public void Combine_FqFile_Component_DetailsScores(FqFile_Component_Details inputDetails)
{
this.sequencerType = inputDetails.sequencerType;
this.TotalNucs += inputDetails.TotalNucs;
this.TotalSequences += inputDetails.TotalSequences;
this.NucleotidesCleaned += inputDetails.NucleotidesCleaned;
this.NCount += inputDetails.NCount;
this.CCount += inputDetails.CCount;
this.GCount += inputDetails.GCount;
this.SequencesRemoved += inputDetails.SequencesRemoved;
if (inputDetails.MaxSeqSize > this.MaxSeqSize)
{
this.MaxSeqSize = inputDetails.MaxSeqSize;
}
if (this.MinSeqSize == 0)
{
this.MinSeqSize = inputDetails.MinSeqSize;
}
else if (inputDetails.MinSeqSize < this.MinSeqSize)
{
this.MinSeqSize = inputDetails.MinSeqSize;
}
CalculatePercents();
CombineDistributionLists(inputDetails.Distribution);
CombineSequenceLengthDistributionLists(inputDetails.SequenceLengthDistribution);
}
private void drawChart(FqFile_Component_Details drawDetails, String chartType)
{
if (FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
Console.WriteLine("Detail to draw: {0} With {1}", drawDetails.FileName, chartType);
charts.DrawCurrentChartSelection(drawDetails, chartType, zedGraphControl1);
}
}
/// <summary>
/// Creates a fqFile_component_details class from the core information that is best still stored within the programs memory.
/// These classes populate a dictionary within the fqfilemap class where the component filename is their key.
/// </summary>
/// <param name="component">The component who's details are to be stored</param>
public void BuildFqFileMap(IFqFile component)
{
FqFile_Component_Details componentDetails = new FqFile_Component_Details();
componentDetails.ContructComponentDetails(component);
fqFileMap.GetFqFileComponentDetailsMap()[component.getFileName()] = componentDetails;
}
/// <summary>
/// Displays details of the components the file was broken into.
/// </summary>
public void DisplayComponentDetais()
{
foreach (String dir in fqMap.getFileComponentDirectories())
{
FqFile_Component_Details componentDetails = fqMap.GetFqFileComponentDetailsMap()[dir];
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Bold);
textBox.AppendText("\t[" + componentDetails.getGraphName() + " CONTENTS]\n\n");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tTotal Sequences: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.TotalSequences.ToString());
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\t\tTotal Nucleotides: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.TotalNucs.ToString() + "\n\n");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tCytosine Count: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.CCount.ToString());
textBox.AppendText("\t" + Math.Round(componentDetails.CPercent, 2).ToString() + "(%) \n");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tGuanine Count: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.GCount.ToString());
textBox.AppendText("\t" + Math.Round(componentDetails.GPercent, 2).ToString() + "(%) \n");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tFailed Read Count: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.NCount.ToString());
textBox.AppendText("\t" + Math.Round(componentDetails.NPercent, 4).ToString() + "(%) \n\n");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tSmallest Sequence Length: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.MinSeqSize.ToString());
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tLargest Sequence Length: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.MaxSeqSize.ToString() + "\n\n");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\tNucleotides Cleaned: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.NucleotidesCleaned.ToString());
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText("\t\tSequences Removed: ");
textBox.SelectionFont = new Font(textBox.Font.ToString(), 8, FontStyle.Regular);
textBox.AppendText(componentDetails.SequencesRemoved.ToString() + "\n\n");
}
}
public void CalculateGlobalFileScores()
{
GlobalDetails = new FqFile_Component_Details();
for (int i = 0; i < fqFileDirectories.Count; i++)
{
FqFile_Component_Details currentDetails = ComponentMap[fqFileDirectories[i]];
GlobalDetails.Combine_FqFile_Component_DetailsScores(currentDetails);
}
}
/// <summary>
/// This method called from the GUI decides which chart to draw and is generally called from the GUI. It checks that the chart type
/// and component details to be drawn are not already the current ones available within the class and then draws
/// a graph based on the chart type string that corresponds to the enum FastqChartTypes within this class.
/// </summary>
/// <param name="details">Current details to draw</param>
/// <param name="chartType">The chart type to draw, based on the enum FastqChartTypes</param>
/// <param name="chart">The ZedGraph control panel. ie the panel the charts are to be drawn on</param>
public void DrawCurrentChartSelection(FqFile_Component_Details details, String chartType, ZedGraphControl chart)
{
if (!chartType.Equals(currentChartType) || !details.Equals(componentDetails))
{
this.componentDetails = details;
this.currentChartType = chartType;
this.graphControl = chart;
Console.WriteLine("Drawing new chart");
if (currentChartType == FastqChartTypes.PerBaseSequenceStatistics.ToString())
DrawSequenceStatistics();
else if (currentChartType == FastqChartTypes.Distribution.ToString())
DrawDistribution();
else if (currentChartType == FastqChartTypes.SequenceLengthDistribution.ToString())
DrawSequenceLengthDistribution();
}
}
/// <summary>
/// This method called from the GUI decides which chart to draw and is generally called from the GUI. It checks that the chart type
/// and component details to be drawn are not already the current ones available within the class and then draws
/// a graph based on the chart type string that corresponds to the enum FastqChartTypes within this class.
/// </summary>
/// <param name="details">Current details to draw</param>
/// <param name="chartType">The chart type to draw, based on the enum FastqChartTypes</param>
/// <param name="chart">The ZedGraph control panel. ie the panel the charts are to be drawn on</param>
public void DrawCurrentChartSelection(FqFile_Component_Details details, String chartType, ZedGraphControl chart)
{
if (!chartType.Equals(currentChartType) || !details.Equals(componentDetails))
{
this.componentDetails = details;
this.currentChartType = chartType;
this.graphControl = chart;
Console.WriteLine("Drawing new chart");
if (currentChartType == FastqChartTypes.PerBaseSequenceStatistics.ToString())
{
DrawSequenceStatistics();
}
else if (currentChartType == FastqChartTypes.Distribution.ToString())
{
DrawDistribution();
}
else if (currentChartType == FastqChartTypes.SequenceLengthDistribution.ToString())
{
DrawSequenceLengthDistribution();
}
}
}
private void drawChart(FqFile_Component_Details drawDetails, String chartType)
{
if (FastqController.CONTROLLER_STATE == FastqController.FastqControllerState.STATE_READY)
{
Console.WriteLine("Detail to draw: {0} With {1}", drawDetails.FileName, chartType);
charts.DrawCurrentChartSelection(drawDetails, chartType, zedGraphControl1);
}
}
public void CalculateGlobalFileScores()
{
GlobalDetails = new FqFile_Component_Details();
for (int i = 0; i < fqFileDirectories.Count; i++)
{
FqFile_Component_Details currentDetails = ComponentMap[fqFileDirectories[i]];
GlobalDetails.Combine_FqFile_Component_DetailsScores(currentDetails);
}
}
/// <summary>
/// Creates a fqFile_component_details class from the core information that is best still stored within the programs memory.
/// These classes populate a dictionary within the fqfilemap class where the component filename is their key.
/// </summary>
/// <param name="component">The component who's details are to be stored</param>
public void BuildFqFileMap(IFqFile component)
{
FqFile_Component_Details componentDetails = new FqFile_Component_Details();
componentDetails.ContructComponentDetails(component);
fqFileMap.GetFqFileComponentDetailsMap()[component.getFileName()] = componentDetails;
}
public void Combine_FqFile_Component_DetailsScores(FqFile_Component_Details inputDetails)
{
this.sequencerType = inputDetails.sequencerType;
this.TotalNucs += inputDetails.TotalNucs;
this.TotalSequences += inputDetails.TotalSequences;
this.NucleotidesCleaned += inputDetails.NucleotidesCleaned;
this.NCount += inputDetails.NCount;
this.CCount += inputDetails.CCount;
this.GCount += inputDetails.GCount;
this.SequencesRemoved += inputDetails.SequencesRemoved;
if (inputDetails.MaxSeqSize > this.MaxSeqSize)
this.MaxSeqSize = inputDetails.MaxSeqSize;
if (this.MinSeqSize == 0)
this.MinSeqSize = inputDetails.MinSeqSize;
else if (inputDetails.MinSeqSize < this.MinSeqSize)
this.MinSeqSize = inputDetails.MinSeqSize;
CalculatePercents();
CombineDistributionLists(inputDetails.Distribution);
CombineSequenceLengthDistributionLists(inputDetails.SequenceLengthDistribution);
}