package org.biojava3.alignment;

import java.io.File; import java.io.PrintStream; import
java.util.ArrayList; import java.util.List;

import org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType;
import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava.nbio.alignment.template.GapPenalty; import
org.biojava.nbio.alignment.template.PairwiseSequenceScorer; import
org.biojava.nbio.alignment.template.Profile; import
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
org.biojava.nbio.core.sequence.ProteinSequence; import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
org.biojava.nbio.core.util.ConcurrencyTools;

public class CookbookMSAProfiler {

   private static class Profiler {

       private long maxMemoryUsed, timeCheckpoint;  
       private final long timeStart;

       private Profiler() {  
           maxMemoryUsed = Runtime.getRuntime().totalMemory();  
           timeStart = timeCheckpoint = System.nanoTime();  
       }

       private long getMaxMemoryUsed() {  
           return maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());  
       }

       private long getTimeSinceCheckpoint() {  
           return System.nanoTime() - timeCheckpoint;  
       }

       private long getTimeSinceStart() {  
           return System.nanoTime() - timeStart;  
       }

       private void setCheckpoint() {  
           maxMemoryUsed = Math.max(maxMemoryUsed, Runtime.getRuntime().totalMemory());  
           timeCheckpoint = System.nanoTime();  
       }

   }

   public static void main(String[] args) throws Exception {

       if (args.length < 1) {  
           System.err.println("The first argument must be a fasta file of protein sequences.");  
           return;  
       }

       // ConcurrencyTools.setThreadPoolSingle();

       PrintStream fout = new PrintStream("msa.txt");  
       Profiler profiler = new Profiler();

       System.out.printf("Loading sequences from %s... ", args[0]);  
       List<ProteinSequence> list = new ArrayList<ProteinSequence>();  
       list.addAll(FastaReaderHelper.readFastaProteinSequence(new File(args[0])).values());  
       if (args.length > 1 && Integer.parseInt(args[1]) < list.size()) {  
           System.out.printf("%s/%d", args[1], list.size());  
           list = list.subList(0, Integer.parseInt(args[1]));  
       } else {  
           System.out.printf("%d", list.size());  
       }  
       System.out.printf(" sequences in %d ms using %d kB%n%n", profiler.getTimeSinceCheckpoint()/1000000,  
               profiler.getMaxMemoryUsed()/1024);

       profiler.setCheckpoint();

       System.out.print("Stage 1: pairwise similarity calculation... ");  
       GapPenalty gaps = new SimpleGapPenalty();  
       SubstitutionMatrix<AminoAcidCompound> blosum62 = new SimpleSubstitutionMatrix<AminoAcidCompound>();  
       List<PairwiseSequenceScorer<ProteinSequence, AminoAcidCompound>> scorers = Alignments.getAllPairsScorers(list,  
               PairwiseSequenceScorerType.GLOBAL_IDENTITIES, gaps, blosum62);  
       Alignments.runPairwiseScorers(scorers);  
       System.out.printf("%d scores in %d ms using %d kB%n%n", scorers.size(),  
               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);

       profiler.setCheckpoint();

       System.out.print("Stage 2: hierarchical clustering into a guide tree... ");  
       GuideTree<ProteinSequence, AminoAcidCompound> tree = new GuideTree<ProteinSequence, AminoAcidCompound>(list,  
               scorers);  
       scorers = null;  
       System.out.printf("%d ms using %d kB%n%n%s%n%n", profiler.getTimeSinceCheckpoint()/1000000,  
               profiler.getMaxMemoryUsed()/1024, tree);

       profiler.setCheckpoint();

       System.out.print("Stage 3: progressive alignment... ");  
       Profile<ProteinSequence, AminoAcidCompound> msa = Alignments.getProgressiveAlignment(tree,  
               ProfileProfileAlignerType.GLOBAL, gaps, blosum62);  
       System.out.printf("%d profile-profile alignments in %d ms using %d kB%n%n", list.size() - 1,  
               profiler.getTimeSinceCheckpoint()/1000000, profiler.getMaxMemoryUsed()/1024);  
       fout.print(msa);  
       fout.close();

       ConcurrencyTools.shutdown();

       System.out.printf("Total time: %d ms%nMemory use: %d kB%n", profiler.getTimeSinceStart()/1000000,  
               profiler.getMaxMemoryUsed()/1024);

   }

}