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com.hfg xml, html, svg, and bioinformatics utility library
package com.hfg.bio.seq;
import java.awt.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import com.hfg.bio.Strand;
import com.hfg.bio.taxonomy.NCBITaxon;
import com.hfg.html.Link;
import com.hfg.math.Range;
import com.hfg.util.collection.CollectionUtil;
//------------------------------------------------------------------------------
/**
* A gene representation.
*
* @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 Gene implements Comparable
{
//##########################################################################
// PRIVATE FIELDS
//##########################################################################
private String mId;
private String mDescription;
private List mURLs;
private Integer mStartLocation;
private Integer mEndLocation;
private GenomicLocation mGenomicLocation;
private Strand mStrand;
private List mExons;
private NCBITaxon mSpecies;
private Color mColor;
private SeqMappingCoverage mSeqMappingCoverage;
//##########################################################################
// CONSTRUCTORS
//##########################################################################
//--------------------------------------------------------------------------
public Gene()
{
}
//##########################################################################
// PUBLIC METHODS
//##########################################################################
//--------------------------------------------------------------------------
public Gene setLocation(GenomicLocation inValue)
{
mGenomicLocation = inValue;
return this;
}
//--------------------------------------------------------------------------
public GenomicLocation getLocation()
{
return mGenomicLocation;
}
//--------------------------------------------------------------------------
public Gene addExons(Collection inValues)
{
if (CollectionUtil.hasValues(inValues))
{
for (Exon exon : inValues)
{
addExon(exon);
}
}
return this;
}
//--------------------------------------------------------------------------
public Gene addExon(Exon inValue)
{
if (null == mExons)
{
mExons = new ArrayList<>();
}
mExons.add(inValue);
if (null == getStrand()
&& inValue.getStrand() != null)
{
setStrand(inValue.getStrand());
}
if (null == getStartLocation()
|| inValue.getLeft() < getStartLocation())
{
setStartLocation(inValue.getLeft());
}
if (null == getEndLocation()
|| inValue.getRight() > getEndLocation())
{
setEndLocation(inValue.getRight());
}
return this;
}
//--------------------------------------------------------------------------
public List getExons()
{
return mExons;
}
//--------------------------------------------------------------------------
public Gene setId(String inValue)
{
mId = inValue;
return this;
}
//--------------------------------------------------------------------------
public String getId()
{
return mId;
}
//--------------------------------------------------------------------------
public Gene setDescription(String inValue)
{
mDescription = inValue;
return this;
}
//--------------------------------------------------------------------------
public String getDescription()
{
return mDescription;
}
//--------------------------------------------------------------------------
public void setSeqMappingCoverage(SeqMappingCoverage inValue)
{
mSeqMappingCoverage = inValue;
}
//--------------------------------------------------------------------------
public SeqMappingCoverage getSeqMappingCoverage()
{
return mSeqMappingCoverage;
}
//--------------------------------------------------------------------------
public Gene setSpecies(NCBITaxon inValue)
{
mSpecies = inValue;
return this;
}
//--------------------------------------------------------------------------
public NCBITaxon getSpecies()
{
return mSpecies;
}
//--------------------------------------------------------------------------
/**
Add a URL to the gene. If more than one URL is defined, a popup menu will be
shown.
@param inValue the link to associate with the gene
*/
public Gene addURL(Link inValue)
{
if (null == mURLs)
{
mURLs = new ArrayList<>(2);
}
mURLs.add(inValue);
return this;
}
//--------------------------------------------------------------------------
public List getURLs()
{
return mURLs;
}
//--------------------------------------------------------------------------
/**
Basepair location of the start of the gene.
@return the 1-based location
*/
public Integer getStartLocation()
{
return mStartLocation != null ? mStartLocation : (mGenomicLocation != null ? mGenomicLocation.toIntRange().getStart() : null);
}
//--------------------------------------------------------------------------
public Gene setStartLocation(int inValue)
{
mStartLocation = inValue;
return this;
}
//--------------------------------------------------------------------------
public Integer getEndLocation()
{
return mEndLocation != null ? mEndLocation : (mGenomicLocation != null ? mGenomicLocation.toIntRange().getEnd() : null);
}
//--------------------------------------------------------------------------
public Gene setEndLocation(int inValue)
{
mEndLocation = inValue;
return this;
}
//--------------------------------------------------------------------------
/**
The leftmost basepair of the gene (the start location if the gene is on the
forward strand or the end location if the gene is on the reverse strand).
@return the 1-based left location
*/
public int getLeft()
{
return Math.min(getStartLocation(), getEndLocation());
}
//--------------------------------------------------------------------------
/**
The rightmost basepair of the gene (the end location if the gene is on the
forward strand or the start location if the gene is on the reverse strand).
@return the 1-based right location
*/
public int getRight()
{
return Math.max(getStartLocation(), getEndLocation());
}
//--------------------------------------------------------------------------
public Gene setStrand(Strand inValue)
{
mStrand = inValue;
return this;
}
//--------------------------------------------------------------------------
public Strand getStrand()
{
return mStrand != null ? mStrand : (mGenomicLocation != null ? mGenomicLocation.getStrand() : null);
}
//--------------------------------------------------------------------------
public Gene setColor(Color inValue)
{
mColor = inValue;
return this;
}
//--------------------------------------------------------------------------
public Color getColor()
{
return mColor;
}
//--------------------------------------------------------------------------
public int compareTo(Object inObj2)
{
int returnValue = -1;
if (inObj2 instanceof Gene)
{
Gene gene2 = (Gene) inObj2;
if (mStartLocation > gene2.mStartLocation)
{
returnValue = 1;
}
else if (mStartLocation < gene2.mStartLocation)
{
returnValue = -1;
}
else
{
if (mEndLocation > gene2.mEndLocation)
{
returnValue = 1;
}
else if (mEndLocation < gene2.mEndLocation)
{
returnValue = -1;
}
}
}
return returnValue;
}
}