public Enzyme(string name, string cleavage, string restrict, SequenceTerminus type)
: this(name,
type == SequenceTerminus.C ? cleavage : null,
type == SequenceTerminus.C ? restrict : null,
type == SequenceTerminus.N ? cleavage : null,
type == SequenceTerminus.N ? restrict : null)
{
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
string name;
if (!helper.ValidateNameTextBox(textName, out name))
{
return;
}
if (_existing.Contains(m => !ReferenceEquals(_measuredIon, m) && Equals(name, m.Name)))
{
helper.ShowTextBoxError(textName, Resources.EditMeasuredIonDlg_OkDialog_The_special_ion__0__already_exists, name);
return;
}
if (radioFragment.Checked)
{
string cleavage;
if (!ValidateAATextBox(helper, textFragment, false, out cleavage))
{
return;
}
string restrict;
if (!ValidateAATextBox(helper, textRestrict, true, out restrict))
{
return;
}
SequenceTerminus direction = (comboDirection.SelectedIndex == 0 ?
SequenceTerminus.C : SequenceTerminus.N);
int minAas;
if (!helper.ValidateNumberTextBox(textMinAas, MeasuredIon.MIN_MIN_FRAGMENT_LENGTH,
MeasuredIon.MAX_MIN_FRAGMENT_LENGTH, out minAas))
{
return;
}
_measuredIon = new MeasuredIon(name, cleavage, restrict, direction, minAas);
}
else
{
var customIon = ValidateCustomIon(name);
if (customIon == null)
{
return;
}
_measuredIon = customIon;
}
DialogResult = DialogResult.OK;
}
private static string GetRegex(string cleavage, string restrict, SequenceTerminus terminus)
{
if (string.IsNullOrEmpty(cleavage))
{
return(null);
}
string cut = "[" + cleavage + "]"; // Not L10N
string nocut = (string.IsNullOrEmpty(restrict) ? "[A-Z]" : "[^" + restrict + "]"); // Not L10N
return(terminus == SequenceTerminus.C ? cut + nocut : nocut + cut);
}
/// <summary>
/// Constructor for a special fragment
/// </summary>
/// <param name="name">The name by which it is stored in the settings list</param>
/// <param name="fragment">Amino acid residues with weak bonds</param>
/// <param name="restrict">Adjacent amino acids that form stronger bonds</param>
/// <param name="terminus">Terminal side which has the weak bond</param>
/// <param name="minFragmentLength">Minimum length to allow as a special fragment</param>
public MeasuredIon(string name,
string fragment,
string restrict,
SequenceTerminus terminus,
int minFragmentLength)
: base(name)
{
Fragment = fragment;
Restrict = restrict;
Terminus = terminus;
MinFragmentLength = minFragmentLength;
Validate();
}
private static string ToString(string cleavage, string restrict, SequenceTerminus term)
{
if (string.IsNullOrEmpty(cleavage))
{
return(string.Empty);
}
if (string.IsNullOrEmpty(restrict))
{
restrict = "-"; // Not L10N
}
return(term == SequenceTerminus.C
? "[" + cleavage + " | " + restrict + "]" // Not L10N
: "[" + restrict + " | " + cleavage + "]"); // Not L10N
}
/// <summary>
/// Constructor for a special fragment
/// </summary>
/// <param name="name">The name by which it is stored in the settings list</param>
/// <param name="fragment">Amino acid residues with weak bonds</param>
/// <param name="restrict">Adjacent amino acids that form stronger bonds</param>
/// <param name="terminus">Terminal side which has the weak bond</param>
/// <param name="minFragmentLength">Minimum length to allow as a special fragment</param>
public MeasuredIon(string name,
string fragment,
string restrict,
SequenceTerminus terminus,
int minFragmentLength)
: base(name)
{
Fragment = fragment;
Restrict = restrict;
Terminus = terminus;
MinFragmentLength = minFragmentLength;
Charge = 1;
Validate();
}
private static string ToString(string cleavage, string restrict, SequenceTerminus term)
{
if (string.IsNullOrEmpty(cleavage))
{
return(string.Empty);
}
if (string.IsNullOrEmpty(restrict))
{
restrict = @"-";
}
return(term == SequenceTerminus.C
? @"[" + cleavage + @" | " + restrict + @"]"
: @"[" + restrict + @" | " + cleavage + @"]");
}
public Protease(string cleavage, string restrict, SequenceTerminus type)
{
Cleavage = cleavage;
Restrict = restrict;
Type = type;
}
private static string ToString(string cleavage, string restrict, SequenceTerminus term)
{
if (string.IsNullOrEmpty(cleavage))
return string.Empty;
if (string.IsNullOrEmpty(restrict))
restrict = "-"; // Not L10N
return term == SequenceTerminus.C
? "[" + cleavage + " | " + restrict + "]" // Not L10N
: "[" + restrict + " | " + cleavage + "]"; // Not L10N
}
private static string GetRegex(string cleavage, string restrict, SequenceTerminus terminus)
{
if (string.IsNullOrEmpty(cleavage))
return null;
string cut = "[" + cleavage + "]"; // Not L10N
string nocut = (string.IsNullOrEmpty(restrict) ? "[A-Z]" : "[^" + restrict + "]"); // Not L10N
return terminus == SequenceTerminus.C ? cut + nocut : nocut + cut;
}
public Enzyme(string name, string cleavage, string restrict, SequenceTerminus type)
: this(name,
type == SequenceTerminus.C ? cleavage : null,
type == SequenceTerminus.C ? restrict : null,
type == SequenceTerminus.N ? cleavage : null,
type == SequenceTerminus.N ? restrict : null)
{
}
public Protease(string cleavage, string restrict, SequenceTerminus type)
{
Cleavage = cleavage;
Restrict = restrict;
Type = type;
}