text += "Protein identification was conducted against a concatenated target/decoy [PMID 20013364] version of the ";
} else {
text += "Protein identification was conducted against a version of the ";
}
FastaIndex fastaIndex = sequenceFactory.getCurrentFastaIndex();
ArrayList<String> species = fastaIndex.getSpecies();
if (species == null || species.isEmpty()) {
text += "[add species]";
} else {
for (int i = 0; i < species.size(); i++) {
if (i > 0) {
if (i == species.size() - 1) {
text += " and ";
} else {
text += ", ";
}
}
text += species;
}
}
text += " complement of the ";
String dbType = fastaIndex.getMainDatabaseType().getFullName();
if (dbType == null) {
dbType = "[add database full name]";
}
String dbRef = fastaIndex.getMainDatabaseType().getPmid();
if (dbRef == null) {
dbRef = "add reference";
} else {
dbRef = "PMID " + dbRef;
}
text += dbType + " [" + dbRef + "] (version of [add database version] , " + fastaIndex.getNTarget() + " (target) sequences).";
return text;
}