public void MatchSeq(SequenceModels sequenceModels)
{
if (!Regex.IsMatch(sequenceModels.Seq.Seq, @"^[ACGTacgt]*$"))
{
sequenceModels.Match.Match = false;
}
}
public SequenceModels SeqFile(SequenceModels sequenceModels)
{
string filePath = "Data/";
string seqLine = string.Empty;
sequenceModels.Seq.Seq = string.Empty;
using (StreamReader stream = new StreamReader(filePath))
{
while ((seqLine = stream.ReadLine()) != null)
{
if (seqLine.Contains(">"))
{
continue;
}
sequenceModels.Seq.Seq += seqLine.ToLower();
}
}
sequenceModels.Seq.SeqLength = sequenceModels.Seq.Seq.Length;
if (sequenceModels.Seq.Seq.Length >= 400)
{
sequenceModels.OutputSeq.OutSeq = sequenceModels.Seq.Seq.Substring(0, 200) + "..." +
sequenceModels.Seq.Seq.Substring(sequenceModels.Seq.Seq.Length - 200);
}
else
{
sequenceModels.OutputSeq.OutSeq = sequenceModels.Seq.Seq;
}
return(sequenceModels);
}
public void Calc(SequenceModels sequenceModels)
{
List <string> dinuc1st = new List <string>();
List <string> dinuc2nd = new List <string>();
char[] nucArray;
int seqLength = sequenceModels.Seq.SeqLength;
Cseq = sequenceModels.Seq.Seq + sequenceModels.Seq.Seq.Substring(0, 2);
nucArray = Cseq.ToCharArray();
try
{
if (seqLength % 2 == 0)
{
for (int i = 0; i < seqLength; i += 2)
{
dinuc1st.Add(nucArray[i].ToString() + nucArray[i + 1].ToString());
dinuc2nd.Add(nucArray[i + 1].ToString() + nucArray[i + 2].ToString());
}
}
else
{
for (int i = 0; i < seqLength - 1; i += 2)
{
dinuc1st.Add(nucArray[i].ToString() + nucArray[i + 1].ToString());
dinuc2nd.Add(nucArray[i + 1].ToString() + nucArray[i + 2].ToString());
}
}
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
foreach (var item in sequenceModels.Dinuc.Dinucs)
{
item.Dinuc1stFrame = dinuc1st.Count(di => di.Contains(item.Dinuc));
item.Dinuc2ndFrame = dinuc2nd.Count(di => di.Contains(item.Dinuc));
item.Dinuc1stFrameFrq = (double)decimal.Divide(item.Dinuc1stFrame, dinuc1st.Count);
item.Dinuc2ndFrameFrq = (double)decimal.Divide(item.Dinuc2ndFrame, dinuc2nd.Count);
item.DinucFrqDiff = Math.Abs(item.Dinuc1stFrameFrq - item.Dinuc2ndFrameFrq);
sequenceModels.Dinuc.DinucDiffSum += item.DinucFrqDiff;
}
}
public ActionResult Calculation(SequenceModels sequenceModels)
{
Match match = new Match();
match.MatchSeq(sequenceModels);
if (sequenceModels.Match.Match)
{
DiCalc diCalc = new DiCalc();
diCalc.Calc(sequenceModels);
sequenceModels.Match.Match = true;
return(View(sequenceModels));
}
else
{
return(View("~/Views/Home/Index.cshtml", sequenceModels));
}
//DinucCalc dinucCalculation = new DinucCalc();
//dinucCalculation.Calculation(multipleModel);
}
public ActionResult SeqIn(SequenceModels sequenceModels, string choose)
{
switch (choose)
{
//case "add-test":
//sequenceModels.TestSeq.TSeq = sequenceModels.TestSeq.TSeq;
//break;
case "make-random":
RandomSeq randomSeq = new RandomSeq();
sequenceModels.Seq.Seq = randomSeq.RandSeq();
break;
case "add-random":
sequenceModels.Seq.Seq = sequenceModels.RandomSeq.Seq;
break;
//case "add-from-list":
//SequenceFile sequenceFile = new SequenceFile();
//sequenceFile.SeqFile(sequenceModels);
//break;
}
return(View("~/Views/Home/Index.cshtml", sequenceModels));
}
public ActionResult Index()
{
Sequence sequence = new Sequence
{
Seq = string.Empty,
SeqName = "SomeSeq"
};
sequence.SeqLength = sequence.Seq.Length;
SeqMatch seqMatch = new SeqMatch
{
Match = true
};
List <TestSequence> testSequence = new List <TestSequence>
{
new TestSequence {
Seq = "aaacagatcacccgctgagcgggttatctgtt", SeqName = "All dinucs"
},
new TestSequence {
Seq = "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa", SeqName = "Mono dinucs"
},
new TestSequence {
Seq = "agcgggctagtgcgtgagcgggctagtgcgtg", SeqName = "Odd seq length"
},
new TestSequence {
Seq = "agcgggctagtgcgtgcagcgggctagtgcgtg", SeqName = "Even seq length"
}
};
TestSequence selectedTestSeq = new TestSequence
{
Seq = string.Empty,
SeqName = string.Empty
};
FileSequence fileSequence = new FileSequence
{
Seq = string.Empty,
SeqName = string.Empty,
SeqFileName = string.Empty
};
List <string> fSeqs = new List <string>
{
"Esherichia coli",
"Lactococcus lactis"
};
SequenceModels sequenceModels = new SequenceModels
{
Seq = sequence,
Match = seqMatch,
TestSeq = testSequence,
SelectedTestSeq = selectedTestSeq,
FSeqs = fSeqs,
FileSeq = fileSequence
};
return(View(sequenceModels));
}
