-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-\r
-import java.net.*;\r
-\r
-\r
-public class FileParse {\r
- public File inFile;\r
- public int fileSize;\r
- public int noLines;\r
- protected String type;\r
- protected BufferedReader dataIn;\r
-\r
- public FileParse() {\r
- }\r
-\r
- public FileParse(String fileStr, String type)\r
- throws MalformedURLException, IOException {\r
- this.type = type;\r
-\r
- if (type.equals("File")) {\r
- this.inFile = new File(fileStr);\r
- this.fileSize = (int) inFile.length();\r
-\r
- dataIn = new BufferedReader(new FileReader(fileStr));\r
- } else if (type.equals("URL")) {\r
- URL url = new URL(fileStr);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
- } else if (type.equals("Paste")) {\r
- dataIn = new BufferedReader(new StringReader(fileStr));\r
- }\r
- }\r
-\r
- public String nextLine() throws IOException {\r
- String next = dataIn.readLine();\r
-\r
- if (next != null) {\r
- noLines++;\r
- }\r
-\r
- return next;\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.zip.GZIPInputStream;
+
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Console;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+/**
+ * implements a random access wrapper around a particular datasource, for
+ * passing to identifyFile and AlignFile objects.
+ */
+public class FileParse
+{
+ protected static final String SPACE = " ";
+
+ protected static final String TAB = "\t";
+
+ /**
+ * text specifying source of data. usually filename or url.
+ */
+ private String dataName = "unknown source";
+
+ public File inFile = null;
+
+ private byte[] bytes; // from JavaScript
+
+ public byte[] getBytes()
+ {
+ return bytes;
+ }
+
+ /**
+ * a viewport associated with the current file operation. May be null. May
+ * move to different object.
+ */
+ private AlignViewportI viewport;
+
+ /**
+ * specific settings for exporting data from the current context
+ */
+ private AlignExportSettingsI exportSettings;
+
+ /**
+ * sequence counter for FileParse object created from same data source
+ */
+ public int index = 1;
+
+ /**
+ * separator for extracting specific 'frame' of a datasource for formats that
+ * support multiple records (e.g. BLC, Stockholm, etc)
+ */
+ protected char suffixSeparator = '#';
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
+ /**
+ * '#' separated string tagged on to end of filename or url that was clipped
+ * off to resolve to valid filename
+ */
+ protected String suffix = null;
+
+ protected DataSourceType dataSourceType = null;
+
+ protected BufferedReader dataIn = null;
+
+ protected String errormessage = "UNINITIALISED SOURCE";
+
+ protected boolean error = true;
+
+ protected String warningMessage = null;
+
+ /**
+ * size of readahead buffer used for when initial stream position is marked.
+ */
+ final int READAHEAD_LIMIT = 2048;
+
+ public FileParse()
+ {
+ }
+
+ /**
+ * Create a new FileParse instance reading from the same datasource starting
+ * at the current position. WARNING! Subsequent reads from either object will
+ * affect the read position of the other, but not the error state.
+ *
+ * @param from
+ */
+ public FileParse(FileParse from) throws IOException
+ {
+ if (from == null)
+ {
+ throw new Error(MessageManager
+ .getString("error.implementation_error_null_fileparse"));
+ }
+ if (from == this)
+ {
+ return;
+ }
+ index = ++from.index;
+ inFile = from.inFile;
+ suffixSeparator = from.suffixSeparator;
+ suffix = from.suffix;
+ errormessage = from.errormessage; // inherit potential error messages
+ error = false; // reset any error condition.
+ dataSourceType = from.dataSourceType;
+ dataIn = from.dataIn;
+ if (dataIn != null)
+ {
+ mark();
+ }
+ dataName = from.dataName;
+ }
+
+ /**
+ * Attempt to open a file as a datasource. Sets error and errormessage if
+ * fileStr was invalid.
+ *
+ * @param fileStr
+ * @return this.error (true if the source was invalid)
+ */
+ private boolean checkFileSource(String fileStr) throws IOException
+ {
+ error = false;
+ this.inFile = new File(fileStr);
+ // check to see if it's a Jar file in disguise.
+ if (!inFile.exists())
+ {
+ errormessage = "FILE NOT FOUND";
+ error = true;
+ }
+ if (!inFile.canRead())
+ {
+ errormessage = "FILE CANNOT BE OPENED FOR READING";
+ error = true;
+ }
+ if (inFile.isDirectory())
+ {
+ // this is really a 'complex' filetype - but we don't handle directory
+ // reads yet.
+ errormessage = "FILE IS A DIRECTORY";
+ error = true;
+ }
+ if (!error)
+ {
+ try
+ {
+ dataIn = checkForGzipStream(new FileInputStream(fileStr));
+ dataName = fileStr;
+ } catch (Exception x)
+ {
+ warningMessage = "Failed to resolve " + fileStr
+ + " as a data source. (" + x.getMessage() + ")";
+ // x.printStackTrace();
+ error = true;
+ }
+ ;
+ }
+ return error;
+ }
+
+ /**
+ * Recognise the 2-byte magic header for gzip streams
+ *
+ * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6
+ *
+ * @param bytes
+ * - at least two bytes
+ * @return
+ * @throws IOException
+ */
+ public static boolean isGzipStream(InputStream input) throws IOException
+ {
+ if (!input.markSupported())
+ {
+ Console.error(
+ "FileParse.izGzipStream: input stream must support mark/reset");
+ return false;
+ }
+ input.mark(4);
+
+ // get first 2 bytes or return false
+ byte[] bytes = new byte[2];
+ int read = input.read(bytes);
+ input.reset();
+ if (read != bytes.length)
+ {
+ return false;
+ }
+
+ int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
+ return (GZIPInputStream.GZIP_MAGIC == header);
+ }
+
+ /**
+ * Returns a Reader for the given input after wrapping it in a buffered input
+ * stream, and then checking if it needs to be wrapped by a GZipInputStream
+ *
+ * @param input
+ * @return
+ */
+ private BufferedReader checkForGzipStream(InputStream input)
+ throws Exception
+ {
+ // NB: stackoverflow
+ // https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped
+ // could use a PushBackInputStream rather than a BufferedInputStream
+ if (!input.markSupported())
+ {
+ input = new BufferedInputStream(input, 16);
+ }
+ if (isGzipStream(input))
+ {
+ return getGzipReader(input);
+ }
+ // return a buffered reader for the stream.
+ InputStreamReader isReader = new InputStreamReader(input);
+ BufferedReader toReadFrom = new BufferedReader(isReader);
+ return toReadFrom;
+ }
+
+ /**
+ * Returns a {@code BufferedReader} which wraps the input stream with a
+ * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error
+ * occurs or the compression method used is unsupported.
+ *
+ * @param inputStream
+ * @return
+ * @throws Exception
+ */
+ private BufferedReader getGzipReader(InputStream inputStream)
+ throws Exception
+ {
+ BufferedReader inData = new BufferedReader(
+ new InputStreamReader(new GZIPInputStream(inputStream)));
+ inData.mark(2048);
+ inData.read();
+ inData.reset();
+ return inData;
+ }
+
+ /**
+ * Tries to read from the given URL. If successful, saves a reader to the
+ * response in field {@code dataIn}, otherwise (on exception, or HTTP response
+ * status not 200), throws an exception.
+ * <p>
+ * If the response status includes
+ *
+ * <pre>
+ * Content-Type : application/x-gzip
+ * </pre>
+ *
+ * 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff