Package mesquite.lib

Examples of mesquite.lib.ListableVector.elementAt()

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    ListableVector taxas = project.getTaxas();
    Taxa t = null;

    for (int i = 0; i < taxas.size(); i++) {
      // One Taxa represents one TAXA block in a Nexus file.
      t = (Taxa) taxas.elementAt(i);
      if (!t.isDoomed()) {
        // a taxa is represented by a TaxonLabelSet
        // name is important:
        TaxonLabelSet labelSet = new TaxonLabelSet();
        labelSet.setStudy(pStudy);
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    TreesManager treeManager = (TreesManager) project.ownerModule
      .findElementManager(TreeVector.class);
    ListableVector treeVectors = treeManager.getTreeBlockVector();
    for (int i = 0; i < treeVectors.size(); i++) {
      // One treeVector represents one tree block
      TreeVector treeVector = (TreeVector) treeVectors.elementAt(i);
      // System.out.println(" treeVector: " + i + " - " + treeVector.getName());

      TreeBlock treeblock = new TreeBlock();
      treeblock.setTitle(treeVector.getName());
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    }

    ListableVector matrices = pMesqProject.getCharacterMatrices();
    mesquite.lib.characters.CharacterData data;
    for (int i = 0; i < matrices.size(); i++) {
      data = (mesquite.lib.characters.CharacterData) matrices.elementAt(i);
      if (!data.isDoomed()) {
        // GOOD matrix
        if (LOGGER.isDebugEnabled()) {
          LOGGER
            .debug("convertMatrices: matrix: " + data.getName() + " -" + data.getNumChars()); //$NON-NLS-1$
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