const wxArrayString &CVolumes::GetKits() const
{
if(m_asKits.IsEmpty())
{
CPersistKitList *pKits = mainApp::GetKitList();
map<wxString,CVolume *>::const_iterator itr;
for(itr = m_mapKitVolume.begin();
itr != m_mapKitVolume.end();
++itr)
{
const wxString &sKit(itr->first);
if(pKits->GetLsArray(sKit) != NULL)
{
m_asKits.Add(sKit);
}
else
{
wxString sError("Cannot find kit: ");
sError.Append(sKit);
sError.Append(" in ILSandLadderInfo.xml");
wxASSERT_MSG(0,sError);
mainApp::LogMessage(sError);
}
}
}
return m_asKits;
}
void CPersistKitList::UnitTest()
{
CPersistKitList kitList;
wxString sError;
if(!kitList.Load())
{
wxString sError("CPersistKitList::Load() failed\n");
wxASSERT_MSG(0,sError);
}
#undef PP12
}
bool CGridLocusColumns::SetupKit(
wxGrid *pGrid,
const wxString &sKitName,
const vector<wxString> &vs,
bool bILS,
bool bAllowAmel,
bool bSetError,
int *pnILScolumn,
unsigned int *pnILSchannel)
{
wxString sProblem;
CPersistKitList *pKit = mainApp::GetKitList();
const CLocusNameList *pLocus =
pKit->GetLocusNameList(sKitName);
if(sKitName.IsEmpty())
{
sProblem = "Marker set name is not specified.";
}
else if(pLocus == NULL)
{
sProblem = "Marker set, ";
sProblem.Append(sKitName);
sProblem.Append(", is unknown");
}
else if(pLocus->size() < 1)
{
sProblem = "Marker set, ";
sProblem.Append(sKitName);
sProblem.Append(", does not have any loci");
}
if(!sProblem.IsEmpty())
{
if(bSetError)
{
nwxGrid::SetError(pGrid,sProblem);
}
}
else
{
vector<unsigned int> vnChannels;
vector<int> vnCounts;
set<unsigned int> snChannelsUsed;
wxFont fnBold = pGrid->GetDefaultCellFont();
int nBeforeLoci = (int)vs.size();
int nCols = (int)(pLocus->size()) + nBeforeLoci + BINT(bILS);
int nRemove = 0;
int nCol;
int nCount = 1;
unsigned int nChannel;
unsigned int nLastChannel = 0; // invalid channel name for default column
unsigned int nILSchannel = 0;
const CSingleKitColors *pKitColors;
const CLocusNameChannel *plc;
pKitColors = mainApp::GetKitColors()->GetKitColors(sKitName);
pGrid->SetMargins(0, wxSystemSettings::GetMetric(wxSYS_HSCROLL_Y) + 4);
fnBold.SetWeight(wxFONTWEIGHT_BOLD);
nwxGrid::SetColCount(pGrid,nCols);
for(nCol = 0; nCol < nCols; nCol++)
{
pGrid->SetCellSize(0,nCol,1,1);
//pGrid->SetReadOnly(0,0,true);
}
vector<wxString>::const_iterator itrs = vs.begin();
for(nCol = 0; nCol < nBeforeLoci; nCol++)
{
pGrid->SetCellBackgroundColour(0,nCol,
pGrid->GetGridLineColour());
pGrid->SetCellValue(0,nCol,wxEmptyString);
pGrid->SetColLabelValue(nCol, *itrs);
//pGrid->SetReadOnly(0,nCol,true);
++itrs;
}
// nCol = nBeforeLoci; // redundant
// Set up column labels
vnCounts.reserve(CHANNEL_MAX);
vnChannels.reserve(CHANNEL_MAX);
for(CLocusNameList::const_iterator itr = pLocus->begin();
itr != pLocus->end();
++itr)
{
plc = *itr;
const wxString &sName(plc->GetName());
if(bAllowAmel || !CLabLocus::IsAmel(sName))
{
nChannel = plc->GetChannel();
if(nChannel != nLastChannel)
{
if(nLastChannel > 0)
{
vnChannels.push_back(nLastChannel);
vnCounts.push_back(nCount);
}
snChannelsUsed.insert(nChannel);
nCount = 1;
nLastChannel = nChannel;
}
else
{
nCount++;
}
pGrid->SetColLabelValue(nCol,plc->GetName());
nCol++;
}
else
{
nRemove++;
}
}
if(nRemove)
{
nCols -= nRemove;
nwxGrid::SetColCount(pGrid,nCols);
}
vnChannels.push_back(nLastChannel);
vnCounts.push_back(nCount);
if(bILS)
{
// figure out which channnel is ILS
int nChannelCount =
pKit->GetChannelCount(sKitName);
for(nChannel = (unsigned int) nChannelCount;
nChannel > 0;
--nChannel)
{
if(snChannelsUsed.find(nChannel) ==
snChannelsUsed.end())
{
nILSchannel = nChannel; // unused channel, assume ILS
if(pnILSchannel != NULL)
{
*pnILSchannel = nChannel;
}
nChannel = 1; // loop exit
}
}
// ILS Column Label
pGrid->SetColLabelValue(nCol,"ILS*");
vnChannels.push_back(nILSchannel);
vnCounts.push_back(1);
if(pnILScolumn != NULL)
{
*pnILScolumn = nCol;
}
}
// column labels are set
pGrid->SetRowLabelValue(0,"Channel");
// now set channel cells in top row
// and colors throughout the table
size_t nSize = vnChannels.size();
size_t i;
nCol = nBeforeLoci;
const CChannelColors *pChannelColors;
wxString sLabel;
bool bColorSet = false;
// set cell colors and set channel numbers/names in
// first row
for(i = 0; i < nSize; i++)
{
bColorSet = false;
nChannel = vnChannels.at(i);
nCount = vnCounts.at(i);
if(nCount > 1)
{
pGrid->SetCellSize(0,nCol,1,nCount);
}
if(nChannel > 0)
{
pChannelColors =
(pKitColors == NULL)
? NULL
: pKitColors->GetColorChannel((unsigned int)nChannel);
const wxChar *psDyeLabel = NULL;
if(pChannelColors != NULL)
{
// int k;
pGrid->SetCellTextColour(0,nCol,*wxWHITE);
pGrid->SetCellBackgroundColour(
0,nCol,pChannelColors->GetColorAnalyzed());
psDyeLabel = (const wxChar *)(pChannelColors->GetDyeName());
bColorSet = true;
}
FORMAT_CHANNEL_DYE(&sLabel,(unsigned int) nChannel, psDyeLabel);
pGrid->SetCellFont(0,nCol,fnBold);
pGrid->SetCellValue(0,nCol,sLabel);
pGrid->SetCellAlignment(0,nCol,wxALIGN_CENTRE, wxALIGN_CENTRE);
}
else
{
pGrid->SetCellValue(0,nCol,wxEmptyString);
}
if(!bColorSet)
{
pGrid->SetCellTextColour(0,nCol,pGrid->GetDefaultCellTextColour());
pGrid->SetCellBackgroundColour(
0,nCol,pGrid->GetDefaultCellBackgroundColour());
}
nCol += nCount;
nwxGrid::SetRowReadOnly(pGrid,0,true);
}
}
return sProblem.IsEmpty();
}
bool CPanelLabGeneral::TransferDataToWindow()
{
bool bRtn = (m_pInfo != NULL) && (m_pMarker != NULL);
if(bRtn)
{
wxString sValue;
wxString s;
const wxString &sKitName = m_pMarker->GetMarkerSetName();
const wxString &sILS = m_pMarker->GetILSName();
CPersistKitList *pKitList = mainApp::GetKitList();
const wxArrayString *psILS = pKitList->GetLsArray(sKitName);
size_t nSize =
(psILS == NULL)
? 0
: psILS->GetCount();
m_pChoiceILS->Clear();
if(!nSize)
{
wxString sError;
bRtn = false;
sError = "Cannot file ILS for kit, ";
sError.Append(sKitName);
mainApp::LogMessage(sError);
wxASSERT_MSG(0,sError);
}
else
{
m_pChoiceILS->Append(*psILS);
if(sILS.IsEmpty() || !m_pChoiceILS->SetStringSelection(sILS))
{
m_pChoiceILS->Select(0);
}
m_pLabelVolumeName->SetLabel(m_pInfo->GetVolumeName());
m_pLabelKitName->SetLabel(sKitName);
const wxDateTime &dt = m_pInfo->GetLastUpdate();
sValue.Empty();
if(dt.GetTicks() > 100)
{
const wxString &sUser = m_pInfo->GetUserID();
sValue = dt.Format();
if(!sUser.IsEmpty())
{
sValue.Append(" by ");
sValue.Append(sUser);
}
}
m_pLabelLastUpdateUser->SetLabel(sValue);
m_pCheckUserOverride->SetValue(m_pMarker->GetAllowUserOverrideILS());
m_pTextProtocol->SetValue(m_pInfo->GetProtocol());
m_pTextLot->SetValue(m_pInfo->GetLot());
m_pTextNotes->SetValue(m_pInfo->GetNotes());
bool bDataAnalyzed = m_pMarker->GetAnalyzed();
m_pRadioRaw->SetValue(!bDataAnalyzed);
m_pRadioAnalyzed->SetValue(bDataAnalyzed);
wxRadioButton *pRadio;
wxString sValue = m_pInfo->GetDataFileType();
size_t nLEN = m_vpRadioFileType.size();
bool bFound = false;
bool b;
if(sValue.Len())
{
for(size_t n = 0; n < nLEN; n++)
{
pRadio = m_vpRadioFileType.at(n);
b = (pRadio->GetLabelText() == sValue);
if(b)
{
bFound = true;
}
pRadio->SetValue(b);
}
}
if(!bFound)
{
m_vpRadioFileType.at(0)->SetValue(true);
}
}
}
return bRtn;
}
void CPersistKitList::UnitTest()
{
CPersistKitList kitList;
wxString sError;
if(!kitList.Load())
{
sError.Append(_T("CPersistKitList::Load() failed\n"));
}
else
{
const wxArrayString *psKitArray;
const wxArrayString *psArray;
psKitArray = &kitList.GetArray();
size_t nCount = psKitArray->GetCount();
#define PP12 _T("PowerPlex 1.2")
#define PP18D _T("PowerPlex 18D")
#define SGM _T("SGM Plus")
#define SEFILER _T("SEfilerPlus")
#define NGM _T("NGMSElect")
#define PP21 _T("PowerPlex 21")
struct
{
size_t n; // number of loci
const wxChar *psName;
} LIST[] =
{
{7, _T("Cofiler")},
{16, _T("Identifiler Less ILS250")},
{16, _T("IdentifilerPlus Less ILS250")},
{16, _T("IdentifilerPlus")},
{16, _T("Identifiler")},
{9, PP12},
{18, PP18D},
{16, _T("PowerPlex 16")},
{11, _T("PowerPlex Y")},
{16, _T("Yfiler")},
{12, SEFILER},
{11, SGM},
{10, _T("ProfilerPlus")},
{17, NGM},
{21,PP21}
};
size_t N_LIST = sizeof(LIST) / sizeof(LIST[0]);
if(nCount != N_LIST)
{
sError.Append(wxString::Format(
_T("\nNumber of kits is %d, expected %d"),
(int)nCount, (int)N_LIST ));
}
map<wxString,size_t> kitLocusCount;
map<wxString,size_t>::iterator itrKL;
size_t i;
for(i = 0; i < N_LIST; i++)
{
kitLocusCount.insert(
map<wxString,size_t>::value_type(
wxString(LIST[i].psName),LIST[i].n));
}
for(i = 0; i < nCount; i++)
{
// verify LS count
const wxString &sItem = psKitArray->Item(i);
psArray = kitList.GetLsArray(sItem);
if(psArray == NULL)
{
sError.Append(_T("\nCannot find ILS for kit: "));
sError.Append(sItem);
}
else
{
size_t nExpected = 4;
if(sItem == PP12 || sItem == PP18D || sItem == NGM || sItem == SEFILER || sItem == PP21)
{ nExpected = 1;
}
else if(sItem == SGM)
{ nExpected = 5;
}
else if(
sItem.StartsWith(_T("Identifiler")) &&
!sItem.Contains(_T("250"))
)
{ nExpected = 5;
}
if(psArray->GetCount() != nExpected)
{
sError.Append(
_T("\nLS count for kit: "));
sError.Append(sItem);
sError.Append(wxString::Format(
_T(", is %d, expected %d"),
(int)psArray->GetCount(),(int)nExpected));
}
}
itrKL = kitLocusCount.find(sItem);
const CLocusNameList *pList = kitList.GetLocusNameList(sItem);
if(pList == NULL)
{
sError.Append(_T("\nCannot find loci for kit: "));
sError.Append(sItem);
}
if(itrKL == kitLocusCount.end())
{
sError.Append(_T("\nUnknown kit name: "));
sError.Append(sItem);
}
else if( (pList != NULL) && (pList->size() != itrKL->second) )
{
sError.Append(_T("\nLocus count for kit: "));
sError.Append(sItem);
sError.Append(wxString::Format(
_T(", is %d, expected %d"),
(int)pList->size(),(int)itrKL->second));
}
}
}
wxASSERT_MSG(sError.IsEmpty(),sError);
#undef PP12
}
