/// <summary>
/// This function handle is called from both the fragmentladder and the dataview.
/// This function handles the case when the user selects a peptide and scan number in dataview.
/// </summary>
/// <param name="ScanNumber">The scan number that relates to the experimental data.</param>
/// <param name="Peptide">The peptide sequence.</param>
public void HandleSelectScanAndPeptide(string ScanNumber, string Peptide)
{
DataLoaded = true;
try
{
SpectrumLook.Views.FragmentLadderView.LadderInstanceBuilder ladderBuilder = new Views.FragmentLadderView.LadderInstanceBuilder();
m_currentScanNumber = Convert.ToInt32(ScanNumber);
m_currentPeptide = Peptide;
//use the builder director to crunch all the data
List <Element> theoreticalList = m_builderDirector.BuildTheoryList(Peptide, m_isFragmentationModeETD, this.m_fragLadder.fragmentLadderOptions.modificationList);
m_experimentalList = m_builderDirector.BuildActualList(Convert.ToInt32(ScanNumber), m_dataFileLocation);
List <Element> comparedList = m_builderDirector.BuildComparedList(m_mainForm.m_currentOptions.toleranceValue, m_mainForm.m_currentOptions.lowerToleranceValue, m_experimentalList, PrecursorMZ, ref theoreticalList);
//now give the data to the views to display
//Send the FragmentLadder and the Plot the data to show
if (m_ladderInstancesTable.ContainsKey(ScanNumber + Peptide))
{
m_currentInstance = m_ladderInstancesTable[ScanNumber + Peptide][0];
m_fragLadder.generateLadderFromSelection(0.0, m_ladderInstancesTable[ScanNumber + Peptide]);
}
else
{
List <LadderInstance> tempList = new List <LadderInstance>();
LadderInstance tempInstance = ladderBuilder.GenerateInstance(theoreticalList, Peptide, m_fragLadder.fragmentLadderOptions.modificationList);
tempInstance.scanAndPeptide = ScanNumber + "|" + Peptide;
tempList.Add(tempInstance);
m_ladderInstancesTable.Add(ScanNumber + Peptide, tempList);
m_currentInstance = m_ladderInstancesTable[ScanNumber + Peptide][0];
m_fragLadder.generateLadderFromSelection(0.0, m_ladderInstancesTable[ScanNumber + Peptide]);
}
m_plot.PlotData(comparedList, ScanNumber, Peptide);
//m_experimentalList.Clear();
//m_experimentalList = null;
}
catch (InvalidProgramException ex)
{
if (ex.Message.Contains("Invalid File Type"))
{
MessageBox.Show("Invalid File Type for the Data file. Only .mzXml, .mzData, and .raw types are allowed.", "File Type Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
else
{
throw ex;
}
}
}
/// <summary>
/// This function handles recalculating all the ladder instances in the hashtable.
/// This is normally called when the fragment ladder options change.
/// </summary>
public void HandleRecalculateAllInHashCode()
{
//Get all the Keys in the HashTable.
string[] allKeyValues = m_ladderInstancesTable.Keys.ToArray();
SpectrumLook.Views.FragmentLadderView.LadderInstanceBuilder ladderBuilder = new Views.FragmentLadderView.LadderInstanceBuilder();
foreach (string currentKey in allKeyValues)
{
List <LadderInstance> currentLadderInstances = m_ladderInstancesTable[currentKey];
m_ladderInstancesTable.Remove(currentKey);
List <LadderInstance> newInstanceList = new List <LadderInstance>();
foreach (LadderInstance currentInstance in currentLadderInstances)
{
//Give Theoretical List the modified Peptide
//Assuming The Frag ladder will add the PeptideString of the modified thing.
List <Element> theoreticalList = m_builderDirector.BuildTheoryList(currentInstance.PeptideString, m_isFragmentationModeETD, this.m_fragLadder.fragmentLadderOptions.modificationList);
//Give experimental List the original Peptide.
//WARNING : ASSUMEING THE SCAN NUMBER KEY IS AN INTERGER
//THIS MAY NOT BE THE CASE IF PARSER CHANGES
List <Element> experimentalList = m_builderDirector.BuildActualList(int.Parse(currentInstance.scanNumberString), m_dataFileLocation);
//build the compared list
List <Element> comparedList = m_builderDirector.BuildComparedList(m_mainForm.m_currentOptions.toleranceValue, m_mainForm.m_currentOptions.lowerToleranceValue, experimentalList, PrecursorMZ, ref theoreticalList);
//Generate the Instance based on the builder.
LadderInstance newLadder = ladderBuilder.GenerateInstance(theoreticalList, currentInstance.PeptideString, m_fragLadder.fragmentLadderOptions.modificationList);
newLadder.scanAndPeptide = currentInstance.scanAndPeptide;
//Add to List
newInstanceList.Add(newLadder);
}
//Add List Of Instances to the HashTable.
m_ladderInstancesTable.Add(currentKey, newInstanceList);
}
if (m_ladderInstancesTable.Count > 0)
{
m_currentInstance = m_ladderInstancesTable[m_currentScanNumber + m_currentPeptide][0];
m_fragLadder.generateLadderFromSelection(0.0, m_ladderInstancesTable[m_currentScanNumber + m_currentPeptide]);
}
}
/// <summary>
/// This handle is called from the fragmentLadder.
/// This is created for the purpose of adding a modified peptide to the current Instance List.
/// </summary>
/// <param name="Peptide">A peptide string.</param>
public bool HandleInputPeptide(string Peptide)
{
if (m_currentScanNumber == 0)
{
MessageBox.Show(
"Please open a synopsis and data file and then load a scan from the data view to calculate: \"" +
Peptide + "\"");
return(false);
}
if (Peptide.Length == 1)
{
MessageBox.Show("Invalid peptide string (single character.");
return(false);
}
/*MG: Generating a regular expression string with the current modification
* symbols to check if the peptide string from the user is a valid peptide string.
* if its not, giving feedback to user and returning out*/
string modList = new string(m_fragLadder.fragmentLadderOptions.modificationList.Keys.ToArray());
string escapedModList = "";
// The manual way, based on a list of metacharacters that need to be escaped
/*foreach (char c in modList)
* {
* // Characters that must be escaped: \[^$.|?*+(){}
* if ("\\[^$.|?*+(){}".Contains(c))
* {
* escapedModList += "\\" + c;
* }
* else
* {
* escapedModList += c;
* }
* }*/
// The automatic way, using .NET
escapedModList = System.Text.RegularExpressions.Regex.Escape(modList);
// One or more characters, A-Z, which may be followed by a valid modification symbol, that does not end with a modification symbol be itself?
// The escaping of all symbols is likely a problem.
//string spattern = "^([A-Z]{1,}[" + escapedModList + "]{0,1})*[^" + escapedModList + "]$";
// Match any set of one or more groups of "character a-z followed by 0-2 valid modification symbols"
string spattern = "([A-Z][" + escapedModList + "]{0,5})+";
// This test will always be evaluate to 'not false' whenever there are lowercase characters or symbols that are not in the modification list,
// or if the peptide begins with a modification symbol.
// TODO: can a peptide begin with a modification symbol? (Not with any software Matt Monroe has written/uses - put mod after first amino acid)
if (!System.Text.RegularExpressions.Regex.IsMatch(Peptide, "^" + spattern + "$"))
{
// Get a string with all invalid characters
string invalid = System.Text.RegularExpressions.Regex.Replace(Peptide, spattern, "");
if (modList.Contains(Peptide[0]))
{
MessageBox.Show("The peptide string cannot start with a modification.");
return(false);
}
if (System.Text.RegularExpressions.Regex.Replace(invalid, "[" + escapedModList + "]", "").Length == 0)
{
MessageBox.Show("Invalid peptide string: Too many modifications on a single amino acid.");
return(false);
}
MessageBox.Show("Invalid characters in peptide string \"" + invalid + "\", please remove the characters or define them in options/fragment ladder");
return(false);
}
// check to see if peptide exists in the ladder instances table and don't add a modification if it does
bool is_same = false;
foreach (var instance in m_ladderInstancesTable[m_currentScanNumber.ToString() + m_currentPeptide])
{
if (instance.PeptideString == Peptide)
{
is_same = true;
}
}
if (!is_same)
{
SpectrumLook.Views.FragmentLadderView.LadderInstanceBuilder ladderBuilder =
new Views.FragmentLadderView.LadderInstanceBuilder();
//use the builder director to crunch all the data
List <Element> theoreticalList = m_builderDirector.BuildTheoryList(Peptide, m_isFragmentationModeETD,
this.m_fragLadder.fragmentLadderOptions.modificationList);
List <Element> comparedList =
m_builderDirector.BuildComparedList(m_mainForm.m_currentOptions.toleranceValue,
m_mainForm.m_currentOptions.lowerToleranceValue, m_experimentalList, PrecursorMZ, ref theoreticalList);
//now give the data to the views to display
//Send the FragmentLadder and the Plot the data to show
if (m_ladderInstancesTable.ContainsKey(m_currentScanNumber.ToString() + m_currentPeptide))
{
m_currentInstance = ladderBuilder.GenerateInstance(theoreticalList, Peptide,
m_fragLadder.fragmentLadderOptions.modificationList);
m_currentInstance.scanAndPeptide = m_currentScanNumber.ToString() + "|" + Peptide;
m_ladderInstancesTable[m_currentScanNumber.ToString() + m_currentPeptide].Add(m_currentInstance);
m_currentInstance = m_ladderInstancesTable[m_currentScanNumber.ToString() + m_currentPeptide][0];
m_fragLadder.generateLadderFromSelection(0.0, m_ladderInstancesTable[m_currentScanNumber.ToString() + m_currentPeptide]);
m_plot.PlotData(comparedList, m_currentScanNumber.ToString(), Peptide);
}
else
{
m_plot.PlotData(comparedList, m_currentScanNumber.ToString(), m_currentPeptide);
}
return(true);
}
return(false);
}