Example #1
0
  /*.................................................................................................................*/
  public void processSingleXMLPreference(String tag, String content) {
    if ("bootStrapReps".equalsIgnoreCase(tag)) bootstrapreps = MesquiteInteger.fromString(content);
    if ("mxram".equalsIgnoreCase(tag)) mxram = MesquiteInteger.fromString(content);
    if ("convertGapsToMissing".equalsIgnoreCase(tag))
      convertGapsToMissing = MesquiteBoolean.fromTrueFalseString(content);
    if ("resamplingAllConsensusTrees".equalsIgnoreCase(tag))
      resamplingAllConsensusTrees = MesquiteBoolean.fromTrueFalseString(content);
    if ("harvestOnlyStrictConsensus".equalsIgnoreCase(tag))
      harvestOnlyStrictConsensus = MesquiteBoolean.fromTrueFalseString(content);
    if ("searchStyle".equalsIgnoreCase(tag)) searchStyle = MesquiteInteger.fromString(content);
    if ("searchArguments".equalsIgnoreCase(tag))
      searchArguments = StringUtil.cleanXMLEscapeCharacters(content);
    if ("bootstrapSearchArguments".equalsIgnoreCase(tag))
      bootstrapSearchArguments = StringUtil.cleanXMLEscapeCharacters(content);
    if ("otherOptions".equalsIgnoreCase(tag))
      otherOptions = StringUtil.cleanXMLEscapeCharacters(content);

    // parallel, etc.
    preferencesSet = true;
  }
 /*.................................................................................................................*/
 public Object doCommand(String commandName, String arguments, CommandChecker checker) {
   if (checker.compare(
       this.getClass(),
       "Sets whether or not to count stops in regions with ambiguous nucleotides that imply a stop OR an amino acid",
       "[on; off]",
       commandName,
       "toggleCountEvenIfOthers")) {
     countEvenIfOthers.toggleValue(parser.getFirstToken(arguments));
     parametersChanged();
   } else if (checker.compare(
       this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
     return matrixSourceTask;
   } else return super.doCommand(commandName, arguments, checker);
   return null;
 }
 public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
   if (result == null) return;
   clearResultAndLastResult(result);
   Taxa taxa = taxon.getTaxa();
   int it = taxa.whichTaxonNumber(taxon);
   if (taxa != currentTaxa || observedStates == null) {
     observedStates = matrixSourceTask.getCurrentMatrix(taxa);
     currentTaxa = taxa;
   }
   if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
   DNAData data = (DNAData) observedStates.getParentData();
   int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
   if (result != null) result.setValue(count);
   if (resultString != null)
     resultString.setValue(
         "Number of stop codons in taxon " + observedStates.getName() + ": " + count);
   saveLastResult(result);
   saveLastResultString(resultString);
 }
Example #4
0
  /*.................................................................................................................*/
  public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
    logln("Preparing to receive TNT trees.");
    boolean success = false;
    taxa = treeList.getTaxa();
    // TODO		finalScore.setValue(finalValue);

    suppressProjectPanelReset();
    CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord();
    CommandRecord scr = new CommandRecord(true);
    MesquiteThread.setCurrentCommandRecord(scr);

    // define file paths and set tree files as needed.
    setFileNames();
    String[] outputFilePaths = externalProcRunner.getOutputFilePaths();

    String treeFilePath = outputFilePaths[OUT_TREEFILE];
    taxonNumberTranslation = getTaxonNumberTranslation(taxa);
    namer.setNumberTranslationTable(taxonNumberTranslation);

    runFilesAvailable();

    // read in the tree files
    success = false;
    Tree t = null;

    MesquiteBoolean readSuccess = new MesquiteBoolean(false);
    // TreeVector tv = new TreeVector(taxa);
    if (bootstrapOrJackknife()) {
      if (resamplingAllConsensusTrees)
        t =
            ZephyrUtil.readTNTTreeFile(
                this,
                treeList,
                taxa,
                treeFilePath,
                "TNT " + getResamplingKindName() + " Rep",
                0,
                readSuccess,
                false,
                false,
                null,
                namer); // set first tree number as 0 as will remove the first one later.
      else
        t =
            ZephyrUtil.readTNTTreeFile(
                this,
                treeList,
                taxa,
                treeFilePath,
                "TNT " + getResamplingKindName() + " Majority Rule Tree",
                1,
                readSuccess,
                false,
                false,
                freqRef,
                namer);
    } else
      t =
          ZephyrUtil.readTNTTreeFile(
              this,
              treeList,
              taxa,
              treeFilePath,
              "TNTTree",
              1,
              readSuccess,
              false,
              harvestOnlyStrictConsensus,
              null,
              namer);
    success = t != null;
    if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) {
      t = t.cloneTree();
      treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree
    }

    MesquiteThread.setCurrentCommandRecord(oldCR);
    success = readSuccess.getValue();
    if (!success) {
      logln("Execution of TNT unsuccessful [2]");
      if (!beanWritten) postBean("unsuccessful [2]", false);
      beanWritten = true;
    } else {
      if (!beanWritten) postBean("successful", false);
      beanWritten = true;
    }

    desuppressProjectPanelReset();
    if (data != null) data.decrementEditInhibition();
    //	manager.deleteElement(tv);  // get rid of temporary tree block
    externalProcRunner.finalCleanup();
    if (success) return t;
    return null;
  }
 /*.................................................................................................................*/
 public Snapshot getSnapshot(MesquiteFile file) {
   Snapshot temp = new Snapshot();
   temp.addLine("getMatrixSource", matrixSourceTask);
   temp.addLine("toggleCountEvenIfOthers " + countEvenIfOthers.toOffOnString());
   return temp;
 }