Examples of org.mcisb.beacon.ui.pedro.NodeUtils

    {
      OutputStream os = null;
      
      try
      {
        final List resultNodes = new NodeUtils().getChildNodes( spotNode, "RESULT" ); //$NON-NLS-1$
      
      for( Iterator iterator = resultNodes.iterator(); iterator.hasNext(); )
      {
        NavigationTreeNode resultNode = (NavigationTreeNode)iterator.next();
        os = new FileOutputStream( new File( directory, new FileUtils().convertCharacters( resultNode.getDisplayName() ) + ".xls" ) ); //$NON-NLS-1$

    if( file != null )
    {
      
      // try
      { 
        final NodeUtils nodeUtils = new NodeUtils();
        int numberOfDishes = nodeUtils.getIntegerFieldValue( node, "numberOfDishes"); //$NON-NLS-1$
        if (numberOfDishes==0) {
          numberOfDishes=1;
        }
        ExperimentDetailsFactory expFactory = new ExperimentDetailsFactory(file);
        ExperimentalDetails expDetails = expFactory.getExperimentalDetails();

            // First get a complete copy of the current node
            final RecordModel array = node.getRecordModel();
            array.setValue( "equipment_file_name", file.getAbsolutePath(), false ); //$NON-NLS-1$


            // Go through the stored model and find the appropriate recording for each spot node at this scope is an Assay
            final NodeUtils nodeUtils = new NodeUtils();


            // Need the microscope recording object here in order to add a microscope:
          MicroscopeRecording recording =null;
          
          String lensNA =""; //$NON-NLS-1$
          String mag=""; //$NON-NLS-1$
          String lensName=""; //$NON-NLS-1$
            // Need to precompute the total number of spots on each dish and cache this    
            final int numberOfDishes = nodeUtils.getIntegerFieldValue( node, "numberOfDishes" ); //$NON-NLS-1$


            for( int i = 0; i < numberOfDishes; i++ )
            {
              final String dishDisplayName = "DISH:-" + ( i + 1 ); //$NON-NLS-1$


              RecordModel microscopeRecordModel = recordModelFactory.createRecordModel( "Microscope" ); //$NON-NLS-1$
              for( Enumeration assayChildren = node.children(); assayChildren.hasMoreElements(); )
              {
                NavigationTreeNode dishNode = (NavigationTreeNode)assayChildren.nextElement();


                if( dishNode.getDisplayName().trim().equals( dishDisplayName ) )
                {      
                  // should have got the appropriate dish by here
                  // Get number of rows/columns from this dish, as each dish could be different :-(
                  final int rows = nodeUtils.getIntegerFieldValue( dishNode, "numberOfRows" ); //$NON-NLS-1$
                  final int columns = nodeUtils.getIntegerFieldValue( dishNode, "numberOfColumns" ); //$NON-NLS-1$


                  final List selectedSpots = new ArrayList();
                  final Collection deselectedSpots = new ArrayList();


                  for( Enumeration spotNodes = dishNode.children(); spotNodes.hasMoreElements(); )
                  {
                    final NavigationTreeNode spotNode = (NavigationTreeNode)spotNodes.nextElement();
                    final int rowNumber = nodeUtils.getIntegerFieldValue( spotNode, "row" ); //$NON-NLS-1$
                    final int columnNumber = nodeUtils.getIntegerFieldValue( spotNode, "column" ); //$NON-NLS-1$


                    final Collection plasmids = new ArrayList();
                    final Spot spot = new Spot( new SpotReading( plasmids, plasmids ) );
                    spot.setRow( rowNumber );
                    spot.setColumn( columnNumber );


                    selectedSpots.add( spot );
                  }


                  // Ask the user about which spots they asked the microscope to track
                  getTrackedSpots( rows, columns, recordings.size(), selectedSpots, deselectedSpots );


                  final boolean deleteNonTrackedSpots = ( deselectedSpots.size() > 0 ) ? deleteNonTrackedSpots() : false;


                  for( Enumeration spotNodes = dishNode.children(); spotNodes.hasMoreElements(); )
                  {
                    final NavigationTreeNode spotNode = (NavigationTreeNode)spotNodes.nextElement();


                    if( spotNode.getDisplayName().trim().startsWith( "SPOTREADING" ) ) //$NON-NLS-1$
                    { 
                      final int rowNumber = nodeUtils.getIntegerFieldValue( spotNode, "row" ); //$NON-NLS-1$
                      final int columnNumber = nodeUtils.getIntegerFieldValue( spotNode, "column" ); //$NON-NLS-1$


                      // Now get the appropriate Microscope model and add it to this spot:
                      recording = getRecording( recordings, selectedSpots, rowNumber, columnNumber );
                      final RecordModel spotRecordModel = spotNode.getRecordModel();

Examples of org.mcisb.beacon.ui.pedro.NodeUtils

Related Classes of org.mcisb.beacon.ui.pedro.NodeUtils