X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=2dec5592664b9889095ed0d9f4618696cc1524d1;hb=5a352aa2f3330ae269d9b70c4a7374c2518bfb2e;hp=0c46a17217a165451a1b52803c7157031dd407db;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 0c46a17..2dec559 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,63 +1,832 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-package jalview.io;
-
-import java.io.*;
-
-import java.net.*;
-
-
-public class FileParse {
- public File inFile;
- public int fileSize;
- public int noLines;
- protected String type;
- protected BufferedReader dataIn;
-
- public FileParse() {
- }
-
- public FileParse(String fileStr, String type)
- throws MalformedURLException, IOException {
- this.type = type;
-
- if (type.equals("File")) {
- this.inFile = new File(fileStr);
- this.fileSize = (int) inFile.length();
-
- dataIn = new BufferedReader(new FileReader(fileStr));
- } else if (type.equals("URL")) {
- URL url = new URL(fileStr);
- this.fileSize = 0;
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
- } else if (type.equals("Paste")) {
- dataIn = new BufferedReader(new StringReader(fileStr));
- }
- }
-
- public String nextLine() throws IOException {
- String next = dataIn.readLine();
-
- if (next != null) {
- noLines++;
- }
-
- return next;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ * 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(urlStr); + URLConnection _conn = url.openConnection(); + if (_conn instanceof HttpURLConnection) + { + HttpURLConnection conn = (HttpURLConnection) _conn; + int rc = conn.getResponseCode(); + if (rc != HttpURLConnection.HTTP_OK) + { + throw new IOException( + "Response status from " + urlStr + " was " + rc); + } + } + else + { + try + { + dataIn = checkForGzipStream(_conn.getInputStream()); + dataName = urlStr; + } catch (IOException ex) + { + throw new IOException("Failed to handle non-HTTP URI stream", ex); + } catch (Exception ex) + { + throw new IOException( + "Failed to determine type of input stream for given URI", + ex); + } + return; + } + String encoding = _conn.getContentEncoding(); + String contentType = _conn.getContentType(); + boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) + || "gzip".equals(encoding); + Exception e = null; + InputStream inputStream = _conn.getInputStream(); + if (isgzipped) + { + try + { + dataIn = getGzipReader(inputStream); + dataName = urlStr; + } catch (Exception e1) + { + throw new IOException(MessageManager + .getString("exception.failed_to_resolve_gzip_stream"), e); + } + return; + } + + dataIn = new BufferedReader(new InputStreamReader(inputStream)); + dataName = urlStr; + return; + } + + /** + * sets the suffix string (if any) and returns remainder (if suffix was + * detected) + * + * @param fileStr + * @return truncated fileStr or null + */ + private String extractSuffix(String fileStr) + { + // first check that there wasn't a suffix string tagged on. + int sfpos = fileStr.lastIndexOf(suffixSeparator); + if (sfpos > -1 && sfpos < fileStr.length() - 1) + { + suffix = fileStr.substring(sfpos + 1); + // System.err.println("DEBUG: Found Suffix:"+suffix); + return fileStr.substring(0, sfpos); + } + return null; + } + + /** + * 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 file + * - datasource locator/content as File or String + * @param sourceType + * - protocol of source + * @throws MalformedURLException + * @throws IOException + */ + public FileParse(Object file, DataSourceType sourceType) + throws MalformedURLException, IOException + { + if (file instanceof File) + { + parse((File) file, ((File) file).getPath(), sourceType, true); + } + else + { + parse(null, file.toString(), sourceType, false); + } + } + + private void parse(File file, String fileStr, DataSourceType sourceType, + boolean isFileObject) throws IOException + { + bytes = Platform.getFileBytes(file); + dataSourceType = sourceType; + error = false; + + if (sourceType == DataSourceType.FILE) + { + + if (bytes != null) + { + // this will be from JavaScript + inFile = file; + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); + dataName = fileStr; + } + else if (checkFileSource(fileStr)) + { + String suffixLess = extractSuffix(fileStr); + if (suffixLess != null) + { + if (checkFileSource(suffixLess)) + { + 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 })); + } + } + } + else if (sourceType == DataSourceType.RELATIVE_URL) + { + // BH 2018 hack for no support for access-origin + bytes = Platform.getFileAsBytes(fileStr); + dataIn = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); + dataName = fileStr; + + } + else if (sourceType == DataSourceType.URL) + { + try + { + try + { + checkURLSource(fileStr); + if (suffixSeparator == '#') + { + extractSuffix(fileStr); // URL lref is stored for later reference. + } + } catch (IOException e) + { + String suffixLess = extractSuffix(fileStr); + if (suffixLess == null) + { + throw (e); + } + else + { + try + { + checkURLSource(suffixLess); + } catch (IOException e2) + { + errormessage = "BAD URL WITH OR WITHOUT SUFFIX"; + throw (e); // just pass back original - everything was wrong. + } + } + } + } catch (Exception e) + { + errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' (" + + e.getMessage() + ")"; + error = true; + } + } + else if (sourceType == DataSourceType.PASTE) + { + errormessage = "PASTE INACCESSIBLE!"; + dataIn = new BufferedReader(new StringReader(fileStr)); + dataName = "Paste"; + } + else if (sourceType == DataSourceType.CLASSLOADER) + { + errormessage = "RESOURCE CANNOT BE LOCATED"; + InputStream is = getClass().getResourceAsStream("/" + fileStr); + if (is == null) + { + String suffixLess = extractSuffix(fileStr); + if (suffixLess != null) + { + is = getClass().getResourceAsStream("/" + suffixLess); + } + } + if (is != null) + { + dataIn = new BufferedReader(new InputStreamReader(is)); + dataName = fileStr; + } + else + { + error = true; + } + } + else + { + errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '" + + (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 })); + } + error = false; + dataIn.mark(READAHEAD_LIMIT); + } + + /** + * mark the current position in the source as start for the purposes of it + * being analysed by IdentifyFile().identify + * + * @throws IOException + */ + public void mark() throws IOException + { + if (dataIn != null) + { + dataIn.mark(READAHEAD_LIMIT); + } + else + { + throw new IOException( + MessageManager.getString("exception.no_init_source_stream")); + } + } + + public String nextLine() throws IOException + { + if (!error) + { + return dataIn.readLine(); + } + 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; + } + + /** + * closes the datasource and tidies up. source will be left in an error state + */ + public void close() throws IOException + { + errormessage = "EXCEPTION ON CLOSE"; + error = true; + dataIn.close(); + dataIn = null; + errormessage = "SOURCE IS CLOSED"; + } + + /** + * Rewinds the datasource to the marked point if possible + * + * @param bytesRead + * + */ + 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")); + } + } + + /** + * + * @return true if there is a warning for the user + */ + public boolean hasWarningMessage() + { + return (warningMessage != null && warningMessage.length() > 0); + } + + /** + * + * @return empty string or warning message about file that was just parsed. + */ + public String getWarningMessage() + { + return warningMessage; + } + + public String getInFile() + { + if (inFile != null) + { + return inFile.getAbsolutePath() + " (" + index + ")"; + } + else + { + return "From Paste + (" + index + ")"; + } + } + + /** + * @return the dataName + */ + public String getDataName() + { + return dataName; + } + + /** + * set the (human readable) name or URI for this datasource + * + * @param dataname + */ + protected void setDataName(String dataname) + { + dataName = dataname; + } + + /** + * get the underlying bufferedReader for this data source. + * + * @return null if no reader available + * @throws IOException + */ + public Reader getReader() + { + if (dataIn != null) // Probably don't need to test for readiness && + // dataIn.ready()) + { + return dataIn; + } + return null; + } + + public AlignViewportI getViewport() + { + return viewport; + } + + public void setViewport(AlignViewportI viewport) + { + this.viewport = viewport; + } + + /** + * @return the currently configured exportSettings for writing data. + */ + public AlignExportSettingsI getExportSettings() + { + return exportSettings; + } + + /** + * Set configuration for export of data. + * + * @param exportSettings + * the exportSettings to set + */ + public void setExportSettings(AlignExportSettingsI 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; + } + + /** + * Returns a buffered reader for the input object. Returns null, or throws + * IOException, on failure. + * + * @param file + * a File, or a String which is a name of a file + * @param sourceType + * @return + * @throws IOException + */ + public BufferedReader getBufferedReader(Object file, + DataSourceType sourceType) throws IOException + { + BufferedReader in = null; + byte[] bytes; + + switch (sourceType) + { + case FILE: + if (file instanceof String) + { + return new BufferedReader(new FileReader((String) file)); + } + bytes = Platform.getFileBytes((File) file); + if (bytes != null) + { + return new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); + } + return new BufferedReader(new FileReader((File) file)); + case URL: + URL url = new URL(file.toString()); + in = new BufferedReader(new InputStreamReader(url.openStream())); + break; + case RELATIVE_URL: // JalviewJS only + bytes = Platform.getFileAsBytes(file.toString()); + if (bytes != null) + { + in = new BufferedReader( + new InputStreamReader(new ByteArrayInputStream(bytes))); + } + break; + case PASTE: + in = new BufferedReader(new StringReader(file.toString())); + break; + case CLASSLOADER: + InputStream is = getClass().getResourceAsStream("/" + file); + if (is != null) + { + in = new BufferedReader(new InputStreamReader(is)); + } + break; + } + + return in; + } +}