com.hfg.automation.platelayer.PlateVolumeAdjustmentLayer Maven / Gradle / Ivy

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com.hfg xml, html, svg, and bioinformatics utility library
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package com.hfg.automation.platelayer;


import java.util.Collection;

import com.hfg.automation.AutomationXML;
import com.hfg.automation.WellRef;
import com.hfg.automation.plateop.VolumeMask;
import com.hfg.units.Quantity;
import com.hfg.xml.XMLNode;

//------------------------------------------------------------------------------
/**
 Plate layer for specifying per-well volume adjustments.
 
 @author J. Alex Taylor, hairyfatguy.com
 
 */
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------

public class PlateVolumeAdjustmentLayer extends PlateLayerImpl
{
   private VolumeMask  mVolumeMask = new VolumeMask();

   //###########################################################################
   // CONSTRUCTORS
   //###########################################################################

   //--------------------------------------------------------------------------
   public PlateVolumeAdjustmentLayer()
   {

   }

   //--------------------------------------------------------------------------
   public PlateVolumeAdjustmentLayer(XMLNode inXML)
   {
      super(inXML);

      XMLNode volumeMaskTag = inXML.getOptionalSubtagByName(AutomationXML.VOLUME_MASK);
      if (volumeMaskTag != null)
      {
         mVolumeMask = new VolumeMask(volumeMaskTag);
      }
   }

   //###########################################################################
   // PUBLIC METHODS
   //###########################################################################

   //---------------------------------------------------------------------------
   public XMLNode toXMLNode()
   {
      XMLNode node = super.toXMLNode();

      if (getVolumeMask() != null)
      {
         node.addSubtag(getVolumeMask().toXMLNode());
      }

      return node;
   }

   //--------------------------------------------------------------------------
   @Override
   public PlateVolumeAdjustmentLayer clone()
   {
      PlateVolumeAdjustmentLayer theClone = (PlateVolumeAdjustmentLayer) super.clone();

      theClone.mVolumeMask = mVolumeMask.clone();

      return theClone;
   }

   //---------------------------------------------------------------------------
   public Quantity getVolumeAdjustment(WellRef inWellRef)
   {
      return getVolumeMask().getVolume(inWellRef);
   }

   //---------------------------------------------------------------------------
   public VolumeMask getVolumeMask()
   {
      return mVolumeMask;
   }

   //---------------------------------------------------------------------------
   public PlateVolumeAdjustmentLayer setVolume(WellRef inWellRef, Quantity inValue)
   {
      getVolumeMask().setVolume(inWellRef, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   public PlateVolumeAdjustmentLayer addVolume(WellRef inWellRef, Quantity inValue)
   {
      getVolumeMask().addVolume(inWellRef, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   public PlateVolumeAdjustmentLayer subtractVolume(WellRef inWellRef, Quantity inValue)
   {
      getVolumeMask().subtractVolume(inWellRef, inValue);
      return this;
   }

   //---------------------------------------------------------------------------
   @Override
   public Collection getOccupiedWellRefs()
   {
      return getVolumeMask().getOccupiedWellRefs();
   }

   //---------------------------------------------------------------------------
   @Override
   public WellLayer getWellLayer(WellRef inWellRef)
   {
      WellVolumeAdjustmentLayer wellLayer = null;

      Quantity volume = getVolumeMask().getVolume(inWellRef);
      if (volume != null)
      {
         wellLayer = new WellVolumeAdjustmentLayer(volume);
         wellLayer.setName(name());
      }

      return wellLayer;
   }
}