/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
+ * 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/>.
+ * 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 jalview.util.MessageManager;
+
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;
+ 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
{
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;
}
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(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+ }
+ throw q;
+ }
// record URL as name of datasource.
dataName = fileStr;
return false;
{
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}));
}
}
}
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"));
}
}
{
if (!error)
return dataIn.readLine();
- throw new IOException("Invalid Source Stream:" + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
}
public boolean isValid()
}
else
{
- throw new IOException(
- "Implementation Error: Reset called for invalid source.");
+ throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
{
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;
}
git://source.jalview.org / jalview.git / blobdiff