public void add(final T line) {
if (standards.containsKey(line.getID())) {
throw new TribbleException(
"Attempting to add multiple standard header lines for ID " + line.getID());
}
standards.put(line.getID(), line);
}
public T repair(final T line) {
final T standard = get(line.getID(), false);
if (standard != null) {
final boolean badCountType = line.getCountType() != standard.getCountType();
final boolean badCount =
line.isFixedCount() && !badCountType && line.getCount() != standard.getCount();
final boolean badType = line.getType() != standard.getType();
final boolean badDesc = !line.getDescription().equals(standard.getDescription());
final boolean needsRepair =
badCountType || badCount || badType || (REPAIR_BAD_DESCRIPTIONS && badDesc);
if (needsRepair) {
if (GeneralUtils.DEBUG_MODE_ENABLED) {
System.err.println(
"Repairing standard header line for field "
+ line.getID()
+ " because"
+ (badCountType
? " -- count types disagree; header has "
+ line.getCountType()
+ " but standard is "
+ standard.getCountType()
: "")
+ (badType
? " -- type disagree; header has "
+ line.getType()
+ " but standard is "
+ standard.getType()
: "")
+ (badCount
? " -- counts disagree; header has "
+ line.getCount()
+ " but standard is "
+ standard.getCount()
: "")
+ (badDesc
? " -- descriptions disagree; header has '"
+ line.getDescription()
+ "' but standard is '"
+ standard.getDescription()
+ "'"
: ""));
}
return standard;
} else {
return line;
}
} else {
return line;
}
}
public String getID() {
if (last == null) {
return null;
}
return last.getID();
}
protected void notifyMediaListeners(T media, Change change) {
if (!canRaiseEvents) {
return;
}
for (ListChangeHandler<T> lch : listeners) {
lch.listChanged(this, change, media.getID(), media);
}
}
/**
* Checks for equality.
*
* @param o the object to check equality against.
* @return <code>true</code> if the object is of the right class and has the same identifier.
*/
@Override
public final boolean equals(final Object o) {
if (this == o) {
return true;
}
if (!checkClass(o)) {
return false;
}
T that = (T) o;
return that.hashCode() == hashCode && id.equals(that.getID());
}
protected void dumpMap() {
try {
tmpFileIndex++;
String outfile = tmpDIR + "/" + tmpFileIndex + ".tmp";
logger.info("dumping memory to file: " + outfile);
PrintStream tmpContentFile = new PrintStream(outfile);
TIntObjectIterator<T> it = id2item.iterator();
while (it.hasNext()) {
it.advance();
T item = it.value();
tmpContentFile.print(item.getID());
tmpContentFile.print("\t");
tmpContentFile.print(Serialization.serialize(item));
tmpContentFile.print("\n");
it.remove();
}
tmpContentFile.close();
} catch (Exception e) {
logger.error(e.toString());
}
}
/**
* Adds a new profile to this typing data, if there is not already an equal one. The new profile
* should have values for all the features considered in this typing data. Otherwise, it will not
* be added.
*
* @param profile the new profile to be added.
* @return the inserted profile.
* @throws Exception on unsuccess.
*/
public T addData(T profile) throws Exception {
// Do we have values for all fields?
if (profile.profileLength() != headers.length - 1) {
throw new Exception(
"Incompatible length: "
+ profile.getID()
+ " has length"
+ profile.profileLength()
+ "(!="
+ (headers.length - 1)
+ ")");
}
if (unique.contains(profile)) {
throw new Exception(
"Duplicated profile: " + profile.getID() + " aka " + this.getEqual(profile).getID());
}
if (idset.contains(profile.getID())) {
throw new Exception("Duplicated profile ID: " + profile.getID());
}
domains[0].add(profile.getID());
for (int i = 0; i < profile.profileLength(); i++) {
domains[i + 1].add(profile.getValue(i));
}
collection.add(profile);
unique.add(profile);
idset.add(profile.getID());
weightOk = false;
return profile;
}
public void addMedia(T media) {
mediaCache.put(media.getID(), media);
notifyMediaListeners(media, Change.ADDED);
}
/**
* Compares two identifiers lexicographically.
*
* @param t the identifiable to compare to.
* @return the value <code>0</code> if the argument identifier is equal to this identifier; a
* value less than <code>0</code> if this identifier is lexicographically less than the
* identifier argument; and a value greater than <code>0</code> if this identifier is
* lexicographically greater than the identifier argument.
*/
public final int compareTo(final T t) {
return getID().compareTo(t.getID());
}
public int compare(T a, T b) {
return CUtil.getStringCompare().compare(a.getID() + "", b.getID() + "");
}
public void setSelecte(T unit) {
list.setSelectedValue(unit, true);
if (unit != null) {
text_unit_name.setText(unit.getID() + "");
}
}