void RGHashTable :: SaveAll (RGFile& f) const {
RGPersistent::SaveAll (f);
f.Write (NumberOfLists);
f.Write (NumberOfEntries);
for (int i=0; i<NumberOfLists; i++)
ListArray [i]->SaveAll (f);
}
void RGHashTable :: RestoreAll (RGFile& f) {
RGPersistent::RestoreAll (f);
ClearAndDelete ();
int TempNumberOfLists;
f.Read (TempNumberOfLists);
RGDList** TempArray;
if (TempNumberOfLists < NumberOfLists) {
TempArray = new RGDList* [TempNumberOfLists];
for (int i=0; i<NumberOfLists; i++) {
if (i >= TempNumberOfLists)
delete ListArray [i];
else
TempArray [i] = ListArray [i];
}
delete[] ListArray;
ListArray = TempArray;
NumberOfLists = TempNumberOfLists;
}
else if (TempNumberOfLists > NumberOfLists) {
TempArray = new RGDList* [TempNumberOfLists];
for (int i=0; i<TempNumberOfLists; i++) {
if (i < NumberOfLists)
TempArray [i] = ListArray [i];
else
TempArray [i] = new RGDList;
}
delete[] ListArray;
ListArray = TempArray;
NumberOfLists = TempNumberOfLists;
}
f.Read (NumberOfEntries);
for (int i=0; i<NumberOfLists; i++)
ListArray [i]->RestoreAll (f);
}
void DataInterval :: SaveAll (RGFile& f) const {
RGPersistent::SaveAll (f);
f.Write (Left);
f.Write (Right);
f.Write (Center);
f.Write (Mass);
f.Write (Height);
f.Write (Mode);
f.Write (MaxAtMode);
f.Write (FixedLeft);
f.Write (FixedRight);
}
void DataInterval :: RestoreAll (RGFile& f) {
RGPersistent::RestoreAll (f);
f.Read (Left);
f.Read (Right);
f.Read (Center);
f.Read (Mass);
f.Read (Height);
f.Read (Mode);
f.Read (MaxAtMode);
f.Read (FixedLeft);
f.Read (FixedRight);
}
void NoiseInterval :: SaveAll (RGFile& f) const {
RGPersistent::SaveAll (f);
f.Write (Left);
f.Write (Right);
f.Write (Maximum);
f.Write (Minimum);
f.Write (Average);
f.Write (NumberOfMaxima);
f.Write (NumberOfMinima);
f.Write (NumberOfSamples);
f.Write (Norm2);
}
void NoiseInterval :: RestoreAll (RGFile& f) {
RGPersistent::RestoreAll (f);
f.Read (Left);
f.Read (Right);
f.Read (Maximum);
f.Read (Minimum);
f.Read (Average);
f.Read (NumberOfMaxima);
f.Read (NumberOfMinima);
f.Read (NumberOfSamples);
f.Read (Norm2);
}
int CopyVolumeFile (const RGString& inputFileName, const RGString& outputFileName) {
RGFile inputFile (inputFileName, "rt");
if (!inputFile.isValid ()) {
cout << "Could not read " << inputFileName.GetData () << " for default volume...exiting" << endl;
return -1;
}
RGString inputFileString;
inputFileString.ReadTextFile (inputFile);
RGTextOutput outputFile (outputFileName, FALSE);
if (!outputFile.FileIsValid ()) {
cout << "Could not create " << outputFileName.GetData () << "...exiting" << endl;
return -1;
}
outputFile << inputFileString;
return 0;
}
void STRBaseAllele :: SaveAll (RGFile& f) const {
BaseAllele::SaveAll (f);
f.Write (BP);
}
void STRBaseAllele :: RestoreAll (RGFile& f) {
BaseAllele::RestoreAll (f);
f.Read (BP);
}
bool GenotypesForAMarkerSet :: AddCollectionToTables (const RGString& xmlString, const RGString& offLadderTag, const RGString& triallelesTag, const RGString& posTriTag) {
RGString XMLString (xmlString);
RGString positiveControlString;
RGString pControlsString;
RGString fullPathControlFileName = GenotypesForAMarkerSet::PathToStandardControlFile + "/LadderSpecifications/StandardPositiveControls.xml";
RGFile* allPositiveControls = new RGFile (fullPathControlFileName, "rt");
if (!allPositiveControls->isValid ()) {
cout << "Could not find positive controls file: " << (char*)fullPathControlFileName.GetData () << endl;
return false;
}
RGString posXMLString;
posXMLString.ReadTextFile (*allPositiveControls);
delete allPositiveControls;
RGXMLTagSearch nameSearch ("MarkerSetName", XMLString);
RGXMLTagSearch positiveControlsSearch ("PositiveControls", posXMLString);
RGXMLTagSearch oldPositiveControlsSearch ("PositiveControls", XMLString);
RGXMLTagSearch posCtrlSearch ("PositiveControl", pControlsString);
RGXMLTagSearch offLadderSearch (offLadderTag, XMLString);
RGXMLTagSearch trialleleSearch (triallelesTag, XMLString);
RGXMLTagSearch posTriSearch (posTriTag, XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
RGString collectionString;
RGString offLadderString;
RGString triString;
RGString posTriString;
size_t startPControls = 0;
size_t endPControls = 0;
bool returnValue = true;
RGString markerSetName;
IndividualGenotype* nextGenotype;
if (!nameSearch.FindNextTag (startOffset, endOffset, markerSetName))
return false;
if (mMarkerSetName.Length () == 0)
mMarkerSetName = markerSetName;
else if (mMarkerSetName != markerSetName)
return false;
startOffset = endOffset;
size_t startOffsetPos = 0;
size_t endOffsetPos = 0;
RGString temp;
if (oldPositiveControlsSearch.FindNextTag (startOffset, endOffset, temp))
startOffset = endOffset;
if (positiveControlsSearch.FindNextTag (startOffsetPos, endOffsetPos, pControlsString)) {
posCtrlSearch.ResetSearch ();
// cout << "Found positive controls in file" << endl;
while (posCtrlSearch.FindNextTag (startPControls, endPControls, positiveControlString)) {
// cout << "Found positive control..." << endl;
startPControls = endPControls;
nextGenotype = new IndividualGenotype (positiveControlString);
if (!nextGenotype->isValid ()) {
returnValue = false;
delete nextGenotype;
}
else {
if (!mGenotypes.Contains (nextGenotype)) {
mGenotypes.Insert (nextGenotype);
// cout << "Inserted genotype in list..." << endl;
}
else {
returnValue = false;
delete nextGenotype;
}
}
}
}
startOffset = endOffset;
if (offLadderSearch.FindNextTag (startOffset, endOffset, offLadderString)) {
if (mOffLadderAlleles == NULL) {
mOffLadderAlleles = new LocusCollection (offLadderString);
if (!mOffLadderAlleles->isValid ())
returnValue = false;
}
else {
if (!mOffLadderAlleles->AddLoci (offLadderString))
returnValue = false;
}
}
startOffset = endOffset;
if (trialleleSearch.FindNextTag (startOffset, endOffset, triString)) {
if (mSampleTriAlleles == NULL) {
mSampleTriAlleles = new LocusCollection (triString);
if (!mSampleTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mSampleTriAlleles->AddLoci (triString))
returnValue = false;
}
}
startOffset = endOffset;
if (posTriSearch.FindNextTag (startOffset, endOffset, posTriString)) {
if (mControlTriAlleles == NULL) {
mControlTriAlleles = new LocusCollection (posTriString);
if (!mControlTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mControlTriAlleles->AddLoci (posTriString))
returnValue = false;
}
}
return returnValue;
}
void RGXmlSizeRestriction :: SaveAll (RGFile& f) const {
RGXmlDataRestriction::SaveAll (f);
f.Write (SizeLimit);
}
void STRTracePrequalification :: SaveAll (RGFile& f) const {
TracePrequalification::SaveAll (f);
f.Write (WindowWidth);
}
int _tmain(int argc, _TCHAR* argv[])
{
MEMDIFF(x);
int nRtn = 1;
// char *ps = strdup("ABCDEFG - ignore this");
#ifdef _DEBUG
if(!fsaFileInput::TESTMEMSTR())
{
cerr << "function fsaFileInput::MEMSTR() failed test." << endl;
}
#endif
if(argc < 3)
{
cerr << "Usage: " << argv[0] << " <infilename> <outfilename>" << endl;
//Pause();
return 1;
}
fsaFileInput fsa(argv[1],true);
// fsaFileIO fsa ("E:/Users/goorrob/My Documents/ABI Info/DataFileConverter/20030707BCOF_B02_2002-011420_016.fsa");
if(fsa.Error())
{
cerr << "Cannot open " << argv[1] << endl;
Pause();
return 2;
}
RGFile file (argv [2], "wt");
// RGFile file ("E:/Users/goorrob/My Documents/ABI Info/DataFileConverter/Test.xml");
if (!file.isValid ()) {
cerr << "Output file name invalid" << endl;
return 5;
}
if(fsa.Warning())
{
cerr << "File has problems, continuing" << endl;
}
fsa.WriteXML (file);
file.Flush ();
file.Close ();
if (argc > 3) {
RGFile notify (argv [3], "a+t");
if (!notify.isValid ()) {
cerr << "Cannot open " << argv [3] << " to notify about " << argv [2] << endl;
return 6;
}
RGString Notification = " <xml>Wrote ";
Notification += argv [2];
Notification += "</xml>";
Notification.WriteTextLine (notify);
notify.Close ();
}
return 0;
}
void STRBaseLocus :: RestoreAll (RGFile& f) {
BaseLocus::RestoreAll (f);
f.Read (MinimumBP);
f.Read (MaximumBP);
}
void RGXmlSizeRestriction :: RestoreAll (RGFile& f) {
RGXmlDataRestriction::RestoreAll (f);
f.Read (SizeLimit);
}
void STRBaseLocus :: SaveAll (RGFile& f) const {
BaseLocus::SaveAll (f);
f.Write (MinimumBP);
f.Write (MaximumBP);
}
void STRTracePrequalification :: RestoreAll (RGFile& f) {
TracePrequalification::RestoreAll (f);
f.Read (WindowWidth);
}