Examples of MesquiteConverter

org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter
MesquiteConverter.java Created on Aug 4, 2006 @author Jin Ruan

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

//
    
//    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);

View Full Code Here

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

    }


    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());

View Full Code Here

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

      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;  
  }

View Full Code Here

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

      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;
  }

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.