
com.hfg.automation.platelayer.PlateReagentLayer Maven / Gradle / Ivy
package com.hfg.automation.platelayer;
import java.lang.reflect.Constructor;
import java.util.Collection;
import com.hfg.automation.AutomationXML;
import com.hfg.automation.WellRange;
import com.hfg.automation.WellRef;
import com.hfg.automation.plateop.VolumeMask;
import com.hfg.bio.HfgBioXML;
import com.hfg.units.Quantity;
import com.hfg.util.StringUtil;
import com.hfg.util.collection.OrderedMap;
import com.hfg.xml.HfgXMLSerializable;
import com.hfg.xml.XMLNode;
import com.hfg.xml.XMLTag;
//------------------------------------------------------------------------------
/**
Plate layer for specifying per-well volumes of a reagent.
@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 PlateReagentLayer extends PlateLayerImpl implements ReagentLayer
{
private R mReagent;
private VolumeMask mVolumeMask = new VolumeMask();
//###########################################################################
// CONSTRUCTORS
//###########################################################################
//---------------------------------------------------------------------------
public PlateReagentLayer(R inValue)
{
setReagent(inValue);
}
//--------------------------------------------------------------------------
public PlateReagentLayer(XMLNode inXML)
{
super(inXML);
// TODO: Best way to deal with the reagent?
XMLNode reagentTag = inXML.getRequiredSubtagByName(AutomationXML.REAGENT);
String reagentClassname = reagentTag.getAttributeValue(HfgBioXML.CLASS_ATT);
if (! StringUtil.isSet(reagentClassname))
{
throw new RuntimeException("No " + AutomationXML.CLASS_ATT + " specified on the layer's reagent XML tag!");
}
if (reagentClassname.equals(String.class.getName()))
{
mReagent = (R) reagentTag.getUnescapedContent();
}
else
{
try
{
Class clazz = Class.forName(reagentClassname);
Constructor constructor = clazz.getConstructor(XMLNode.class);
mReagent = (R) constructor.newInstance(reagentTag.getSubtags().get(0));
}
catch (Exception e)
{
throw new RuntimeException("Error during plate instantiation from its XML tag!", e);
}
}
XMLNode volumeMaskTag = inXML.getOptionalSubtagByName(AutomationXML.VOLUME_MASK);
if (volumeMaskTag != null)
{
mVolumeMask = new VolumeMask(volumeMaskTag);
}
}
//###########################################################################
// PUBLIC METHODS
//###########################################################################
//---------------------------------------------------------------------------
public XMLNode toXMLNode()
{
XMLNode node = super.toXMLNode();
XMLNode reagentTag = new XMLTag(AutomationXML.REAGENT);
reagentTag.setAttribute(AutomationXML.CLASS_ATT, mReagent.getClass().getName());
if (mReagent.getClass().equals(String.class))
{
reagentTag.setContent(mReagent.toString());
}
else
{
reagentTag.addSubtag(((HfgXMLSerializable) mReagent).toXMLNode());
}
node.addSubtag(reagentTag);
if (getVolumeMask() != null)
{
node.addSubtag(getVolumeMask().toXMLNode());
}
return node;
}
//--------------------------------------------------------------------------
@Override
public PlateReagentLayer clone()
{
PlateReagentLayer theClone = (PlateReagentLayer) super.clone();
theClone.mVolumeMask = mVolumeMask.clone();
return theClone;
}
//---------------------------------------------------------------------------
public PlateReagentLayer setReagent(R inValue)
{
mReagent = inValue;
return this;
}
//---------------------------------------------------------------------------
public R getReagent()
{
return mReagent;
}
//---------------------------------------------------------------------------
public PlateReagentLayer setVolume(WellRange inWellRange, Quantity inQuantity)
{
getVolumeMask().setVolume(inWellRange, inQuantity);
return this;
}
//---------------------------------------------------------------------------
public PlateReagentLayer setVolume(WellRef inWellRef, Quantity inQuantity)
{
getVolumeMask().setVolume(inWellRef, inQuantity);
return this;
}
//---------------------------------------------------------------------------
public Quantity getVolume(WellRef inWellRef)
{
return getVolumeMask().getVolume(inWellRef);
}
//---------------------------------------------------------------------------
public VolumeMask getVolumeMask()
{
return mVolumeMask;
}
//---------------------------------------------------------------------------
@Override
public Collection getOccupiedWellRefs()
{
return getVolumeMask().getOccupiedWellRefs();
}
//---------------------------------------------------------------------------
@Override
public WellLayer getWellLayer(WellRef inWellRef)
{
WellReagentLayer wellLayer = null;
Quantity volume = getVolumeMask().getVolume(inWellRef);
if (volume != null)
{
wellLayer = new WellReagentLayer().setReagent(getReagent()).setVolume(volume);
wellLayer.setName(name());
}
return wellLayer;
}
}
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