/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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
+ * 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.*;
import java.net.*;
+import java.util.zip.GZIPInputStream;
/**
* implements a random access wrapper around a particular datasource, for
*/
public class FileParse
{
+ /**
+ * 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
+
+ // same data source
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
*/
{
mark();
}
+ dataName = from.dataName;
}
/**
}
if (!error)
{
+ if (fileStr.toLowerCase().endsWith(".gz"))
+ {
+ try
+ {
+ dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+ dataName = fileStr;
+ return error;
+ } catch (Exception x)
+ {
+ warningMessage = "Failed to resolve as a GZ stream ("
+ + x.getMessage() + ")";
+ x.printStackTrace();
+ }
+ ;
+ }
+
dataIn = new BufferedReader(new FileReader(fileStr));
+ dataName = fileStr;
}
return error;
}
-
+ private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception
+ {
+ BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+ inData.mark(2048);
+ inData.read();
+ inData.reset();
+ return inData;
+ }
private boolean checkURLSource(String fileStr) throws IOException,
MalformedURLException
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+ //
+ // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
+ Exception e=null;
+ if (fileStr.toLowerCase().endsWith(".gz")) {
+ try {
+ InputStream inputStream = url.openStream();
+ dataIn = tryAsGzipSource(inputStream);
+ dataName = fileStr;
+ return false;
+ } catch (Exception ex) {
+ e=ex;
+ }
+ }
+
+ try {
+ dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+ } catch (IOException q) {
+ if (e!=null)
+ {
+ throw new IOException("Failed to resolve GZIP stream", e);
+ }
+ throw q;
+ }
+ // record URL as name of datasource.
+ dataName = fileStr;
return false;
}
* 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 type
+ * - protocol of source
* @throws MalformedURLException
* @throws IOException
*/
{
errormessage = "PASTE INACCESSIBLE!";
dataIn = new BufferedReader(new StringReader(fileStr));
+ dataName = "Paste";
}
else if (type.equals(AppletFormatAdapter.CLASSLOADER))
{
if (is != null)
{
dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+ dataName = fileStr;
}
else
{
}
}
- 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)
+ {
+ dataName = dataname;
+ }
+
+ /**
+ * get the underlying bufferedReader for this data source.
+ *
+ * @return null if no reader available
+ * @throws IOException
+ */
+ public Reader getReader()
{
- if (dataIn != null && dataIn.ready())
+ if (dataIn != null) // Probably don't need to test for readiness &&
+ // dataIn.ready())
{
return dataIn;
}
git://source.jalview.org / jalview.git / blobdiff