private void onProfileChange(String oldProfileName) {
SharedPreferences settings = PreferenceManager.getDefaultSharedPreferences(this);
mProfile.getProfile(settings);
Editor ed = settings.edit();
ed.putString(oldProfileName, mProfile.toString());
ed.commit();
String profileString = settings.getString(profile, "");
if (profileString.equals("")) {
mProfile.init();
mProfile.setName(getProfileName(profile));
} else {
mProfile.decodeJson(profileString);
}
hostText.setText(mProfile.getHost());
userText.setText(mProfile.getUser());
passwordText.setText(mProfile.getPassword());
domainText.setText(mProfile.getDomain());
certificateText.setText(mProfile.getCertificate());
proxyTypeList.setValue(mProfile.getProxyType());
ssidList.setValue(mProfile.getSsid());
isAuthCheck.setChecked(mProfile.isAuth());
isNTLMCheck.setChecked(mProfile.isNTLM());
isAutoConnectCheck.setChecked(mProfile.isAutoConnect());
isAutoSetProxyCheck.setChecked(mProfile.isAutoSetProxy());
isBypassAppsCheck.setChecked(mProfile.isBypassApps());
isDNSProxyCheck.setChecked(mProfile.isDNSProxy());
isPACCheck.setChecked(mProfile.isPAC());
portText.setText(Integer.toString(mProfile.getPort()));
Log.d(TAG, mProfile.toString());
mProfile.setProfile(settings);
}
private void loadList(JList list) {
list.removeAll();
List<Profile> profiles = getProfiles();
DefaultListModel model = new DefaultListModel();
int i = 0;
int foundLastProfile = -1;
for (Profile p : profiles) {
model.addElement(p);
if (p.toString().equals(Base.preferences.get("lastGeneratorProfileSelected", "---"))) {
Base.logger.fine("Selecting last used element: " + p);
foundLastProfile = i;
}
i++;
}
list.setModel(model);
list.clearSelection();
if (foundLastProfile != -1) {
list.setSelectedIndex(foundLastProfile);
generate.setEnabled(true);
generate.requestFocusInWindow();
generate.setFocusPainted(true);
}
}
void save(Profile profile)
{
Validate.notNull(profile, "profile");
profile = profile.toJSONObject();
if (profile != null)
{
sharedPreferences.edit().putString("com.facebook.ProfileManager.CachedProfile", profile.toString()).apply();
}
}
private void computeCorrelations() {
log.info("Filling repository with most correlated profiles");
List<String> referenceProfile;
for (AssayType assayType : AssayType.values()) {
referenceProfile = getReferenceProfile(assayType);
List<Profile> profiles = profileRepository.findByAssayType(assayType);
String[] profileNames = new String[profiles.size()];
double[][] distanceMatrix = new double[profiles.size()][profiles.size()];
int i = 0;
for (Profile profileA : profiles) {
profileNames[i] = profileA.getId().toString();
Double maxPearson = Double.MIN_VALUE;
Profile maxProfile = profileA;
int j = 0;
for (Profile profileB : profiles) {
if (profileA.equals(profileB)) {
distanceMatrix[i][j] = 0;
j++;
continue;
}
double[] vectorA = profileA.getVector();
double[] vectorB = profileB.getVector();
PearsonsCorrelation pearson = new PearsonsCorrelation();
Double pearsonCorrelation = pearson.correlation(vectorA, vectorB);
if (pearsonCorrelation >= maxPearson) {
maxPearson = pearsonCorrelation;
maxProfile = profileB;
}
double[] profileAasDouble = UtilsTransform.intArrayToDouble(profileA.getColors());
double[] profileBasDouble = UtilsTransform.intArrayToDouble(profileB.getColors());
Double pearsonOfColors = pearson.correlation(profileAasDouble, profileBasDouble);
distanceMatrix[i][j] = pearsonOfColors;
j++;
}
profileA.setCorrelatedVector(maxProfile.getListWrapper());
SortedSet<StringDouble> positivePeptides =
UtilsStatistics.influentialPeptides(
profileA.getVector(), maxProfile.getVector(), referenceProfile, true);
profileA.setPositivePeptides(UtilsTransform.SortedSetToHTML(positivePeptides, false));
DecimalFormat df = new DecimalFormat("0.0000");
String peptideCorrelation = " <br/><br/><b style=\"color: #23527c;\">%s</b>";
profileA.setPositiveCorrelation(
maxProfile.toString() + String.format(peptideCorrelation, df.format(maxPearson)));
profileRepository.save(profileA);
i++;
}
}
}
@Override
public String toString() {
return "P: " + profile.toString() + " L: " + level.toString();
}