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/* Copyright (c) 2011 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library 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 Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.ws.client;
import static compbio.ws.client.Constraints.pseparator;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Writer;
import java.util.ArrayList;
import java.util.List;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.ClustalAlignmentUtil;
import compbio.data.sequence.ScoreManager;
public class IOHelper {
/**
* Checks -i options and return the File if one was provided, null otherwise
*
* @param cmd
* @param key
* @param mustExist
* @return
* @throws IOException
*/
static File getFile(String[] cmd, String key, boolean mustExist)
throws IOException {
assert key != null && key.trim().length() != 0;
for (String c : cmd) {
String filename = c;
filename = filename.trim();
if (filename.toLowerCase().startsWith(key + pseparator)) {
filename = filename.substring((key + pseparator).length());
File file = new File(filename);
if (mustExist && !file.exists()) {
System.out.println(key + " file " + file.getAbsolutePath()
+ " does not exist");
return null;
}
if (!mustExist && !file.exists()) {
file.createNewFile();
}
if (!file.canRead()) {
System.out.println("Cannot read " + key + " file "
+ file.getAbsolutePath());
return null;
}
return file;
}
}
return null;
}
/**
* Load parameters from file
*
* @throws IOException
*/
static List<String> loadParameters(File paramsfile) throws IOException {
assert paramsfile != null && paramsfile.exists();
BufferedReader reader = new BufferedReader(new FileReader(paramsfile));
String line = null;
ArrayList<String> params = new ArrayList<String>();
while ((line = reader.readLine()) != null) {
line = line.trim();
if (line.length() == 0)
continue;
params.add(line);
}
return params;
}
static Writer getWriter(File file) throws IOException {
assert file != null && file.exists();
return new FileWriter(file);
}
/**
* Outputs clustal formatted alignment into the file represented by the
* outStream
*
* @param outStream
* @param align
* the alignment to output
*/
static void writeOut(Writer writer, Alignment align) {
try {
ClustalAlignmentUtil.writeClustalAlignment(writer, align);
} catch (IOException e) {
System.err
.println("Problems writing output file! Stack trace is below: ");
e.printStackTrace();
} finally {
if (writer != null) {
try {
writer.close();
} catch (IOException ignored) {
// e.printStackTrace();
}
}
}
}
/**
* Outputs AAcon results into the file represented by the outStream
*
* @param outStream
* @param result
* the AACon scores to output
*/
static void writeOut(Writer writer, ScoreManager results) {
if (results == null) {
return;
}
try {
results.writeOut(writer);
} catch (IOException e) {
System.err
.println("Problems writing output file! Stack trace is below: ");
e.printStackTrace();
} finally {
if (writer != null) {
try {
writer.close();
} catch (IOException ignored) {
// e.printStackTrace();
}
}
}
}
}
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