public static double GetDistance(DistanceMeasure distanceMeasure, double x1, double y1, double x2, double y2)
{
switch (distanceMeasure)
{
case DistanceMeasure.Att:
return(AttDistance(x1, y1, x2, y2));
case DistanceMeasure.Direct:
throw new ArgumentException("Direct distance measure requires distance matrix for distance calculation.");
case DistanceMeasure.Euclidean:
return(EuclideanDistance(x1, y1, x2, y2));
case DistanceMeasure.Geo:
return(GeoDistance(x1, y1, x2, y2));
case DistanceMeasure.Manhattan:
return(ManhattanDistance(x1, y1, x2, y2));
case DistanceMeasure.Maximum:
return(MaximumDistance(x1, y1, x2, y2));
case DistanceMeasure.RoundedEuclidean:
return(Math.Round(EuclideanDistance(x1, y1, x2, y2)));
case DistanceMeasure.UpperEuclidean:
return(Math.Ceiling(EuclideanDistance(x1, y1, x2, y2)));
default:
throw new InvalidOperationException("Distance measure is not known.");
}
}
private void RunHierarchicalCluster(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
DistanceMeasure distance = null;
//distance.CalcDistMatrix(distance.structNames);
// opt.hierarchical.atoms = PDB.PDBMODE.ALL_ATOMS;
if (dcd != null)
{
distance = CreateMeasureForDCD(dcd, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryAglom,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileAglom);
}
else
{
distance = CreateMeasure(name, dirName, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryAglom,
alignFile, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileAglom);
}
DebugClass.WriteMessage("Measure Created");
hierarchicalCluster hk = new hierarchicalCluster(distance, opt.hierarchical, dirName);
if (beginJob != null)
{
beginJob(currentProcessName, hk.ToString(), dirName, distance.ToString());
}
clType = hk.ToString();
ClusterOutput output;
progressDic.Add(name, hk);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
output = hk.HierarchicalClustering(new List <string>(distance.structNames.Keys));
UpdateOutput(name, dirName, alignFile, output, distance.ToString(), cpuPart1, cpuPart2, hk);
}
private void RunFastHCluster(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput clustOut = null;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryFast,
alignFile, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileFast);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryFast,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileFast);
}
FastDendrog km;
km = new FastDendrog(distance, opt.hierarchical, dirName);
if (beginJob != null)
{
beginJob(currentProcessName, km.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, km);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
clType = km.ToString();
clustOut = km.Run(new List <string>(distance.structNames.Keys));
UpdateOutput(name, dirName, alignFile, clustOut, distance.ToString(), cpuPart1, cpuPart2, km);
}
public Jury3D(DistanceMeasure dMeasure)
{
this.dMeasure = dMeasure;
maxV = 1;
currentV = 0;
}
/* private Dictionary<string,double> SableDist(List<string> refStructures)
* {
* StreamReader sableFile = new StreamReader(textBox3.Text);
* string line = sableFile.ReadLine();
* string prefix=refStructures[0];
* protInfo pr_SS=new protInfo();
* protInfo pr_SA = new protInfo();
* string seq, ss, sa;
* if(prefix.Contains("\\"))
* {
* string []aux=prefix.Split('\\');
* prefix=aux[aux.Length-2];
* }
* while (line !=null)
* {
* if(line.StartsWith("Query:"))
* {
* string[] aux = line.Split(' ');
* aux = aux[1].Split('.');
* if (prefix.Contains(aux[0]))
* {
* pr_SS.sequence = sableFile.ReadLine();
* string ww=sableFile.ReadLine();
* pr_SS.profile = new List<byte>();
* for (int i = 0; i < ww.Length;i++ )
* pr_SS.profile.Add(ww[i].ToString());
* line = sableFile.ReadLine();
* pr_SA.sequence = pr_SS.sequence;
* pr_SA.profile = new List<string>(Regex.Replace(sableFile.ReadLine(),@"\s+"," ").Trim().Split(' '));
* for (int i = 0; i < pr_SA.profile.Count; i++)
* pr_SA.profile[i] = (Convert.ToInt16(pr_SA.profile[i]) / 10).ToString();
*
* }
* }
* line = sableFile.ReadLine();
* }
*
* sableFile.Close();
* Settings set=new Settings();
* set.Load();
* Alignment al=new Alignment(refStructures,set,"H:\\profiels\\SS3_SA9_internal.profiles");
* al.MyAlign(null);
* al.AddStructureToAlignment("sable_res","SS", ref pr_SS);
* al.AddStructureToAlignment("sable_res", "SA", ref pr_SA);
*
* Dictionary<string, Dictionary<string, protInfo>> allProf = new Dictionary<string, Dictionary<string, protInfo>>();
* allProf.Add("SS", new Dictionary<string, protInfo>());
* allProf["SS"].Add("sable_res", pr_SS);
* allProf.Add("SA", new Dictionary<string, protInfo>());
* allProf["SA"].Add("sable_res", pr_SA);
* Dictionary<string,List<string>> protCombineStates = al.CombineProfiles("sable_res", allProf);
*
*
* JuryDistance dist = new JuryDistance(al, false);
*
* Dictionary<string, double> distRes = new Dictionary<string, double>();
*
* foreach (var item in refStructures)
* {
* distRes.Add(Path.GetFileName(item), dist.GetDistance("sable_res",Path.GetFileName(item)));
* currentV++;
* }
*
*
* return distRes;
*
* }*/
private DistanceMeasure PrepareDistanceMeasure(List <string> cluster, DistanceMeasures measure, string dirName)
{
DistanceMeasure distRes = null;
List <string> clustFiles = new List <string>();
foreach (var item in cluster)
{
clustFiles.Add(dirName + Path.DirectorySeparatorChar + item);
}
switch (measure)
{
case DistanceMeasures.HAMMING:
distRes = new JuryDistance(clustFiles, alignFile, true, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
{
distRes = new MaxSub(clustFiles, alignFile, distanceControl1.reference);
}
break;
case DistanceMeasures.RMSD:
distRes = new Rmsd(clustFiles, alignFile, distanceControl1.reference, distanceControl1.CAtoms, distanceControl1.referenceProfile);
break;
}
distRes.InitMeasure();
return(distRes);
}
private static double GetDistance(int i, int j, DistanceMeasure distanceMeasure, double[,] coordinates, double[,] distances)
{
switch (distanceMeasure)
{
case DistanceMeasure.Att:
return(AttDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
case DistanceMeasure.Direct:
return(distances[i, j]);
case DistanceMeasure.Euclidean:
return(EuclideanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
case DistanceMeasure.Geo:
return(GeoDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
case DistanceMeasure.Manhattan:
return(ManhattanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
case DistanceMeasure.Maximum:
return(MaximumDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
case DistanceMeasure.RoundedEuclidean:
return(Math.Round(EuclideanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1])));
case DistanceMeasure.UpperEuclidean:
return(Math.Ceiling(EuclideanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1])));
default:
throw new InvalidOperationException("Distance measure is not known.");
}
}
public void SetGeoCode(ICoordinates coordinates, int radius, DistanceMeasure measure)
{
GeoCode = _geoCodeUnityFactory.Create();
GeoCode.Coordinates = coordinates;
GeoCode.Radius = radius;
GeoCode.DistanceMeasure = measure;
}
public void setFont(Font font)
{
style.font = font;
DistanceMeasure fontSize = null;
if (font == CrhcConstants.FONT_NORMAL)
{
fontSize = CrhcConstants.FONT_HEIGHT_NORMAL;
}
else if (font == CrhcConstants.FONT_TITLE)
{
fontSize = CrhcConstants.FONT_HEIGHT_TITLE;
}
else if (font == CrhcConstants.FONT_SUBTITLE)
{
fontSize = CrhcConstants.FONT_HEIGHT_SUBTITLE;
}
else if (font == CrhcConstants.FONT_SOURCE)
{
fontSize = CrhcConstants.FONT_HEIGHT_SOURCE;
}
if (fontSize != null)
{
style.fontSize = (int)fontSize.getAs(NumberType.PIXELS);
}
//invalidateHeight();
}
public IList <TPredictionResult> Predict(IDataFrame queryDataFrame, IPredictionModel model, int dependentFeatureIndex)
{
ValidateModel(model);
var knnModel = model as IKnnPredictionModel <TPredictionResult>;
var results = new ConcurrentBag <RowIndexDistanceDto <TPredictionResult> >();
var normalizedData = NormalizeData(queryDataFrame, knnModel, dependentFeatureIndex);
var normalizedTrainingData = normalizedData.Item1;
var queryMatrix = normalizedData.Item2;
Parallel.For(0, queryDataFrame.RowCount, queryRowIdx =>
{
var rowVector = queryMatrix.Row(queryRowIdx);
var distances = new ConcurrentBag <RowIndexDistanceDto <TPredictionResult> >();
for (int trainingRowIdx = 0; trainingRowIdx < normalizedTrainingData.RowCount; trainingRowIdx++)
{
var trainingRow = normalizedTrainingData.Row(trainingRowIdx);
TPredictionResult dependentFeatureValue = knnModel.ExpectedTrainingOutcomes[trainingRowIdx];
double distance = DistanceMeasure.Distance(rowVector, trainingRow);
var distanceDto = new RowIndexDistanceDto <TPredictionResult>(trainingRowIdx, distance, dependentFeatureValue);
distances.Add(distanceDto);
}
var sortedDistances = distances.OrderBy(distDto => distDto.Distance).Take(knnModel.KNeighbors);
var result = new RowIndexDistanceDto <TPredictionResult>(queryRowIdx, 0, _resultHandler(sortedDistances, WeightingFunction));
results.Add(result);
});
return(results.OrderBy(res => res.RowIndex).Select(res => res.DependentFeatureValue).ToList());
}
private DistanceMeasure CreateMeasureForDCD(DCDFile dcd, DistanceMeasures measure, PDB.PDBMODE atoms, bool jury1d, string alignFileName,
string profileName = null, string refJuryProfile = null)
{
DistanceMeasure dist = null;
switch (measure)
{
case DistanceMeasures.HAMMING:
if (refJuryProfile == null || !jury1d)
{
throw new Exception("Sorry but for jury measure you have to define 1djury profile to find reference structure");
}
else
{
dist = new JuryDistance(dcd, alignFileName, true, profileName, refJuryProfile);
}
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(dcd, alignFileName, jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(dcd, alignFileName, jury1d, refJuryProfile);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(dcd, alignFileName, jury1d, refJuryProfile);
break;
}
dist.InitMeasure();
return(dist);
}
int GetDist(DistanceMeasures distance,string dirName,string item1,string item2)
{
DistanceMeasure dist = null;
List<string> targets = new List<string>();
if(!item1.Contains(dirName))
targets.Add(dirName + Path.DirectorySeparatorChar + item1);
else
targets.Add(item1);
targets.Add(dirName + Path.DirectorySeparatorChar + item2);
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, "", false, "");
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, "", false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, "", false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, "", false);
break;
}
dist.InitMeasure();
return GetDist(dist, item1, item2);
}
private void RunBakerCluster(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput output = null;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.threshold.hDistance, opt.threshold.hAtoms, opt.threshold.reference1Djury,
alignFile, opt.threshold.hammingProfile, null);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.threshold.hDistance, opt.threshold.hAtoms, opt.threshold.reference1Djury,
opt.threshold.alignmentFileName, opt.threshold.hammingProfile, null);
}
ThresholdCluster bk = new ThresholdCluster(distance, opt.threshold.distThresh, opt.threshold.bakerNumberofStruct);
if (beginJob != null)
{
beginJob(currentProcessName, bk.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, bk);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
clType = bk.ToString();
output = bk.OrgClustering();
UpdateOutput(name, dirName, alignFile, output, distance.ToString(), cpuPart1, cpuPart2, bk);
}
public hierarchicalCluster(DistanceMeasure dMeasure, HierarchicalCInput hier, string dirName)
{
this.dMeasure = dMeasure;
this.linkageType = hier.linkageType;
this.dirName = dirName;
progressRead = 0;
hierOpt = hier;
}
int GetDist(DistanceMeasure distance, string item1, string item2)
{
string[] aux1 = item1.Split(Path.DirectorySeparatorChar);
string[] aux2 = item2.Split(Path.DirectorySeparatorChar);
int v = distance.GetDistance(aux1[aux1.Length - 1], aux2[aux2.Length - 1]);
if (v == distance.errorValue)
v = errorValue;
return v;
}
public ThresholdCluster(DistanceMeasure dMeasure, float threshold, int minCluster)
{
this.dMeasure = dMeasure;
this.threshold = threshold * 100;
this.minCluster = minCluster;
//dist = cBase.CalcRmsd(cBase.structNames);
}
public FastDendrog(DistanceMeasure dMeasure, HierarchicalCInput input, string dirName)
{
this.dMeasure = dMeasure;
this.initNodesNum = input.numInitNodes;
this.linkage = input.linkageType;
this.useKMeans = input.ItMeans;
this.hConcensus = input.HConsensus;
this.kMeansIter = input.ItNum;
this.dirName = dirName;
this.input = input;
}
/// <summary>
/// Initialize class that performs multivariate DTW calculation for given series and settings.
/// </summary>
/// <param name="seriesVariables">Array of series value pairs for different variables with additional options for data preprocessing and weights.</param>
/// <param name="distanceMeasure">Distance measure used (how distance for value pair (p,q) of signal elements is calculated from multiple variables).</param>
/// <param name="boundaryConstraintStart">Apply boundary constraint at (1, 1).</param>
/// <param name="boundaryConstraintEnd">Apply boundary constraint at (m, n).</param>
/// <param name="slopeStepSizeDiagonal">Diagonal steps in local window for calculation. Results in Ikatura paralelogram shaped dtw-candidate space. Use in combination with slopeStepSizeAside parameter. Leave null for no constraint.</param>
/// <param name="slopeStepSizeAside">Side steps in local window for calculation. Results in Ikatura paralelogram shaped dtw-candidate space. Use in combination with slopeStepSizeDiagonal parameter. Leave null for no constraint.</param>
/// <param name="sakoeChibaMaxShift">Sakoe-Chiba max shift constraint (side steps). Leave null for no constraint.</param>
public Dtw(SeriesVariable[] seriesVariables, DistanceMeasure distanceMeasure = DistanceMeasure.Euclidean, bool boundaryConstraintStart = true, bool boundaryConstraintEnd = true, int? slopeStepSizeDiagonal = null, int? slopeStepSizeAside = null, int? sakoeChibaMaxShift = null)
{
_seriesVariables = seriesVariables;
_distanceMeasure = distanceMeasure;
_boundaryConstraintStart = boundaryConstraintStart;
_boundaryConstraintEnd = boundaryConstraintEnd;
if (seriesVariables == null || seriesVariables.Length == 0)
throw new ArgumentException("Series should have values for at least one variable.");
for (int i = 1; i < _seriesVariables.Length; i++)
{
if (_seriesVariables[i].OriginalXSeries.Length != _seriesVariables[0].OriginalXSeries.Length)
throw new ArgumentException("All variables withing series should have the same number of values.");
if (_seriesVariables[i].OriginalYSeries.Length != _seriesVariables[0].OriginalYSeries.Length)
throw new ArgumentException("All variables withing series should have the same number of values.");
}
_xLen = _seriesVariables[0].OriginalXSeries.Length;
_yLen = _seriesVariables[0].OriginalYSeries.Length;
if(_xLen == 0 || _yLen == 0)
throw new ArgumentException("Both series should have at least one value.");
if (sakoeChibaMaxShift != null && sakoeChibaMaxShift < 0)
throw new ArgumentException("Sakoe-Chiba max shift value should be positive or null.");
_isXLongerOrEqualThanY = _xLen >= _yLen;
_signalsLengthDifference = Math.Abs(_xLen - _yLen);
_sakoeChibaConstraint = sakoeChibaMaxShift.HasValue;
_sakoeChibaMaxShift = sakoeChibaMaxShift.HasValue ? sakoeChibaMaxShift.Value : int.MaxValue;
if (slopeStepSizeAside != null || slopeStepSizeDiagonal != null)
{
if (slopeStepSizeAside == null || slopeStepSizeDiagonal == null)
throw new ArgumentException("Both values or none for slope constraint must be specified.");
if (slopeStepSizeDiagonal < 1)
throw new ArgumentException("Diagonal slope constraint parameter must be greater than 0.");
if (slopeStepSizeAside < 0)
throw new ArgumentException("Diagonal slope constraint parameter must be greater or equal to 0.");
_useSlopeConstraint = true;
_slopeStepSizeAside = slopeStepSizeAside.Value;
_slopeStepSizeDiagonal = slopeStepSizeDiagonal.Value;
_slopeMatrixLookbehind = slopeStepSizeDiagonal.Value + slopeStepSizeAside.Value;
}
//todo: throw error when solution (path from (1, 1) to (m, n) is not even possible due to slope constraints)
}
public FastDendrog(DistanceMeasure dMeasure,HierarchicalCInput input,string dirName)
{
this.dMeasure = dMeasure;
this.initNodesNum = input.numInitNodes;
this.linkage = input.linkageType;
this.useKMeans = input.ItMeans;
this.hConcensus = input.HConsensus;
this.kMeansIter = input.ItNum;
this.dirName = dirName;
this.input = input;
}
/// <summary>
/// If only the coordinates are given, can calculate the distance matrix.
/// </summary>
/// <returns>A full distance matrix between all cities.</returns>
public static double[,] GetDistanceMatrix(DistanceMeasure distanceMeasure, double[,] coordinates, double[,] distances, int dimension) {
if (distances != null) return distances;
distances = new double[dimension, dimension];
for (int i = 0; i < dimension - 1; i++)
for (int j = i + 1; j < dimension; j++) {
distances[i, j] = GetDistance(i, j, distanceMeasure, coordinates, distances);
distances[j, i] = distances[i, j];
}
return distances;
}
public override double GetDistance(AudioFeature f, AudioFeature.DistanceType t)
{
if (!(f is Scms))
{
new Exception("Can only handle AudioFeatures of type Scms, not of: " + f);
return(-1);
}
Scms other = (Scms)f;
DistanceMeasure distanceMeasure = DistanceMeasure.Euclidean;
switch (t)
{
case AudioFeature.DistanceType.Dtw_Euclidean:
distanceMeasure = DistanceMeasure.Euclidean;
break;
case AudioFeature.DistanceType.Dtw_SquaredEuclidean:
distanceMeasure = DistanceMeasure.SquaredEuclidean;
break;
case AudioFeature.DistanceType.Dtw_Manhattan:
distanceMeasure = DistanceMeasure.Manhattan;
break;
case AudioFeature.DistanceType.Dtw_Maximum:
distanceMeasure = DistanceMeasure.Maximum;
break;
case AudioFeature.DistanceType.UCR_Dtw:
return(UCRCSharp.UCR.DTW(this.GetArray(), other.GetArray()));
case AudioFeature.DistanceType.CosineSimilarity:
return(CosineSimilarity(this, other));
case AudioFeature.DistanceType.BitStringHamming:
return(Imghash.ImagePHash.HammingDistance(this.BitString, other.BitString));
case AudioFeature.DistanceType.KullbackLeiblerDivergence:
default:
return(Distance(this, other, new ScmsConfiguration(Analyzer.MFCC_COEFFICIENTS)));
}
Dtw dtw = new Dtw(this.GetArray(), other.GetArray(), distanceMeasure, true, true, null, null, null);
return(dtw.GetCost());
}
// Note: The latitude/longitude order here is reversed compared to the various
// signatures in Tweetinvi (see the GeoCode constructor below for example),
// for ease of copy-and-pasting coordinates from the web
static ISearchResult SearchTweetsTaggedWithGeo(string query,
double latitude,
double longitude,
double radius = 15,
DistanceMeasure distanceMeasure = DistanceMeasure.Miles)
{
var searchParameters = new TweetSearchParameters(query)
{
GeoCode = new GeoCode(longitude, latitude, radius, distanceMeasure),
Lang = Language.English,
SearchType = SearchResultType.Recent,
MaximumNumberOfResults = 15,
Locale = "new york"
};
return Search.SearchTweetsWithMetadata(searchParameters);
}
private double Distance(double lat1, double lon1, double lat2, double lon2, DistanceMeasure unit)
{
double dist = Math.Sin(Deg2rad(lat1)) * Math.Sin(Deg2rad(lat2)) + Math.Cos(Deg2rad(lat1)) * Math.Cos(Deg2rad(lat2)) * Math.Cos(Deg2rad(lon1 - lon2));
dist = Math.Acos(dist);
dist = Rad2deg(dist);
dist = dist * 60 * 1.1515;
if (unit == DistanceMeasure.Kilometers)
{
dist = dist * 1.609344;
}
else if (unit == DistanceMeasure.Nautical)
{
dist = dist * 0.8684;
}
return(dist);
}
// Note: The latitude/longitude order here is reversed compared to the various
// signatures in Tweetinvi (see the GeoCode constructor below for example),
// for ease of copy-and-pasting coordinates from the web
static ISearchResult SearchTweetsTaggedWithGeo(string query,
double latitude,
double longitude,
double radius = 15,
DistanceMeasure distanceMeasure = DistanceMeasure.Miles)
{
var searchParameters = new TweetSearchParameters(query)
{
GeoCode = new GeoCode(longitude, latitude, radius, distanceMeasure),
Lang = Language.English,
SearchType = SearchResultType.Recent,
MaximumNumberOfResults = 15,
Locale = "new york"
};
return(Search.SearchTweetsWithMetadata(searchParameters));
}
private void RunKMeans(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput clustOut;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.kmeans.kDistance, opt.kmeans.kAtoms, opt.kmeans.reference1Djury,
alignFile, opt.kmeans.hammingProfile, opt.kmeans.jury1DProfile);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.kmeans.kDistance, opt.kmeans.kAtoms, opt.kmeans.reference1Djury,
opt.kmeans.alignmentFileName, opt.kmeans.hammingProfile, opt.kmeans.jury1DProfile);
}
kMeans km;
km = new kMeans(distance, opt.kmeans.kMeans_init);
if (beginJob != null)
{
beginJob(currentProcessName, km.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, km);
distance.InitMeasure();
DateTime cpuPart2 = DateTime.Now;
clType = km.ToString();
if ((int)opt.kmeans.maxK <= 1)
{
throw new Exception("k in k-Means must be bigger then 1, right now is: " + (int)opt.kmeans.maxK);
}
if (distance.structNames.Count < 10)
{
throw new Exception("Number of structures to cluster must be bigger then 10 right now is: " + distance.structNames.Count);
}
clustOut = km.kMeansLevel((int)opt.kmeans.maxK, opt.kmeans.maxIter, new List <string>(distance.structNames.Keys));
UpdateOutput(name, dirName, alignFile, clustOut, distance.ToString(), cpuPart1, cpuPart2, km);
GC.SuppressFinalize(distance);
}
/// <summary>
/// If only the coordinates are given, can calculate the distance matrix.
/// </summary>
/// <returns>A full distance matrix between all cities.</returns>
public static double[,] GetDistanceMatrix(DistanceMeasure distanceMeasure, double[,] coordinates, double[,] distances, int dimension)
{
if (distances != null)
{
return(distances);
}
distances = new double[dimension, dimension];
for (int i = 0; i < dimension - 1; i++)
{
for (int j = i + 1; j < dimension; j++)
{
distances[i, j] = GetDistance(i, j, distanceMeasure, coordinates, distances);
distances[j, i] = distances[i, j];
}
}
return(distances);
}
public static Geopath CreateGeopath(BasicGeoposition center, double radius, DistanceMeasure units)
{
var earthRadius = (units == DistanceMeasure.Miles ? Geohelper.EarthRadiusInMiles : Geohelper.EarthRadiusInKilometers);
var lat = ToRadian(center.Latitude); //radians
var lng = ToRadian(center.Longitude); //radians
var d = radius / earthRadius; // d = angular distance covered on earth's surface
var locations = new List <BasicGeoposition>();
for (var x = 0; x <= 360; x++)
{
var brng = ToRadian(x);
var latRadians = Math.Asin(Math.Sin(lat) * Math.Cos(d) + Math.Cos(lat) * Math.Sin(d) * Math.Cos(brng));
var lngRadians = lng + Math.Atan2(Math.Sin(brng) * Math.Sin(d) * Math.Cos(lat), Math.Cos(d) - Math.Sin(lat) * Math.Sin(latRadians));
locations.Add(new BasicGeoposition {
Latitude = ToDegrees(latRadians), Longitude = ToDegrees(lngRadians)
});
}
return(new Geopath(locations));
}
private void RunHKMeans(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
ClusterOutput clustOut = null;
DistanceMeasure distance = null;
if (dcd == null)
{
distance = CreateMeasure(name, dirName, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryKmeans,
alignFile, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileKmeans);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.hierarchical.distance, opt.hierarchical.atoms, opt.hierarchical.reference1DjuryKmeans,
opt.hierarchical.alignmentFileName, opt.hierarchical.hammingProfile, opt.hierarchical.jury1DProfileKmeans);
}
kMeans km;
km = new kMeans(distance, true);
if (beginJob != null)
{
beginJob(currentProcessName, km.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, km);
DateTime cpuPart2 = DateTime.Now;
distance.InitMeasure();
clType = km.ToString();
km.BMIndex = opt.hierarchical.indexDB;
km.threshold = opt.hierarchical.numberOfStruct;
km.maxRepeat = opt.hierarchical.repeatTime;
km.maxK = opt.hierarchical.maxK;
clustOut = km.HierarchicalKMeans();
UpdateOutput(name, dirName, alignFile, clustOut, distance.ToString(), cpuPart1, cpuPart2, km);
}
private static double GetDistance(int i, int j, DistanceMeasure distanceMeasure, double[,] coordinates, double[,] distances) {
switch (distanceMeasure) {
case DistanceMeasure.Att:
return AttDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]);
case DistanceMeasure.Direct:
return distances[i, j];
case DistanceMeasure.Euclidean:
return EuclideanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]);
case DistanceMeasure.Geo:
return GeoDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]);
case DistanceMeasure.Manhattan:
return ManhattanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]);
case DistanceMeasure.Maximum:
return MaximumDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]);
case DistanceMeasure.RoundedEuclidean:
return Math.Round(EuclideanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
case DistanceMeasure.UpperEuclidean:
return Math.Ceiling(EuclideanDistance(coordinates[i, 0], coordinates[i, 1], coordinates[j, 0], coordinates[j, 1]));
default:
throw new InvalidOperationException("Distance measure is not known.");
}
}
public static double GetDistance(DistanceMeasure distanceMeasure, double x1, double y1, double x2, double y2) {
switch (distanceMeasure) {
case DistanceMeasure.Att:
return AttDistance(x1, y1, x2, y2);
case DistanceMeasure.Direct:
throw new ArgumentException("Direct distance measure requires distance matrix for distance calculation.");
case DistanceMeasure.Euclidean:
return EuclideanDistance(x1, y1, x2, y2);
case DistanceMeasure.Geo:
return GeoDistance(x1, y1, x2, y2);
case DistanceMeasure.Manhattan:
return ManhattanDistance(x1, y1, x2, y2);
case DistanceMeasure.Maximum:
return MaximumDistance(x1, y1, x2, y2);
case DistanceMeasure.RoundedEuclidean:
return Math.Round(EuclideanDistance(x1, y1, x2, y2));
case DistanceMeasure.UpperEuclidean:
return Math.Ceiling(EuclideanDistance(x1, y1, x2, y2));
default:
throw new InvalidOperationException("Distance measure is not known.");
}
}
DistanceMeasure PrepareDistance(DistanceMeasures distance,List <string> targets,string alignFile,string profileName)
{
DistanceMeasure dist=null;
switch (distance)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(targets, alignFile, false, profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(targets, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(targets, alignFile, false, PDB.PDBMODE.ONLY_CA);
break;
case DistanceMeasures.GDT_TS:
dist = new GDT_TS(targets, alignFile, false);
break;
}
dist.InitMeasure();
return dist;
}
private double CalcDevCluster(DistanceMeasure dd, List <string> cluster, string refStruct)
{
double sum = 0;
double v1 = 0, v2 = 0;
if (dd == null)
{
dd = PrepareDistanceMeasure(cluster, distanceControl1.distDef, dirName);
}
foreach (var item in cluster)
{
int x = dd.GetDistance(refStruct, item) / 100;
v1 += x;
v2 += x * x;
}
v1 = v1 / cluster.Count;
v1 *= v1;
v2 = v2 / cluster.Count;
sum = Math.Sqrt(v2 - v1);
return(sum);
}
/// <summary>Get Distance</summary>
/// <seealso cref="">comirva.audio.feature.AudioFeature#GetDistance(comirva.audio.feature.AudioFeature)</seealso>
public override double GetDistance(AudioFeature f, AudioFeature.DistanceType t)
{
if (!(f is MandelEllis))
{
new Exception("Can only handle AudioFeatures of type Mandel Ellis, not of: " + f);
return(-1);
}
MandelEllis other = (MandelEllis)f;
DistanceMeasure distanceMeasure = DistanceMeasure.Euclidean;
switch (t)
{
case AudioFeature.DistanceType.Dtw_Euclidean:
distanceMeasure = DistanceMeasure.Euclidean;
break;
case AudioFeature.DistanceType.Dtw_SquaredEuclidean:
distanceMeasure = DistanceMeasure.SquaredEuclidean;
break;
case AudioFeature.DistanceType.Dtw_Manhattan:
distanceMeasure = DistanceMeasure.Manhattan;
break;
case AudioFeature.DistanceType.Dtw_Maximum:
distanceMeasure = DistanceMeasure.Maximum;
break;
case AudioFeature.DistanceType.KullbackLeiblerDivergence:
default:
return(KullbackLeibler(this.gmmMe, other.gmmMe) + KullbackLeibler(other.gmmMe, this.gmmMe));
}
Dtw dtw = new Dtw(this.GetArray(), other.GetArray(), distanceMeasure, true, true, null, null, null);
return(dtw.GetCost());
}
private void Run3DJury(string name, string dirName, string alignFile = null, DCDFile dcd = null)
{
DateTime cpuStart = DateTime.Now;
ClusterOutput output;
DistanceMeasure distance = null;
if (alignFile != null)
{
distance = CreateMeasure(name, null, opt.other.oDistance, opt.other.oAtoms, opt.other.reference1Djury,
alignFile, opt.other.hammingProfile, opt.other.referenceProfile);
}
else
if (dirName != null)
{
distance = CreateMeasure(name, dirName, opt.other.oDistance, opt.other.oAtoms, opt.other.reference1Djury,
alignFile, opt.other.hammingProfile, opt.other.referenceProfile);
}
else
{
distance = CreateMeasureForDCD(dcd, opt.other.oDistance, opt.other.oAtoms, opt.other.reference1Djury,
opt.other.alignFileName, opt.other.hammingProfile, opt.other.referenceProfile);
}
Jury3D ju = new Jury3D(distance);
if (beginJob != null)
{
beginJob(currentProcessName, ju.ToString(), dirName, distance.ToString());
}
progressDic.Add(name, ju);
distance.InitMeasure();
clType = ju.ToString();
output = ju.Run3DJury();
UpdateOutput(name, dirName, alignFile, output, distance.ToString(), cpuStart, DateTime.Now, ju);
progressDic.Remove(name);
}
string CLusterRepresent(DistanceMeasure distance, List<string> targets)
{
return distance.GetReferenceStructure(targets);
}
public static ITweetSearchParameters GenerateSearchTweetParameter(ICoordinates coordinates, int radius, DistanceMeasure measure)
{
return(SearchQueryGenerator.GenerateSearchTweetParameter(coordinates, radius, measure));
}
public void CalcStat()
{
List<string> fileNames = new List<string>();
List<string> refStructures = new List<string>();
DistanceMeasures measure = distanceControl1.distDef;
DistanceMeasure distTemp = null;
double distRes=0;
maxV = selected.Count;
distList.Clear();
try
{
tableRes = new DataTable();
tableRes.Columns.Add("Cluster Size", typeof(int));
tableRes.Columns.Add("Reference structure", typeof(string));
tableRes.Columns.Add("Distance", typeof(double));
tableRes.Columns.Add("Hidden1", typeof(int));
tableRes.Columns.Add("Hidden2", typeof(string));
if (checkBoxSable.Checked)
{
tableRes.Columns.Add("Dist to Sable", typeof(double));
maxV *= 2;
}
if (checkBox1.Checked)
{
for (int i = 0; i < selected.Count; i++)
maxV += selected[i].Count;
}
fileNames.Add(textBox1.Text);
jury1D jury = new jury1D();
if (distanceControl1.reference)
jury.PrepareJury(dirName, alignFile, distanceControl1.referenceProfile);
refStructures.Clear();
selected.Sort(delegate(List<string> first, List<string> second)
{ return first.Count.CompareTo(second.Count); });
selected.Reverse();
// dataGridView1.Rows.Add(selected.Count);
for (int i = 0; i < selected.Count; i++)
{
string refD = selected[i][0];
ClusterOutput juryO = null;
if (distanceControl1.reference)
{
if (selected[i].Count > 5)
{
juryO = jury.JuryOptWeights(selected[i]);
if (juryO == null)
continue;
refD = juryO.juryLike[0].Key;
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + juryO.juryLike[0].Key);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
}
else
if (!fileNames.Contains(dirName + Path.DirectorySeparatorChar + selected[i][0]))
{
fileNames.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
refStructures.Add(dirName + Path.DirectorySeparatorChar + selected[i][0]);
}
}
else
{
dist = PrepareDistanceMeasure(selected[i], measure, dirName);
distTemp = dist;
refD = dist.GetReferenceStructure(selected[i]);
fileNames.Add(dirName + Path.DirectorySeparatorChar + refD);
refStructures.Add(dirName + Path.DirectorySeparatorChar + refD);
}
if (fileNames.Count == 2)
{
switch (measure)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, null, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, null, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
distRes = Convert.ToDouble(String.Format("{0:0.00}", dist.GetDistance(native, refD) / 100.0));
}
fileNames.RemoveAt(fileNames.Count - 1);
if (checkBoxSable.Checked && refStructures.Count > 0)
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName, 0.0);
else
tableRes.Rows.Add(selected[i].Count, refD, distRes, i, dirName);
currentV++;
}
if (checkBoxSable.Checked && refStructures.Count > 0)
{
Dictionary<string, double> res = null;// SableDist(refStructures);
for (int i = 0; i < refStructures.Count; i++)
{
if (res.ContainsKey(Path.GetFileName(refStructures[i])))
{
DataRow dr = tableDist.Rows[i];
dr[5] = Convert.ToDouble(String.Format("{0:0.00}", res[Path.GetFileName(refStructures[i])]));
}
}
}
if (checkBox1.Checked)
{
CalculateDistToAll();
}
}
catch(Exception ex)
{
exc = ex;
}
}
/// <summary>
/// Initialize class that performs single variable DTW calculation for given series and settings.
/// </summary>
/// <param name="x">Series A, array of values.</param>
/// <param name="y">Series B, array of values.</param>
/// /// <param name="distanceMeasure">Distance measure used (how distance for value pair (p,q) of signal elements is calculated from multiple variables).</param>
/// <param name="boundaryConstraintStart">Apply boundary constraint at (1, 1).</param>
/// <param name="boundaryConstraintEnd">Apply boundary constraint at (m, n).</param>
/// <param name="slopeStepSizeDiagonal">Diagonal steps in local window for calculation. Results in Ikatura paralelogram shaped dtw-candidate space. Use in combination with slopeStepSizeAside parameter. Leave null for no constraint.</param>
/// <param name="slopeStepSizeAside">Side steps in local window for calculation. Results in Ikatura paralelogram shaped dtw-candidate space. Use in combination with slopeStepSizeDiagonal parameter. Leave null for no constraint.</param>
/// <param name="sakoeChibaMaxShift">Sakoe-Chiba max shift constraint (side steps). Leave null for no constraint.</param>
public Dtw(double[] x, double[] y, DistanceMeasure distanceMeasure = DistanceMeasure.Euclidean, bool boundaryConstraintStart = true, bool boundaryConstraintEnd = true, int? slopeStepSizeDiagonal = null, int? slopeStepSizeAside = null, int? sakoeChibaMaxShift = null)
: this(new [] { new SeriesVariable(x, y) }, distanceMeasure, boundaryConstraintStart, boundaryConstraintEnd, slopeStepSizeDiagonal, slopeStepSizeAside, sakoeChibaMaxShift)
{
}
//private jury1D jury;
public hierarchicalCluster (DistanceMeasure dMeasure, AglomerativeType linkageType,string dirName)
{
this.dMeasure=dMeasure;
this.linkageType = linkageType;
this.dirName = dirName;
}
public GeoCode(double longitude, double latitude, double radius, DistanceMeasure distanceMeasure)
{
Coordinates = new Coordinates(longitude, latitude);
Radius = radius;
DistanceMeasure = distanceMeasure;
}
public static IGeoCode GenerateGeoCode(ICoordinates coordinates, double radius, DistanceMeasure measure)
{
return _geoFactory.GenerateGeoCode(coordinates, radius, measure);
}
public ITweetSearchParameters CreateSearchTweetParameter(double longitude, double latitude, int radius, DistanceMeasure measure)
{
return new TweetSearchParameters(longitude, latitude, radius, measure);
}
public void SetGeoCode(double longitude, double latitude, double radius, DistanceMeasure measure)
{
GeoCode = new GeoCode(longitude, latitude, radius, measure);
}
public ClusterOutput DendrogUsingMeasures(List<string> structures)
{
jury1D juryLocal = new jury1D();
juryLocal.PrepareJury(al);
ClusterOutput outC = null;
Dictionary<string, List<int>> dic;
//Console.WriteLine("Start after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
maxV = 4;
currentV = 0;
dic = PrepareKeys(structures,false);
currentV++;
//DebugClass.DebugOn();
//dic = HashEntropyCombine(dic, structures,input.reqClusters);
//Console.WriteLine("Entropy ready after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
DebugClass.WriteMessage("Entropy ready");
//Alternative way to start of UQclust Tree must be finished
//input.relClusters = 10000;
input.relClusters = input.reqClusters;
input.perData = 90;
//dic = FastCombineKeys(dic, structures, false);
dic = FastCombineKeys(dic, structures, true);
DebugClass.WriteMessage("dic size" + dic.Count);
currentV++;
//Console.WriteLine("Combine ready after jury " + Process.GetCurrentProcess().PeakWorkingSet64);
DebugClass.WriteMessage("Combine Keys ready");
Dictionary<string, string> translateToCluster = new Dictionary<string, string>(dic.Count);
List<string> structuresToDendrogram = new List<string>(dic.Count);
List<string> structuresFullPath = new List<string>(dic.Count);
DebugClass.WriteMessage("Number of clusters: "+dic.Count);
int cc = 0;
foreach (var item in dic)
{
if (item.Value.Count > 2)
{
List<string> cluster = new List<string>(item.Value.Count);
foreach (var str in item.Value)
cluster.Add(structures[str]);
ClusterOutput output = juryLocal.JuryOptWeights(cluster);
structuresToDendrogram.Add(output.juryLike[0].Key);
if(alignFile==null)
structuresFullPath.Add(dirName + Path.DirectorySeparatorChar + output.juryLike[0].Key);
else
structuresFullPath.Add(output.juryLike[0].Key);
translateToCluster.Add(output.juryLike[0].Key, item.Key);
}
else
{
structuresToDendrogram.Add(structures[item.Value[0]]);
if(alignFile==null)
structuresFullPath.Add(dirName + Path.DirectorySeparatorChar + structures[item.Value[0]]);
else
structuresFullPath.Add(structures[item.Value[0]]);
translateToCluster.Add(structures[item.Value[0]], item.Key);
}
cc++;
}
currentV++;
DebugClass.WriteMessage("Jury finished");
switch (dMeasure)
{
case DistanceMeasures.HAMMING:
if (refJuryProfile == null || !jury1d)
throw new Exception("Sorry but for jury measure you have to define 1djury profile to find reference structure");
else
dist = new JuryDistance(structuresFullPath, alignFile, true, profileName, refJuryProfile);
break;
case DistanceMeasures.COSINE:
dist = new CosineDistance(structuresFullPath, alignFile, jury1d, profileName, refJuryProfile);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(structuresFullPath, "", jury1d, atoms, refJuryProfile);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(structuresFullPath, "", jury1d, refJuryProfile);
break;
}
// return new ClusterOutput();
DebugClass.WriteMessage("Start hierarchical");
//Console.WriteLine("Start hierarchical " + Process.GetCurrentProcess().PeakWorkingSet64);
currentV = maxV;
hk = new hierarchicalCluster(dist, linkageType, dirName);
dist.InitMeasure();
//Now just add strctures to the leaves
outC = hk.HierarchicalClustering(structuresToDendrogram);
DebugClass.WriteMessage("Stop hierarchical");
List<HClusterNode> hLeaves = outC.hNode.GetLeaves();
foreach(var item in hLeaves)
{
if (translateToCluster.ContainsKey(item.setStruct[0]))
{
foreach (var str in dic[translateToCluster[item.setStruct[0]]])
if (item.setStruct[0] != structures[str])
item.setStruct.Add(structures[str]);
}
else
throw new Exception("Cannot add structure. Something is wrong");
}
outC.hNode.RedoSetStructures();
return outC;
}
public void SetGeoCode(ICoordinates coordinates, double radius, DistanceMeasure measure)
{
GeoCode = new GeoCode(coordinates, radius, measure);
}
public TweetSearchParameters(double longitude, double latitude, int radius, DistanceMeasure measure) : this()
{
GeoCode = new GeoCode(longitude, latitude, radius, measure);
}
public TweetSearchParameters(ICoordinates coordinates, int radius, DistanceMeasure measure) : this()
{
GeoCode = new GeoCode(coordinates, radius, measure);
}
public static ITweetSearchParameters GenerateSearchTweetParameter(double longitude, double latitude, int radius, DistanceMeasure measure)
{
return(SearchQueryGenerator.GenerateSearchTweetParameter(longitude, latitude, radius, measure));
}
private PoolItem GetBestItem(IList <PoolItem> items, CombinatorialSemantics semantics, DistanceMeasure distanceMeasure)
{
double bestDistance = Double.MaxValue;
PoolItem bestItem = null;
var allSemantics = items.Where(item => item is ISemanticsHolder && ((ISemanticsHolder)item.Node).SemanticsEvaluated)
.Select(item => ((ISemanticsHolder)item.Node).Semantics);
foreach (var item in items)
{
var semanticsNode = item.Node as ISemanticsHolder;
if (semanticsNode != null && semanticsNode.SemanticsEvaluated)
{
var distance = distanceMeasure(semantics, semanticsNode.Semantics, allSemantics);
if (distance < bestDistance)
{
bestDistance = distance;
bestItem = item;
}
}
}
return(bestItem);
}
public ITweetSearchParameters CreateSearchTweetParameter(ICoordinates coordinates, int radius, DistanceMeasure measure)
{
return new TweetSearchParameters(coordinates, radius, measure);
}
private double CalcDevCluster(DistanceMeasure dd, List<string> cluster, string refStruct)
{
double sum = 0;
double v1 = 0, v2 = 0;
if(dd==null)
dd = PrepareDistanceMeasure(cluster, distanceControl1.distDef, dirName);
foreach (var item in cluster)
{
int x = dd.GetDistance(refStruct, item) / 100;
v1 += x;
v2 += x * x;
}
v1 = v1 / cluster.Count;
v1 *= v1;
v2 = v2 / cluster.Count;
sum = Math.Sqrt(v2 - v1);
return sum;
}
// Note: The latitude/longitude order here is reversed compared to the various
// signatures in Tweetinvi (see the GeoCode constructor below for example),
// for ease of copy-and-pasting coordinates from the web
static ISearchResult SearchTweetsTaggedWithGeo(string query,
double latitude,
double longitude,
double radius = 15,
DistanceMeasure distanceMeasure = DistanceMeasure.Miles)
{
var searchParameters = new TweetSearchParameters(query)
{
GeoCode = new GeoCode(longitude, latitude, radius, distanceMeasure),
Lang = Language.English,
SearchType = SearchResultType.Recent,
MaximumNumberOfResults = 15
};
try
{
var result = Search.SearchTweetsWithMetadata(searchParameters);
return result;
}
catch (Exception e)
{
PrintStackTrace(e);
Log(e);
return null;
}
}
private void CalculateDistToAll()
{
tableDist = new DataTable();
tableDist.Columns.Add("Reference structure", typeof(string));
tableDist.Columns.Add("Distance", typeof(double));
tableDist.Columns.Add("Cluster size", typeof(int));
List <string> fileNames=new List<string>();
if (textBox1.Text != null && textBox1.Text.Length > 5 && File.Exists(textBox1.Text))
{
fileNames.Add(textBox1.Text);
string[] tmp = textBox1.Text.Split(Path.DirectorySeparatorChar);
native = tmp[tmp.Length - 1];
}
bestStr = float.MaxValue;
foreach (var item in selected)
{
foreach (var lItem in item)
{
fileNames.Add(dirName+Path.DirectorySeparatorChar+lItem);
switch (distanceControl1.distDef)
{
case DistanceMeasures.HAMMING:
dist = new JuryDistance(fileNames, alignFile, false, distanceControl1.profileName);
break;
case DistanceMeasures.MAXSUB:
dist = new MaxSub(fileNames, alignFile, false);
break;
case DistanceMeasures.RMSD:
dist = new Rmsd(fileNames, alignFile, false, distanceControl1.CAtoms);
break;
}
dist.InitMeasure();
float distF = float.MaxValue;
if (distanceControl1.distDef != DistanceMeasures.HAMMING)
{
if (!dist.pdbs.molDic.ContainsKey(native) || !dist.pdbs.molDic.ContainsKey(lItem))
continue;
if (dist.pdbs.molDic[native].mol.Chains[0].chainSequence.Length > dist.pdbs.molDic[lItem].mol.Chains[0].chainSequence.Length)
distF = dist.GetDistance(native, lItem) / 100.0f;
else
distF = dist.GetDistance(lItem, native) / 100.0f;
}
else
distF=dist.GetDistance(native, lItem) / 100.0f;
tableDist.Rows.Add(lItem, Convert.ToDouble(String.Format("{0:0.00}", distF)),item.Count);
distList.Add(lItem, distF);
if (bestStr > distF)
bestStr = distF;
fileNames.RemoveAt(fileNames.Count - 1);
currentV++;
}
}
}
public static ITweetSearchParameters CreateTweetSearchParameter(ICoordinates coordinates, int radius, DistanceMeasure measure)
{
return SearchQueryParameterGenerator.CreateSearchTweetParameter(coordinates, radius, measure);
}
public GeoCode(ICoordinates coordinates, double radius, DistanceMeasure distanceMeasure)
{
Coordinates = coordinates;
Radius = radius;
DistanceMeasure = distanceMeasure;
}
public void SetGeoCode(double longitude, double latitude, int radius, DistanceMeasure measure)
{
var coordinates = _geoFactory.GenerateCoordinates(longitude, latitude);
SetGeoCode(coordinates, radius, measure);
}
public static ITweetSearchParameters CreateTweetSearchParameter(double longitude, double latitude, int radius, DistanceMeasure measure)
{
return SearchQueryParameterGenerator.CreateSearchTweetParameter(longitude, latitude, radius, measure);
}
public void GetFraction(object param)
{
float fraction = 0;
float avrDiff=0;
int counter = 0;
int end;
DistanceMeasures distance=((fractionParams)param).distance;
string profileName = ((fractionParams)param).profileName;
double distThreshold = ((fractionParams)param).distThreshold;
int clustersNum = ((fractionParams)param).clustersNum;
results = new DataTable();
try
{
DataColumn col;
col=results.Columns.Add("Output", typeof(string));
col.AllowDBNull = true;
col=results.Columns.Add("Best Model", typeof(string));
col.AllowDBNull = true;
col=results.Columns.Add("Distance To Native", typeof(double));
col.AllowDBNull = true;
col=results.Columns.Add("Best found", typeof(string));
col.AllowDBNull = true;
col=results.Columns.Add("Distance to best model", typeof(double));
col.AllowDBNull = true;
maxV = output.Count;
foreach (var item in output)
{
string[] kkk = item.dirName.Split(Path.DirectorySeparatorChar);
List<List<string>> clusters = item.GetClusters(10);
List<string> list = new List<string>();
foreach (var cl in clusters)
foreach (var target in cl)
list.Add(target);
string native = item.dirName + ".pdb";
if (item.dirName.Contains("."))
{
string[] aux = item.dirName.Split('.');
native = aux[0] + ".pdb";
}
string fileBestModel = item.dirName + "_" + distance.ToString() + "_bestmodel.dat";
BestModel bestToNative;
if (!File.Exists(fileBestModel))
{
bestToNative = FindBestToModel(list, distance, item.dirName, "", "", native);
StreamWriter st = new StreamWriter(fileBestModel);
st.WriteLine(bestToNative.modelName + " " + bestToNative.value);
st.Close();
}
else
{
StreamReader st = new StreamReader(fileBestModel);
string line = st.ReadLine();
string[] aux = line.Split(' ');
bestToNative.modelName = aux[0];
bestToNative.value = Convert.ToInt32(aux[1]);
st.Close();
}
if (bestToNative.value == int.MaxValue)
continue;
// list.Clear();
if (clusters.Count > 0)
clusters.Sort(delegate(List<string> first, List<string> second)
{ return second.Count.CompareTo(first.Count); });
string represent = "";
//And now best five
BestModel vOut = new BestModel();
InitBestModel(distance, ref vOut);
end = clustersNum;
if (clusters.Count < clustersNum)
end = clusters.Count;
for (int i = 0; i < end; i++)
//for (int i = 0; i < clusters.Count; i++)
{
if (profileName != null)
represent = CLusterRepresentJury(item.dirName, clusters[i], profileName)[0].Key;
else
{
if (item.juryLike != null)
represent = item.juryLike[i].Key;
else
{
/* if (clusters.Count > 1)
{
represent = CLusterRepresent(distance,item.dirName, clusters[i],"",profileName);
}
else*/
represent = clusters[i][0];
}
}
//int vDist = GetDist(distance, item.dirName, bestToNative.modelName, represent);
int vDist = GetDist(distance, item.dirName, native, represent);
CheckBest(distance, vDist, represent, ref vOut);
}
if (bestToNative.value == errorValue || vOut.value == errorValue)
{
if (bestToNative.value == errorValue && vOut.value != errorValue)
results.Rows.Add(item.name, bestToNative.modelName, double.NaN, vOut.modelName, vOut.value / 100.0);
else
if(bestToNative.value != errorValue && vOut.value == errorValue)
results.Rows.Add(item.name, bestToNative.modelName, bestToNative.value / 100.0, vOut.modelName, double.NaN);
else
results.Rows.Add(item.name, bestToNative.modelName, double.NaN, vOut.modelName, double.NaN);
}
else
results.Rows.Add(item.name, bestToNative.modelName, bestToNative.value / 100.0, vOut.modelName, vOut.value / 100.0);
if (vOut.value!=errorValue && Math.Abs(vOut.value-bestToNative.value) < distThreshold * 100)
{
fraction++;
}
if (vOut.value!=errorValue)
{
counter++;
avrDiff += vOut.value;
}
dist = null;
GC.Collect();
currentV++;
}
avrDiff /= counter;
fraction /= counter;
results.Rows.Add(null, null, null, null, null);
results.Rows.Add("AVR:"," "+Math.Round(avrDiff / 100,2),null,"Fraction:",Math.Round(fraction,2));
}
catch(Exception ex)
{
exc = ex;
}
//Console.WriteLine("avrDiff=" + avrDiff + " fraction=" + fraction+" pearson="+Pearson());
currentV = maxV;
}
string CLusterRepresent(DistanceMeasures distance,string dirName, List<string> targets,string alignFile, string profileName)
{
DistanceMeasure dist;
List<string> fileNames=new List<string>();
foreach (var item in targets)
fileNames.Add(dirName + Path.DirectorySeparatorChar + item);
dist = PrepareDistance(distance, fileNames, alignFile, profileName);
return dist.GetReferenceStructure(targets);
}
public kMeans(DistanceMeasure dMeasure,bool hierarchical=false)
{
this.dMeasure = dMeasure;
// this.initialization = initialization;
this.hierarchical = hierarchical;
}
public IGeoCode GenerateGeoCode(ICoordinates coordinates, double radius, DistanceMeasure measure)
{
return new GeoCode(coordinates, radius, measure);
}