+ public static void setStartupFilesFromParameterString(String p) {
+ // multiple files *might* be passed in as space separated quoted filenames
+ String q = "\"";
+ if (!StringUtil.isBlank(p)) {
+ String[] filenames;
+ // split quoted params or treat as single string array
+ if (p.startsWith(q) && p.endsWith(q)) {
+ // this fails if, e.g.
+ // p=q("stupidfilename\" " "otherfilename")
+ // let's hope no-one ever ends a filename with '" '
+ filenames = p.substring(q.length(),p.length()-q.length()).split(q+" "+q);
+ } else {
+ // single unquoted filename
+ filenames = new String[]{p};
+ }
+
+ // check for locator file. Only allow one locator file to be double clicked (if multiple files opened, ignore locator files)
+ String locatorFilename = filenames.length >= 1 ? filenames[0] : null;
+ if (
+ !StringUtil.isBlank(locatorFilename)
+ && locatorFilename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)
+ ) {
+ setLocatorFile(locatorFilename);
+ // remove the locator filename from the filenames array
+ String[] otherFilenames = new String[filenames.length - 1];
+ System.arraycopy(filenames, 1, otherFilenames, 0, otherFilenames.length);
+ filenames = otherFilenames;
+ }
+
+ for (int i = 0; i < filenames.length; i++) {
+ String filename = filenames[i];
+ // skip any other locator files in a multiple file list
+ if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) {
+ setJalviewUri(filename);
+ } else if (! filename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+ addStartupFile(filename);
+ }
+ }
+ }
+ }
+
+ public static void setLocatorFile(String filename) {
+ _locatorFile = new File(filename);
+ }
+
+ public static void addStartupFile(String filename) {
+ _startupFiles.add(new File(filename));
+ }
+
+ public static void setJalviewUri(String uri) {
+ _jalviewUri = uri;
+ }
+
+ private Config createLocatorConfig(Config.ParseOpts opts) {
+ if (_locatorFile == null) {
+ return null;
+ }
+
+ Config locatorConfig = null;
+
+ try {
+ Config tmpConfig = null;
+ Map<String, Object> tmpData = new HashMap<>();
+ if (_locatorFile.exists()) {
+ tmpConfig = Config.parseConfig(_locatorFile, opts);
+ // appbase is sanitised in HostWhitelist
+ Map<String, Object> tmpConfigData = tmpConfig.getData();
+ if (tmpConfig != null) {
+ for (Map.Entry<String, Object> entry : tmpConfigData.entrySet()) {
+ String key = entry.getKey();
+ Object value = entry.getValue();
+ String mkey = key.indexOf('.') > -1 ? key.substring(key.indexOf('.') + 1) : key;
+ if (Config.allowedReplaceKeys.contains(mkey) || Config.allowedMergeKeys.contains(mkey)) {
+ tmpData.put(key, value);
+ }
+ }
+ } else {
+ log.warning("Error occurred reading config file", "file", _locatorFile);
+ }
+ } else {
+ log.warning("Given locator file does not exist", "file", _locatorFile);
+ }
+
+ locatorConfig = new Config(tmpData);
+
+ } catch (Exception e) {
+ log.warning("Failure reading locator file", "file", _locatorFile, e);
+ }
+
+ return locatorConfig;
+ }
+
+ public String getAppbase() {
+ return _appbase;
+ }
+