private static void GenerateHtmlContent(string htmlFile, ManxcatSection config)
{
using (var writer = new StreamWriter(htmlFile))
{
using (Stream stream = Assembly.GetExecutingAssembly().GetManifestResourceStream("Manxcat.Web.template")
)
{
if (stream != null)
{
using (var reader = new StreamReader(stream))
{
while (!reader.EndOfStream)
{
string line = reader.ReadLine();
if (!string.IsNullOrEmpty(line))
{
writer.WriteLine(!line.Contains(ManxcatConstants.Tag)
? line
: ProcessTagLine(line, config));
}
}
}
}
else
{
throw new Exception(ManxcatErrorMessages.TemplateHtmlNotAvailable);
}
}
}
}
private static string ProcessTagLine(string line, ManxcatSection config)
{
int tagStartIdx = line.IndexOf(ManxcatConstants.Tag);
int tagEndIdx = line.IndexOf(ManxcatConstants.Tag, tagStartIdx + ManxcatConstants.Tag.Length) +
(ManxcatConstants.Tag.Length - 1);
string prefix = line.Substring(0, tagStartIdx);
string suffix = line.Substring(tagEndIdx + 1);
string meat = line.Substring(tagStartIdx + ManxcatConstants.Tag.Length,
((tagEndIdx + 1) - (tagStartIdx + 2 * ManxcatConstants.Tag.Length)));
switch (meat)
{
case ManxcatConstants.TagManxcatName:
return(prefix + config.ManxcatRunName + suffix);
case ManxcatConstants.TagManxcatDescription:
return(prefix + config.ManxcatRunDescription + suffix);
case ManxcatConstants.TagManxcatConfig:
return(GenerateConfig(config));
case ManxcatConstants.TagManxcatLinks:
return(prefix + GenerateLinks(config) + suffix);
default:
throw new Exception(ManxcatErrorMessages.UnidentifiedTagInHTMLGeneration);
}
}
public ConfigurationMgr()
{
_global = new GlobalSection();
_manxcat = new ManxcatSection();
_pairwise = new PairwiseSection();
_smithWaterman = new SmithWatermanSection();
_needlemanWunsch = new NeedlemanWunschSection();
_smithWatermanMS = new SmithWatermanMS();
_daVectorSpongeSection = new DAVectorSpongeSection();
}
private static string GenerateLinks(ManxcatSection config)
{
const string liTemplate = "<li><a href=\"{0}\">{1}</a></li>";
const string txtExt = ".txt";
string dotslash = string.IsNullOrEmpty(config.ServerUrlPrefix)
? "./"
: (config.ServerUrlPrefix + "/" + config.ManxcatRunName + "/");
var sb = new StringBuilder("<ul>");
string reducedVectorFileNameTag = Path.GetFileNameWithoutExtension(config.ReducedVectorOutputFileName);
string link = dotslash + ManxcatConstants.SimplePointsPrefix + reducedVectorFileNameTag + txtExt;
string name = "Simple Points";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + reducedVectorFileNameTag + ManxcatConstants.ColonPointsSuffix + txtExt;
name = "Colon Points";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + reducedVectorFileNameTag + ManxcatConstants.GroupPointsSuffix + txtExt;
name = "Group Points";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + Path.GetFileName(config.SummaryOutputFileName);
name = "Summary File";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + Path.GetFileName(config.TimingOutputFileName);
name = "Timing File";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + ManxcatConstants.OutFileNameTag + txtExt;
name = "Manxcat Ouput";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + "whole-plot.png";
name = "Density Graph";
sb.AppendLine(string.Format(liTemplate, link, name));
if (SALSAUtility.IsClustersSelected)
{
link = dotslash + "selected-plot.png";
name = "Density Graph for Selected Clusters (Intra Cluster Distances)";
sb.AppendLine(string.Format(liTemplate, link, name));
link = dotslash + "selected-inter-plot.png";
name = "Density Graph for Selected Clusters (Inter Cluster Distances)";
sb.AppendLine(string.Format(liTemplate, link, name));
}
return(sb.ToString());
}
// End SALSAStatus
// todo: saliya - Possible Improvement: handle comments in this function to use the List instead of the string
// you will have to search for the places where comment is manipulated in other
// places as well
public static void SALSAUpdateMetaData(ManxcatSection Configuration)
{
string Comment = Configuration.Comment;
for (int i = 0; i < CosmicOutput.Count; i++)
{
if (i == 0)
{
continue;
}
Comment += "\n" + CosmicOutput[i];
}
Comment = Comment.Replace(':', '-');
Configuration.Comment = Comment;
}
/// <summary>
/// Generates a Web page linking to output files
/// </summary>
public static void WriteHTML()
{
ManxcatSection config = ManxcatCentral.Configuration;
string directoryPath = Path.GetDirectoryName(config.ReducedVectorOutputFileName);
directoryPath = string.IsNullOrEmpty(directoryPath) ? string.Empty : directoryPath;
string stylesFile = Path.Combine(directoryPath, ManxcatConstants.StyleFileNameTag) + ".css";
CopyStylesCSS(stylesFile);
string htmlFile = Path.Combine(directoryPath, ManxcatConstants.HtmlFileNameTag) + ".html";
GenerateHtmlContent(htmlFile, config);
}
private static string GenerateConfig(ManxcatSection config)
{
var sb = new StringBuilder();
sb.AppendLine("I/O");
sb.AppendLine("\tCoordinateWriteFrequency: " + config.CoordinateWriteFrequency);
sb.AppendLine("\tDistanceMatrixFile: " + config.DistanceMatrixFile);
sb.AppendLine("\n\nManxcatCore");
sb.AppendLine("\tAddonforQcomputation: " + config.AddonforQcomputation);
sb.AppendLine("\tCalcFixedCrossFixed: " + config.CalcFixedCrossFixed);
sb.AppendLine("\tCGResidualLimit: " + config.CGResidualLimit);
sb.AppendLine("\tChisqChangePerPoint: " + config.ChisqChangePerPoint);
sb.AppendLine("\tChisqnorm: " + config.Chisqnorm);
sb.AppendLine("\tChisqPrintConstant: " + config.ChisqPrintConstant);
sb.AppendLine("\tConversionInformation: " + config.ConversionInformation);
sb.AppendLine("\tConversionOption: " + config.ConversionOption);
sb.AppendLine("\tDataPoints: " + config.DataPoints);
sb.AppendLine("\tDerivtest: " + config.Derivtest);
sb.AppendLine("\tDiskDistanceOption: " + config.DiskDistanceOption);
sb.AppendLine("\tDistanceCut: " + config.DistanceCut);
sb.AppendLine("\tDistanceFormula: " + config.DistanceFormula);
sb.AppendLine("\tDistanceProcessingOption: " + config.DistanceProcessingOption);
sb.AppendLine("\tDistanceWeigthsCuts: " + config.DistanceWeightsCuts);
sb.AppendLine("\tEigenvaluechange: " + config.Eigenvaluechange);
sb.AppendLine("\tEigenvectorchange: " + config.Eigenvectorchange);
sb.AppendLine("\tExtraOption1: " + config.ExtraOption1);
sb.AppendLine("\tExtraprecision: " + config.Extraprecision);
sb.AppendLine("\tFixedPointCriterion: " + config.FixedPointCriterion);
sb.AppendLine("\tFletcherRho: " + config.FletcherRho);
sb.AppendLine("\tFletcherSigma: " + config.FletcherSigma);
sb.AppendLine("\tFullSecondDerivativeOption: " + config.FullSecondDerivativeOption);
sb.AppendLine("\tFunctionErrorCalcMultiplier: " + config.FunctionErrorCalcMultiplier);
sb.AppendLine("\tHistogramBinCount " + config.HistogramBinCount);
sb.AppendLine("\tInitializationLoops: " + config.InitializationLoops);
sb.AppendLine("\tInitializationOption: " + config.InitializationOption);
sb.AppendLine("\tInitialSteepestDescents: " + config.InitialSteepestDescents);
sb.AppendLine("\tLinkCut: " + config.LinkCut);
sb.AppendLine("\tLocalVectorDimension: " + config.LocalVectorDimension);
sb.AppendLine("\tMaxit: " + config.Maxit);
sb.AppendLine("\tMinimumDistance: " + config.MinimumDistance);
sb.AppendLine("\tMPIIOStrategy: " + config.MPIIOStrategy);
sb.AppendLine("\tNbadgo: " + config.Nbadgo);
sb.AppendLine("\tOmega: " + config.Omega);
sb.AppendLine("\tOmegaOption: " + config.OmegaOption);
sb.AppendLine("\tPowerIterationLimit: " + config.PowerIterationLimit);
sb.AppendLine("\tProcessingOption: " + config.ProcessingOption);
sb.AppendLine("\tQgoodReductionFactor: " + config.QgoodReductionFactor);
sb.AppendLine("\tQHighInitialFactor: " + config.QHighInitialFactor);
sb.AppendLine("\tQLimiscalecalculationInterval: " + config.QLimitscalculationInterval);
sb.AppendLine("\tRotationOption: " + config.RotationOption);
sb.AppendLine("\tSelectedfixedpoints: " + config.Selectedfixedpoints);
sb.AppendLine("\tSelectedvariedpoints: " + config.Selectedvariedpoints);
sb.AppendLine("\tStoredDistanceOption: " + config.StoredDistanceOption);
sb.AppendLine("\tTimeCutmillisec: " + config.TimeCutmillisec);
sb.AppendLine("\tTransformMethod: " + config.TransformMethod);
sb.AppendLine("\tTransformParameter: " + config.TransformParameter);
sb.AppendLine("\tUndefindDistanceValue: " + config.UndefinedDistanceValue);
sb.AppendLine("\tVariedPointCriterion: " + config.VariedPointCriterion);
sb.AppendLine("\tWeightingOption: " + config.WeightingOption);
sb.AppendLine("\tWrite2Das3D: " + config.Write2Das3D);
sb.AppendLine("\n\nDensity");
sb.AppendLine("\tAlpha: " + config.Alpha);
sb.AppendLine("\tPcutf: " + config.Pcutf);
sb.AppendLine("\tSelectedClusters: " + config.SelectedClusters);
sb.AppendLine("\tXmaxBound: " + config.XmaxBound);
sb.AppendLine("\tXres: " + config.Xres);
sb.AppendLine("\tYmaxBound: " + config.YmaxBound);
sb.AppendLine("\tYres: " + config.Yres);
return(sb.ToString());
}
public static void WriteRotateMDS(string fname, int OutputOption, double[][] param, double[][] perr)
{
int LocalVectorDimension = param[0].GetLength(0);
if (LocalVectorDimension != perr[0].GetLength(0))
{
SALSAUtility.SALSAError("Inconsistent Dimensions Labels " + LocalVectorDimension.ToString() + " Perr " +
perr[0].GetLength(0).ToString());
}
ManxcatSection Configuration = ManxcatCentral.Configuration;
// set current cosmic scaling
for (int LocalVectorIndex1 = 0; LocalVectorIndex1 < PointVectorDimension; LocalVectorIndex1++)
{
for (int LocalVectorIndex2 = 0; LocalVectorIndex2 < PointVectorDimension; LocalVectorIndex2++)
{
CurrentCosmicScaling[LocalVectorIndex1, LocalVectorIndex2] =
SavedCosmicScaling[Hotsun.BestChisqLoop][LocalVectorIndex1, LocalVectorIndex2];
}
}
// Write SALSA Properties File Header
if (OutputOption == 0)
{
int filetype = 2;
if ((SALSAUtility.NumberFixedPoints > 0) ||
(SALSAUtility.NumberVariedPoints < SALSAUtility.NumberOriginalPoints))
{
filetype = 4;
}
RotationFileProperties.GroupName = "MDS Run:" + Configuration.RunNumber.ToString();
RotationFileProperties.FileGenerationType = filetype;
RotationFileProperties.OriginalPointStartIndex = 0;
RotationFileProperties.LocalPointStartIndex = 0;
// Rotation parameters
RotationFileProperties.NumberRotationParameters = Hotsun.npar;
RotationFileProperties.RotationParameters = "";
for (int CountRotPars = 0; CountRotPars < Hotsun.npar; CountRotPars++)
{
RotationFileProperties.RotationParameters += " " + param[CountRotPars][0].ToString("E4") + ",";
}
for (int Cosmicdiagonals = 0; Cosmicdiagonals < PointVectorDimension; Cosmicdiagonals++)
{
RotationFileProperties.RotationParameters += " " +
CurrentCosmicScaling[Cosmicdiagonals, Cosmicdiagonals].
ToString("E4") + ",";
}
// Comment should have key features of Run
string OldComment = RotationFileProperties.Comment;
if (OldComment != "")
{
OldComment += "\n";
}
OldComment += "MDS ROTATION Run " + Configuration.RunNumber.ToString() + " Start Time " +
SALSAUtility.startTime.ToLocalTime() + " *** ";
OldComment += "\n RotationOption " + Configuration.RotationOption + " First Scale " +
FirstScale.ToString("E4") + " Second Scale " + SecondScale.ToString()
+ "\n First Mean";
for (int PointIndex = 0; PointIndex < PointVectorDimension; PointIndex++)
{
OldComment += " " + FirstMean[PointIndex].ToString("E4");
}
OldComment += " Second Mean";
for (int PointIndex = 0; PointIndex < PointVectorDimension; PointIndex++)
{
OldComment += " " + SecondMean[PointIndex].ToString("E4");
}
RotationFileProperties.Comment = OldComment;
SALSA_Properties.WriteDataPointFile(fname, ManxcatCentral.Configuration.Write2Das3D, "all ",
RotationFileProperties,
RotationPointProperties, SALSAUtility.NumberOriginalPoints);
return;
}
// Option OutputOption = 1 -- write ROTATED Second Data
try
{
StreamWriter sw = null;
if (!string.IsNullOrEmpty(fname))
{
sw = new StreamWriter(fname, false, Encoding.UTF8);
}
if (sw != null)
{
double[] FullTranslation;
double[,] FullRotation;
SetupFinalTransforamation(param, out FullTranslation, out FullRotation);
for (int UsedDataPoint = 0; UsedDataPoint < SALSAUtility.PointCount_Global; UsedDataPoint++)
{
var Vector = new double[PointVectorDimension];
MatrixVectorProduct(Vector, FullRotation, SecondData[UsedDataPoint]);
VectorSum(Vector, FullTranslation, +1.0, Vector);
string Coordinates = "";
int SingleCluster = 1;
for (int LocalVectorIndex = 0; LocalVectorIndex < PointVectorDimension; LocalVectorIndex++)
{
Coordinates += Vector[LocalVectorIndex].ToString("E4") + "\t";
}
sw.WriteLine(
String.Format((UsedDataPoint + 1).ToString() + "\t" + Coordinates + SingleCluster.ToString()));
}
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed writing data" + e);
throw (e);
}
}
// Write label-cluster results into a file
public static void WriteMDS(string fname, int OutputOption, double[][] param, double[][] perr)
{
int LocalVectorDimension = param[0].GetLength(0);
if (LocalVectorDimension != perr[0].GetLength(0))
{
SALSAUtility.SALSAError("Inconsistent Dimensions Labels " + LocalVectorDimension.ToString() + " Perr " +
perr[0].GetLength(0).ToString());
}
ManxcatSection Configuration = ManxcatCentral.Configuration;
// Write SALSA Properties File Header
if (OutputOption == 0)
{
int filetype = 2;
if ((SALSAUtility.NumberFixedPoints > 0) ||
(SALSAUtility.NumberVariedPoints < SALSAUtility.NumberOriginalPoints))
{
filetype = 4;
}
string cleandate = SALSAUtility.startTime.ToLocalTime().ToString();
cleandate = cleandate.Replace(":", ".");
cleandate = cleandate.Replace(" ", "-");
SALSAUtility.GlobalFileProperties.GroupName = "MDSasChisq-" + Configuration.RunSetLabel + "-Run" +
Configuration.RunNumber.ToString() + "-Date-" + cleandate;
SALSAUtility.GlobalFileProperties.FileGenerationType = filetype;
SALSAUtility.GlobalFileProperties.OriginalPointStartIndex = 0;
SALSAUtility.GlobalFileProperties.LocalPointStartIndex = 0;
SALSAUtility.GlobalFileProperties.NumberOriginalPoints = SALSAUtility.NumberOriginalPoints;
SALSAUtility.GlobalFileProperties.NumberPointsinFile = SALSAUtility.PointCount_Global;
// Comment should have key features of Run
string OldComment = SALSAUtility.GlobalFileProperties.Comment;
if (OldComment != "")
{
OldComment += "\n";
}
OldComment += "MDSasChisq " + Configuration.RunNumber.ToString() + " StartTime " + cleandate + " ****";
OldComment += "\n Distance Input Option " + Configuration.DistanceProcessingOption.ToString() +
" Distance Formula " + Configuration.DistanceFormula.ToString() + " Weighting Option " +
Configuration.Chisqnorm.ToString() + " Minimum Distance Value " +
Configuration.MinimumDistance.ToString();
OldComment += "\n" + Hotsun.HotsunComment;
SALSAUtility.GlobalFileProperties.Comment = OldComment;
for (int GlobalPointIndex = 0; GlobalPointIndex < SALSAUtility.PointCount_Global; GlobalPointIndex++)
{
int OriginalPointIndex = SALSAUtility.UsedPointtoOriginalPointMap[GlobalPointIndex];
int groupnumber = -1;
string grouplabel = "Ignored";
SALSAUtility.GlobalPointProperties[GlobalPointIndex].FixedorVaried = 0;
if (ManxcatMDS.PointStatus[GlobalPointIndex] == -1)
{
groupnumber = 3;
grouplabel = "Deleted";
}
else
{
if (SALSAUtility.OriginalPointDisposition[GlobalPointIndex] <= -SALSAUtility.SALSASHIFT)
{
groupnumber = 2;
grouplabel = "Fixed";
SALSAUtility.GlobalPointProperties[GlobalPointIndex].FixedorVaried = 2;
}
if (SALSAUtility.OriginalPointDisposition[GlobalPointIndex] >= SALSAUtility.SALSASHIFT)
{
groupnumber = 1;
grouplabel = "Varied";
SALSAUtility.GlobalPointProperties[GlobalPointIndex].source = "MDSasChisq-" +
Configuration.RunSetLabel +
"-Run" +
Configuration.RunNumber.
ToString() + "-Date-" +
cleandate;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].FixedorVaried = 1;
}
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].group = groupnumber;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].grouplabel = grouplabel;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].OriginalPointNumber = OriginalPointIndex;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].LocalPointNumber = GlobalPointIndex;
}
for (int GlobalPointIndex = 0; GlobalPointIndex < SALSAUtility.PointCount_Global; GlobalPointIndex++)
{
if (ManxcatMDS.PointStatus[GlobalPointIndex] == -1)
{
SALSAUtility.GlobalPointProperties[GlobalPointIndex].valuesset = false;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].errorsset = false;
continue;
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].x = param[GlobalPointIndex][0];
SALSAUtility.GlobalPointProperties[GlobalPointIndex].y = param[GlobalPointIndex][1];
if (LocalVectorDimension > 2)
{
SALSAUtility.GlobalPointProperties[GlobalPointIndex].z = param[GlobalPointIndex][2];
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].xerr = perr[GlobalPointIndex][0];
SALSAUtility.GlobalPointProperties[GlobalPointIndex].yerr = perr[GlobalPointIndex][1];
if (LocalVectorDimension > 2)
{
SALSAUtility.GlobalPointProperties[GlobalPointIndex].zerr = perr[GlobalPointIndex][2];
}
SALSAUtility.GlobalPointProperties[GlobalPointIndex].valuesset = true;
SALSAUtility.GlobalPointProperties[GlobalPointIndex].errorsset = true;
}
if (SALSAUtility.Usedreordered)
{
var NaivePointProperties = new SALSADataPointProperties[SALSAUtility.PointCount_Global];
for (int GlobalPointIndex = 0;
GlobalPointIndex < SALSAUtility.PointCount_Global;
GlobalPointIndex++)
{
int NaivePointIndex = SALSAUtility.ActualtoNaiveUsedOrder[GlobalPointIndex];
NaivePointProperties[NaivePointIndex] =
SALSAUtility.GlobalPointProperties[GlobalPointIndex].ShallowCopy();
}
SALSA_Properties.WriteDataPointFile(fname, ManxcatCentral.Configuration.Write2Das3D, "all ",
SALSAUtility.GlobalFileProperties,
NaivePointProperties, SALSAUtility.PointCount_Global);
return;
}
SALSA_Properties.WriteDataPointFile(fname, ManxcatCentral.Configuration.Write2Das3D, "all ",
SALSAUtility.GlobalFileProperties,
SALSAUtility.GlobalPointProperties, SALSAUtility.PointCount_Global);
return;
}
// Option OutputOption = 1
// Simple output of Used in ORIGINAL not Loadbalanced Order
try
{
StreamWriter sw = null;
if (!string.IsNullOrEmpty(fname))
{
sw = new StreamWriter(fname, false, Encoding.UTF8);
}
if (sw != null)
{
for (int GlobalPointIndex = 0;
GlobalPointIndex < SALSAUtility.PointCount_Global;
GlobalPointIndex++)
{
if (ManxcatMDS.PointStatus[GlobalPointIndex] == -1)
{
continue;
}
string Coordinates = "";
int SingleCluster = 1;
int UsedPointIndex = SALSAUtility.NaivetoActualUsedOrder[GlobalPointIndex];
for (int LocalVectorIndex = 0; LocalVectorIndex < LocalVectorDimension; LocalVectorIndex++)
{
Coordinates += param[UsedPointIndex][LocalVectorIndex].ToString("E4") + "\t";
}
sw.WriteLine(
String.Format((GlobalPointIndex).ToString() + "\t" + Coordinates + SingleCluster.ToString()));
}
}
sw.Flush();
sw.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed writing data" + e);
throw (e);
}
}
