/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * 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.
- *
- * 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 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
+ * 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.*;
-/**
- * implements a random access wrapper around a particular datasource, for passing to
- * identifyFile and AlignFile objects.
+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
+ * passing to identifyFile and AlignFile objects.
*/
public class FileParse
{
- public File inFile=null;
+ /**
+ * text specifying source of data. usually filename or url.
+ */
+ private String dataName = "unknown source";
+
+ public File inFile = null;
+
+ /**
+ * 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;
+
+ /**
+ * 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 = '#';
+
/**
- * '#' separated string tagged on to end of filename
- * or url that was clipped off to resolve to valid filename
+ * character used to write newlines
*/
- protected String suffix=null;
- protected String type=null;
- protected BufferedReader dataIn=null;
- protected String errormessage="UNITIALISED SOURCE";
- protected boolean error=true;
- protected String warningMessage=null;
+ 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
+ */
+ protected String suffix = null;
+
+ protected String type = null;
+
+ protected BufferedReader dataIn = null;
+
+ protected String errormessage = "UNINITIALISED SOURCE";
+
+ protected boolean error = true;
+
+ protected String warningMessage = null;
+
/**
* size of readahead buffer used for when initial stream position is marked.
*/
- final int READAHEAD_LIMIT=2048;
+ final int READAHEAD_LIMIT = 2048;
+
public FileParse()
{
}
+
+ /**
+ * Create a new FileParse instance reading from the same datasource starting
+ * at the current position. WARNING! Subsequent reads from either object will
+ * affect the read position of the other, but not the error state.
+ *
+ * @param from
+ */
+ public FileParse(FileParse from) throws IOException
+ {
+ if (from == null)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_null_fileparse"));
+ }
+ if (from == this)
+ {
+ return;
+ }
+ index = ++from.index;
+ inFile = from.inFile;
+ suffixSeparator = from.suffixSeparator;
+ suffix = from.suffix;
+ errormessage = from.errormessage; // inherit potential error messages
+ error = false; // reset any error condition.
+ type = from.type;
+ dataIn = from.dataIn;
+ if (dataIn != null)
+ {
+ mark();
+ }
+ dataName = from.dataName;
+ }
+
/**
- * Attempt to open a file as a datasource.
- * Sets error and errormessage if fileStr was invalid.
+ * Attempt to open a file as a datasource. Sets error and errormessage if
+ * fileStr was invalid.
+ *
* @param fileStr
* @return this.error (true if the source was invalid)
*/
- private boolean checkFileSource(String fileStr) throws IOException {
- error=false;
+ private boolean checkFileSource(String fileStr) throws IOException
+ {
+ error = false;
this.inFile = new File(fileStr);
// check to see if it's a Jar file in disguise.
- if (!inFile.exists()) {
+ if (!inFile.exists())
+ {
errormessage = "FILE NOT FOUND";
- error=true;
+ error = true;
}
- if (!inFile.canRead()) {
+ if (!inFile.canRead())
+ {
errormessage = "FILE CANNOT BE OPENED FOR READING";
- error=true;
+ error = true;
}
- if (inFile.isDirectory()) {
- // this is really a 'complex' filetype - but we don't handle directory reads yet.
+ if (inFile.isDirectory())
+ {
+ // this is really a 'complex' filetype - but we don't handle directory
+ // reads yet.
errormessage = "FILE IS A DIRECTORY";
- error=true;
+ error = true;
}
- if (!error) {
+ 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 boolean checkURLSource(String fileStr) throws IOException, MalformedURLException
+
+ 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;
}
+
/**
- * sets the suffix string (if any) and returns remainder (if suffix was detected)
+ * sets the suffix string (if any) and returns remainder (if suffix was
+ * detected)
+ *
* @param fileStr
* @return truncated fileStr or null
*/
- private String extractSuffix(String fileStr) {
+ private String extractSuffix(String fileStr)
+ {
// first check that there wasn't a suffix string tagged on.
int sfpos = fileStr.lastIndexOf(suffixSeparator);
- if (sfpos>-1 && sfpos<fileStr.length()-1) {
- suffix = fileStr.substring(sfpos+1);
+ if (sfpos > -1 && sfpos < fileStr.length() - 1)
+ {
+ suffix = fileStr.substring(sfpos + 1);
// System.err.println("DEBUG: Found Suffix:"+suffix);
- return fileStr.substring(0,sfpos);
+ return fileStr.substring(0, sfpos);
}
return null;
}
+
/**
- * 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
+ * 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
* @throws MalformedURLException
* @throws IOException
*/
public FileParse(String fileStr, String type)
- throws MalformedURLException, IOException
+ throws MalformedURLException, IOException
{
this.type = type;
- error=false;
+ error = false;
if (type.equals(AppletFormatAdapter.FILE))
{
- if (checkFileSource(fileStr)) {
+ if (checkFileSource(fileStr))
+ {
String suffixLess = extractSuffix(fileStr);
- if (suffixLess!=null)
+ if (suffixLess != null)
{
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
+ }
+ else
{
- throw new IOException("Problem opening "+inFile+" : "+errormessage);
+ throw new IOException(MessageManager.formatMessage(
+ "exception.problem_opening_file",
+ new String[] { inFile.getName(), errormessage }));
}
}
}
else if (type.equals(AppletFormatAdapter.URL))
{
- try {
- checkURLSource(fileStr);
- if (suffixSeparator=='#')
- extractSuffix(fileStr); // URL lref is stored for later reference.
- } catch (IOException e) {
- String suffixLess = extractSuffix(fileStr);
- if (suffixLess==null)
+ try
+ {
+ try
{
- throw(e);
- } else {
- try {
- checkURLSource(suffixLess);
+ checkURLSource(fileStr);
+ if (suffixSeparator == '#')
+ {
+ extractSuffix(fileStr); // URL lref is stored for later reference.
}
- catch (IOException e2) {
- errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
- throw(e); // just pass back original - everything was wrong.
+ } catch (IOException e)
+ {
+ String suffixLess = extractSuffix(fileStr);
+ if (suffixLess == null)
+ {
+ throw (e);
+ }
+ else
+ {
+ try
+ {
+ checkURLSource(suffixLess);
+ } catch (IOException e2)
+ {
+ errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+ throw (e); // just pass back original - everything was wrong.
+ }
}
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
- errormessage = "CANNOT ACCESS DATA AT URL '"+fileStr+"' ("+e.getMessage()+")";
- error=true;
+ errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' ("
+ + e.getMessage() + ")";
+ error = true;
}
}
else if (type.equals(AppletFormatAdapter.PASTE))
{
errormessage = "PASTE INACCESSIBLE!";
dataIn = new BufferedReader(new StringReader(fileStr));
+ dataName = "Paste";
}
else if (type.equals(AppletFormatAdapter.CLASSLOADER))
{
errormessage = "RESOURCE CANNOT BE LOCATED";
- java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
- if (is==null) {
+ java.io.InputStream is = getClass()
+ .getResourceAsStream("/" + fileStr);
+ if (is == null)
+ {
String suffixLess = extractSuffix(fileStr);
- if (suffixLess!=null)
+ if (suffixLess != null)
+ {
is = getClass().getResourceAsStream("/" + suffixLess);
+ }
}
if (is != null)
{
dataIn = new BufferedReader(new java.io.InputStreamReader(is));
- } else {
+ dataName = fileStr;
+ }
+ else
+ {
error = true;
}
}
- if (dataIn==null)
+ else
+ {
+ errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
+ + (type != null ? type : "null") + "'";
+ error = true;
+ }
+ 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;
+ error = false;
dataIn.mark(READAHEAD_LIMIT);
}
- public String nextLine()
- throws IOException
+
+ /**
+ * mark the current position in the source as start for the purposes of it
+ * being analysed by IdentifyFile().identify
+ *
+ * @throws IOException
+ */
+ public void mark() throws IOException
+ {
+ if (dataIn != null)
+ {
+ dataIn.mark(READAHEAD_LIMIT);
+ }
+ else
+ {
+ 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;
}
+
/**
- * closes the datasource and tidies up.
- * source will be left in an error state
+ * closes the datasource and tidies up. source will be left in an error state
*/
public void close() throws IOException
{
- errormessage="EXCEPTION ON CLOSE";
- error=true;
+ errormessage = "EXCEPTION ON CLOSE";
+ error = true;
dataIn.close();
- dataIn=null;
- errormessage="SOURCE IS CLOSED";
+ dataIn = null;
+ errormessage = "SOURCE IS CLOSED";
}
+
/**
* rewinds the datasource the beginning.
- *
+ *
*/
public void reset() throws IOException
{
- if (dataIn!=null && !error) {
+ if (dataIn != null && !error)
+ {
dataIn.reset();
- } else {
- throw new IOException("Implementation Error: Reset called for invalid source.");
+ }
+ else
+ {
+ throw new IOException(
+ MessageManager
+ .getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
+
/**
*
* @return true if there is a warning for the user
*/
- public boolean hasWarningMessage() {
- return (warningMessage!=null && warningMessage.length()>0);
+ public boolean hasWarningMessage()
+ {
+ return (warningMessage != null && warningMessage.length() > 0);
}
+
/**
*
* @return empty string or warning message about file that was just parsed.
*/
- public String getWarningMessage() {
+ public String getWarningMessage()
+ {
return warningMessage;
}
+
+ public String getInFile()
+ {
+ if (inFile != null)
+ {
+ return inFile.getAbsolutePath() + " (" + index + ")";
+ }
+ else
+ {
+ return "From Paste + (" + index + ")";
+ }
+ }
+
+ /**
+ * @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) // Probably don't need to test for readiness &&
+ // dataIn.ready())
+ {
+ return dataIn;
+ }
+ 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