Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
package net.maizegenetics.analysis.distance;
import com.google.common.collect.Range;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.plugindef.PluginParameter;
import net.maizegenetics.taxa.distance.DistanceMatrix;
import javax.swing.*;
import java.net.URL;
import java.awt.Frame;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
/**
* @author Terry Casstevens
* @author Zhiwu Zhang
* @author Peter Bradbury
*
*/
public class KinshipPlugin extends AbstractPlugin {
private static final Logger myLogger = LogManager.getLogger(KinshipPlugin.class);
public static enum KINSHIP_METHOD {
Centered_IBS,
Normalized_IBS,
Dominance_Centered_IBS,
Dominance_Normalized_IBS
};
public static enum ALGORITHM_VARIATION {
Observed_Allele_Freq,
Proportion_Heterozygous
};
private PluginParameter myMethod = new PluginParameter.Builder<>("method", KINSHIP_METHOD.Centered_IBS, KINSHIP_METHOD.class)
.guiName("Kinship method")
.range(KINSHIP_METHOD.values())
.description("The Centered_IBS (Endelman - previously Scaled_IBS) method produces a kinship matrix that is scaled to give a reasonable estimate of additive "
+ "genetic variance. Uses algorithm http://www.g3journal.org/content/2/11/1405.full.pdf Equation-13. "
+ "The Normalized_IBS (Previously GCTA) uses the algorithm published here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014363/pdf/main.pdf.")
.build();
private PluginParameter myMaxAlleles = new PluginParameter.Builder<>("maxAlleles", 6, Integer.class)
.description("")
.range(Range.closed(2, 6))
.dependentOnParameter(myMethod, new Object[]{KINSHIP_METHOD.Centered_IBS, KINSHIP_METHOD.Dominance_Centered_IBS})
.build();
private PluginParameter myAlgorithmVariation = new PluginParameter.Builder<>("algorithmVariation", ALGORITHM_VARIATION.Observed_Allele_Freq, ALGORITHM_VARIATION.class)
.description("")
.range(ALGORITHM_VARIATION.values())
.dependentOnParameter(myMethod, new Object[]{KINSHIP_METHOD.Dominance_Centered_IBS})
.build();
public KinshipPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
@Override
protected void preProcessParameters(DataSet input) {
List alignInList = input.getDataOfType(GenotypeTable.class);
if ((alignInList == null) || (alignInList.isEmpty())) {
throw new IllegalArgumentException("KinshipPlugin: Nothing selected. Please select a genotype.");
}
}
@Override
public void setParameters(String[] args) {
try {
for (int i = 0; i < args.length; i++) {
if (args[i].equals("-method")) {
if (args[i + 1].equalsIgnoreCase("GCTA")) {
args[i + 1] = KINSHIP_METHOD.Normalized_IBS.name();
myLogger.warn("setParameters: Notice GCTA has been changed to Normalized_IBS");
} else if (args[i + 1].equalsIgnoreCase("Scaled_IBS")) {
args[i + 1] = KINSHIP_METHOD.Centered_IBS.name();
myLogger.warn("setParameters: Notice Scaled_IBS has been changed to Centered_IBS");
} else if (args[i + 1].equalsIgnoreCase("Dominance")) {
args[i + 1] = KINSHIP_METHOD.Dominance_Centered_IBS.name();
myLogger.warn("setParameters: Notice Dominance has been changed to Dominance_Centered_IBS");
}
}
break;
}
} catch (Exception e) {
// do nothing
myLogger.debug(e.getMessage(), e);
}
super.setParameters(args);
}
@Override
public DataSet processData(DataSet input) {
List alignInList = input.getDataOfType(GenotypeTable.class);
List result = new ArrayList<>();
Iterator itr = alignInList.iterator();
while (itr.hasNext()) {
Datum current = itr.next();
String datasetName = current.getName();
DistanceMatrix kin = null;
if (current.getData() instanceof GenotypeTable) {
GenotypeTable myGenotype = (GenotypeTable) current.getData();
if (kinshipMethod() == KINSHIP_METHOD.Centered_IBS) {
kin = EndelmanDistanceMatrix.getInstance(myGenotype, maxAlleles(), this);
} else if (kinshipMethod() == KINSHIP_METHOD.Normalized_IBS) {
kin = GCTADistanceMatrix.getInstance(myGenotype, this);
} else if (kinshipMethod() == KINSHIP_METHOD.Dominance_Centered_IBS) {
kin = DominanceRelationshipMatrix.getInstance(myGenotype, maxAlleles(), algorithmVariation(), this);
} else if (kinshipMethod() == KINSHIP_METHOD.Dominance_Normalized_IBS) {
kin = DominanceNormalizedIBSMatrix.getInstance(myGenotype, this);
} else {
throw new IllegalArgumentException("Unknown method to calculate kinship: " + kinshipMethod());
}
} else {
throw new IllegalArgumentException("Invalid selection. Can't create kinship matrix from: " + datasetName);
}
if (kin != null) {
StringBuilder comment = new StringBuilder();
comment.append(kinshipMethod());
if (kinshipMethod() == KINSHIP_METHOD.Dominance_Centered_IBS) {
comment.append("(variation: ");
comment.append(algorithmVariation());
comment.append(")");
}
comment.append(" matrix created from ");
comment.append(datasetName);
Datum ds = new Datum(kinshipMethod() + "_" + datasetName, kin, comment.toString());
result.add(ds);
}
}
return new DataSet(result, this);
}
@Override
public String pluginUserManualURL() {
return "https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Kinship/Kinship";
}
@Override
public ImageIcon getIcon() {
URL imageURL = KinshipPlugin.class.getResource("/net/maizegenetics/analysis/images/Kin.gif");
if (imageURL == null) {
return null;
} else {
return new ImageIcon(imageURL);
}
}
@Override
public String getButtonName() {
return "Kinship";
}
@Override
public String getToolTipText() {
return "Calculate kinship from marker data";
}
/**
* Convenience method to run plugin with one return object.
*/
public DistanceMatrix runPlugin(DataSet input) {
return (DistanceMatrix) performFunction(input).getData(0).getData();
}
/**
* Convenience method to run plugin with one return object.
*/
public DistanceMatrix runPlugin(GenotypeTable input) {
return (DistanceMatrix) performFunction(DataSet.getDataSet(input)).getData(0).getData();
}
/**
* The scaled_IBS method produces a kinship matrix that is scaled to give a
* reasonable estimate of additive genetic variance. The pairwise_IBS
* method, which is the method used by TASSEL ver.4, may result in an
* inflated estimate of genetic variance. Either will do a good job of
* controlling population structure in MLM. The pedigree method is used to
* calculate a kinship matrix from a pedigree information.
*
* @return Kinship method
*/
public KINSHIP_METHOD kinshipMethod() {
return myMethod.value();
}
/**
* Set Kinship method. The scaled_IBS method produces a kinship matrix that
* is scaled to give a reasonable estimate of additive genetic variance. The
* pairwise_IBS method, which is the method used by TASSEL ver.4, may result
* in an inflated estimate of genetic variance. Either will do a good job of
* controlling population structure in MLM. The pedigree method is used to
* calculate a kinship matrix from a pedigree information.
*
* @param value Kinship method
*
* @return this plugin
*/
public KinshipPlugin kinshipMethod(KINSHIP_METHOD value) {
myMethod = new PluginParameter<>(myMethod, value);
return this;
}
/**
* Max Alleles
*
* @return Max Alleles
*/
public Integer maxAlleles() {
return myMaxAlleles.value();
}
/**
* Set Max Alleles. Max Alleles
*
* @param value Max Alleles
*
* @return this plugin
*/
public KinshipPlugin maxAlleles(Integer value) {
myMaxAlleles = new PluginParameter<>(myMaxAlleles, value);
return this;
}
/**
* Algorithm Variation
*
* @return Algorithm Variation
*/
public ALGORITHM_VARIATION algorithmVariation() {
return myAlgorithmVariation.value();
}
/**
* Set Algorithm Variation. Algorithm Variation
*
* @param value Algorithm Variation
*
* @return this plugin
*/
public KinshipPlugin algorithmVariation(ALGORITHM_VARIATION value) {
myAlgorithmVariation = new PluginParameter<>(myAlgorithmVariation, value);
return this;
}
}
