Package org.cipres.treebase.domain.nexus.mesquite

Examples of org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter

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//
   
//    String newick = "[&R] (5,(4,1,3,2))";
   
    // 2. test
    MesquiteConverter converter = new MesquiteConverter();
    converter.buildNodesFromNewick(tree, labels, newick);
   
    //3. verify:
    tree.updateNewickString();
    logger.debug("treenode size=" + tree.getTreeNodesReadOnly().size() + "\n" + tree.getNewickString());
    //assertTrue(condition);
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    }

    List<TaxonLabel> taxonLabels = new ArrayList<TaxonLabel>();
    taxonLabels.addAll(tree.getAllTaxonLabels());
   
    MesquiteConverter converter = new MesquiteConverter();
    //List<PhyloTreeNode> allnodes = new ArrayList<PhyloTreeNode>(tree.getTreeNodesReadOnly());
   
    getPhyloTreeHome().deleteNodes(tree);
   
    converter.buildNodesFromNewick(tree, taxonLabels, pNewick);
   
    //ALERT: for whatever reason, needs to save tree nodes explicitly.
    //seems the tree.treenodes merge cascade does not work!
    getDomainHome().storeAll(tree.getTreeNodesReadOnly());
   
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      return null;
    }

    NexusDataSet data = new NexusDataSet();

    MesquiteConverter converter = new MesquiteConverter();
    converter.setMatrixDataTypeHome(getMatrixDataTypeHome());
    converter.setItemDefinitionHome(getItemDefinitionHome());
    converter.setTaxonLabelHome(getTaxonLabelHome());

    //converter.processLoadFile(pNexusFiles, pStudy, data, pListener);
    if ( LOGGER.isInfoEnabled() ) {
      LOGGER.info("Mesquite is located at: '"+System.getProperty(MESQUITE_FOLDER_DIR_KEY)+"'");
    }
   
    converter.parseOneFile(pNexusFile, pStudy, data);

    return data; 
  }
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      return null;
    }

    NexusDataSet data = new NexusDataSet();

    MesquiteConverter converter = new MesquiteConverter();
    converter.setMatrixDataTypeHome(getMatrixDataTypeHome());
    converter.setItemDefinitionHome(getItemDefinitionHome());
    converter.setTaxonLabelHome(getTaxonLabelHome());

    converter.processLoadFile(pNexusFiles, pStudy, data, pListener);

    return data;
  }
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Related Classes of org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter

  • mesquite.lib.duties.TreesManager
  • mesquite.lib.ListableVector
  • mesquite.lib.MesquiteProject
  • mesquite.lib.MesquiteTree
  • mesquite.lib.Parser
  • mesquite.lib.Taxa
  • mesquite.lib.Taxon
  • mesquite.lib.Tree
  • mesquite.lib.TreeVector
  • org.cipres.treebase.domain.nexus.MesquiteConverterTest
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