public PairedEndPeakFinder(string BAMFile, string prefix, string mtDNAName = "MT")
{
// ReasonForFailure = "NOT SET";
PeakEdgeWindowSize = 3;
ScanningWindowSize = 11;
if (String.IsNullOrEmpty(BAMFile) || String.IsNullOrEmpty(mtDNAName) || String.IsNullOrEmpty(prefix))
{
throw new ArgumentException("Tried to load the paired peak finder without the a BAM file, output file Prefix or mt DNA chromosome name");
}
if (!File.Exists(BAMFile))
{
throw new IOException("Could not find BAM file: " + BAMFile);
}
rInt = new RInterface();
FileName = BAMFile;
this.mtDNAName = mtDNAName;
this.OutputFilePrefix = prefix;
bp = new BAMParser();
//create count array
countsOfSize = new double[StaticResources.CRS_LENGTH];
}
/// <summary>
/// Render a PDF image to the file with the given name
/// </summary>
/// <param name="rInt"></param>
/// <param name="filename"></param>
public void Render(RInterface rInt, string filename)
{
//#if FALSE
var e = rInt.CurrentEngine;
lock (e)
{
if (this.slices.Count == 0 || !Assembly.SuccessfulAssembly)
{
return;
}
//load the file
// string rFile = System.Reflection.Assembly.GetExecutingAssembly().Location;
//char splitChar = '\\';
//if (Bio.CrossPlatform.Environment.RunningInMono) {
// splitChar = '/';
//}
//var tempSplit=rFile.Split(splitChar);
//rFile=String.Join("/",tempSplit.Take(tempSplit.Length-1))+"/Visualization/MakeGenomeAssemblyPlot.r";
//rFile=rFile.Replace('\\','/');
//string loadFile="source('"+rFile+"')";
//e.Evaluate(loadFile);
try
{
var fname = System.IO.Path.GetTempFileName();
var sw = new StreamWriter(fname);
sw.Write(VisualizationRScript.FILE_AS_STRING);
sw.Close();
var rFile = fname.Replace('\\', '/');
string loadFile = "source('" + rFile + "')";
e.Evaluate(loadFile);
File.Delete(fname);
}
catch (Exception thrown)
{
Console.WriteLine("\n\nCould not render assembly graphic!\n" + thrown.Message);
return;
}
//var strings = VisualizationRScript.FILE_AS_STRING.Split(new char[] {'\n','\r'},StringSplitOptions.RemoveEmptyEntries);
//foreach (var str in strings)
//{
// e.Evaluate(str);
//}
//TODO: THIS LOGIC REALLY NEEDS SOME CLEANING
var curMax = Math.Max(this.slices.Max(x => x.ActualLeftGraphicalPosition.Value), this.slices.Max(x => x.ActualRightGraphicalPosition.Value));
//e.Evaluate("assemblyLength="+Assembly.AssemblyLength.ToString());
e.Evaluate("assemblyLength=" + curMax.ToString());
double outer = e.GetSymbol("outerRadius").AsNumeric().First();
e.Evaluate("createPlot(\"" + filename + "\")");
double total = Assembly.AssemblyLength;
//TODO: Not sure how this ever could have been possible
if (Math.Abs(total) < double.Epsilon)
{
return;
}
foreach (var slice in this.slices)
{
Dictionary <string, object> args = new Dictionary <string, object>();
//drawSegment<-function(start,end,low,height)
args["start"] = slice.ActualLeftGraphicalPosition;
args["end"] = slice.ActualRightGraphicalPosition;
args["low"] = slice.MagnitudeLow;
args["height"] = slice.Height;
RDotNet.SymbolicExpression se;
bool worked = e.EvaluateMethodWithNamedArguments("drawSegment", args, out se);
if (!worked)
{
e.Evaluate("traceback()");
throw new RInterfaceException("Could not draw a segment from the assembly");
}
}
//now the arrows
//drawArrow<-function(sMag,sAng,eMag,eAng)
foreach (var arrow in this.arrows)
{
Dictionary <string, object> args = new Dictionary <string, object>();
//drawSegment<-function(start,end,low,height)
args["sMag"] = arrow.sMag;
args["sAng"] = arrow.sAng;
args["eMag"] = arrow.eMag;
args["eAng"] = arrow.eAng;
RDotNet.SymbolicExpression se;
bool worked = e.EvaluateMethodWithNamedArguments("drawArrow", args, out se);
if (!worked)
{
throw new RInterfaceException("Could not draw an arrow from the assembly");
}
}
e.Evaluate("dev.off()");
}
//#endif
}
private bool active; //true while game is playing; false when rewinding; basically if objects are active
void Start()
{
active = true;
otherScript = (RInterface)gameObject.GetComponent(typeof(RInterface));
}
