/**
* Returns a list of descriptions corresponding to every item matching the search.
*
* @return a list of descriptions
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
public ArrayList<String> getPossibilitiesDescriptions()
throws SQLException, ClassNotFoundException, IOException, InterruptedException {
Identification identification = reporterGUI.getIdentification();
// some necessary pre-caching
ArrayList<Type> typeList = types.get(jumpType);
ArrayList<String> keys = possibilities.get(jumpType);
ArrayList<String> proteinKeys = new ArrayList<String>();
for (int i = 0; i < keys.size(); i++) {
String key = keys.get(i);
if (typeList.get(i) == Type.PROTEIN) {
proteinKeys.add(key);
}
}
if (!proteinKeys.isEmpty()) {
identification.loadProteinMatches(proteinKeys, null, false);
}
ArrayList<String> descriptions = new ArrayList<String>();
for (int i = 0; i < keys.size(); i++) {
String key = keys.get(i);
Type type = typeList.get(i);
String description = getItemDescription(key, type);
descriptions.add(description);
}
return descriptions;
}
/** Updates the item selection in the selected tab. */
public void updateSelectionInTab() {
indexLabel.setForeground(Color.BLACK);
if (types.get(jumpType).get(currentSelection.get(jumpType)) == Type.PROTEIN) {
String selectedProtein = possibilities.get(jumpType).get(currentSelection.get(jumpType));
ArrayList<String> selectedProteins = new ArrayList<String>();
selectedProteins.add(selectedProtein);
reporterGUI.minimizeChart();
reporterGUI.setSelectedProteins(selectedProteins, true, true);
}
String label =
"("
+ (currentSelection.get(jumpType) + 1)
+ " of "
+ possibilities.get(jumpType).size()
+ ")";
indexLabel.setText(label);
lastLabel.put(jumpType, label);
}
/**
* Returns the description of an item.
*
* @param key the key of the item
* @param itemType the type of the item
* @return the description of an item
* @throws SQLException thrown if an SQLException occurs
* @throws ClassNotFoundException thrown if a ClassNotFoundException occurs
* @throws IOException thrown if an IOException occurs
* @throws InterruptedException thrown if an InterruptedException occurs
*/
private String getItemDescription(String key, Type itemType)
throws IllegalArgumentException, SQLException, IOException, ClassNotFoundException,
InterruptedException {
Identification identification = reporterGUI.getIdentification();
switch (itemType) {
case PROTEIN:
ProteinMatch proteinMatch = identification.getProteinMatch(key);
String mainMatch = proteinMatch.getMainMatch();
String description = sequenceFactory.getHeader(mainMatch).getSimpleProteinDescription();
String result = mainMatch;
for (String accession : ProteinMatch.getAccessions(key)) {
if (!accession.equals(mainMatch)) {
if (!result.equals(mainMatch)) {
result += ", ";
}
result += accession;
}
}
result += " - " + description;
return result;
default:
return "Unknown";
}
}
