/**
* Updates the available settings according to the opened file. This should be called e.g. after
* loading a PIA intermediate file
*/
public void applyLoadedSettings(NodeSettingsRO settings) {
checkCreatePSMSets.setSelected(
settings.getBoolean(
PIASettings.CREATE_PSMSETS.getKey(), PIASettings.CREATE_PSMSETS.getDefaultBoolean()));
fdrThreshold.setValue(
settings.getDouble(
PIASettings.FDR_THRESHOLD.getKey(), PIASettings.FDR_THRESHOLD.getDefaultDouble()));
if (settings
.getString(
PIASettings.ALL_DECOY_STRATEGY.getKey(),
PIASettings.ALL_DECOY_STRATEGY.getDefaultString())
.equals(FDRData.DecoyStrategy.ACCESSIONPATTERN.toString())) {
decoyStrategy_pattern.setSelected(true);
} else {
decoyStrategy_searchengine.setSelected(true);
}
decoyPattern_pattern.setText(
settings.getString(
PIASettings.ALL_DECOY_PATTERN.getKey(),
PIASettings.ALL_DECOY_PATTERN.getDefaultString()));
if (settings.getInt(
PIASettings.ALL_USED_IDENTIFICATIONS.getKey(),
PIASettings.ALL_USED_IDENTIFICATIONS.getDefaultInteger())
== 0) {
usedIdentifications_all.setSelected(true);
} else {
usedIdentifications_top.setSelected(true);
}
preferredScoresModel.removeAllElements();
for (String scoreShort :
settings.getStringArray(
PIASettings.FDR_PREFERRED_SCORES.getKey(),
PIASettings.FDR_PREFERRED_SCORES.getDefaultStringArray())) {
ScoreModelEnum modelType = ScoreModelEnum.getModelByDescription(scoreShort);
ScoreModel model;
if (modelType.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
model = new ScoreModel(0.0, scoreShort, scoreShort);
} else {
model = new ScoreModel(0.0, modelType);
}
preferredScoresModel.addElement(model);
}
}
/**
* creates a settings map with the current settings
*
* @param key
* @return
*/
public Map<String, Object> getSettings() {
HashMap<String, Object> settings = new HashMap<String, Object>();
settings.put(PIASettings.CREATE_PSMSETS.getKey(), checkCreatePSMSets.isSelected());
settings.put(PIASettings.FDR_THRESHOLD.getKey(), (Double) fdrThreshold.getValue());
settings.put(
PIASettings.ALL_DECOY_STRATEGY.getKey(),
decoyStrategyGroup.getSelection().getActionCommand());
settings.put(PIASettings.ALL_DECOY_PATTERN.getKey(), decoyPattern_pattern.getText());
settings.put(
PIASettings.ALL_USED_IDENTIFICATIONS.getKey(),
Integer.parseInt(usedIdentificationsGroup.getSelection().getActionCommand()));
String[] preferredScoreShorts = new String[preferredScoresModel.getSize()];
for (int i = 0; i < preferredScoresModel.getSize(); i++) {
preferredScoreShorts[i] = preferredScoresModel.getElementAt(i).getShortName();
}
settings.put(PIASettings.FDR_PREFERRED_SCORES.getKey(), preferredScoreShorts);
return settings;
}