public void GetTranscriptToCodingBlocks_SingleBaseBlock()
{
var intervalArray = new IInterval[]
{
new Interval(1, 10),
new Interval(21, 21),
new Interval(41, 50),
new Interval(65, 70)
};
var phasedIntervalArrays = new List <PhasedIntervalArray> {
new PhasedIntervalArray(0, intervalArray)
};
var codingBlocklists = CodonInfoProvider.GetTranscriptToCodingBlocks(phasedIntervalArrays, false);
var expectedBlockList = new List <CodingBlock>
{
new CodingBlock(1, 10, 0),
new CodingBlock(21, 21, 1),
new CodingBlock(41, 50, 2),
new CodingBlock(65, 70, 0)
};
Assert.True(expectedBlockList.SequenceEqual(codingBlocklists[0]));
}
public void GetCodonRange_AsExpected()
{
const int position = 73115941;
var codingBlock = new CodingBlock(73115838, 73116000, 1);
int range = CodonInfoProvider.GetCodonRange(position, codingBlock);
Assert.Equal(73115941, range);
}
private void ResetBuffer(ISimplePosition simplePosition, bool recomposable)
{
var functionBlockRanges = recomposable ? new List <int> {
CodonInfoProvider.GetLongestFunctionBlockDistance(simplePosition)
} : new List <int>();
BufferedPositions = new BufferedPositions(new List <ISimplePosition> {
simplePosition
}, new List <bool> {
recomposable
}, functionBlockRanges);
CurrentChromosome = simplePosition.Chromosome;
}
public void GetTranscriptToCodingBlocks_AlternativeTranslationStartInCodingExon()
{
var intervalArray1 = new IInterval[]
{
new Interval(1, 50),
new Interval(61, 70)
};
var intervalArray2 = new IInterval[]
{
new Interval(40, 50),
new Interval(61, 70)
};
var phasedIntervalArrays = new List <PhasedIntervalArray>
{
new PhasedIntervalArray(0, intervalArray1),
new PhasedIntervalArray(0, intervalArray2)
};
var codingBlocklists = CodonInfoProvider.GetTranscriptToCodingBlocks(phasedIntervalArrays, false);
var expectedBlockList1 = new List <CodingBlock>
{
new CodingBlock(1, 39, 0),
new CodingBlock(40, 50, 0),
new CodingBlock(61, 70, 2)
};
var expectedBlockList2 = new List <CodingBlock>
{
new CodingBlock(40, 50, 0),
new CodingBlock(61, 70, 2)
};
var expectedBlockLists = new[] { expectedBlockList1, expectedBlockList2 };
for (var i = 0; i < 2; i++)
{
Assert.True(expectedBlockLists[i].SequenceEqual(codingBlocklists[i]));
}
}
public void UpdateFunctionBlockRanges(ISimplePosition simplePosition)
{
BufferedPositions.FunctionBlockRanges.Add(CodonInfoProvider.GetLongestFunctionBlockDistance(simplePosition));
}
public void GetTranscriptToCodingBlocks_AsExpected()
{
var intervalArray1 = new IInterval[]
{
new Interval(1, 10),
new Interval(21, 30),
new Interval(41, 50),
new Interval(65, 70)
};
var intervalArray2 = new IInterval[]
{
new Interval(1, 10),
new Interval(41, 50),
new Interval(61, 70)
};
var intervalArray3 = new IInterval[]
{
new Interval(1, 10),
new Interval(21, 26),
new Interval(41, 50),
new Interval(61, 70)
};
var phasedIntervalArrays = new List <PhasedIntervalArray>
{
new PhasedIntervalArray(0, intervalArray1),
new PhasedIntervalArray(0, intervalArray2),
new PhasedIntervalArray(0, intervalArray3)
};
var codingBlocklists = CodonInfoProvider.GetTranscriptToCodingBlocks(phasedIntervalArrays, false);
var expectedBlockList1 = new List <CodingBlock>
{
new CodingBlock(1, 10, 0),
new CodingBlock(21, 26, 1),
new CodingBlock(27, 30, 1),
new CodingBlock(41, 50, 2),
new CodingBlock(65, 70, 0)
};
var expectedBlockList2 = new List <CodingBlock>
{
new CodingBlock(1, 10, 0),
new CodingBlock(41, 50, 1),
new CodingBlock(61, 64, 2),
new CodingBlock(65, 70, 0)
};
var expectedBlockList3 = new List <CodingBlock>
{
new CodingBlock(1, 10, 0),
new CodingBlock(21, 26, 1),
new CodingBlock(41, 50, 1),
new CodingBlock(61, 64, 2),
new CodingBlock(65, 70, 0)
};
var expectedBlockLists = new[] { expectedBlockList1, expectedBlockList2, expectedBlockList3 };
for (var i = 0; i < 3; i++)
{
Assert.True(expectedBlockLists[i].SequenceEqual(codingBlocklists[i]));
}
}
