public void Initialize(IDataset dataset, XmlElement filterNode)
{
intronSize = new double[dataset.Rows][];
antiSense = new bool[dataset.Rows];
int strandIdx = dataset.IndexOfColumn("Strand");
for (int row = 0; row < dataset.Rows; row++)
{
string[] beginList = dataset.GetDataAt(row, 3).Split(',');
string[] endList = dataset.GetDataAt(row, 4).Split(',');
if (beginList.Length != endList.Length)
{
continue;
}
double[] R = new double[beginList.Length - 1];
intronSize[row] = R;
for (int col = 0; col < R.Length; col++)
{
R[col] = int.Parse(beginList[col + 1]) - int.Parse(endList[col]) - 1;
}
antiSense[row] = (dataset.GetDataAt(row, strandIdx) == "-1");
if (antiSense[row])
{
Array.Reverse(intronSize[row]);
}
// normalize
double sum = R.Sum();
for (int col = 0; col < R.Length; col++)
{
R[col] /= sum;
}
}
}
public void Initialize(IDataset dataset, XmlElement filterNode)
{
seqList = new int[dataset.Rows][];
cdsLength = new int[dataset.Rows];
geneSpan = new int[dataset.Rows];
antiSense = new bool[dataset.Rows];
int strandIdx = dataset.IndexOfColumn("Strand");
for (int row = 0; row < dataset.Rows; row++)
{
string[] beginList = dataset.GetDataAt(row, 3).Split(',');
string[] endList = dataset.GetDataAt(row, 4).Split(',');
if (beginList.Length != endList.Length)
{
continue;
}
seqList[row] = new int[2 * beginList.Length];
int cdsLen = 0;
int minBegin = int.MaxValue;
int maxEnd = int.MinValue;
int[] R = seqList[row];
for (int col = 0; col < beginList.Length; col++)
{
int idxBegin = int.Parse(beginList[col]) - 1;
int idxEnd = int.Parse(endList[col]) - 1;
R[2 * col] = idxBegin;
R[2 * col + 1] = idxEnd;
cdsLen += idxEnd - idxBegin + 1;
minBegin = Math.Min(minBegin, idxBegin);
maxEnd = Math.Max(maxEnd, idxEnd);
}
cdsLength[row] = cdsLen;
geneSpan[row] = maxEnd - minBegin + 1;
antiSense[row] = (dataset.GetDataAt(row, strandIdx) == "-1");
for (int col = 0; col < R.Length; col++)
{
R[col] -= minBegin;
}
if (antiSense[row])
{
int maxIdx = R[R.Length - 1];
for (int col = 0; col < R.Length; col++)
{
R[col] = maxIdx - R[col];
}
Array.Reverse(R);
}
}
}
public void Initialize(IDataset dataset, XmlElement filterNode)
{
IList <IColumnSpec> columnList = dataset.ColumnSpecList;
columns = 0;
foreach (IColumnSpec cs in columnList)
{
if (cs.DataType == 'n')
{
columns++;
}
}
table = new double[dataset.Rows][];
for (int row = 0; row < dataset.Rows; row++)
{
table[row] = new double[columns];
int col = 0;
for (int ch = 0; ch < dataset.Columns; ch++)
{
if (columnList[ch].DataType == 'n')
{
table[row][col] = double.Parse(dataset.GetDataAt(row, ch));
col++;
}
}
}
}
public void Initialize(IDataset dataset, XmlElement filterNode)
{
vecList = new double[dataset.Rows][];
var rg = new Random();
String ACGT = "ACGT";
double[] amplitudes1 = new double[L];
for (int k = 0; k < L; k++)
{
amplitudes1[k] = rg.NextDouble();
}
double[] amplitudes2 = new double[L];
for (int k = 0; k < L; k++)
{
amplitudes2[k] = rg.NextDouble();
}
for (int row = 0; row < dataset.Rows; row++)
{
vecList[row] = new double[8];
var s = dataset.GetDataAt(row, 0);
for (int k = 0; k < s.Length; k++)
{
int kk = k % L;
int ii = ACGT.IndexOf(s[k]);
vecList[row][ii] += amplitudes1[kk];
vecList[row][4 + ii] += amplitudes2[kk];
}
}
}
public void Initialize(IDataset dataset, XmlElement filterNode)
{
motifPos = new int[dataset.Rows][];
for (int row = 0; row < dataset.Rows; row++)
{
string[] posList = dataset.GetDataAt(row, 0).Split(',');
int[] R = new int[posList.Length];
for (int i = 0; i < R.Length; i++)
{
R[i] = int.Parse(posList[i]);
}
motifPos[row] = R;
}
}
public void Initialize(IDataset dataset, XmlElement filterNode)
{
motifs = new string[dataset.Rows];
for (int row = 0; row < dataset.Rows; row++)
{
motifs[row] = dataset.GetDataAt(row, 0);
}
maxLength = motifs.Max(s => s.Length);
mem = null; // This is only for the single threaded execution.
string settings = GeneticAnalysis.App.ScriptApp.GetProperty("GeneticAnalysis.NeedlemanWunsch", null);
if (settings != null)
{
string[] fs = settings.Split(new char[] { ' ', '\t' }, StringSplitOptions.RemoveEmptyEntries);
gapCost = short.Parse(fs[0]);
matchCost = short.Parse(fs[1]);
mismatchCost = short.Parse(fs[2]);
}
}
public void Initialize(IDataset dataset, XmlElement filterNode)
{
int sparseSetColumn = 0;
var csList = dataset.ColumnSpecList;
string flags = null;
if (filterNode != null)
{
XmlNamespaceManager nsmgr = new XmlNamespaceManager(new NameTable());
nsmgr.AddNamespace("vm", "urn:VisuMap.Technologies:VisuMap");
flags = filterNode.SelectSingleNode("vm:EnabledFlag", nsmgr).InnerText;
}
for (int col = 0; col < csList.Count; col++)
{
if (csList[col].Name == "SparseSet")
{
sparseSetColumn = col;
sparseTable = new int[dataset.Rows][];
break;
}
}
if (sparseTable != null)
{
for (int row = 0; row < dataset.Rows; row++)
{
string[] fs = dataset.GetDataAt(row, sparseSetColumn).Split(',');
sparseTable[row] = new int[fs.Length];
int col2 = 0;
for (int col = 0; col < fs.Length; col++)
{
if ((fs[col] != null) && (fs[col] != ""))
{
sparseTable[row][col2++] = int.Parse(fs[col]);
}
}
if (col2 < fs.Length)
{
Array.Resize(ref sparseTable[row], col2);
}
}
}
else
{
int columns = 0;
for (int col = 0; col < csList.Count; col++)
{
if (csList[col].IsNumber && ((flags == null) || flags[col] == 'y'))
{
columns++;
}
}
setTable = new bool[dataset.Rows][];
for (int row = 0; row < dataset.Rows; row++)
{
setTable[row] = new bool[columns];
int idx = 0;
for (int col = 0; col < csList.Count; col++)
{
if (csList[col].IsNumber && ((flags == null) || flags[col] == 'y'))
{
setTable[row][idx] = (double.Parse(dataset.GetDataAt(row, col)) != 0);
idx++;
}
}
}
}
}
