/*
- * 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 2.9)
+ * Copyright (C) 2015 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 java.io.*;
-import java.net.*;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.zip.GZIPInputStream;
/**
* implements a random access wrapper around a particular datasource, for
public File inFile = null;
- public int index = 1; // sequence counter for FileParse object created from
+ /**
+ * 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;
- // same data source
+ /**
+ * 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 = '#';
/**
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");
+ MessageManager
+ .getString("error.implementation_error_null_fileparse"));
}
if (from == this)
+ {
return;
+ }
index = ++from.index;
inFile = from.inFile;
suffixSeparator = from.suffixSeparator;
}
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 }));
}
}
}
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
+ }
} catch (IOException e)
{
String suffixLess = extractSuffix(fileStr);
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess != null)
+ {
is = getClass().getResourceAsStream("/" + suffixLess);
+ }
}
if (is != null)
{
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;
else
{
throw new IOException(
- "Implementation Error: Reset called for invalid source.");
+ MessageManager
+ .getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
}
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
+ }
}
git://source.jalview.org / jalview.git / blobdiff