/// <summary>
/// Gets a block from the cache at the specified index.
/// </summary>
/// <param name="index">The zero-based index of the block.</param>
/// <returns>The cached sequence block.</returns>
private CacheBox <byte[]> GetCacheBlock(int index)
{
CacheBox <byte[]> block = _virtualData.FirstOrDefault(C => index >= C.StartRange && index <= C.EndRange);
if (block != null)
{
return(block);
}
else
{
int startIndex = index - (index % BlockSize);
byte[] seq = _parser.ParseRange(startIndex, BlockSize, SequencePointerInstance);
if (seq == null)
{
return(null);
}
else
{
block = new CacheBox <byte[]>(seq.Length)
{
StartRange = startIndex
};
block.EndRange = block.StartRange + seq.Length - 1;
block.Data = seq;
_virtualData.Add(block);
return(block);
}
}
}
/// <summary>
/// Gets a block from the cache at the specified index.
/// </summary>
/// <param name="index">The zero-based index of the block.</param>
/// <returns>The cached sequence block.</returns>
private CacheBox <byte[]> GetCacheBlock(int index)
{
CacheBox <byte[]> block = _virtualData.FirstOrDefault(C => index >= C.StartRange && index <= C.EndRange);
if (block != null)
{
return(block);
}
else
{
int startIndex = index;
int blockStartingIndex = index - (index % BlockSize);
int sequenceLength = (int)(SequencePointerInstance.IndexOffsets[1] - SequencePointerInstance.IndexOffsets[0]);
int count = sequenceLength > BlockSize ? BlockSize : sequenceLength;
if (sequenceLength > BlockSize && _sidecarProvider != null)
{
blockStartingIndex = _sidecarProvider.GetBlockToLoad(_sequenceIndex, index, ref startIndex, ref count);
}
else
{
blockStartingIndex = 0;
startIndex = 0;
}
byte[] seq = _parser.ParseRange(blockStartingIndex, count, SequencePointerInstance);
if (seq == null)
{
return(null);
}
else
{
block = new CacheBox <byte[]>(seq.Length)
{
StartRange = startIndex
};
block.EndRange = block.StartRange + seq.Length - 1;
block.Data = seq;
_virtualData.Add(block);
return(block);
}
}
}
/// <summary>
/// General method to validate virtual data class.
/// <param name="addParam">Additional parameter.</param>
/// </summary>
static void ValidateGeneralVirtualDataTestCases(AdditionalParameters addParam)
{
VirtualData <Sequence> vdObj = new VirtualData <Sequence>();
// Sets the Initial Properties and required Cache box
vdObj.MaxNumberOfBlocks = 5;
vdObj.BlockSize = 5;
CacheBox <Sequence> cb1 = new CacheBox <Sequence>(11);
cb1.StartRange = 0;
cb1.EndRange = 10;
cb1.Data = new Sequence(Alphabets.DNA, "GGGGGGGGGGGGG");
CacheBox <Sequence> cb2 = new CacheBox <Sequence>(11);
cb2.StartRange = 0;
cb2.EndRange = 10;
cb2.Data = new Sequence(Alphabets.DNA, "TTTTTTTTTTTTT");
CacheBox <Sequence> cb3 = new CacheBox <Sequence>(11);
cb3.StartRange = 0;
cb3.EndRange = 10;
cb3.Data = new Sequence(Alphabets.DNA, "CCCCCCCCCCCCC");
CacheBox <Sequence> cb4 = new CacheBox <Sequence>(11);
cb4.StartRange = 0;
cb4.EndRange = 10;
cb4.Data = new Sequence(Alphabets.DNA, "AAAAAAAAAAAAAA");
List <CacheBox <Sequence> > cbList = new List <CacheBox <Sequence> >();
cbList.Add(cb1);
cbList.Add(cb2);
cbList.Add(cb3);
cbList.Add(cb4);
switch (addParam)
{
case AdditionalParameters.Add:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbList[i].Data, vdObj[i].Data);
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the Add() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the Add() method.");
break;
case AdditionalParameters.AddData:
vdObj.AddData(new Sequence(Alphabets.DNA, "GGGGGGGGGGGGG"), 0, 10);
vdObj.AddData(new Sequence(Alphabets.DNA, "TTTTTTTTTTTTT"), 0, 10);
vdObj.AddData(new Sequence(Alphabets.DNA, "CCCCCCCCCCCCC"), 0, 10);
vdObj.AddData(new Sequence(Alphabets.DNA, "AAAAAAAAAAAAAA"), 0, 10);
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbList[i].Data.ToString(), vdObj[i].Data.ToString());
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the AddData() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the AddData() method.");
break;
case AdditionalParameters.AddDelay:
vdObj.MaxNumberOfBlocks = 2;
vdObj.Add(cb1);
vdObj.Add(cb2);
// Sleep for 20 seconds so that the cache box would be cleared
// and the count of items in the VirtualData would be reduced
Thread.Sleep(20000);
vdObj.Add(cb3);
vdObj.Add(cb4);
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbList[i + 2].Data, vdObj[i].Data);
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the Add() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the Add() method.");
break;
case AdditionalParameters.AddDataDelay:
vdObj.MaxNumberOfBlocks = 2;
vdObj.AddData(new Sequence(Alphabets.DNA, "GGGGGGGGGGGGG"), 0, 10);
vdObj.AddData(new Sequence(Alphabets.DNA, "TTTTTTTTTTTTT"), 0, 10);
// Sleep for 20 seconds so that the cache box would be cleared
// and the count of items in the VirtualData would be reduced
Thread.Sleep(20000);
vdObj.AddData(new Sequence(Alphabets.DNA, "CCCCCCCCCCCCC"), 0, 10);
vdObj.AddData(new Sequence(Alphabets.DNA, "AAAAAAAAAAAAAA"), 0, 10);
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbList[i + 2].Data.ToString(), vdObj[i].Data.ToString());
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the AddData() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the AddData() method.");
break;
case AdditionalParameters.Clear:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
vdObj.Clear();
Assert.AreEqual(0, vdObj.Count);
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the Clear() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the Clear() method.");
break;
case AdditionalParameters.ClearStaleData:
vdObj.MaxNumberOfBlocks = 2;
vdObj.Add(cb1);
vdObj.Add(cb2);
// Sleep for 20 seconds so that the cache box would be cleared
// and the count of items in the VirtualData would be reduced
Thread.Sleep(20000);
vdObj.Add(cb3);
vdObj.Add(cb4);
Assert.IsTrue(3 > vdObj.Count);
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the ClearStaleData() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the ClearStaleData() method.");
break;
case AdditionalParameters.GetAllData:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
// Gets all the data in Virtual data object
IList <Sequence> allSeqData = vdObj.GetAllData();
for (int i = 0; i < allSeqData.Count; i++)
{
Assert.AreEqual(cbList[i].Data.ToString(), allSeqData[i].ToString());
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the GetAllData() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the GetAllData() method.");
break;
case AdditionalParameters.GetData:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
// Gets the data in Virtual data object
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbList[i].Data.ToString(), vdObj.GetData(i).ToString());
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the GetData() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the GetData() method.");
break;
case AdditionalParameters.GetEnumerator:
vdObj.Add(cb1);
vdObj.Add(cb2);
IEnumerator <CacheBox <Sequence> > enumObj = vdObj.GetEnumerator();
Assert.IsTrue(null != enumObj);
Assert.AreEqual(cb1, vdObj.FirstOrDefault(C => 0 >= C.StartRange && 0 <= C.EndRange));
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the GetEnumerator() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the GetEnumerator() method.");
break;
case AdditionalParameters.Insert:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
// Inserts the cache box in Virtual data object
vdObj.Insert(3, cb4);
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbList[i].Data, vdObj[i].Data);
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the Insert() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the Insert() method.");
break;
case AdditionalParameters.Remove:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
// Add a Cache Box and remove the same
CacheBox <Sequence> cb5 = new CacheBox <Sequence>(11);
cb5.StartRange = 0;
cb5.EndRange = 10;
cb5.Data = new Sequence(Alphabets.DNA, "AAAAAATTTTTTT");
vdObj.Add(cb5);
vdObj.Remove(cb5);
// Removes the cache box from the virtual data list
for (int i = 0; i < cbList.Count; i++)
{
Assert.AreEqual(cbList[i].Data, vdObj[i].Data);
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the Remove() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the Remove() method.");
break;
case AdditionalParameters.RemoveAt:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
// Add a Cache Box and remove the same
CacheBox <Sequence> cbRemove = new CacheBox <Sequence>(11);
cbRemove.StartRange = 0;
cbRemove.EndRange = 10;
cbRemove.Data = new Sequence(Alphabets.DNA, "AAAAAATTTTTTT");
vdObj.Add(cbRemove);
vdObj.RemoveAt(4);
for (int i = 0; i < cbList.Count; i++)
{
Assert.AreEqual(cbList[i].Data, vdObj[i].Data);
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the RemoveAt() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the RemoveAt() method.");
break;
case AdditionalParameters.Contains:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
// Validates the contains block
Assert.IsTrue(vdObj.Contains(cb4));
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the Contains() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the Contains() method.");
break;
case AdditionalParameters.CopyTo:
vdObj.Add(cb1);
vdObj.Add(cb2);
vdObj.Add(cb3);
vdObj.Add(cb4);
CacheBox <Sequence>[] cbArray = new CacheBox <Sequence> [vdObj.Count];
vdObj.CopyTo(cbArray, 0);
for (int i = 0; i < vdObj.Count; i++)
{
Assert.AreEqual(cbArray[i].Data, vdObj[i].Data);
}
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Virtual Data BVT : Successfully validated the CopyTo() method.");
ApplicationLog.WriteLine(
"Virtual Data BVT : Successfully validated the CopyTo() method.");
break;
default:
break;
}
}
