private static EnzymeType makeEnzymeType() {
EnzymeType enzymeType = new EnzymeType();
enzymeType.setId("Enz1");
enzymeType.setCTermGain("OH");
enzymeType.setNTermGain("H");
enzymeType.setMinDistance(1);
return enzymeType;
}
public static EnzymeType makeNoEnzyme() {
EnzymeType enzymeType = new EnzymeType();
enzymeType.setId("Enz1");
ParamListType nameParam = new ParamListType();
nameParam
.getParamGroup()
.add(CvParamMaker.getInstance().make("MS:1001091", "NoEnzyme", CvConstants.PSI_CV));
enzymeType.setEnzymeName(nameParam);
return enzymeType;
}
public static EnzymeType makeLysC_OR_TrypsinK() {
/*
[Term]
id: MS:1001310
name: Lys-C/P
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001336 ! (?<=K)
*/
EnzymeType enzymeType = makeEnzymeType();
ParamListType nameParam = new ParamListType();
nameParam
.getParamGroup()
.add(CvParamMaker.getInstance().make("MS:1001310", "Lys-C/P", CvConstants.PSI_CV));
enzymeType.setEnzymeName(nameParam);
return enzymeType;
}
public static EnzymeType makeModifiedChymotrypsin() {
/*
[Term]
id: MS:1001306
name: Chymotrypsin
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P)
*/
EnzymeType enzymeType = makeEnzymeType();
ParamListType nameParam = new ParamListType();
nameParam
.getParamGroup()
.add(CvParamMaker.getInstance().make("MS:1001306", "Chymotrypsin", CvConstants.PSI_CV));
enzymeType.setEnzymeName(nameParam);
return enzymeType;
}
public static EnzymeType makeArgC_OR_TrypsinR() {
// 9. Trypsin_R 1 R P
/*
[Term]
id: MS:1001303
name: Arg-C
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001272 ! (?<=R)(?!P)
*/
EnzymeType enzymeType = makeEnzymeType();
ParamListType nameParam = new ParamListType();
nameParam
.getParamGroup()
.add(CvParamMaker.getInstance().make("MS:1001303", "Arg-C", CvConstants.PSI_CV));
enzymeType.setEnzymeName(nameParam);
return enzymeType;
}
public static EnzymeType makeCyanogenBromide() {
// 4. Cyanogen_Bromide 1 M -
/*
[Term]
id: MS:1001307
name: CNBr
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001333 ! (?<=M)
*/
EnzymeType enzymeType = makeEnzymeType();
ParamListType nameParam = new ParamListType();
nameParam
.getParamGroup()
.add(CvParamMaker.getInstance().make("MS:1001307", "CNBr", CvConstants.PSI_CV));
enzymeType.setEnzymeName(nameParam);
return enzymeType;
}
public static EnzymeType makeTrypsin() {
// 1. Trypsin 1 KR P
/*
[Term]
id: MS:1001251
name: Trypsin
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P)
*/
EnzymeType enzymeType = makeEnzymeType();
ParamListType nameParam = new ParamListType();
nameParam
.getParamGroup()
.add(CvParamMaker.getInstance().make("MS:1001251", "Trypsin", CvConstants.PSI_CV));
enzymeType.setEnzymeName(nameParam);
return enzymeType;
}
