void EpsilonVor::ReadIt(std::ifstream & fin){
Matrix co0,oc0;
fin.read((char *) &nnx, sizeof nnx);
fin.read((char *) &nny, sizeof nny);
fin.read((char *) &nnz, sizeof nnz);
fin.read((char *) &co0, sizeof co0);
fin.read((char *) &oc0, sizeof oc0);
fin.read((char *) &nresid, sizeof nresid);
Deallocate();
is_xRefset=true;
is_COset=true;
setMetric(co0);
Allocate();
int ntoken;
fin.read((char *) &ntoken, sizeof ntoken);
char * css=new char [ntoken];
fin.read(css, (sizeof css[0])*ntoken);
string token(css);
ResLabel.clear();
boost::split(ResLabel,token, boost::is_any_of("\t "));
fin.read((char *) &TotalCount, sizeof TotalCount);
fin.read((char *) &M_avg[0], (sizeof M_avg[0])*DIM);
fin.read((char *) &VoroVol[0], (sizeof VoroVol[0])*nresid);
fin.read((char *) &D[0][0][0], (sizeof D[0][0][0])*DIM*DIM*nresid);
fin.read((char *) &G[0][0][0], (sizeof G[0][0][0])*DIM*DIM*nresid);
fin.read((char *) &M[0][0], (sizeof M[0][0])*DIM*nresid);
fin.read((char *) &E[0][0], (sizeof E[0][0])*DIM*nresid);
}
NetDeviceFace::NetDeviceFace(Ptr<Node> node, const Ptr<NetDevice>& netDevice)
: Face(FaceUri("netDeviceFace://"), FaceUri("netDeviceFace://"),getLevelFromNode(node),false)
, m_node(node)
, m_netDevice(netDevice)
{
NS_LOG_FUNCTION(this << netDevice);
setMetric(1); // default metric
NS_ASSERT_MSG(m_netDevice != 0, "NetDeviceFace needs to be assigned a valid NetDevice");
m_node->RegisterProtocolHandler(MakeCallback(&NetDeviceFace::receiveFromNetDevice, this),
L3Protocol::ETHERNET_FRAME_TYPE, m_netDevice,
true /*promiscuous mode*/);
}
EpsilonVor & EpsilonVor::operator=(const Epsilon & z){
const EpsilonVor & z1=dynamic_cast<const EpsilonVor &> (z);
Matrix co0=z1.co;
nresid=z1.nresid;
Deallocate();
is_xRefset=true;
is_COset=true;
setMetric(co0);
Allocate();
ResLabel=z1.ResLabel;
TotalCount=z1.TotalCount;
M_avg=z1.M_avg;
VoroVol=z1.VoroVol;
D=z1.D;
G=z1.G;
M=z1.M;
E=z1.E;
return *this;
}
MetEngLayout::MetEngLayout(bool state, QWidget *parent) :
QHBoxLayout(parent)
{
// Create the Edit boxes for ft/cm and inches. We can set the width of
// the inch edit box now, since that won't change.
//
ftcmEdit = new WLineEdit;
inchEdit = new WLineEdit;
inchEdit->setFixedWidth(INWID);
// Connect these editboxes to their validators
//
ftcmEdit->setValidator(&ftcmValidator);
inchEdit->setValidator(&inchValidator);
inchValidator.setRange(MIN_IN, MAX_IN);
// Create the labels for ft/cm and inches. We can put the text into the
// inches label now, since that won't change, either.
//
ftcmLabel = new QLabel;
inchLabel = new QLabel("in");
// Initialize the state of the metenglayout object. If the object was
// instantiated without a state argument, the default is "true", which
// means the default measurement system is metric.
//
state ? setMetric() : setEnglish();
// When adding the ftcmEdit and ftcmLabel widgets, we want them to fill
// the available space and align left within the QHBoxLayout. The secret
// is to set the stretch (second arg) = 1, and the alignment (third arg)
// = QtAlignLeft.
// See http://lists.qt.nokia.com/public/qt-interest/2011-March/031994.html
//
addWidget(ftcmEdit, 1, Qt::AlignLeft);
addWidget(ftcmLabel, 1, Qt::AlignLeft);
// Add the inch Edit box and label.
//
addWidget(inchEdit);
addWidget(inchLabel);
}
NetDeviceFace::NetDeviceFace(Ptr<Node> node, const Ptr<NetDevice>& netDevice)
: Face(FaceUri("netDeviceFace://"),
FaceUri("netDeviceFace://"),
false,
// this is the mod mentioned above
( netDevice->GetObject<Object>
( TypeId::LookupByName( "ndntac::IsEdgeFlag" ) )
? true : false ),
false )
, m_node(node)
, m_netDevice(netDevice)
{
NS_LOG_FUNCTION(this << netDevice);
setMetric(1); // default metric
NS_ASSERT_MSG(m_netDevice != 0, "NetDeviceFace needs to be assigned a valid NetDevice");
m_node->RegisterProtocolHandler(MakeCallback(&NetDeviceFace::receiveFromNetDevice, this),
L3Protocol::ETHERNET_FRAME_TYPE, m_netDevice,
true /*promiscuous mode*/);
}
StartNodePicker::StartNodePicker(RRTMetric* m) {
setMetric(m);
}
/**
* Process another cel files worth of data.
*/
void
MultiChannelNonOverlapCelListener::newChip(affymetrix_fusion_io::FusionCELData* cel)
{
// remember the pointer for later.
m_cel=cel;
//
m_CelNames.push_back(cel->GetFileName());
// Get Contrast Values
vector<double> ATcontrastValues;
vector<double> GCcontrastValues;
// Get LogDiff values
vector<double> ATLogDiffValues;
vector<double> GCLogDiffValues;
vector<double> ATSaturationValues;
vector<double> GCSaturationValues;
// Vincent Bressler 11/15/2012
//vector<float> intensities;
//double sat_gc = 0;
//double sat_at = 0;
//{
// int n = cel->GetNumCells ();
// intensities.resize (n);
// int check = cel->GetIntensities (0,intensities); // GC is channel 0
// int nsat = 0;
// for (int i=0; i<n; i++)
// {
// if (intensities[i] >= 3800)
// nsat++;
// }
// sat_gc = (double)nsat / (double)n;
//}
//{
// int n = cel->GetNumCells ();
// cel->GetIntensities (1,intensities); // AT is channel 1
// int nsat = 0;
// for (int i=0; i<n; i++)
// {
// if (intensities[i] >= 3800)
// nsat++;
// }
// sat_at = (double)nsat / (double)n;
//}
//need to edit here to change the contrast
GimmeContrast(m_ProbeSets,
ATcontrastValues, GCcontrastValues,
ATLogDiffValues, GCLogDiffValues,
ATSaturationValues, GCSaturationValues,
m_K);
Verbose::out(4, "AT nonpolymorphic probeset size is: " + ToStr(ATcontrastValues.size()));
Verbose::out(4, "GC nonpolymorphic probeset size is: " + ToStr(GCcontrastValues.size()));
Verbose::out(4, "calculate new log diff score");
double atLogDiffScore, gcLogDiffScore, logDiffQC ;
calcLogDiff(ATLogDiffValues, atLogDiffScore);
calcLogDiff(GCLogDiffValues, gcLogDiffScore);
logDiffQC = atLogDiffScore + gcLogDiffScore;
CumulativeStats<double> GCstats;
CumulativeStats<double> ATstats_full;
CumulativeStats<double> GCstats_full;
double nonOverlap = calcNonOverlap(ATcontrastValues, GCcontrastValues, GCstats);
// difference between median / avg IQR
//double medianDiff = calcMedianDiff(ATcontrastValues, GCcontrastValues, GCstats_full, ATstats_full);
int chipIdx=getNextChipIdx();
setMetric(chipIdx,m_Label+"_DQC" , nonOverlap);
//setMetric(chipIdx,m_Label+"_median_diff_over_iqr", medianDiff);
//setMetric(chipIdx,m_Label+"_AT_median" , ATstats_full.getMedian());
//setMetric(chipIdx,m_Label+"_GC_median" , GCstats_full.getMedian());
setMetric(chipIdx,m_Label+"_log_diff_qc" , logDiffQC);
setMetric(chipIdx,"saturation_GC" , GCSaturationValues[0]);
setMetric(chipIdx,"saturation_AT" , ATSaturationValues[0]);
setValid(true);
}
Route4::Route4(const in_addr_t addr, const std::string & mask,
const int metric)
: Addr4(addr, mask)
{
setMetric(metric);
}
Route4::Route4(const in_addr_t addr, const uint32_t mask,
const MaskType type, const int metric)
: Addr4(addr, mask, type)
{
setMetric(metric);
}
Route4::Route4(const std::string & addr, const uint32_t mask,
const MaskType type, const int metric)
: Addr4(addr, mask, type)
{
setMetric(metric);
}
