/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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
*
* 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
import java.io.*;
import java.net.*;
+import java.util.zip.GZIPInputStream;
/**
* implements a random access wrapper around a particular datasource, for
// same data source
protected char suffixSeparator = '#';
+
/**
- * character used to write newlines
+ * 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
{
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.endsWith(".gz")) {
+ try {
+ InputStream inputStream = url.openStream();
+ dataIn = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+ dataIn.mark(2048);
+ dataIn.read();
+ dataIn.reset();
+
+ 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;
{
return dataName;
}
+
/**
* set the (human readable) name or URI for this datasource
+ *
* @param dataname
*/
- protected void setDataName(String 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())
+ if (dataIn != null) // Probably don't need to test for readiness &&
+ // dataIn.ready())
{
return dataIn;
}