com.hfg.automation.platelayer.PlateLayerImpl 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 java.util.Iterator;

import com.hfg.automation.AutomationXML;
import com.hfg.automation.PlateLayout;
import com.hfg.automation.WellRef;
import com.hfg.util.CompareUtil;
import com.hfg.util.StringUtil;
import com.hfg.xml.XMLNode;
import com.hfg.xml.XMLTag;

//------------------------------------------------------------------------------
/**
 Abstract base plate layer.
 
 @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 abstract class PlateLayerImpl implements PlateLayer, Comparable
{
   private String      mName;
   private LayerPlate  mPlate;
   private PlateLayout mLayout;


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

   //--------------------------------------------------------------------------
   public PlateLayerImpl()
   {

   }

   //--------------------------------------------------------------------------
   public PlateLayerImpl(String inName)
   {
      this();
      setName(inName);
   }

   //--------------------------------------------------------------------------
   public PlateLayerImpl(XMLNode inXML)
   {
      inXML.verifyTagName(AutomationXML.PLATE_LAYER);

      setName(inXML.getAttributeValue(AutomationXML.NAME_ATT));

      XMLNode layoutTag = inXML.getOptionalSubtagByName(AutomationXML.PLATE_LAYOUT);
      if (layoutTag != null)
      {
         setLayout(new PlateLayout(layoutTag));
      }
   }

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

   //---------------------------------------------------------------------------
   public XMLNode toXMLNode()
   {
      XMLNode node = new XMLTag(AutomationXML.PLATE_LAYER);
      node.setAttribute(AutomationXML.CLASS_ATT, getClass().getName());

      if (StringUtil.isSet(name()))
      {
         node.setAttribute(AutomationXML.NAME_ATT, name());
      }

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

      return node;
   }

   //--------------------------------------------------------------------------
   @Override
   public PlateLayerImpl clone()
   {
      PlateLayerImpl theClone;
      try
      {
         theClone = (PlateLayerImpl) super.clone();
      }
      catch (CloneNotSupportedException e)
      {
         throw new RuntimeException(e);
      }

      return theClone;
   }

   //---------------------------------------------------------------------------
   @Override
   public int hashCode()
   {
      int hashCode = super.hashCode();
      if (StringUtil.isSet(name()))
      {
         hashCode += 31 * name().hashCode();
      }

      if (getLayout() != null)
      {
         hashCode += 31 * getLayout().hashCode();
      }

      return hashCode;
   }

   //---------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      return (0 == compareTo(inObj2));
   }

   //---------------------------------------------------------------------------
   @Override
   public int compareTo(Object inObj2)
   {
      int result = -1;

      if (inObj2 != null
            && inObj2 instanceof PlateLayer)
      {
         result = 0;
         if (this != inObj2)
         {
            PlateLayer plateLayer2 = (PlateLayer) inObj2;

            result = CompareUtil.compare(name(), plateLayer2.name());

            if (0 == result)
            {
               result = CompareUtil.compare(getLayout(), plateLayer2.getLayout());
            }
         }
      }

      return result;
   }

   //--------------------------------------------------------------------------
   public PlateLayer setName(String inValue)
   {
      mName = inValue;
      return this;
   }

   //--------------------------------------------------------------------------
   public String name()
   {
      return mName;
   }

   //---------------------------------------------------------------------------
   public PlateLayer setPlate(LayerPlate inValue)
   {
      mPlate = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public PlateLayer setLayout(PlateLayout inValue)
   {
      mLayout = inValue;
      return this;
   }

   //---------------------------------------------------------------------------
   public PlateLayout getLayout()
   {
      if (null == mLayout)
      {
         // Default to the plate's layout
         mLayout = mPlate.getLayout();
      }

      return mLayout;
   }

   //---------------------------------------------------------------------------
   public WellRef getNextAvailableWellRef()
   {
      WellRef nextWellRef = null;

      Collection occupiedWellRefs = getOccupiedWellRefs();

      Iterator iterator = getLayout().wellRefIterator();
      while (iterator.hasNext())
      {
         WellRef wellRef = iterator.next();
         if (null == occupiedWellRefs
               || ! occupiedWellRefs.contains(wellRef))
         {
            nextWellRef = wellRef;
            break;
         }
      }

      return nextWellRef;
   }

}