/**
* Maps database (SO) keys to EMBl keys. It will add any extra qualifiers found in the 3rd column
* of DATABASE_MAP_KEYS.
*
* @param key
* @return
*/
private Key map(final Key key, final QualifierVector qualifiers) {
if (DATABASE_MAP_KEYS == null) initDatabaseMappings();
for (int i = 0; i < DATABASE_MAP_KEYS.length; i++) {
if (key.getKeyString().equals(DATABASE_MAP_KEYS[i][0])) {
Key mappedKey = new Key((String) DATABASE_MAP_KEYS[i][1]);
if (DATABASE_MAP_KEYS[i][2] != null) {
Qualifier newQualifier = (Qualifier) DATABASE_MAP_KEYS[i][2];
if (!getEntryInformation().isValidQualifier(mappedKey, newQualifier.getName())) {
try {
final int nvalues;
if (newQualifier.getValues() == null) nvalues = 0;
else nvalues = newQualifier.getValues().size();
final int type;
if (nvalues == 0) type = QualifierInfo.NO_VALUE;
else type = QualifierInfo.QUOTED_TEXT;
getEntryInformation()
.addQualifierInfo(
new QualifierInfo(newQualifier.getName(), type, null, null, false));
} catch (QualifierInfoException e) {
}
}
qualifiers.addQualifierValues(newQualifier);
}
return mappedKey;
}
}
return key;
}
/**
* Change the name of a qualifier
*
* @param qualifiers
* @param oldName
* @param newName
*/
private void changeQualifierName(
QualifierVector qualifiers, final String oldName, final String newName) {
QualifierVector tmpQualifiers = new QualifierVector();
for (int i = 0; i < qualifiers.size(); i++) {
Qualifier qualifier = (Qualifier) qualifiers.elementAt(i);
if (!qualifier.getName().equals(oldName)) {
tmpQualifiers.addElement(qualifier);
continue;
}
Qualifier newQualifier = new Qualifier(newName, qualifier.getValues());
tmpQualifiers.addQualifierValues(newQualifier);
}
qualifiers.removeAllElements();
for (int i = 0; i < tmpQualifiers.size(); i++)
qualifiers.addElement(tmpQualifiers.elementAt(i));
}
/**
* Read some embl feature qualifiers from a stream into a QualifierVector object. The stream
* should contain qualifiers in this form:
*
* <PRE> /name1=value1/name2="value2"/name3=[value3] </PRE>
*
* @param in_stream the qualifiers are read from this stream
* @exception IOException thrown if there is a problem reading the qualifiers, such as end of
* file.
* @exception QualifierParseException Thrown if the format of the value String is not appropriate
* for a Qualifier with the given name. Each qualifier has a specific format for the value
* part which depends on the name, for example the value part of /codon_start qualifier must
* be a number: 1, 2 or 3.
* @return A Vector containing one Qualifier object for each name/value pair read from the stream.
*/
public static QualifierVector readQualifiers(
final Reader in_stream, final EntryInformation entry_information)
throws QualifierParseException, IOException {
QualifierVector return_vector = new QualifierVector();
BufferedReader buffered_reader = new BufferedReader(in_stream);
String name;
String value;
// loop until end of file
while ((name = StreamQualifier.readName(buffered_reader)) != null) {
// save one character in case the next char is not a '='
buffered_reader.mark(1);
final int next_char = buffered_reader.read();
if (next_char == -1) value = null;
else {
if (next_char == '=') value = StreamQualifier.readValue(buffered_reader);
else {
// this qualifier doesn't have a value
value = null;
buffered_reader.reset();
}
}
final Qualifier new_qualifier;
if (value == null) new_qualifier = new Qualifier(name);
else {
new_qualifier = StreamQualifier.makeStreamQualifier(name, value, entry_information);
}
return_vector.addQualifierValues(new_qualifier);
}
return return_vector;
}
