Exemple #1
0
  public void run() {
    if (in.verbosity > 1) System.err.println("Config : " + conf);

    try {

      if (AlignmentMaker_SingleSequences.consistency) {
        int increase = AlignmentMaker_SingleSequences.consistency_subs_increase;
        conf.cost.increaseCosts(
            increase); // arbitrary number ... just trying to make w-w identities non-zero cost, and
                       // high enough to avoid rounding effects
        conf.cost.multiplyCosts(2);

        conf.increaseGapCosts(increase / 2);
        conf.multiplyGapCosts(2);
      }

      if (Tree.treeType == Tree.TreeType.entered) {
        Tree.iterations = 1;
      }

      FacetAlignment fa = null;
      if (in.justDoSubOpt) {
        am = new AlignmentMaker_SuboptimalityTester();
        // am.initialize(in.fileA, in.structFileA);
        am.initialize(conf, in);
        alignmentInstance = am.buildAlignment();
        if (in.structFileA != null) {
          fa =
              new FacetAlignment(
                  conf.sc.convertIntsToSeqs(alignmentInstance), in.structure.structure);
        }
      } else if (in.justDoConvert) {
        am = new AlignmentMaker_Converter();
        // am.initialize(in.fileA, in.structFileA);
        am.initialize(conf, in);
        alignmentInstance = am.buildAlignment();
        if (in.structFileA != null) {
          fa =
              new FacetAlignment(
                  conf.sc.convertIntsToSeqs(alignmentInstance), in.structure.structure);
        }
      } else if (in.fileB != null) { // alignalign call
        am = new AlignmentMaker_TwoAlignments();
        // am.initialize(in.fileA, in.fileB);
        // Aligner.useStructure = false;
        am.initialize(conf, in);
        alignmentInstance = am.buildAlignment();
        if (in.structFileA != null) {
          fa =
              new FacetAlignment(
                  ((AlignmentMaker_TwoAlignments) am).result, in.structure.structure);
        }

      } else if (in.justTree || Tree.justPWDists) { //
        am = new AlignmentMaker_SingleSequences();
        // am.initialize(in.fileA, in.structFileA);
        am.initialize(conf, in);
        ((AlignmentMaker_SingleSequences) am).buildTree(conf, in);
      } else { // multiple alignment call
        am = new AlignmentMaker_SingleSequences();
        // am.initialize(in.fileA, in.structFileA);
        am.initialize(conf, in);
        // final Timer queueRunner = new Timer();
        // ShutdownHandler sh = new ShutdownHandler(queueRunner,
        // (AlignmentMaker_SingleSequences)am);
        // Runtime.getRuntime().addShutdownHook(sh);
        // Thread.setDefaultUncaughtExceptionHandler(sh);  // this should be available for all calls
        // ... but this is the one I use a lot, so it's all I've implemented it for

        alignmentInstance = am.buildAlignment();

        if (in.structFileA != null) {

          if (realignmentConfigList != null) {
            Configuration newRealignmentConfigList[] =
                new Configuration[realignmentConfigList.length];
            for (int rNum = 0; rNum < realignmentConfigList.length; rNum++) {
              newRealignmentConfigList[rNum] = new Configuration(realignmentConfigList[rNum]);
            }
            preRealignmentAlignmentInstance = alignmentInstance.clone();
            preRealignmentFacetScore =
                Facet.defaultValue(
                    new FacetAlignment(
                        conf.sc.convertIntsToSeqs(preRealignmentAlignmentInstance),
                        in.structure.structure),
                    conf.useLegacyFacetFunction);
            if (conf.useTCSforAdvising)
              preRealignmentFacetScore = TCS.TCSValue(preRealignmentAlignmentInstance, am, conf);
            realignmentDriver realigner =
                new realignmentDriver(
                    conf.sc.convertIntsToSeqs(preRealignmentAlignmentInstance),
                    in.structure.structure,
                    newRealignmentConfigList,
                    conf,
                    (float) preRealignmentFacetScore,
                    am);
            if (conf.realignment_window_type == Configuration.WINDOW_SIZE.VALUE)
              realigner.simpleRealignment((int) conf.realignment_window_value);
            else if (conf.realignment_window_type == Configuration.WINDOW_SIZE.PERCENTAGE) {
              int window_size =
                  (int)
                      (conf.realignment_window_value
                          * (float) preRealignmentAlignmentInstance[0].length);
              if (window_size > conf.maximum_realignment_window_value)
                window_size = (int) conf.maximum_realignment_window_value;
              if (window_size < conf.minimum_realignment_window_value)
                window_size = (int) conf.minimum_realignment_window_value;
              realigner.simpleRealignment(window_size);
            }
            alignmentInstance = realigner.newAlignment();
            newRealignmentConfigList = null;
          }
          fa =
              new FacetAlignment(
                  conf.sc.convertIntsToSeqs(alignmentInstance), in.structure.structure);
        }
      }

      if (fa != null) {
        if (in.featureOutputFile != null) {
          String fname = in.featureOutputFile.replace("__CONFIG__", conf.toString());
          if (conf.repetition >= 0)
            fname = fname.replace("__ITTERATION__", Integer.toString(conf.repetition));
          Facet.outputDefaultFeatures(fname, fa);
        }
        facetScore = Facet.defaultValue(fa, conf.useLegacyFacetFunction);
        if (conf.useTCSforAdvising) facetScore = TCS.TCSValue(alignmentInstance, am, conf);
      }
      // in.structFileA = "";
      // System.err.println("File: " + in.structFileA);

      // System.err.printf("facet value --  %.6f\n\n",facetScore);
    } catch (GenericOpalException e) {
      System.exit(1);
    } /*catch (FileNotFoundException e){
      	System.err.println("File Error:" + e.toString());
      	System.exit(15);
      }*/
  }
Exemple #2
0
  public static void main(String[] argv) {

    OpalLogWriter.setLogger(new DefaultLogger());

    ArgumentHandler argHandler = new ArgumentHandler(argv);

    if (argHandler.getVerbosity() > 0) {
      OpalLogWriter.printVersion();
      OpalLogWriter.stdErrLogln("");
    }

    /*String fileA = argHandler.getFileA();
    String fileB = argHandler.getFileB();
    String structFileA = argHandler.getStructFileA();
    String structFileB = argHandler.getStructFileB();



    String costName = argHandler.getCostName();
    int gamma = argHandler.getGamma();
    int lambda = argHandler.getLambda();
    int gammaTerm = argHandler.getGammaTerm();
    int lambdaTerm = argHandler.getLambdaTerm();

    int verbosity = argHandler.getVerbosity();
    boolean toUpper = argHandler.isToUpper();
    boolean justDoConvert= argHandler.isJustDoConvert();
    boolean justDoSubOpt= argHandler.isJustDoSubOpt();
    boolean justTree= argHandler.isJustTree();*/

    Date start = new Date();

    Configuration[] advising_config = argHandler.getAdvisingConfigs();
    Configuration[] realignment_config = argHandler.getRealignmentConfigs();
    Inputs input = argHandler.getInputs();
    runAlignment[] thread = new runAlignment[advising_config.length];

    int last_joined = -1;
    int max_threads = Runtime.getRuntime().availableProcessors();
    if (argHandler.getMaxThreads() > -1) max_threads = argHandler.getMaxThreads();
    if (input.verbosity > 0) {
      OpalLogWriter.stdErrLogln(
          "The number of available threads is "
              + Runtime.getRuntime().availableProcessors()
              + ", Opal will use "
              + max_threads);
    }

    int maxIndex = 0;
    int maxPreRealignmentIndex = 0;
    for (int i = 0; i < advising_config.length; i++) {
      thread[i] = new runAlignment(advising_config[i], input, realignment_config);
      // thread[i] = new printLine(config[i],i);
      thread[i].start();
      if (i - last_joined >= max_threads) {
        last_joined++;
        try {
          thread[last_joined].join();
          if (input.configOutputFile != null) thread[last_joined].print();
          if (input.configOutputFile != null && realignment_config != null)
            thread[last_joined].printPreRealignment();
          if (thread[last_joined].facetScore > thread[maxIndex].facetScore) {
            if (maxPreRealignmentIndex != maxIndex) thread[maxIndex] = null;
            maxIndex = last_joined;
          }
          if (thread[last_joined].preRealignmentFacetScore
              > thread[maxPreRealignmentIndex].preRealignmentFacetScore) {
            if (maxPreRealignmentIndex != maxIndex) thread[maxPreRealignmentIndex] = null;
            maxPreRealignmentIndex = last_joined;
          }
          if (last_joined != maxIndex && last_joined != maxPreRealignmentIndex)
            thread[last_joined] = null;
        } catch (InterruptedException e) {
          OpalLogWriter.stdErrLogln("InterruptedException " + e.toString());
          throw new GenericOpalException("InterruptedException " + e.toString());
        }
      }
    }

    for (last_joined++; last_joined < advising_config.length; last_joined++) {
      try {
        thread[last_joined].join();
        if (input.configOutputFile != null) thread[last_joined].print();
        if (input.configOutputFile != null && realignment_config != null)
          thread[last_joined].printPreRealignment();
        if (thread[last_joined].facetScore > thread[maxIndex].facetScore) {
          if (maxPreRealignmentIndex != maxIndex) thread[maxIndex] = null;
          maxIndex = last_joined;
        }
        if (thread[last_joined].preRealignmentFacetScore
            > thread[maxPreRealignmentIndex].preRealignmentFacetScore) {
          if (maxPreRealignmentIndex != maxIndex) thread[maxPreRealignmentIndex] = null;
          maxPreRealignmentIndex = last_joined;
        }
        if (last_joined != maxIndex && last_joined != maxPreRealignmentIndex)
          thread[last_joined] = null;
      } catch (InterruptedException e) {
        OpalLogWriter.stdErrLogln("InterruptedException " + e.toString());
        throw new GenericOpalException("InterruptedException " + e.toString());
      }
    }

    // if(advising_config.length>1 && thread[maxIndex]!=null && thread[maxIndex].facetScore>=0)
    if (!thread[maxIndex].printBest()) System.err.println("Print returned false");

    if (advising_config.length > 1
        && realignment_config != null
        && thread[maxPreRealignmentIndex] != null
        && thread[maxPreRealignmentIndex].facetScore >= 0) {
      if (input.bestPreRealignmentOutputFile != null)
        if (!thread[maxPreRealignmentIndex].printBestPreRealignment())
          System.err.println("Print returned false");
      if (input.bestPreRealignmentsRealignmentOutputFile != null)
        if (!thread[maxPreRealignmentIndex].printBestPreRealignmentsRealignment())
          System.err.println("Print returned false");
      if (input.bestPreRealignmentsRealignmentOutputFileIncludePreRealignment != null)
        if (!thread[maxPreRealignmentIndex]
            .printBestPreRealignmentsRealignmentIncludePreRealignment())
          System.err.println("Print returned false");
    }

    if (advising_config.length > 1
        && realignment_config != null
        && thread[maxIndex] != null
        && thread[maxIndex].facetScore >= 0
        && thread[maxPreRealignmentIndex] != null
        && thread[maxPreRealignmentIndex].facetScore >= 0
        && thread[maxPreRealignmentIndex].preRealignmentFacetScore < thread[maxIndex].facetScore) {
      if (input.bestOutputFileIncludePreRealignment != null)
        if (!thread[maxIndex].printBestIncludePreRealignment())
          System.err.println("Print returned false");
    } else if (advising_config.length > 1
        && thread[maxPreRealignmentIndex] != null
        && thread[maxPreRealignmentIndex].facetScore >= 0) {
      if (input.bestOutputFileIncludePreRealignment != null)
        if (!thread[maxPreRealignmentIndex].printBestIncludePreRealignment())
          System.err.println("Print returned false");
    }

    if (input.verbosity > 0) {
      Date now = new Date();
      long diff = now.getTime() - start.getTime();
      System.err.printf("Total time for job: %.1f seconds\n\n", ((float) diff / 1000 + .05));
    }

    System.exit(0);
  }