+ * 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; } /** @@ -253,23 +302,47 @@ 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)) { @@ -278,16 +351,21 @@ public class FileParse { if (checkFileSource(suffixLess)) { - throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage})); + throw new IOException(MessageManager.formatMessage( + "exception.problem_opening_file_also_tried", + new String[] + { inFile.getName(), suffixLess, errormessage })); } } else { - throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage})); + throw new IOException(MessageManager.formatMessage( + "exception.problem_opening_file", new String[] + { inFile.getName(), errormessage })); } } } - else if (type.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { try { @@ -295,7 +373,7 @@ public class FileParse { checkURLSource(fileStr); if (suffixSeparator == '#') - { + { extractSuffix(fileStr); // URL lref is stored for later reference. } } catch (IOException e) @@ -324,13 +402,13 @@ 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() @@ -356,13 +434,15 @@ 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})); + throw new IOException(MessageManager.formatMessage( + "exception.failed_to_read_data_from_source", new String[] + { errormessage })); } error = false; dataIn.mark(READAHEAD_LIMIT); @@ -382,7 +462,8 @@ public class FileParse } else { - throw new IOException(MessageManager.getString("exception.no_init_source_stream")); + throw new IOException( + MessageManager.getString("exception.no_init_source_stream")); } } @@ -392,9 +473,24 @@ 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 })); } + /** + * + * @return true if this FileParse is configured for Export only + */ + public boolean isExporting() + { + return !error && dataIn == null; + } + + /** + * + * @return true if the data source is valid + */ public boolean isValid() { return !error; @@ -413,18 +509,27 @@ public class FileParse } /** - * rewinds the datasource the beginning. + * Rewinds the datasource to the marked point if possible + * + * @param bytesRead * */ - public void reset() throws IOException + public void reset(int bytesRead) throws IOException { + if (bytesRead >= READAHEAD_LIMIT) + { + System.err.println(String.format( + "File reset error: read %d bytes but reset limit is %d", + bytesRead, READAHEAD_LIMIT)); + } if (dataIn != null && !error) { dataIn.reset(); } 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")); } } @@ -501,4 +606,54 @@ public class FileParse { this.viewport = viewport; } + + /** + * @return the currently configured exportSettings for writing data. + */ + public AlignExportSettingI getExportSettings() + { + return exportSettings; + } + + /** + * Set configuration for export of data. + * + * @param exportSettings + * the exportSettings to set + */ + public void setExportSettings(AlignExportSettingI exportSettings) + { + this.exportSettings = exportSettings; + } + + /** + * method overridden by complex file exporter/importers which support + * exporting visualisation and layout settings for a view + * + * @param avpanel + */ + public void configureForView(AlignmentViewPanel avpanel) + { + if (avpanel != null) + { + setViewport(avpanel.getAlignViewport()); + } + // 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; + } }