//Constructor - user provides a filename for existing file as a c string.
Oligowalk_object::Oligowalk_object(const char filename[], const int type)
:RNA(filename, type) {
CommonConstructor();
}
//Pass the constructor parameters directly to the parent TwoRNA class.
Dynalign_object::Dynalign_object(const char sequence1[], const char sequence2[], const bool IsRNA)
:TwoRNA(sequence1, sequence2, IsRNA) {
//Do some initilaizations
CommonConstructor();
}
//Constructor - user provides a sequence as a c string.
Oligowalk_object::Oligowalk_object(const char sequence[])
:RNA(sequence) {
CommonConstructor();
}
Dynalign_object::Dynalign_object(const char filename1[], const int type1, const char filename2[], const int type2, const bool IsRNA)
: TwoRNA(filename1, type1, filename2, type2, IsRNA) {
//Do some initilaizations
CommonConstructor();
}
Hdf5DataReader::Hdf5DataReader(const FileFinder& rDirectory,
const std::string& rBaseName,
std::string datasetName)
: AbstractHdf5Access(rDirectory, rBaseName, datasetName),
mNumberTimesteps(1),
mClosed(false)
{
CommonConstructor();
}
GTimer::GTimer ()
: m_ConditionVar(&m_Mutex),
m_bTimerRunning(false),
m_bOneShot(false),
m_pCommand(NULL),
m_u32MillisecondInterval(0),
m_bShuttingdown(false),
m_bThreadStarted(false),
m_bStopInProgress(false),
m_pInitConditionVar(NULL)
{
// This will not return until the timer's thread has entered run_undetached().
CommonConstructor();
}
OutputFileHandler::OutputFileHandler(const FileFinder& rDirectory,
bool cleanOutputDirectory)
{
FileFinder output_root("", RelativeTo::ChasteTestOutput);
std::string relative_path;
try
{
relative_path = rDirectory.GetRelativePath(output_root);
}
catch (const Exception&)
{
EXCEPTION("The location provided to OutputFileHandler must be inside CHASTE_TEST_OUTPUT; '"
<< rDirectory.GetAbsolutePath() << "' is not under '"
<< output_root.GetAbsolutePath() << "'.");
}
if (*output_root.GetAbsolutePath().rbegin() != '/' && !relative_path.empty())
{
assert(*relative_path.begin() == '/');
relative_path.erase(0, 1); // Remove leading slash
}
CommonConstructor(relative_path, cleanOutputDirectory);
}
//Constructor
//This constructor is used to perform Dynaligh refolding.
Dynalign_object::Dynalign_object(const char* filename, const short maxtrace, const short bpwin, const short awin, const short percent): TwoRNA() {
int i;
CommonConstructor();
//Make sure the filename exists:
if ((fopen(filename, "r"))== NULL) {
//the file is not found
ErrorCodeTwo=106;
return;
}
//open the save file to peek at the sizes needed to allocate arrays:
std::ifstream sav(filename,std::ios::binary);
read(&sav, &modificationflag);
//start with structure information
read(&sav,&GetRNA1()->GetStructure()->numofbases);
read(&sav,&GetRNA2()->GetStructure()->numofbases);
sav.close();
//allocate space for the alignment
align = new short *[maxtrace];//maximum number of tracebacks and next line and below at delete
for (i=0;i<maxtrace;i++) align[i] = new short [GetRNA1()->GetStructure()->numofbases+1];
refolddynalign(filename,GetRNA1()->GetStructure(),GetRNA2()->GetStructure(),align,maxtrace,bpwin,awin,percent);
//No errors encountered.
ErrorCodeTwo=0;
return;
}
GTimer::GTimer (const GAbsCommand* pCommand, UINT32 u32MillisecondInterval, bool bOneShot, bool bAutoStart)
: m_ConditionVar(&m_Mutex),
m_bTimerRunning(false),
m_bOneShot(false),
m_pCommand(NULL),
m_u32MillisecondInterval(0),
m_bShuttingdown(false),
m_bThreadStarted(false),
m_bStopInProgress(false),
m_pInitConditionVar(NULL)
{
m_pCommand = const_cast<GAbsCommand*>(pCommand);
m_u32MillisecondInterval = u32MillisecondInterval;
m_bOneShot = bOneShot;
// This will not return until the timer's thread has entered run_undetached().
CommonConstructor();
if(bAutoStart)
{
Start();
}
}
CEditPoly::CEditPoly( CEditPoly *pCopyFrom )
{
CommonConstructor( );
CopyEditPoly( pCopyFrom );
}
ActiveXConstructor(JSContext *cx, JSObject *obj, uintN argc, jsval *argv,
jsval *rval)
{
return CommonConstructor(cx, XPCJSRuntime::IDX_ACTIVEX_OBJECT, obj, argc, argv,
rval, PR_TRUE);
}
COMObjectConstructor(JSContext *cx, JSObject *obj, uintN argc, jsval *argv,
jsval *rval)
{
return CommonConstructor(cx, XPCJSRuntime::IDX_COM_OBJECT, obj, argc,
argv, rval, PR_FALSE);
}
TRfd::TRfd(TComponent * owner)
{
CommonConstructor(owner);
} // End of constructor
//Constructor for reading a dynalign save file.
Dynalign_object::Dynalign_object(const char filename[]): TwoRNA() {
//Open the save file, make the output file
int ir,ip,jp,kp,cp;
short i,j,k,l;
integersize en1;
short maxsep;
integersize crit;
dynalignheap heap;
//Do some initializations
CommonConstructor();
//Make sure the filename exists:
if ((fopen(filename, "r"))== NULL) {
//the file is not found
ErrorCodeTwo=106;
return;
}
data = new datatable;
bool singleinsert,local;
bool **allowed_alignments;
//indicate that a save file was read so that the destructor can do the cleanup
savefileread=true;
//open the save file to peek at the sizes needed to allocate arrays:
std::ifstream sav(filename,std::ios::binary);
read(&sav, &modificationflag);
//start with structure information
read(&sav,&(GetRNA1()->GetStructure()->numofbases));
read(&sav,&(GetRNA2()->GetStructure()->numofbases));
read(&sav,&maxsep);
sav.close();
if (maxsep<0) {
//This means that the allowed alignments were constrained by the HMM alignment
//probs and not by the traditional M parameter.
//Therefore, space must be allocated for the allowed_alignment arrays.
allowed_alignments=new bool *[GetRNA1()->GetStructure()->numofbases+1];
for (i=0;i<=GetRNA1()->GetStructure()->numofbases;i++) allowed_alignments[i]=new bool [GetRNA2()->GetStructure()->numofbases+1];
}
else allowed_alignments=NULL;
//fill the low and highend arrays:
//allocate space:
lowend = new short [2*GetRNA1()->GetStructure()->numofbases];
highend = new short [2*GetRNA1()->GetStructure()->numofbases];
if (modificationflag==1) {
vmod = new dynalignarray();
}
else vmod=NULL;
v = new varray();
w = new dynalignarray();
w3 = new wendarray();
w5 = new wendarray();
opendynalignsavefile(filename, GetRNA1()->GetStructure(), GetRNA2()->GetStructure(), v, w, vmod, w3, w5, data, &singleinsert, &maxsep, &gap, &lowest, &local, allowed_alignments,lowend,highend);
if (maxsep<0) {
for (i=0;i<=GetRNA1()->GetStructure()->numofbases;i++) delete[] allowed_alignments[i];
delete[] allowed_alignments;
}
//delete[] pair[0];
//delete[] pair[1];
//delete[] pair;
//No errors encounted
ErrorCodeTwo=0;
return;
}
OutputFileHandler::OutputFileHandler(const std::string& rDirectory,
bool cleanOutputDirectory)
{
CommonConstructor(rDirectory, cleanOutputDirectory);
}
CSocketAddress::CSocketAddress(const sockaddr& addr)
{
CommonConstructor(addr);
}
CSocketAddress::CSocketAddress(const sockaddr_storage& addr)
{
CommonConstructor(*(sockaddr*)&addr);
}
CEditPoly::CEditPoly()
{
CommonConstructor( );
}
//Default Constructor - user provides nothing.
Oligowalk_object::Oligowalk_object(const bool IsRNA)
:RNA(IsRNA) {
CommonConstructor();
}
CEditPoly::CEditPoly( CEditBrush *pBrush )
{
CommonConstructor( );
m_pBrush = pBrush;
}