/// <summary>
/// This function generates a LadderInstance based upon the given theoryList and the given peptide.
/// </summary>
/// <param name="theoryList">A list of elements that have been processed through the ComparedListBuilder.</param>
/// <param name="peptide">The Peptide sequence that the List of Elements are generated from.</param>
/// <returns></returns>
public LadderInstance GenerateInstance(List <SpectrumLook.Builders.Element> theoryList, string peptide, Dictionary <char, double> modificationValues)
{
int i = 0;
List <string[]> tempListHolder = new List <string[]>();
List <string> tempListColumnOptions = new List <string>();
LadderInstance returnedLadderInstance = new LadderInstance();
foreach (SpectrumLook.Builders.Element currentElement in theoryList)
{
i = 0;
if (!(tempListColumnOptions.Contains(spliceNumberFromAnnotation(currentElement.Annotation))))
{
//Need to filter out Modification values when calculating the length of the string.
tempListHolder.Add(new string[peptideLength(peptide, modificationValues)]);
tempListColumnOptions.Add(spliceNumberFromAnnotation(currentElement.Annotation));
}
//Find the index to add.
while (tempListColumnOptions[i] != spliceNumberFromAnnotation(currentElement.Annotation))
{
++i;
}
string tempDoubleString = string.Format("{0:#.00}", currentElement.Mz);
try
{
tempListHolder[i][unformatAnnotation(currentElement.Annotation) - 1] = tempDoubleString + "|" + currentElement.Matched.ToString();
}
catch { }
}
for (i = 0; i < tempListColumnOptions.Count; ++i)
{
for (int j = 0; j < tempListHolder[i].Length; ++j)
{
if (tempListHolder[i][j] == null)
{
tempListHolder[i][j] = "";
}
}
}
returnedLadderInstance.mzValue = tempListHolder;
returnedLadderInstance.mzValueHeaders = tempListColumnOptions;
return(returnedLadderInstance);
}
/// <summary>
/// Adds annotations from the matchedPoints to the Graph Pane
/// Plot Options specify how much of the top % of annotations to display, along with size and color.
/// </summary>
/// <param name="pointsList"></param>
/// <param name="myPane"></param>
private void AddAnnotations(IPointList pointsList, GraphPane myPane)
{
//add the annotations for the matched items
double offset = 5;
double minIntensityToDisplay = FindMinIntensityToDisplay(pointsList);
LadderInstance currentInstance = m_manager.GetCurrentInstance();
for (int i = 0; i < pointsList.Count; i++)
{
bool usingCustomAnnotation = false;
TextObj text = new TextObj();
//look for if the user has defined a custom annotation if they have we deal with that instead of making a new one
for (int j = 0; j < currentInstance.annotations.Count; j++)
{
if ((currentInstance.annotations[j].m_point.X == pointsList[i].X) &&
(currentInstance.annotations[j].m_point.Y == pointsList[i].Y))
{
usingCustomAnnotation = true;
Annotation customAnnotation = currentInstance.annotations[j];
PointPair pt = pointsList[i];
// Create a text label from the Y data value
text = new TextObj(customAnnotation.m_text, pt.X, pt.Y + offset,
CoordType.AxisXYScale, AlignH.Left, AlignV.Center);
// Store the point into the text object's tag
text.Tag = (object)pt;
if (customAnnotation.m_showHideAuto > 0)
{
// Always show this annotation
text.IsVisible = true;
}
else if (customAnnotation.m_showHideAuto < 0)
{
// Always hide this annotation
text.IsVisible = false;
}
else if (pt.Y <= minIntensityToDisplay)
{
// Auto Determine if we are going to show the annotation for this point
text.IsVisible = false;
}
break;
}
}
if (!usingCustomAnnotation)
{
// Get the pointpair
PointPair pt = pointsList[i];
// Create a text label from the Y data value
string tagText;
if (pt.Tag != null)
{
tagText = pt.Tag as string;
}
else
{
tagText = string.Empty;
}
text = new TextObj(tagText, pt.X, pt.Y + offset,
CoordType.AxisXYScale, AlignH.Left, AlignV.Center);
// Store the point into the text object's tag
text.Tag = (object)pt;
// Determine if we are going to show the annotation for this point
if (pt.Y <= minIntensityToDisplay)
{
text.IsVisible = false;
}
}
text.IsClippedToChartRect = true; //set true because we want the annotations to hide when they go off the borders of the graph
text.FontSpec.Size = m_options.annotationTextSize;
text.FontSpec.FontColor = m_options.annotationColor;
text.ZOrder = ZOrder.C_BehindChartBorder;
// Hide the border and the fill
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
// Rotate the text to 90 degrees
text.FontSpec.Angle = 90;
myPane.GraphObjList.Add(text);
}
}
/// <summary>
/// Handles selecting the nearest peptide to edit the annotation for, and showing the editAnnotation form
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void msPlot_DoubleClick(object sender, EventArgs e)
{
bool usingCustomAnnotation = false;
MouseEventArgs mouseArgs = (MouseEventArgs)e;
Graphics g = msPlot.CreateGraphics();
GraphPane closestPane;
PointPair closestPoint;
PointF mousePt = new PointF(mouseArgs.X, mouseArgs.Y);
TextObj selectedTextObj = null;
//retrieve the text object that the user may have selected
if (msPlot.FindClosestPoint(mousePt, out closestPoint, out closestPane))
{
foreach (GraphObj textObject in closestPane.GraphObjList)
{
if (textObject.Tag == closestPoint)
{
//zed graph found the annotation object, use that text object
selectedTextObj = textObject as TextObj;
break;
}
}
}
else
{
//couldn't find the annotation from where the user clicked
return;
}
if (selectedTextObj == null)
{
return; //no obj, so don't do anything
}
//see if we have a custom annotation for this annotation we selected
LadderInstance currentInstance = m_manager.GetCurrentInstance();
Annotation selectedAnnotation = new Annotation();
foreach (Annotation annotation in currentInstance.annotations)
{
if (annotation.m_point == (PointPair)selectedTextObj.Tag)
{
usingCustomAnnotation = true;
selectedAnnotation = annotation;
currentInstance.annotations.Remove(annotation);
break;
}
}
if (selectedAnnotation.m_point == null && selectedAnnotation.m_text == null)
{
selectedAnnotation.m_showHideAuto = 0;
selectedAnnotation.m_text = selectedTextObj.Text;
selectedAnnotation.m_point = (PointPair)selectedTextObj.Tag;
}
// Open the AnnotationEdit form
PlotView.AnnotationEdit editForm = new PlotView.AnnotationEdit(selectedAnnotation);
if (editForm.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
if (editForm.m_annotation.m_showHideAuto < 0)
{
selectedTextObj.IsVisible = false;
}
else if (editForm.m_annotation.m_showHideAuto > 0)
{
selectedTextObj.IsVisible = true;
}
selectedTextObj.Text = editForm.m_annotation.m_text;
currentInstance.annotations.Add(editForm.m_annotation);
}
else if (usingCustomAnnotation)
{
//recreate the annotation we thought we were replacing
currentInstance.annotations.Add(selectedAnnotation);
}
msPlot.ReevaluateAnnotations();
msPlot.Invalidate();
return;
}
