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Merge branch 'master' of github.com:biojava/biojava.github.io
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‎_wikis/BioJava:CookBook3:MSAProfiler.md‎

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@@ -25,95 +25,95 @@ org.biojava.nbio.core.util.ConcurrencyTools;
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public class CookbookMSAProfiler {
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`   private static class Profiler {`
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`       private long maxMemoryUsed, timeCheckpoint;`
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`       private final long timeStart;`
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`       private Profiler() {`
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`           maxMemoryUsed = Runtime.getRuntime().totalMemory();`
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`           timeStart = timeCheckpoint = System.nanoTime();`
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`       }`
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`       private long getMaxMemoryUsed() {`
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`           return maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());`
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`       }`
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`       private long getTimeSinceCheckpoint() {`
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`           return System.nanoTime() - timeCheckpoint;`
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`       }`
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`       private long getTimeSinceStart() {`
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`           return System.nanoTime() - timeStart;`
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`       }`
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`       private void setCheckpoint() {`
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`           maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());`
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`           timeCheckpoint = System.nanoTime();`
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`       }`
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`   }`
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`   public static void main(String[] args) throws Exception {`
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`       if (args.length < 1) {`
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`           System.err.println("The first argument must be a fasta file of protein sequences.");`
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`           return;`
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`       }`
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`       // ConcurrencyTools.setThreadPoolSingle();`
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`       PrintStream fout = new PrintStream("msa.txt");`
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`       Profiler profiler = new Profiler();`
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`       System.out.printf("Loading sequences from %s... ", args[0]);`
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`       List`<ProteinSequence>` list = new ArrayList`<ProteinSequence>`();`
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`       list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());`
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`       if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {`
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`           System.out.printf("%s/%d", args[1], list.size());`
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`           list = list.subList(0, Integer.parseInt(args[1]));`
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`       } else {`
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`           System.out.printf("%d", list.size());`
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`       }`
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`       System.out.printf(" sequences in %d ms using %d kB%n%n", profiler.getTimeSinceCheckpoint()/1000000,`
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`               profiler.getMaxMemoryUsed()/1024);`
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`       profiler.setCheckpoint();`
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`       System.out.print("Stage 1: pairwise similarity calculation... ");`
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`       GapPenalty gaps = new SimpleGapPenalty();`
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`       SubstitutionMatrix`<AminoAcidCompound>` blosum62 = new SimpleSubstitutionMatrix`<AminoAcidCompound>`();`
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`       List`<PairwiseSequenceScorer<ProteinSequence, AminoAcidCompound>`> scorers = Alignments.getAllPairsScorers(list,`
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`               PairwiseSequenceScorerType.GLOBAL_IDENTITIES, gaps, blosum62);`
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`       Alignments.runPairwiseScorers(scorers);`
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`       System.out.printf("%d scores in %d ms using %d kB%n%n", scorers.size(),`
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`               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);`
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`       profiler.setCheckpoint();`
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`       System.out.print("Stage 2: hierarchical clustering into a guide tree... ");`
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`       GuideTree`<ProteinSequence, AminoAcidCompound>` tree = new GuideTree`<ProteinSequence, AminoAcidCompound>`(list,`
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`               scorers);`
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`       scorers = null;`
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`       System.out.printf("%d ms using %d kB%n%n%s%n%n", profiler.getTimeSinceCheckpoint()/1000000,`
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`               profiler.getMaxMemoryUsed()/1024, tree);`
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`       profiler.setCheckpoint();`
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`       System.out.print("Stage 3: progressive alignment... ");`
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`       Profile`<ProteinSequence, AminoAcidCompound>` msa = Alignments.getProgressiveAlignment(tree,`
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`               ProfileProfileAlignerType.GLOBAL, gaps, blosum62);`
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`       System.out.printf("%d profile-profile alignments in %d ms using %d kB%n%n", list.size() - 1,`
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`               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);`
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`       fout.print(msa);`
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`       fout.close();`
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`       ConcurrencyTools.shutdown();`
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`       System.out.printf("Total time: %d ms%nMemory use: %d kB%n", profiler.getTimeSinceStart()/1000000,`
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`               profiler.getMaxMemoryUsed()/1024);`
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`   }`
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   private static class Profiler {
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       private long maxMemoryUsed, timeCheckpoint;
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       private final long timeStart;
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       private Profiler() {
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           maxMemoryUsed = Runtime.getRuntime().totalMemory();
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           timeStart = timeCheckpoint = System.nanoTime();
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       }
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       private long getMaxMemoryUsed() {
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           return maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());
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       }
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       private long getTimeSinceCheckpoint() {
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           return System.nanoTime() - timeCheckpoint;
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       }
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       private long getTimeSinceStart() {
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           return System.nanoTime() - timeStart;
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       }
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       private void setCheckpoint() {
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           maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());
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           timeCheckpoint = System.nanoTime();
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       }
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   }
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   public static void main(String[] args) throws Exception {
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       if (args.length < 1) {
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           System.err.println("The first argument must be a fasta file of protein sequences.");
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           return;
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       }
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       // ConcurrencyTools.setThreadPoolSingle();
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       PrintStream fout = new PrintStream("msa.txt");
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       Profiler profiler = new Profiler();
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       System.out.printf("Loading sequences from %s... ", args[0]);
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       List<ProteinSequence> list = new ArrayList<ProteinSequence>();
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       list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());
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       if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {
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           System.out.printf("%s/%d", args[1], list.size());
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           list = list.subList(0, Integer.parseInt(args[1]));
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       } else {
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           System.out.printf("%d", list.size());
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       }
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       System.out.printf(" sequences in %d ms using %d kB%n%n", profiler.getTimeSinceCheckpoint()/1000000,
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               profiler.getMaxMemoryUsed()/1024);
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       profiler.setCheckpoint();
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       System.out.print("Stage 1: pairwise similarity calculation... ");
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       GapPenalty gaps = new SimpleGapPenalty();
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       SubstitutionMatrix<AminoAcidCompound> blosum62 = new SimpleSubstitutionMatrix<AminoAcidCompound>();
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       List<PairwiseSequenceScorer<ProteinSequence, AminoAcidCompound>> scorers = Alignments.getAllPairsScorers(list,
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               PairwiseSequenceScorerType.GLOBAL_IDENTITIES, gaps, blosum62);
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       Alignments.runPairwiseScorers(scorers);
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       System.out.printf("%d scores in %d ms using %d kB%n%n", scorers.size(),
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               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);
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       profiler.setCheckpoint();
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       System.out.print("Stage 2: hierarchical clustering into a guide tree... ");
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       GuideTree<ProteinSequence, AminoAcidCompound> tree = new GuideTree<ProteinSequence, AminoAcidCompound>(list,
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               scorers);
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       scorers = null;
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       System.out.printf("%d ms using %d kB%n%n%s%n%n", profiler.getTimeSinceCheckpoint()/1000000,
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               profiler.getMaxMemoryUsed()/1024, tree);
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       profiler.setCheckpoint();
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       System.out.print("Stage 3: progressive alignment... ");
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       Profile<ProteinSequence, AminoAcidCompound> msa = Alignments.getProgressiveAlignment(tree,
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               ProfileProfileAlignerType.GLOBAL, gaps, blosum62);
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       System.out.printf("%d profile-profile alignments in %d ms using %d kB%n%n", list.size() - 1,
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               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);
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       fout.print(msa);
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       fout.close();
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       ConcurrencyTools.shutdown();
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       System.out.printf("Total time: %d ms%nMemory use: %d kB%n", profiler.getTimeSinceStart()/1000000,
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               profiler.getMaxMemoryUsed()/1024);
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   }
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}
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