public InstrumentParam(Instrument[] instruments, CVLookUp cv)
: base(null)
{
_cv = cv;
_count = instruments.Length;
Value = instruments;
Default = instruments;
}
public ModificationParam(Mod[] contacts, CVLookUp cv)
: base(null)
{
_cv = cv;
_count = contacts.Length;
Value = contacts;
Default = contacts;
}
public SampleProcessingParam(SplitList<Lib.Model.Param>[] steps, CVLookUp cv)
: base(null)
{
_cv = cv;
_count = steps.Length;
Value = steps;
Default = steps;
}
public ContactParam(Contact[] contacts, CVLookUp cv)
: base(null)
{
_cv = cv;
_count = contacts.Length;
Value = contacts;
Default = contacts;
}
public PublicationParam(Publication[] publications, CVLookUp cv)
: base(null)
{
_cv = cv;
_count = publications.Length;
Value = publications;
Default = publications;
}
public SoftwareParam(Software[] software, CVLookUp cv, Dictionary<string, string> parameters)
: base(null)
{
_count = software.Length;
_cv = cv;
_parameters = parameters;
Value = software;
Default = software;
}
public AssayParam(int count, Assay[] assays, bool reduced, CVLookUp cv, string name = null)
: base(name)
{
_reduced = reduced;
_cv = cv;
_count = count;
Value = assays;
Default = assays;
}
public SampleProcessingPanel(SplitList<Lib.Model.Param>[] steps, CVLookUp cv)
{
_cv = cv;
_count = steps.Length;
InitializeComponent();
Value = steps;
}
public SampleParam(Sample[] samples, bool reduced, CVLookUp cv, string name = null)
: base(name)
{
_reduced = reduced;
_cv = cv;
_count = samples == null ? 0 : samples.Length;
Value = samples;
Default = samples;
}
public StudyVariableParam(StudyVariable[] studyVariables, bool reduced, CVLookUp cv, string name = null)
: base(name)
{
_reduced = reduced;
_cv = cv;
_count = studyVariables.Length;
Value = studyVariables;
Default = studyVariables;
}
public MsRunPanel1(int count, MsRunImpl[] msRunsImpl, CVLookUp cv)
{
_count = count;
_cv = cv;
InitializeComponent();
Value = msRunsImpl;
}
public MsRunParam(int groups, MsRunImpl[] msRunsImpl, CVLookUp cv, bool compact, string name = null)
: base(name)
{
_count = groups;
_cv = cv;
_compact = compact;
Value = msRunsImpl;
Default = msRunsImpl;
}
public ModificationPanel(Mod[] value, CVLookUp cv)
{
_count = value.Length;
_type = value.Length > 0 && value.First() != null ? value.First().Element : MetadataElement.FIXED_MOD;
_cv = cv;
InitializeComponent();
Value = value;
}
public SamplePanel(Sample[] value, bool variable, CVLookUp cv)
{
_variable = variable;
_cv = cv;
_count = value == null ? 0 : value.Length;
InitializeComponent();
Value = value;
}
public InstrumentPanel(Instrument[] instruments, CVLookUp cv)
{
_cv = cv;
_count = instruments.Length;
_defaultName = _cv.GetNameOfTerm("MS:1000449", "MS");
_defaultSource = _cv.GetNameOfTerm("MS:1000073", "MS");
_defaultAnalyzer = _cv.GetNameOfTerm("MS:1000484", "MS");
_defaultDetector = null;
InitializeComponent();
Value = instruments;
}
public SoftwarePanel(Software[] value, CVLookUp cv, Dictionary<string, string> parameters)
{
MaxWidth = 800;
_count = value.Length;
_cv = cv;
_parameters = parameters;
defaultName = _cv.GetNameOfTerm("MS:1001583", "MS");
defaultVersion = parameters.ContainsKey("Version") ? parameters["Version"] : null;
InitializeComponent();
Value = value;
}
public AssayPanel2(int count, Assay[] value, CVLookUp cv)
{
_cv = cv;
_count = count;
foreach (var assay in value){
if (assay == null){
continue;
}
if (assay.MsRun != null){
_msRunText.Add(MsRunToString(assay.MsRun));
_msRunList.Add(assay.MsRun as MsRunImpl);
}
if (assay.Sample != null){
_sampleText.Add(SampleToString(assay.Sample));
_sampleList.Add(assay.Sample);
}
}
_uniqueSamples = ArrayUtils.UniqueValues(_sampleText);
InitializeComponent();
Value = value;
}
public AssayPanel1(int count, Assay[] value, CVLookUp cv)
{
_cv = cv;
_count = count;
InitializeComponent();
Value = value;
}
protected IEnumerable<AssayQuantificationMod> GetModifications(Assay assay, ListSelectorControl listBox,
CVLookUp cv)
{
List<AssayQuantificationMod> result = new List<AssayQuantificationMod>();
foreach (var item in listBox.SelectedItems){
string name = item.ToString();
Lib.Model.Param param = cv.GetParam(name, "MOD");
if (param == null){
continue;
}
string position = null;
string site = null;
if (Tables.Modifications.ContainsKey(name)){
var m = Tables.Modifications[name];
if (m != null){
switch (m.Position){
case ModificationPosition.anywhere:
position = "Anywhere";
break;
case ModificationPosition.anyNterm:
position = "Any N-term";
break;
case ModificationPosition.anyCterm:
position = "Any C-term";
break;
case ModificationPosition.proteinNterm:
position = "Protein N-term";
break;
case ModificationPosition.proteinCterm:
position = "Protein C-term";
break;
default:
position = m.Position.ToString();
break;
}
site = m.GetSiteArray() != null ? StringUtils.Concat("|", m.GetSiteArray()) : "-";
}
}
result.Add(new AssayQuantificationMod(assay, result.Count + 1){
Param = param,
Position = position,
Site = site
});
}
return result;
}
protected Assay GetAssay(int id, int _count, string text, CVLookUp _cv)
{
Assay assay = new Assay(id);
if (!string.IsNullOrEmpty(text)){
assay.QuantificationReagent = _cv.GetParam(text, "PRIDE");
}
return assay;
}
public MsRunPanel2(int count, MsRunImpl[] msRunsImpl, CVLookUp cv)
{
HorizontalAlignment = HorizontalAlignment.Stretch;
_cv = cv;
_count = count;
_defaultFormat = new string[2];
_defaultFormat[0] = _cv.GetNameOfTerm("MS:1000563", "MS");
_defaultFormat[1] = _cv.GetNameOfTerm("Andromeda Peak list file", "MS");
_defaultIdFormat = new string[2];
_defaultIdFormat[0] = _cv.GetNameOfTerm("MS:1000768", "MS");
_defaultIdFormat[1] = _cv.GetNameOfTerm("MS:1000774", "MS");
InitializeComponent();
Value = msRunsImpl;
}
