/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.indexdb;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import org.biojava.bio.AbstractAnnotation;
import org.biojava.utils.AssertionFailure;
import org.biojava.utils.CommitFailure;
import org.biojava.utils.Commitable;
/**
* ConfigFile
implements reading, updating and writing
* of OBDA tab-delimited index files.
*
* @author Matthew Pocock
* @author Keith James
*/
class ConfigFile
extends AbstractAnnotation
implements Commitable
{
private File file;
private Map map;
/**
* Creates a new ConfigFile
using the specified
* File
, which may or may not already exist.
*
* @param file a File
.
*
* @exception IOException if an error occurs.
*/
public ConfigFile(File file)
throws IOException {
this.file = file;
map = new HashMap();
if(file.exists()) {
parseFile();
}
}
public void commit()
throws CommitFailure {
try {
writeFile();
} catch (IOException e) {
throw new CommitFailure("Couldn't commit", e);
}
}
public void rollback() {
try {
parseFile();
} catch (IOException e) {
throw new AssertionFailure("Couldn't roll back: your data may be invalid", e);
}
}
private void parseFile()
throws IOException {
BufferedReader reader = new BufferedReader(new FileReader(file));
for(String line = reader.readLine();
line != null;
line = reader.readLine()) {
int tab = line.indexOf("\t");
String key = line.substring(0, tab).trim();
String value = line.substring(tab+1).trim();
map.put(key, value);
}
}
private void writeFile()
throws IOException {
PrintWriter writer = new PrintWriter(new FileWriter(file));
writer.println("index\t" + map.get("index"));
for(Iterator i = map.entrySet().iterator(); i.hasNext(); ) {
Map.Entry me = (Map.Entry) i.next();
if(!me.getKey().equals("index")) {
writer.println(me.getKey() + "\t" + me.getValue());
}
}
writer.flush();
}
protected Map getProperties() {
return map;
}
protected boolean propertiesAllocated() {
return true;
}
}