);
//////////////////
PropertiesInsertItem temp;
WatchPropertiesListType* ValList = new std::list< PropertiesInsertItem >;
//////////////////////
DWORD pc = pCPU->Geteip(); // PC
/*dword func_id = pCPU->Getdreg()[ 1 ];*/
dword func_id = m_funcId.top(); //每次都去栈顶
//m_funcId.push(func_id);
Table* table;
auto iter=env.m_tableList.begin();
for (;iter!=env.m_tableList.end();iter++)
{
if( iter->second.GetID()==func_id)
{
break;
}
}
if ( iter == env.m_tableList.end() ) return;
table = &iter->second;
/*(table)->m_symbolList;*/
for ( auto symbol = table->GetLocalVarTable().begin(); symbol != table->GetLocalVarTable().end(); ++symbol )
{
temp.varname=symbol->second.name;
temp.val=*(dword_pointer)( ((uchar_pointer)pebp) - symbol->second.offset);
ValList->push_back(temp);
}
/*table->m_paramSymbolList;*/
for ( auto symbol = table->GetParamTable().begin(); symbol != table->GetParamTable().end(); ++symbol )
{
temp.varname=symbol->second.name;
temp.val=*(dword_pointer)( ((uchar_pointer)pebp) - symbol->second.offset + 4);
ValList->push_back(temp);
}
if ( listComp != *ValList )
{
listComp = *ValList;
//pProWnd->PostMessageA( WM_CLEAR_ALL_ITEMS );
pProWnd->PostMessageA( WM_INSERT_ITEM, (WPARAM)ValList, 0 );
}
else
{
delete ValList;
}
}
}
//////////////////////////////////////////////////////////////////////////
//
// Class WatchDogDebugger
//
// 罗嘉飞 2011/5/26 需要看到的内存
//
void WatchDogDebugger::Debug( VCPU* pCPU, LPVOID param )
{
auto IR = pCPU->GetIR();
if ( IR->m_elements[ 0 ] == "leave" ) {flag = 0; m_funcId.pop();}
else if ( IR->m_elements[ 0 ] == "mov" && IR->m_elements[ 1 ] == "d1" ) {flag = 1;m_funcId.push( pCPU->Getdreg()[ 1 ] );}
if ( !m_funcId.empty() )
{
if ( m_funcId.top() != pCPU->Getdreg()[ 1 ] )
flag = 1;
}
if( flag==1)
{
// 获取语法器
IParser* pParser = (IParser*)m_callBack( 0 );
// 获取符号表
Environment& env = (Environment)pParser->GetTables();
dword_pointer pebp = pCPU->Getebp();
dword_pointer pesp = pCPU->Getesp();
dword eip = pCPU->Geteip();
std::list<std::string>* pList = (std::list<std::string>*)m_callBack( (LPVOID)1 );
PropertiesInsertItem temp;
std::list< PropertiesInsertItem >* ValList = new std::list< PropertiesInsertItem >;
//////////////////////
DWORD pc = pCPU->Geteip(); // PC
dword func_id = m_funcId.top();
Table* table;
auto iter=env.m_tableList.begin();
for (;iter!=env.m_tableList.end();iter++)
{
if( iter->second.GetID()==func_id)
{
break;
}
}
if ( iter == env.m_tableList.end() ) return;
table = &iter->second;
for ( auto symbol = table->GetLocalVarTable().begin(); symbol != table->GetLocalVarTable().end(); ++symbol )
{
//在关键字List里才取出
for (auto iter = pList->begin(); iter != pList->end(); ++iter)
{
if ( *iter == symbol->second.name)
{
temp.varname=symbol->second.name;
temp.val=*(dword_pointer)( ((uchar_pointer)pebp) - symbol->second.offset);
ValList->push_back(temp);
}
}
}
for ( auto symbol = table->GetParamTable().begin(); symbol != table->GetParamTable().end(); ++symbol )
{
//在关键字List里才取出
for (auto iter = pList->begin(); iter != pList->end(); ++iter)
{
if ( *iter == symbol->second.name)
{
temp.varname=symbol->second.name;
temp.val=*(dword_pointer)( ((uchar_pointer)pebp) - symbol->second.offset+4);
ValList->push_back(temp);
}
}
}
m_callBack( (LPVOID)ValList );
/* CPropertiesWnd* pProWnd = *(CPropertiesWnd**)m_callBack( (LPVOID)2 );
if ( listComp != *ValList )
{
listComp = *ValList;
pProWnd->PostMessageA( WM_CLEAR_ALL_ITEMS );
pProWnd->PostMessageA( WM_INSERT_ITEM, (WPARAM)ValList, 0 );
}*/
//static int i = 0;
//if ( ! ValList->empty() )
//{
// std::ofstream out("d:\\data\\" + itoa( i++ ) + ".txt",std::ios::out);
// out << eip << std::endl;
// for (auto iter = ValList->begin(); iter!=ValList->end(); ++iter)
// {
// out << iter->varname << " ";
// out << iter->val << std::endl;
// }
//}
}
}
unsigned int SubsetPartition::output_partitioned_file(const std::string infilename,
const std::string outputfile,
bool output_unassigned,
CallbackFn callback,
void * callback_data)
{
IParser* parser = IParser::get_parser(infilename);
ofstream outfile(outputfile.c_str());
unsigned int total_reads = 0;
unsigned int reads_kept = 0;
unsigned int n_singletons = 0;
PartitionSet partitions;
Read read;
string seq;
std::string first_kmer;
HashIntoType kmer = 0;
const unsigned int ksize = _ht->ksize();
//
// go through all the reads, and take those with assigned partitions
// and output them.
//
while(!parser->is_complete()) {
read = parser->get_next_read();
seq = read.seq;
if (_ht->check_read(seq)) {
const char * kmer_s = seq.c_str();
bool found_tag = false;
for (unsigned int i = 0; i < seq.length() - ksize + 1; i++) {
kmer = _hash(kmer_s + i, ksize);
// is this a known tag?
if (partition_map.find(kmer) != partition_map.end()) {
found_tag = true;
break;
}
}
// all sequences should have at least one tag in them.
// assert(found_tag); @CTB currently breaks tests. give fn flag to
// disable.
PartitionID partition_id = 0;
if (found_tag) {
PartitionID * partition_p = partition_map[kmer];
if (partition_p == NULL ){
partition_id = 0;
n_singletons++;
} else {
partition_id = *partition_p;
partitions.insert(partition_id);
}
}
if (partition_id > 0 || output_unassigned) {
outfile << ">" << read.name << "\t" << partition_id;
outfile << "\n" << seq << "\n";
}
#ifdef VALIDATE_PARTITIONS
std::cout << "checking: " << read.name << "\n";
assert(is_single_partition(seq));
#endif // VALIDATE_PARTITIONS
total_reads++;
// run callback, if specified
if (total_reads % CALLBACK_PERIOD == 0 && callback) {
try {
callback("output_partitions", callback_data,
total_reads, reads_kept);
} catch (...) {
delete parser; parser = NULL;
outfile.close();
throw;
}
}
}
}
delete parser; parser = NULL;
return partitions.size() + n_singletons;
}
void Hashtable::consume_fasta(const std::string &filename,
unsigned int &total_reads,
unsigned long long &n_consumed,
HashIntoType lower_bound,
HashIntoType upper_bound,
ReadMaskTable ** orig_readmask,
bool update_readmask,
CallbackFn callback,
void * callback_data)
{
total_reads = 0;
n_consumed = 0;
IParser* parser = IParser::get_parser(filename.c_str());
Read read;
string currName = "";
string currSeq = "";
//
// readmask stuff: were we given one? do we want to update it?
//
ReadMaskTable * readmask = NULL;
std::list<unsigned int> masklist;
if (orig_readmask && *orig_readmask) {
readmask = *orig_readmask;
}
//
// iterate through the FASTA file & consume the reads.
//
while(!parser->is_complete()) {
read = parser->get_next_read();
currSeq = read.seq;
currName = read.name;
// do we want to process it?
if (!readmask || readmask->get(total_reads)) {
// yep! process.
unsigned int this_n_consumed;
bool is_valid;
this_n_consumed = check_and_process_read(currSeq,
is_valid,
lower_bound,
upper_bound);
// was this an invalid sequence -> mark as bad?
if (!is_valid && update_readmask) {
if (readmask) {
readmask->set(total_reads, false);
} else {
masklist.push_back(total_reads);
}
} else { // nope -- count it!
n_consumed += this_n_consumed;
}
}
// reset the sequence info, increment read number
total_reads++;
// run callback, if specified
if (total_reads % CALLBACK_PERIOD == 0 && callback) {
try {
callback("consume_fasta", callback_data, total_reads, n_consumed);
} catch (...) {
throw;
}
}
}
//
// We've either updated the readmask in place, OR we need to create a
// new one.
//
if (orig_readmask && update_readmask && readmask == NULL) {
// allocate, fill in from masklist
readmask = new ReadMaskTable(total_reads);
list<unsigned int>::const_iterator it;
for(it = masklist.begin(); it != masklist.end(); ++it) {
readmask->set(*it, false);
}
*orig_readmask = readmask;
}
}
