C++ AlignmentConstPtr::getNewickTree方法代码示例

void LodExtract::createInterpolatedAlignment(AlignmentConstPtr inAlignment,
                                             AlignmentPtr outAlignment,
                                             double scale,
                                             const string& tree,
                                             const string& rootName,
                                             bool keepSequences,
                                             bool allSequences,
                                             double probeFrac,
                                             double minSeqFrac)
{
  _inAlignment = inAlignment;
  _outAlignment = outAlignment;
  _keepSequences = keepSequences;
  _allSequences = allSequences;
  _probeFrac = probeFrac;
  _minSeqFrac = minSeqFrac;
  
  string newTree = tree.empty() ? inAlignment->getNewickTree() : tree;
  createTree(newTree, rootName);
  cout << "tree = " << _outAlignment->getNewickTree() << endl;
  
  deque<string> bfQueue;
  bfQueue.push_front(_outAlignment->getRootName());
  while (!bfQueue.empty())
  {
    string genomeName = bfQueue.back();
    bfQueue.pop_back();
    vector<string> childNames = _outAlignment->getChildNames(genomeName);
    if (!childNames.empty())
    {
      convertInternalNode(genomeName, scale);
      for (size_t childIdx = 0; childIdx < childNames.size(); childIdx++)
      {
        bfQueue.push_back(childNames[childIdx]);
      } 
    }
  }
}

//.........这里部分代码省略.........
    if (bottomSegments != "\"\"") ++optCount;
    if (allCoverage) ++optCount;
    if (optCount > 1)
    {
      throw hal_exception("--genomes, --sequences, --tree, --span, --spanRoot, "
                          "--branches, --sequenceStats, --children, --parent, "
                          "--bedSequences, --root, --numSegments, --baseComp, "
                          "--genomeMetaData, --chromSizes, --percentID, "
                          "--coverage,  --topSegments, --bottomSegments, "
                          "--allCoverage "
                          "and --branchLength options are exclusive");
    }
  }
  catch(exception& e)
  {
    cerr << e.what() << endl;
    optionsParser->printUsage(cerr);
    exit(1);
  }
  try
  {
    AlignmentConstPtr alignment = openHalAlignmentReadOnly(path, optionsParser);

    if (listGenomes == true && alignment->getNumGenomes() > 0)
    {
      printGenomes(cout, alignment);
    }
    else if (sequencesFromGenome != "\"\"")
    {
      printSequences(cout, alignment, sequencesFromGenome);
    }
    else if (tree == true)
    {
      cout << alignment->getNewickTree() << endl;
    }
    else if (sequenceStatsFromGenome != "\"\"")
    {
      printSequenceStats(cout, alignment, sequenceStatsFromGenome);
    }
    else if (bedSequencesFromGenome != "\"\"")
    {
      printBedSequenceStats(cout, alignment, bedSequencesFromGenome);
    }
    else if (spanGenomes !=  "\"\"")
    {
      printBranchPath(cout, alignment, chopString(spanGenomes, ","), false);
    }
    else if (spanRootGenomes !=  "\"\"")
    {
      printBranchPath(cout, alignment, chopString(spanRootGenomes, ","), true);
    }
    else if (branches == true)
    {
      printBranches(cout, alignment);
    }
    else if (childrenFromGenome != "\"\"")
    {
      printChildren(cout, alignment, childrenFromGenome);
    }
    else if (parentFromGenome != "\"\"")
    {
      printParent(cout, alignment, parentFromGenome);
    }
    else if (printRoot == true)
    {
      printRootName(cout, alignment);

int main(int argc, char** argv)
{
  CLParserPtr optionsParser = hdf5CLParserInstance();
  optionsParser->setDescription("Rertrieve basic statics from a hal database");
  optionsParser->addArgument("halFile", "path to hal file to analyze");
  optionsParser->addOptionFlag("genomes", "print only a list of genomes "
                               "in alignment", false);
  optionsParser->addOption("sequences", "print list of sequences in given "
                           "genome", "\"\"");
  optionsParser->addOption("sequenceStats", "print stats for each sequence in "
                           "given genome", "\"\"");
  optionsParser->addOptionFlag("tree", "print only the NEWICK tree", false);
  optionsParser->addOptionFlag("branches", "print list of branches. "
                               "Each branch is specified by the child genome", 
                               false);
  optionsParser->addOption("span", "print branches on path (or spanning tree) "
                           "between comma "
                           "separated list of genomes", "\"\"");
  optionsParser->addOption("spanRoot", "print genomes on path" 
                           "(or spanning tree) between comma "
                           "separated list of genomes.  Different from --path"
                           "only in that the spanning tree root is also "
                           "given", "\"\"");

  string path;
  bool listGenomes;
  string sequencesFromGenome;
  string sequenceStatsFromGenome;
  string spanGenomes;
  string spanRootGenomes;
  bool tree;
  bool branches;
  try
  {
    optionsParser->parseOptions(argc, argv);
    path = optionsParser->getArgument<string>("halFile");
    listGenomes = optionsParser->getFlag("genomes");
    sequencesFromGenome = optionsParser->getOption<string>("sequences");
    sequenceStatsFromGenome = optionsParser->getOption<string>("sequenceStats");
    tree = optionsParser->getFlag("tree");
    spanGenomes = optionsParser->getOption<string>("span");
    spanRootGenomes = optionsParser->getOption<string>("spanRoot");
    branches = optionsParser->getFlag("branches");

    size_t optCount = listGenomes == true ? 1 : 0;
    if (sequencesFromGenome != "\"\"") ++optCount;
    if (tree == true) ++optCount;
    if (sequenceStatsFromGenome != "\"\"") ++optCount;
    if (spanGenomes != "\"\"") ++optCount;
    if (spanRootGenomes != "\"\"") ++optCount;
    if (branches) ++optCount;
    if (optCount > 1)
    {
      throw hal_exception("--genomes, --sequences, --tree, --span, "
                          "--spanRoot, --branches "
                          "and --sequenceStats " 
                          "options are mutually exclusive");
    }        
  }
  catch(exception& e)
  {
    cerr << e.what() << endl;
    optionsParser->printUsage(cerr);
    exit(1);
  }
  try
  {
    AlignmentConstPtr alignment = openHalAlignmentReadOnly(path, optionsParser);

    if (listGenomes == true && alignment->getNumGenomes() > 0)
    {
      printGenomes(cout, alignment);
    }
    else if (sequencesFromGenome != "\"\"")
    {
      printSequences(cout, alignment, sequencesFromGenome);
    }
    else if (tree == true)
    {
      cout << alignment->getNewickTree() << endl;
    }
    else if (sequenceStatsFromGenome != "\"\"")
    {
      printSequenceStats(cout, alignment, sequenceStatsFromGenome);
    }
    else if (spanGenomes !=  "\"\"")
    {
      printBranchPath(cout, alignment, chopString(spanGenomes, ","), false);
    }
    else if (spanRootGenomes !=  "\"\"")
    {
      printBranchPath(cout, alignment, chopString(spanRootGenomes, ","), true);
    }
    else if (branches == true)
    {
      printBranches(cout, alignment);
    }
    else
    {
      HalStats halStats(alignment);
//.........这里部分代码省略.........