/*
- * 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
- * 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.
- *
- * 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
+ * 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
+ *
+ * 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
+ * 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/>.
*/
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.
+
+/**
+ * implements a random access wrapper around a particular datasource, for
+ * passing to identifyFile and AlignFile objects.
*/
public class FileParse
{
- public File inFile=null;
- public int index = 1; // sequence counter for FileParse object created from same data source
+ /**
+ * text specifying source of data. usually filename or url.
+ */
+ private String dataName = "unknown source";
+
+ public File inFile = null;
+
+ public int index = 1; // sequence counter for FileParse object created from
+
+ // same data source
+
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 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="UNITIALISED SOURCE";
- protected boolean error=true;
- protected String warningMessage=null;
+ 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;
+
/**
* 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.
+ * 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)
+ if (from == null)
{
- throw new Error("Implementation error. Null FileParse in copy constructor");
+ throw new Error(
+ "Implementation error. Null FileParse in copy constructor");
}
- if (from==this)
+ if (from == this)
return;
index = ++from.index;
inFile = from.inFile;
error = false; // reset any error condition.
type = from.type;
dataIn = from.dataIn;
- if (dataIn!=null)
+ 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)
+ {
dataIn = new BufferedReader(new FileReader(fileStr));
+ dataName = fileStr;
}
return error;
}
- private boolean checkURLSource(String fileStr) throws IOException, MalformedURLException
+
+ private boolean checkURLSource(String fileStr) throws IOException,
+ MalformedURLException
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+ // 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("Problem opening " + inFile
+ + " (also tried " + suffixLess + ") : " + errormessage);
}
- } else
+ }
+ else
{
- throw new IOException("Problem opening "+inFile+" : "+errormessage);
+ throw new IOException("Problem opening " + inFile + " : "
+ + errormessage);
}
}
}
else if (type.equals(AppletFormatAdapter.URL))
{
- try {
- 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
+ {
+ checkURLSource(fileStr);
+ if (suffixSeparator == '#')
+ extractSuffix(fileStr); // URL lref is stored for later reference.
+ } catch (IOException e)
{
- throw(e);
- } else {
- try {
- checkURLSource(suffixLess);
+ String suffixLess = extractSuffix(fileStr);
+ if (suffixLess == null)
+ {
+ throw (e);
}
- catch (IOException e2) {
- errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
- throw(e); // just pass back original - everything was wrong.
+ 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("Failed to read data from source:\n"
+ + errormessage);
}
- error=false;
+ error = false;
dataIn.mark(READAHEAD_LIMIT);
}
+
/**
- * mark the current position in the source as start
- * for the purposes of it being analysed by IdentifyFile().identify
+ * 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)
+ if (dataIn != null)
{
dataIn.mark(READAHEAD_LIMIT);
- } else {
+ }
+ else
+ {
throw new IOException("Unitialised Source Stream");
}
}
- public String nextLine()
- throws IOException
+
+ public String nextLine() throws IOException
{
if (!error)
return dataIn.readLine();
- throw new IOException("Invalid Source Stream:"+errormessage);
+ throw new IOException("Invalid Source Stream:" + errormessage);
}
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(
+ "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)
+ if (inFile != null)
{
- return inFile.getAbsolutePath()+" ("+index+")";
+ return inFile.getAbsolutePath() + " (" + index + ")";
}
else
{
- return "From Paste + ("+index+")";
+ 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;
}
}
git://source.jalview.org / jalview.git / blobdiff