/**
* Create a publication item.
*
* @param type SHOULD NOT set null
* @param accession SHOULD NOT empty
*/
public PublicationItem(Type type, String accession) {
if (type == null) {
throw new NullPointerException("Publication type can not set null!");
}
if (MZTabUtils.isEmpty(accession)) {
throw new IllegalArgumentException("Publication accession can not empty!");
}
this.type = type;
this.accession = accession;
}
/**
* Find modification type by name with case-insensitive.
*
* @param name SHOULD not be empty.
* @return If not find, return null value.
*/
public static Type findType(String name) {
if (MZTabUtils.isEmpty(name)) {
throw new IllegalArgumentException("Modification type name should not be empty!");
}
Type type;
try {
type = Type.valueOf(name.trim().toUpperCase());
} catch (IllegalArgumentException e) {
type = null;
}
return type;
}
/**
* Create a modification in columns of the protein, peptide, small molecule and PSM sections. The
* structure like: {Type:accession}
*
* <p>NOTICE: {position} is mandatory. However, if it is not known (e.g. MS1 Peptide Mass
* Fingerprinting), "null" must be used. Thus, in construct method we not provide position
* parameter. User can define this by using {@link #addPosition(Integer, CVParam)} method.
*
* @param section SHOULD be {@link Section#Protein}, {@link Section#Peptide}, {@link Section#PSM}
* or {@link Section#Small_Molecule}
* @param type SHOULD NOT be null.
* @param accession SHOULD not be empty.
*/
public Modification(Section section, Type type, String accession) {
if (!section.isData()) {
throw new IllegalArgumentException(
"Section should use Protein, Peptide, PSM or SmallMolecule.");
}
this.section = section;
if (type == null) {
throw new NullPointerException("Modification type should not be null!");
}
this.type = type;
if (MZTabUtils.isEmpty(accession)) {
throw new IllegalArgumentException("Modification accession can not empty!");
}
this.accession = accession;
}
