+ * If the response status includes + * + *
+ * Content-Type : application/x-gzip + *+ * + * then tries to read as gzipped content. + * + * @param urlStr + * @throws IOException + * @throws MalformedURLException + */ + private void checkURLSource(String urlStr) + throws IOException, MalformedURLException { errormessage = "URL NOT FOUND"; - URL url = new URL(fileStr); - // - // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via - // Kenny Sabir + URL url = new URL(urlStr); + HttpURLConnection conn = (HttpURLConnection) url.openConnection(); + int rc = conn.getResponseCode(); + if (rc != HttpURLConnection.HTTP_OK) + { + throw new IOException( + "Response status from " + urlStr + " was " + rc); + } + String encoding = conn.getContentEncoding(); + String contentType = conn.getContentType(); + boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) + || "gzip".equals(encoding); Exception e = null; - if (fileStr.toLowerCase().endsWith(".gz")) + InputStream inputStream = conn.getInputStream(); + if (isgzipped) { try { - InputStream inputStream = url.openStream(); - dataIn = tryAsGzipSource(inputStream); - dataName = fileStr; - return false; - } catch (Exception ex) + dataIn = getGzipReader(inputStream); + dataName = urlStr; + } catch (Exception e1) { - e = ex; + throw new IOException(MessageManager + .getString("exception.failed_to_resolve_gzip_stream"), e); } + return; } - try - { - dataIn = new BufferedReader(new InputStreamReader(url.openStream())); - } catch (IOException q) - { - if (e != null) - { - throw new IOException( - MessageManager - .getString("exception.failed_to_resolve_gzip_stream"), - e); - } - throw q; - } - // record URL as name of datasource. - dataName = fileStr; - return false; + dataIn = new BufferedReader(new InputStreamReader(inputStream)); + dataName = urlStr; + return; } /** @@ -274,23 +338,47 @@ public class FileParse } /** + * not for general use, creates a fileParse object for an existing reader with + * configurable values for the origin and the type of the source + */ + public FileParse(BufferedReader source, String originString, + DataSourceType sourceType) + { + dataSourceType = sourceType; + error = false; + inFile = null; + dataName = originString; + dataIn = source; + try + { + if (dataIn.markSupported()) + { + dataIn.mark(READAHEAD_LIMIT); + } + } catch (IOException q) + { + + } + } + + /** * Create a datasource for input to Jalview. See AppletFormatAdapter for the * types of sources that are handled. * * @param fileStr * - datasource locator/content - * @param type + * @param sourceType * - protocol of source * @throws MalformedURLException * @throws IOException */ - public FileParse(String fileStr, String type) + public FileParse(String fileStr, DataSourceType sourceType) throws MalformedURLException, IOException { - this.type = type; + this.dataSourceType = sourceType; error = false; - if (type.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { if (checkFileSource(fileStr)) { @@ -301,19 +389,19 @@ public class FileParse { throw new IOException(MessageManager.formatMessage( "exception.problem_opening_file_also_tried", - new String[] { inFile.getName(), suffixLess, - errormessage })); + new String[] + { inFile.getName(), suffixLess, errormessage })); } } else { throw new IOException(MessageManager.formatMessage( - "exception.problem_opening_file", - new String[] { inFile.getName(), errormessage })); + "exception.problem_opening_file", new String[] + { inFile.getName(), errormessage })); } } } - else if (type.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { try { @@ -350,13 +438,13 @@ public class FileParse error = true; } } - else if (type.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { errormessage = "PASTE INACCESSIBLE!"; dataIn = new BufferedReader(new StringReader(fileStr)); dataName = "Paste"; } - else if (type.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { errormessage = "RESOURCE CANNOT BE LOCATED"; java.io.InputStream is = getClass() @@ -382,15 +470,15 @@ public class FileParse else { errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" - + (type != null ? type : "null") + "'"; + + (sourceType != null ? sourceType : "null") + "'"; error = true; } if (dataIn == null || error) { // pass up the reason why we have no source to read from throw new IOException(MessageManager.formatMessage( - "exception.failed_to_read_data_from_source", - new String[] { errormessage })); + "exception.failed_to_read_data_from_source", new String[] + { errormessage })); } error = false; dataIn.mark(READAHEAD_LIMIT); @@ -421,9 +509,9 @@ public class FileParse { return dataIn.readLine(); } - throw new IOException(MessageManager.formatMessage( - "exception.invalid_source_stream", - new String[] { errormessage })); + throw new IOException(MessageManager + .formatMessage("exception.invalid_source_stream", new String[] + { errormessage })); } /** @@ -476,9 +564,8 @@ public class FileParse } else { - throw new IOException( - MessageManager - .getString("error.implementation_error_reset_called_for_invalid_source")); + throw new IOException(MessageManager.getString( + "error.implementation_error_reset_called_for_invalid_source")); } } @@ -589,4 +676,20 @@ public class FileParse } // could also set export/import settings } + + /** + * Returns the preferred feature colour configuration if there is one, else + * null + * + * @return + */ + public FeatureSettingsModelI getFeatureColourScheme() + { + return null; + } + + public DataSourceType getDataSourceType() + { + return dataSourceType; + } }