public static void WriteDataFile(string fileName, NumericalText nt)
{
if (((nt.Data != null) && (nt.Data.Count > 0)) || ((nt.Tags != null) && (nt.Tags.Count > 0)))
{
int useLen = Math.Min(nt.Titles.Count, (nt.Data.Count + nt.Tags.Count));
int dataLen = nt.Data [0].Count;
List <int> counts = new List <int> ();
List <int> currentIndexes = new List <int> ();
List <PrintOutNext> printTypes = new List <PrintOutNext> ();
if (nt.Tags != null)
{
int tagInd = 0;
foreach (List <string> sl in nt.Tags)
{
counts.Add(sl.Count - 1);
printTypes.Add(PrintOutNext.Tag);
dataLen = Math.Max(dataLen, sl.Count);
currentIndexes.Add(tagInd);
tagInd++;
}
}
if (nt.Data != null)
{
int datInd = 0;
foreach (List <Double> ld in nt.Data)
{
counts.Add(ld.Count - 1);
printTypes.Add(PrintOutNext.Data);
dataLen = Math.Max(dataLen, ld.Count);
currentIndexes.Add(datInd);
datInd++;
}
}
using (StreamWriter sw = new StreamWriter(fileName)) {
for (int i = 0; i < useLen; i++)
{
if (i > 0)
{
sw.Write("\t");
}
sw.Write(nt.Titles [i]);
}
sw.Write("\n");
for (int j = 0; j < dataLen; j++)
{
for (int i = 0; i < useLen; i++)
{
if (i > 0)
{
sw.Write("\t");
}
if (counts [i] >= j)
{
if (printTypes [i] == PrintOutNext.Data)
{
sw.Write(nt.Data [currentIndexes[i]] [j]);
}
else
{
sw.Write(nt.Tags [currentIndexes [i]] [j]);
}
}
else
{
sw.Write("x");
}
}
sw.Write("\n");
}
}
MainData.UpdateLog("Saved " + MainData.MainWindow.MaxLenString(fileName, 20), false);
}
else
{
MainData.ShowMessageWindow("There isn't any data there to save!", false);
}
}
public void LoadGFF3(string fileName)
{
string idTag = AppSettings.Loading.GFF3_ID_TAG.Item;
int tagSize = idTag.Length;
string line = "";
string parentTag = "arent=";
int pTagSize = parentTag.Length;
int count = 0;
long modulo = MainData.ScanFileForModulo(fileName, 5);
long lineCount = modulo * 5;
MainData.UpdateLog("Reading... ", true);
char[] spChar = { '\t' }; char[] spChar2 = { ';' };
using (StreamReader sr = new StreamReader(fileName)) {
while ((line = sr.ReadLine()) != null)
{
if (line.Length > 10)
{
string[] spstr = line.Split(spChar, 10);
string[] spstr2 = spstr [8].Split(spChar2, 20);
string ID = "";
string pID = "";
foreach (string st in spstr2)
{
if (st.Contains(idTag))
{
ID = st;
break;
}
}
foreach (string st in spstr2)
{
if (st.Contains(parentTag))
{
pID = st;
break;
}
}
ID = ID.Substring(tagSize);
GFF3ApplyOptionsToID(ref ID);
if (pID != "")
{
GFF3ApplyOptionsToID(ref pID);
}
Sense sn = Sense.Sense;
if (spstr [6].Equals("-"))
{
sn = Sense.AntiSense;
}
else if (spstr [6].Equals("."))
{
sn = Sense.None;
}
string nameOfType = ID + "#" + spstr [2] + "#" + pID;;
int sta, end;
bool A = int.TryParse(spstr [3], out sta);
bool B = int.TryParse(spstr [4], out end);
if (A && B)
{
if (Scaffolds.ContainsKey(spstr [0]))
{
Scaffolds [spstr [0]].SendComponent(nameOfType, sta, end, sn);
}
else
{
throw new Exception("Gff3 references scaffold not found in genome!");
}
}
}
count++;
if (count % modulo == 0)
{
long perc = (long)(((float)count / (float)lineCount) * 100);
MainData.UpdateLog("Read " + perc + "% of gff3..", true);
}
}
}
if (AppSettings.Genes.GENERATE_ANY_PROMO.Item || AppSettings.Genes.GENERATE_FLANK3.Item)
{
MainData.UpdateLog("Generating GFF3 additional elements as described in Settings -> Genes", true);
foreach (KeyValuePair <string, Scaffold> kvp in Scaffolds)
{
kvp.Value.RunGenePostLoad();
}
}
}