internal void Parse()
{
int sections = ReadSections(0);
int numPoints = 0, numBases = 0;
float fspacing = 0; /* average base spacing */
int no_bases = 0;
int indexO = 0; /* File offset where the index is */
int baseO = 0; /* File offset where the bases are stored */
int fwo_ = 0; /* base . lane mapping */
int dataCO = 0; /* File offset where the C trace is stored */
int dataAO = 0; /* File offset where the A trace is stored */
int dataGO = 0; /* File offset where the G trace is stored */
int dataTO = 0; /* File offset where the T trace is stored */
if ((indexO = GetABIIndexOffset()) < 0)
{
return;
}
GetABIIndexEntryLW(indexO, DataLabel, DataCount[0], 3, ref numPoints);
if (GetABIIndexEntryLW(indexO, BaseEntryLabel, 1, 3, ref numBases) == 0)
{
no_bases = 1;
numBases = 0;
}
DataInfo = new ABIDataInfo(numPoints, numBases);
if (GetABIIndexEntryLW(indexO, FWO_Label, 1, 5, ref fwo_) == 0)
{
fwo_ = 0x43414754;
}
if ((sections & READ_SAMPLES) > 0)
{
int[] dataxO = new int[4];
/*Get the positions of the four traces */
GetABIIndexEntryLW(indexO, DataLabel, DataCount[0], 5, ref dataxO[BaseIdnex((char)(fwo_ >> 24 & 255))]);
GetABIIndexEntryLW(indexO, DataLabel, DataCount[1], 5, ref dataxO[BaseIdnex((char)(fwo_ >> 16 & 255))]);
GetABIIndexEntryLW(indexO, DataLabel, DataCount[2], 5, ref dataxO[BaseIdnex((char)(fwo_ >> 8 & 255))]);
GetABIIndexEntryLW(indexO, DataLabel, DataCount[3], 5, ref dataxO[BaseIdnex((char)(fwo_ & 255))]);
dataCO = dataxO[0];
dataAO = dataxO[1];
dataGO = dataxO[2];
dataTO = dataxO[3];
// Read the traces and bases information
if ((sections & READ_SAMPLES) > 0)
{
/* Read in the C trace */
fs.Seek(header_fudge + dataCO, SeekOrigin.Begin);
GetABIint2(0, string.Empty, 0, DataInfo.TraceC, DataInfo.NPoints);
/* Read in the A trace */
fs.Seek(header_fudge + dataAO, SeekOrigin.Begin);
GetABIint2(0, string.Empty, 0, DataInfo.TraceA, DataInfo.NPoints);
/* Read in the G trace */
fs.Seek(header_fudge + dataGO, SeekOrigin.Begin);
GetABIint2(0, string.Empty, 0, DataInfo.TraceG, DataInfo.NPoints);
/* Read in the T trace */
fs.Seek(header_fudge + dataTO, SeekOrigin.Begin);
GetABIint2(0, string.Empty, 0, DataInfo.TraceT, DataInfo.NPoints);
/* Compute highest trace peak */
for (int i = 0; i < DataInfo.NPoints; i++)
{
if (DataInfo.MaxTraceVal < DataInfo.TraceA[i])
{
DataInfo.MaxTraceVal = DataInfo.TraceA[i];
}
if (DataInfo.MaxTraceVal < DataInfo.TraceC[i])
{
DataInfo.MaxTraceVal = DataInfo.TraceC[i];
}
if (DataInfo.MaxTraceVal < DataInfo.TraceG[i])
{
DataInfo.MaxTraceVal = DataInfo.TraceG[i];
}
if (DataInfo.MaxTraceVal < DataInfo.TraceT[i])
{
DataInfo.MaxTraceVal = DataInfo.TraceT[i];
}
}
}
byte[] conf = new byte[DataInfo.NBases];
GetABIint1(indexO, BaseConfLabel, 1, conf, DataInfo.NBases);
GetABIIndexEntryLW(indexO, BaseEntryLabel, 1, 5, ref baseO);
fs.Seek(header_fudge + baseO, SeekOrigin.Begin);
for (int i = 0; i < DataInfo.NBases; ++i)
{
int ch = MFGetC();
DataInfo.Bases[i] = (((char)ch) == 'N') ? '-' : (char)ch;
switch (DataInfo.Bases[i])
{
case 'A':
case 'a':
DataInfo.Prob_A[i] = conf[i];
DataInfo.Prob_C[i] = 0;
DataInfo.Prob_G[i] = 0;
DataInfo.Prob_T[i] = 0;
break;
case 'C':
case 'c':
DataInfo.Prob_A[i] = 0;
DataInfo.Prob_C[i] = conf[i];
DataInfo.Prob_G[i] = 0;
DataInfo.Prob_T[i] = 0;
break;
case 'G':
case 'g':
DataInfo.Prob_A[i] = 0;
DataInfo.Prob_C[i] = 0;
DataInfo.Prob_G[i] = conf[i];
DataInfo.Prob_T[i] = 0;
break;
case 'T':
case 't':
DataInfo.Prob_A[i] = 0;
DataInfo.Prob_C[i] = 0;
DataInfo.Prob_G[i] = 0;
DataInfo.Prob_T[i] = conf[i];
break;
default:
DataInfo.Prob_A[i] = 0;
DataInfo.Prob_C[i] = 0;
DataInfo.Prob_G[i] = 0;
DataInfo.Prob_T[i] = 0;
break;
}
}
DataInfo.Bases[DataInfo.Bases.Length - 1] = ' ';
}
GetABIint2(indexO, BasePosEntryLabel, 1, DataInfo.BasePos, DataInfo.NBases);
fs.Close();
}
public TraceConvert(ABIDataInfo dataInfo)
{
this.dataInfo = dataInfo;
}
