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Add support for downloading genomes including sequence and annotations.
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89 changes: 89 additions & 0 deletions
89
src/main/java/org/broad/igv/feature/genome/DotGenomeUtils.java
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| package org.broad.igv.feature.genome; | ||
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| import org.broad.igv.DirectoryManager; | ||
| import org.broad.igv.feature.genome.load.GenomeDescriptor; | ||
| import org.broad.igv.feature.genome.load.GenomeLoader; | ||
| import org.broad.igv.logging.LogManager; | ||
| import org.broad.igv.logging.Logger; | ||
| import org.broad.igv.ui.IGV; | ||
| import org.broad.igv.ui.util.download.Downloader; | ||
| import org.broad.igv.util.HttpUtils; | ||
| import org.broad.igv.util.Utilities; | ||
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| import java.awt.*; | ||
| import java.io.*; | ||
| import java.net.MalformedURLException; | ||
| import java.net.URL; | ||
| import java.net.URLDecoder; | ||
| import java.util.Map; | ||
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| /** | ||
| * Utilities for the ".genome" format. These files are not created anymore, having been replaced by the genome json | ||
| * format, but we need to maintain support for reading and managing them. | ||
| */ | ||
| public class DotGenomeUtils { | ||
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| private static Logger log = LogManager.getLogger(DotGenomeUtils.class); | ||
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| /** | ||
| * Returns a File of the provided genomePath. If the genomePath is a URL, it will be downloaded | ||
| * and saved in the genome cache directory. | ||
| * | ||
| * @param genomePath | ||
| * @return | ||
| * @throws MalformedURLException | ||
| * @throws UnsupportedEncodingException | ||
| */ | ||
| public static File getDotGenomeFile(String genomePath) throws MalformedURLException, UnsupportedEncodingException { | ||
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| File archiveFile; | ||
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| if (HttpUtils.isRemoteURL(genomePath.toLowerCase())) { | ||
| // We need a local copy, as there is no http zip file reader | ||
| URL genomeArchiveURL = HttpUtils.createURL(genomePath); | ||
| final String tmp = URLDecoder.decode(genomeArchiveURL.getFile(), "UTF-8"); | ||
| String cachedFilename = Utilities.getFileNameFromURL(tmp); | ||
| if (!DirectoryManager.getGenomeCacheDirectory().exists()) { | ||
| DirectoryManager.getGenomeCacheDirectory().mkdir(); | ||
| } | ||
| archiveFile = new File(DirectoryManager.getGenomeCacheDirectory(), cachedFilename); | ||
| Frame parent = IGV.hasInstance() ? IGV.getInstance().getMainFrame() : null; | ||
| Downloader.download(genomeArchiveURL, archiveFile, parent); | ||
| } else { | ||
| archiveFile = new File(genomePath); | ||
| } | ||
| return archiveFile; | ||
| } | ||
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| public static File getLocalFasta(String id) { | ||
| return GenomeLoader.localSequenceMap.get(id); | ||
| } | ||
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| public static void removeLocalFasta(String id) { | ||
| GenomeLoader.localSequenceMap.remove(id); | ||
| updateSequenceMapFile(); | ||
| } | ||
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| private static void updateSequenceMapFile() { | ||
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| PrintWriter pw = null; | ||
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| try { | ||
| File sequenceFile = new File(DirectoryManager.getGenomeCacheDirectory(), GenomeDescriptor.SEQUENCE_MAP_FILE); | ||
| pw = new PrintWriter(new BufferedWriter(new FileWriter(sequenceFile))); | ||
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| for (Map.Entry<String, File> entry : GenomeLoader.localSequenceMap.entrySet()) { | ||
| pw.println(entry.getKey() + "\t" + entry.getValue()); | ||
| } | ||
| } catch (IOException e) { | ||
| log.error("Error writing sequence map", e); | ||
| } finally { | ||
| if (pw != null) pw.close(); | ||
| } | ||
| } | ||
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| } |
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