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/*
* Copyright 2013 Brian Tjaden
*
* This file is part of Rockhopper.
*
* Rockhopper 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
* any later version.
*
* Rockhopper 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
* (in the file gpl.txt) along with Rockhopper.
* If not, see <http://www.gnu.org/licenses/>.
*/
import java.util.ArrayList;
import java.io.PrintWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.broad.igv.feature.genome.GenomeImporter;
public class IGV_Ops {
/**
* Creates a genome registry for IGV. File is named genomes.txt.
*/
public static boolean createGenomeRegistry(File genomeRegistryFile, ArrayList<Genome> genomes) {
try {
PrintWriter writer = new PrintWriter(genomeRegistryFile);
writer.println("<Server-Side Genome List>");
for (Genome genome : genomes)
writer.println(getGenomeDisplayName(genome.getName()) + "\t" + genome.getBaseFileName() + ".genome" + "\t" + genome.getName().replace(' ', '_'));
writer.close();
return true;
} catch (FileNotFoundException ex) {
return false;
}
}
/**
* Creates a genome archive file for use by IGV. This method
* utilizes IGV code.
*/
public static boolean createGenomeArchive(String genomeArchiveFileName, String genomeName, String fastaFileName, String geneFileName) {
try {
(new GenomeImporter()).createGenomeArchive(new File(genomeArchiveFileName), genomeName.replace(' ', '_'), getGenomeDisplayName(genomeName), fastaFileName, new File(geneFileName), null, null);
return true;
} catch (IOException ex) {
return false;
}
}
/**
* Create a batch script to execute when IGV launches to load
* the sequencing reads data.
*/
public static boolean createBatchFileToLoadData(String batchFileName, String genomeName, String dataFiles, String rockhopperFiles) {
try {
PrintWriter writer = new PrintWriter(new File(batchFileName));
writer.println("new");
writer.println("genome " + genomeName.replace(' ', '_'));
if (dataFiles.length() > 0) writer.println("load " + dataFiles);
if (rockhopperFiles.length() > 0) writer.println("load " + rockhopperFiles);
writer.close();
return true;
} catch (FileNotFoundException ex) {
return false;
}
}
/**
* Returns the name of the genome to display in IGV's drop-down menu.
*/
private static String getGenomeDisplayName(String genomeName) {
genomeName = genomeName.trim();
int indexOfSpace = genomeName.indexOf(' ');
if (indexOfSpace >= 0) genomeName = genomeName.charAt(0) + "." + genomeName.substring(indexOfSpace);
return genomeName;
}
}
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