@Override public void start() throws PluginConfigurationException { setOptionalArguements(); getInputAndStart(); GeneralOutputEvent so1 = new GeneralOutputEvent( "OXL parsing finished.", "[Parser - start]"); so1.setLog4jLevel(Level.INFO); fireEventOccurred(so1); }
GeneralOutputEvent goe = new GeneralOutputEvent( "Extract enzyme details...", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); "Successfully extracted details and file closed.", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); } catch (FileNotFoundException fnfe) {
goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe); + entries.size() + " enzyme classes.", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe);
"Reading EC import files...", ONDEXParser.getCurrentMethodName()); goe.setLog4jLevel(Level.INFO); Parser.propagateEventOccurred(goe);
"Using taxonomy flatfile " + filename, "[Validator - validate]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe);
/** * Takes a given AbstractONDEXGraph and builds the index around it. * * @param aog * AbstractONDEXGraph * @throws AccessDeniedException */ public void setONDEXGraph(ONDEXGraph aog) throws AccessDeniedException { GeneralOutputEvent so = new GeneralOutputEvent( "Using Lucene with index dir: " + this.indexdir, "[LuceneEnv - setONDEXGraph]"); so.setLog4jLevel(Level.INFO); // todo: fix this - should be configured // externally fireEventOccurred(so); // start indexing indexONDEXGraph(aog, create); // make the ONDEXGraph immutable og = new LuceneONDEXGraph(aog); }
@Override public void start() throws Exception { GeneralOutputEvent goe = new GeneralOutputEvent("Start parsing Phytozome organism...", "[Parser - start()]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe); //parse FASTA, GFF3 and SYNONYM files GenomicParser genomic = new GenomicParser(genomeReg); genomic.start(graph, args, this); goe = new GeneralOutputEvent("Successfully parsed Phytozome.", "[Parser - start()]"); fireEventOccurred(goe); }
Config.properties.getProperty("persistent.BerkeleyEnv.UsingBerkeley") + path, "[BerkeleyEnv - constructor]"); so.setLog4jLevel(Level.INFO); fireEventOccurred(so);
so.setLog4jLevel(Level.INFO); fireEventOccurred(so); so.setLog4jLevel(Level.INFO); fireEventOccurred(so);
so.setLog4jLevel(Level.INFO); fireEventOccurred(so); so.setLog4jLevel(Level.INFO); fireEventOccurred(so);
public void start() throws InvalidPluginArgumentException { GeneralOutputEvent so = new GeneralOutputEvent("Started TAIR Database Parser...", getCurrentMethodName()); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); File dir = new File((String) args.getUniqueValue(FileArgumentDefinition.INPUT_DIR)); //Get Dir for the tair files: String inFilesDir = dir.getAbsolutePath() + File.separator; //Parse The Genome ParseGenome genome = new ParseGenome(); genome.parseGenome(inFilesDir, graph); boolean parseAnnotation = (Boolean) args.getUniqueValue(ArgumentNames.ANNOTATION); if (parseAnnotation) { //parse protein domain information ParseProtein protDomain = new ParseProtein(); protDomain.parse(inFilesDir, graph, genome.getProteinsMap()); //parse publications ParseAnnotation genePubs = new ParseAnnotation(); genePubs.parse(inFilesDir, graph, genome.getProteinsMap()); } //Parse ... (other things) so = new GeneralOutputEvent("Finished TAIR Database Parser...", getCurrentMethodName()); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); }
@Override public void start() throws Exception { GeneralOutputEvent goe = new GeneralOutputEvent("Start parsing Poplar genome...", "[Parser - start()]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe);
@Override public void start() throws Exception { GeneralOutputEvent goe = new GeneralOutputEvent("Start parsing Poplar QTLs...", "[Parser - start()]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe);
goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe);