/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.*;
-import java.net.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+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;
+
/**
* implements a random access wrapper around a particular datasource, for
*/
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;
- public int index = 1; // sequence counter for FileParse object created from
- // same data source
+ /**
+ * 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 AlignExportSettingI 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 String type = null;
+ protected DataSourceType dataSourceType = null;
protected BufferedReader dataIn = null;
- protected String errormessage = "UNITIALISED SOURCE";
+ protected String errormessage = "UNINITIALISED SOURCE";
protected boolean error = true;
{
if (from == null)
{
- throw new Error(
- "Implementation error. Null FileParse in copy constructor");
+ 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.
- type = from.type;
+ dataSourceType = from.dataSourceType;
dataIn = from.dataIn;
if (dataIn != null)
{
mark();
}
+ dataName = from.dataName;
}
/**
}
if (!error)
{
- dataIn = new BufferedReader(new FileReader(fileStr));
+ 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;
}
- private boolean checkURLSource(String fileStr) throws IOException,
- MalformedURLException
+ /**
+ * Recognise the 2-byte magic header indicating a gzipped stream
+ *
+ * see
+ * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6
+ *
+ * @param input
+ * - input stream that supports mark and contains at least two bytes
+ *
+ * @return false if mark not supported or no magic header found
+ *
+ * @throws IOException
+ */
+ public static boolean isGzipStream(InputStream input) throws IOException
+ {
+ if (!input.markSupported())
+ {
+ Cache.log.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(fileStr);
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
- return false;
+ 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;
}
/**
}
/**
+ * 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 -
- * protocol of source
+ * @param fileStr
+ * - datasource locator/content
+ * @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))
{
{
if (checkFileSource(suffixLess))
{
- throw new IOException("Problem opening " + inFile
- + " (also tried " + suffixLess + ") : " + errormessage);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.problem_opening_file_also_tried",
+ new String[]
+ { inFile.getName(), suffixLess, errormessage }));
}
}
else
{
- throw new IOException("Problem opening " + inFile + " : "
- + 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
{
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
+ }
} catch (IOException e)
{
String suffixLess = extractSuffix(fileStr);
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()
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess != null)
+ {
is = getClass().getResourceAsStream("/" + suffixLess);
+ }
}
if (is != null)
{
dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+ dataName = fileStr;
}
else
{
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("Failed to read data from source:\n"
- + errormessage);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.failed_to_read_data_from_source", new String[]
+ { errormessage }));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
}
else
{
- throw new IOException("Unitialised Source Stream");
+ throw new IOException(
+ MessageManager.getString("exception.no_init_source_stream"));
}
}
public String nextLine() throws IOException
{
if (!error)
+ {
return dataIn.readLine();
- throw new IOException("Invalid Source Stream:" + 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;
}
/**
- * 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(
- "Implementation Error: Reset called for invalid source.");
+ throw new IOException(MessageManager.getString(
+ "error.implementation_error_reset_called_for_invalid_source"));
}
}
}
}
- public Reader getReader() throws IOException
+ /**
+ * @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)
{
- if (dataIn != null && dataIn.ready())
+ 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 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff