public static double VectorDistanceValue(VectorDistanceMeasurementValues vectorDistanceMeasurementValues, bool[] isInteraction1, bool[] isInteraction2)
{
if (vectorDistanceMeasurementValues == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMeasurementValues));
}
if (isInteraction1 == null)
{
throw new ArgumentNullException(nameof(isInteraction1));
}
if (isInteraction2 == null)
{
throw new ArgumentNullException(nameof(isInteraction2));
}
if (isInteraction1.Length != isInteraction2.Length)
{
throw new ArgumentOutOfRangeException(nameof(isInteraction1), "Interaction vectors must be the same size");
}
double distance = 0;
for (var index = 0; index < isInteraction1.Length; index++)
{
distance += VectorDistanceValue(vectorDistanceMeasurementValues, isInteraction1[index], isInteraction2[index]);
}
return(distance);
}
public static void CustomDistance(bool[] array1, bool[] array2, VectorDistanceMeasurementValues vectorDistanceMeasurementValues, out double optimisticDistance /*, out double pessimisticDistance*/, int offsetStep = 1)
{
if (array1 == null)
{
throw new ArgumentNullException(nameof(array1));
}
if (array2 == null)
{
throw new ArgumentNullException(nameof(array2));
}
if (vectorDistanceMeasurementValues == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMeasurementValues));
}
var lengthDifference = Math.Abs(array1.Length - array2.Length);
optimisticDistance = double.MaxValue;
//pessimisticDistance = double.MinValue;
for (var index = 0; index <= lengthDifference; index += offsetStep)
{
double neutralOffsetDistance = CustomDistanceOffset(array1, array2, vectorDistanceMeasurementValues, index);
if (neutralOffsetDistance < optimisticDistance)
{
optimisticDistance = neutralOffsetDistance;
}
//if (neutralOffsetDistance > pessimisticDistance)
//{
// pessimisticDistance = neutralOffsetDistance;
//}
}
}
public static double VectorDistanceValue(VectorDistanceMeasurementValues vectorDistanceMeasurementValues, bool isInteraction1, bool isInteraction2)
{
if (vectorDistanceMeasurementValues == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMeasurementValues));
}
if (isInteraction1 && isInteraction2)
{
return(vectorDistanceMeasurementValues.InteractionAndInteraction);
}
if (!isInteraction1 && !isInteraction2)
{
return(vectorDistanceMeasurementValues.NonInteractionAndNonInteraction);
}
return(vectorDistanceMeasurementValues.InteractionAndNonInteraction);
}
public static double CustomDistanceOffset(bool[] array1, bool[] array2, VectorDistanceMeasurementValues vectorDistanceMeasurementValues, int offset)
{
if (array1 == null)
{
throw new ArgumentNullException(nameof(array1));
}
if (array2 == null)
{
throw new ArgumentNullException(nameof(array2));
}
if (vectorDistanceMeasurementValues == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMeasurementValues));
}
if (offset > array1.Length && offset > array2.Length)
{
throw new ArgumentOutOfRangeException(nameof(offset));
}
if (array1 == null || array1.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(array1));
}
if (array2 == null || array2.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(array2));
}
bool[] shorterArray;
bool[] longerArray;
if (array1.Length > array2.Length)
{
if (offset + array2.Length > array1.Length)
{
throw new ArgumentOutOfRangeException(nameof(offset));
}
longerArray = array1;
shorterArray = new bool[longerArray.Length];
Array.Copy(array2, 0, shorterArray, offset, array2.Length);
}
else if (array2.Length > array1.Length)
{
if (offset + array1.Length > array2.Length)
{
throw new ArgumentOutOfRangeException(nameof(offset));
}
longerArray = array2;
shorterArray = new bool[longerArray.Length];
Array.Copy(array1, 0, shorterArray, offset, array1.Length);
}
else
{
shorterArray = array1;
longerArray = array2;
}
var distance = VectorDistanceValue(vectorDistanceMeasurementValues, shorterArray, longerArray);
return(distance);
}
/*
* public static void ClusterVectorDistanceMatrixUpgma(List<VectorProteinInterfaceWhole> vectorProteinInterfaceWholeList, decimal[,] vectorDistanceMatrix, int minimumOutputTreeLeafs, out List<string> vectorNames, out List<List<UpgmaNode>> nodeList, out List<List<string>> treeList, ProgressActionSet progressActionSet)
* {
* if (vectorProteinInterfaceWholeList == null) throw new ArgumentNullException(nameof(vectorProteinInterfaceWholeList));
* if (vectorDistanceMatrix == null) throw new ArgumentNullException(nameof(vectorDistanceMatrix));
*
* vectorNames = vectorProteinInterfaceWholeList.Select(VectorProteinInterfaceWholeTreeHeader).ToList();
*
* List<string> finalTreeLeafOrderList;
* UpgmaClustering.Upgma(vectorDistanceMatrix, vectorNames, minimumOutputTreeLeafs, out nodeList, out treeList, out finalTreeLeafOrderList, false, progressActionSet);
* }
*/
public static void BestDistanceMatrixWithPartsAlignment(CancellationToken cancellationToken, List <VectorProteinInterfaceWhole> vectorProteinInterfaceWholeList, VectorDistanceMeasurementValues vectorDistanceMeasurementValues, out double[,] optimisticDistanceMatrix, /* out double[,] pessimisticDistanceMatrix,*/ ProgressActionSet progressActionSet)
{
if (vectorProteinInterfaceWholeList == null)
{
throw new ArgumentNullException(nameof(vectorProteinInterfaceWholeList));
}
if (vectorDistanceMeasurementValues == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMeasurementValues));
}
var totalVectors = vectorProteinInterfaceWholeList.Count;
var optimisticDistanceMatrix2 = new double[totalVectors, totalVectors];
//var pessimisticDistanceMatrix2 = new double[totalVectors, totalVectors];
var workDivision = new WorkDivision(vectorProteinInterfaceWholeList.Count, -1);
ProgressActionSet.StartAction(vectorProteinInterfaceWholeList.Count, progressActionSet);
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
var task = Task.Run(() =>
{
for (int indexX = workDivision.ThreadFirstIndex[localThreadIndex]; indexX <= workDivision.ThreadLastIndex[localThreadIndex]; indexX++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
var vectorProteinInterfaceWholeX = vectorProteinInterfaceWholeList[indexX];
for (int indexY = 0; indexY < vectorProteinInterfaceWholeList.Count; indexY++)
{
if (indexX >= indexY)
{
continue;
}
var vectorProteinInterfaceWholeY = vectorProteinInterfaceWholeList[indexY];
if (vectorProteinInterfaceWholeX.FullProteinInterfaceId == vectorProteinInterfaceWholeY.FullProteinInterfaceId)
{
continue;
}
double optimisticDistance;
//double pessimisticDistance;
BestDistanceWithPartsAlignment(vectorProteinInterfaceWholeX, vectorProteinInterfaceWholeY, vectorDistanceMeasurementValues, out optimisticDistance /*, out pessimisticDistance*/);
var lengthDifference = Math.Abs(vectorProteinInterfaceWholeX.ProteinInterfaceLength - vectorProteinInterfaceWholeY.ProteinInterfaceLength);
var lengthDistance = lengthDifference * vectorDistanceMeasurementValues.DifferentLengthProteinInterface;
optimisticDistance += lengthDistance;
//pessimisticDistance += lengthDistance;
optimisticDistanceMatrix2[indexX, indexY] = optimisticDistance;
//pessimisticDistanceMatrix2[indexX, indexY] = pessimisticDistance;
optimisticDistanceMatrix2[indexY, indexX] = optimisticDistance;
//pessimisticDistanceMatrix2[indexY, indexX] = pessimisticDistance;
}
workDivision.IncrementItemsCompleted(1);
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(workDivision.StartTicks, workDivision.ItemsCompleted, workDivision.ItemsToProcess, progressActionSet);
}
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
ProgressActionSet.FinishAction(true, progressActionSet);
optimisticDistanceMatrix = optimisticDistanceMatrix2;
//pessimisticDistanceMatrix = pessimisticDistanceMatrix2;
}
public static void BestDistanceWithPartsAlignment(VectorProteinInterfaceWhole vectorProteinInterfaceWhole1, VectorProteinInterfaceWhole vectorProteinInterfaceWhole2, VectorDistanceMeasurementValues vectorDistanceMeasurementValues, out double optimisticDistance /*, out double pessimisticDistance*/)
{
if (vectorProteinInterfaceWhole1 == null)
{
throw new ArgumentNullException(nameof(vectorProteinInterfaceWhole1));
}
if (vectorProteinInterfaceWhole2 == null)
{
throw new ArgumentNullException(nameof(vectorProteinInterfaceWhole2));
}
if (vectorDistanceMeasurementValues == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMeasurementValues));
}
var proteinInterfaceLength1 = vectorProteinInterfaceWhole1.ProteinInterfaceLength;
var proteinInterfaceLength2 = vectorProteinInterfaceWhole2.ProteinInterfaceLength;
var proteinInterfaceLengthDifference = Math.Abs(proteinInterfaceLength1 - proteinInterfaceLength2);
var longerProteinInterfaceLength = proteinInterfaceLength1 > proteinInterfaceLength2 ? proteinInterfaceLength1 : proteinInterfaceLength2;
var shorterProteinInterfaceLength = proteinInterfaceLength1 < proteinInterfaceLength2 ? proteinInterfaceLength1 : proteinInterfaceLength2;
var longerProteinInterface = proteinInterfaceLength1 > proteinInterfaceLength2 ? vectorProteinInterfaceWhole1 : vectorProteinInterfaceWhole2;
var shorterProteinInterface = longerProteinInterface == vectorProteinInterfaceWhole1 ? vectorProteinInterfaceWhole2 : vectorProteinInterfaceWhole1;
/*
* A: Longer ProteinInterface
* B: Shorter ProteinInterface
*
* A: Length 5
* 0 1 2 3 4
* A: 0000 0000 0000 0000 0000
*
* B: Length 3
* 0 1 2 3 4 [proteinInterfacePartIndex]
* B: 0: 0000 0000 0000 ____ ____ [shorterPartOffset = 0;] 3: proteinInterfacePartIndex>shorterProteinInterfaceLength+shorterPartOffset
* B: 1: ____ 0000 0000 0000 ____ [shorterPartOffset = 1;] 1: proteinInterfacePartIndex<shorterPartOffset
* B: 2: ____ ____ 0000 0000 0000 [shorterPartOffset = 2;]
* []
*
* LEN(A) - LEN(B) = 2
*
* 1. Loop through every proteinInterface part
* 2. If (part offset > proteinInterface part index OR part offset)
*
*/
/* F 111000
* F 101010
*
* F 111000
* R 010101
*
* R 000111
* R 010101
*
* R 000111
* F 101010
*
*/
optimisticDistance = double.MaxValue;
//pessimisticDistance = double.MinValue;
const int directionCount = 1;
for (var direction = 0; direction < directionCount; direction++)
{
for (var shorterPartOffset = 0; shorterPartOffset <= proteinInterfaceLengthDifference; shorterPartOffset++)
{
double optimisticOffsetDistanceResult = 0;
//double pessimisticOffsetDistanceResult = 0;
for (var proteinInterfacePartIndex = 0; proteinInterfacePartIndex < longerProteinInterfaceLength; proteinInterfacePartIndex++)
{
double optimisticPartDistanceResult = 0;
//double pessimisticPartDistanceResult = 0;
if (proteinInterfacePartIndex < shorterPartOffset || proteinInterfacePartIndex >= shorterProteinInterfaceLength + shorterPartOffset)
{
var longerProteinInterfaceBools = longerProteinInterface.VectorProteinInterfacePartList[proteinInterfacePartIndex].InteractionFlagBools;
var distanceForProteinInterface = VectorDistanceValue(vectorDistanceMeasurementValues, longerProteinInterfaceBools, new bool[longerProteinInterfaceBools.Length]);
optimisticPartDistanceResult = distanceForProteinInterface;
//pessimisticPartDistanceResult = distanceForProteinInterface;
var distanceForNonProteinInterface = VectorDistanceValue(vectorDistanceMeasurementValues, longerProteinInterface.VectorProteinInterfacePartList[proteinInterfacePartIndex].InteractionToNonProteinInterface, false);
optimisticPartDistanceResult += distanceForNonProteinInterface;
//pessimisticPartDistanceResult += distanceForNonProteinInterface;
}
else
{
var longerProteinInterfaceBools = longerProteinInterface.VectorProteinInterfacePartList[proteinInterfacePartIndex].InteractionFlagBools;
var shorterProteinInterfaceBools = shorterProteinInterface.VectorProteinInterfacePartList[proteinInterfacePartIndex - shorterPartOffset].InteractionFlagBools;
var longerProteinInterfaceBoolsCopy = new bool[longerProteinInterfaceBools.Length];
Array.Copy(longerProteinInterfaceBools, longerProteinInterfaceBoolsCopy, longerProteinInterfaceBools.Length);
var shorterProteinInterfaceBoolsCopy = new bool[shorterProteinInterfaceBools.Length];
Array.Copy(shorterProteinInterfaceBools, shorterProteinInterfaceBoolsCopy, shorterProteinInterfaceBools.Length);
if (direction == 1)
{
Array.Reverse(longerProteinInterfaceBoolsCopy);
}
double optimisticPartDistance;
//double pessimisticPartDistance;
CustomDistance(longerProteinInterfaceBoolsCopy, shorterProteinInterfaceBoolsCopy, vectorDistanceMeasurementValues, out optimisticPartDistance /*, out pessimisticPartDistance*/);
optimisticPartDistanceResult = optimisticPartDistance;
//pessimisticPartDistanceResult = pessimisticPartDistance;
var isInteractionToNonProteinInterface1 = longerProteinInterface.VectorProteinInterfacePartList[proteinInterfacePartIndex].InteractionToNonProteinInterface;
var isInteractionToNonProteinInterface2 = shorterProteinInterface.VectorProteinInterfacePartList[proteinInterfacePartIndex - shorterPartOffset].InteractionToNonProteinInterface;
var distanceForNonProteinInterface = VectorDistanceValue(vectorDistanceMeasurementValues, isInteractionToNonProteinInterface1, isInteractionToNonProteinInterface2);
optimisticPartDistanceResult += distanceForNonProteinInterface;
//pessimisticPartDistanceResult += distanceForNonProteinInterface;
}
optimisticOffsetDistanceResult += optimisticPartDistanceResult;
//pessimisticOffsetDistanceResult += pessimisticPartDistanceResult;
}
if (optimisticOffsetDistanceResult < optimisticDistance)
{
optimisticDistance = optimisticOffsetDistanceResult;
}
//if (pessimisticOffsetDistanceResult > pessimisticDistance)
//{
// pessimisticDistance = pessimisticOffsetDistanceResult;
//}
}
}
}
