/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.*;
import java.net.*;
+import java.util.zip.GZIPInputStream;
/**
* implements a random access wrapper around a particular datasource, for
}
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;