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net.maizegenetics.analysis.data.ExportPlugin Maven / Gradle / Ivy
/*
* ExportPlugin.java
*
* Created on December 18, 2009
*
*/
package net.maizegenetics.analysis.data;
import net.maizegenetics.analysis.avro.ExportAvro;
import net.maizegenetics.dna.map.PositionList;
import net.maizegenetics.dna.map.PositionListTableReport;
import net.maizegenetics.dna.snp.ExportUtils;
import net.maizegenetics.dna.snp.FilterList;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.dna.snp.io.FilterJSONUtils;
import net.maizegenetics.dna.snp.io.FlapjackUtils;
import net.maizegenetics.dna.snp.io.JSONUtils;
import net.maizegenetics.dna.snp.io.SiteScoresIO;
import net.maizegenetics.phenotype.Phenotype;
import net.maizegenetics.phenotype.PhenotypeUtils;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.PluginParameter;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.TaxaListTableReport;
import net.maizegenetics.taxa.distance.DistanceMatrix;
import net.maizegenetics.taxa.distance.DistanceMatrixUtils;
import net.maizegenetics.taxa.distance.WriteDistanceMatrix;
import net.maizegenetics.taxa.tree.NewickUtils;
import net.maizegenetics.taxa.tree.SimpleTree;
import net.maizegenetics.util.TableReport;
import net.maizegenetics.util.TableReportUtils;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import javax.swing.*;
import java.awt.*;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* @author Terry Casstevens
*/
public class ExportPlugin extends AbstractPlugin {
private static final Logger myLogger = LogManager.getLogger(ExportPlugin.class);
private PluginParameter mySaveFile = new PluginParameter.Builder<>("saveAs", null, String.class)
.description("Save file as...")
.outFile()
.required(true)
.build();
private PluginParameter myFileType = new PluginParameter.Builder<>("format", null, FileLoadPlugin.TasselFileType.class)
.description("Export file format (Default format depends on data being exported)")
.required(true)
.objectListSingleSelect()
.range(FileLoadPlugin.TasselFileType.values())
.build();
private PluginParameter myKeepDepth = new PluginParameter.Builder<>("keepDepth", true, Boolean.class)
.description("Whether to keep depth if format supports depth.")
.dependentOnParameter(myFileType, new FileLoadPlugin.TasselFileType[]{FileLoadPlugin.TasselFileType.VCF,
FileLoadPlugin.TasselFileType.HDF5})
.build();
private PluginParameter myIncludeTaxaAnnotations = new PluginParameter.Builder<>("includeTaxaAnnotations", true, Boolean.class)
.description("Whether to include taxa annotations if format supports taxa annotations.")
.dependentOnParameter(myFileType, new FileLoadPlugin.TasselFileType[]{FileLoadPlugin.TasselFileType.VCF,
FileLoadPlugin.TasselFileType.HDF5,
FileLoadPlugin.TasselFileType.Hapmap,
FileLoadPlugin.TasselFileType.HapmapDiploid,
FileLoadPlugin.TasselFileType.HapmapLIX})
.build();
private PluginParameter myIncludeBranchLengths = new PluginParameter.Builder<>("includeBranchLengths", true, Boolean.class)
.description("Whether to include branch lengths for Newick formatted files.")
.dependentOnParameter(myFileType, new FileLoadPlugin.TasselFileType[]{FileLoadPlugin.TasselFileType.Newick})
.build();
/**
* Creates a new instance of ExportPlugin
*/
public ExportPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
@Override
protected void preProcessParameters(DataSet input) {
if (input.getSize() != 1) {
throw new IllegalArgumentException("Please select only one item.");
}
Object data = input.getData(0).getData();
if (data instanceof GenotypeTable) {
GenotypeTable genotype = (GenotypeTable) data;
List temp = new ArrayList<>();
if (genotype.hasGenotype()) {
temp.add(FileLoadPlugin.TasselFileType.Hapmap);
temp.add(FileLoadPlugin.TasselFileType.HapmapDiploid);
temp.add(FileLoadPlugin.TasselFileType.HDF5);
temp.add(FileLoadPlugin.TasselFileType.VCF);
temp.add(FileLoadPlugin.TasselFileType.Plink);
temp.add(FileLoadPlugin.TasselFileType.Flapjack);
temp.add(FileLoadPlugin.TasselFileType.Phylip_Seq);
temp.add(FileLoadPlugin.TasselFileType.Phylip_Inter);
temp.add(FileLoadPlugin.TasselFileType.Table);
}
if (genotype.hasDepth()) {
temp.add(FileLoadPlugin.TasselFileType.Depth);
}
if (genotype.hasReferenceProbablity()) {
temp.add(FileLoadPlugin.TasselFileType.ReferenceProbability);
}
myFileType = new PluginParameter<>(myFileType, temp);
} else if (data instanceof Phenotype) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.Phenotype,
FileLoadPlugin.TasselFileType.PlinkPhenotype}));
} else if (data instanceof FilterList) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{FileLoadPlugin.TasselFileType.Filter}));
} else if (data instanceof DistanceMatrix) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.SqrMatrix,
FileLoadPlugin.TasselFileType.SqrMatrixBin,
FileLoadPlugin.TasselFileType.SqrMatrixRaw,
FileLoadPlugin.TasselFileType.SqrMatrixDARwinDIS}));
} else if (data instanceof TaxaList) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.TaxaList,
FileLoadPlugin.TasselFileType.Table}));
} else if (data instanceof TaxaListTableReport) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.TaxaList,
FileLoadPlugin.TasselFileType.Table}));
} else if (data instanceof PositionList) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.PositionList,
FileLoadPlugin.TasselFileType.Table}));
} else if (data instanceof PositionListTableReport) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.PositionList,
FileLoadPlugin.TasselFileType.Table}));
} else if (data instanceof TableReport) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{FileLoadPlugin.TasselFileType.Table}));
} else if (data instanceof SimpleTree) {
myFileType = new PluginParameter<>(myFileType,
Arrays.asList(new FileLoadPlugin.TasselFileType[]{
FileLoadPlugin.TasselFileType.Newick,
FileLoadPlugin.TasselFileType.Report}));
} else {
throw new IllegalStateException("Don't know how to export data type: " + data.getClass().getName());
}
if (!isInteractive() && myFileType.isEmpty() && myFileType.hasPossibleValues()) {
fileType(myFileType.possibleValues().get(0));
}
}
@Override
public DataSet processData(DataSet input) {
String filename = null;
Object data = input.getData(0).getData();
if (data instanceof GenotypeTable) {
filename = performFunctionForAlignment((GenotypeTable) data);
} else if (data instanceof Phenotype) {
filename = performFunctionForPhenotype((Phenotype) data);
} else if (data instanceof FilterList) {
filename = performFunctionForFilter((FilterList) data);
} else if (data instanceof DistanceMatrix) {
filename = performFunctionForDistanceMatrix((DistanceMatrix) data);
} else if (data instanceof TaxaList) {
filename = performFunctionForTaxaList((TaxaList) data);
} else if (data instanceof TaxaListTableReport) {
filename = performFunctionForTaxaList(((TaxaListTableReport) data).getTaxaList());
} else if (data instanceof PositionList) {
filename = performFunctionForPositionList((PositionList) data);
} else if (data instanceof PositionListTableReport) {
filename = performFunctionForPositionList(((PositionListTableReport) data).getPositionList());
} else if (data instanceof TableReport) {
filename = performFunctionForTableReport((TableReport) data);
} else if (data instanceof SimpleTree) {
filename = performFunctionForSimpleTree((SimpleTree) data);
} else {
throw new IllegalStateException("Don't know how to export data type: " + data.getClass().getName());
}
if (filename != null) {
myLogger.info("performFunction: wrote dataset: " + input.getData(0).getName() + " to file: " + filename);
}
return null;
}
public String performFunctionForDistanceMatrix(DistanceMatrix input) {
if (fileType() == FileLoadPlugin.TasselFileType.SqrMatrix) {
String filename = Utils.addSuffixIfNeeded(saveFile(), ".txt", new String[]{".txt", ".txt.gz"});
WriteDistanceMatrix.saveDelimitedDistanceMatrix(input, filename);
return filename;
} else if (fileType() == FileLoadPlugin.TasselFileType.SqrMatrixRaw) {
String[] grmFiles = DistanceMatrixUtils.getGRMFilenames(saveFile());
WriteDistanceMatrix.saveRawMultiBlupMatrix(input, grmFiles[0], grmFiles[3]);
return grmFiles[3];
} else if (fileType() == FileLoadPlugin.TasselFileType.SqrMatrixBin) {
String[] grmFiles = DistanceMatrixUtils.getGRMFilenames(saveFile());
WriteDistanceMatrix.saveBinMultiBlupMatrix(input, grmFiles[0], grmFiles[1], grmFiles[2]);
return grmFiles[1];
} else if (fileType() == FileLoadPlugin.TasselFileType.SqrMatrixDARwinDIS) {
String filename = Utils.addSuffixIfNeeded(saveFile(), ".dis");
WriteDistanceMatrix.saveDARwinMatrix(input, filename);
return filename;
} else {
throw new IllegalArgumentException("ExportPlugin: performFunctionForDistanceMatrix: Unknown file type: " + fileType());
}
}
public String performFunctionForTableReport(TableReport input) {
File theFile = new File(Utils.addSuffixIfNeeded(saveFile(), ".txt"));
TableReportUtils.saveDelimitedTableReport(input, "\t", theFile);
return theFile.getAbsolutePath();
}
public String performFunctionForFilter(FilterList filter) {
return FilterJSONUtils.exportFilterToJSON(filter, saveFile());
}
public String performFunctionForPhenotype(Phenotype input) {
String filename = Utils.addSuffixIfNeeded(saveFile(), ".txt");
if (fileType() == FileLoadPlugin.TasselFileType.Phenotype) {
PhenotypeUtils.write(input, filename);
} else if (fileType() == FileLoadPlugin.TasselFileType.PlinkPhenotype) {
PhenotypeUtils.writePlink(input, filename);
}
return new File(filename).getAbsolutePath();
}
public String performFunctionForAlignment(GenotypeTable inputAlignment) {
String resultFile = saveFile();
if (fileType() == FileLoadPlugin.TasselFileType.ReferenceProbability) {
resultFile = SiteScoresIO.writeReferenceProbability(inputAlignment, resultFile);
} else if (fileType() == FileLoadPlugin.TasselFileType.Depth) {
resultFile = SiteScoresIO.writeDepth(inputAlignment, resultFile);
} else if (fileType() == FileLoadPlugin.TasselFileType.Hapmap) {
resultFile = ExportUtils.writeToHapmap(inputAlignment, false, saveFile(), '\t', includeTaxaAnnotations(), this);
} else if (fileType() == FileLoadPlugin.TasselFileType.HapmapDiploid) {
resultFile = ExportUtils.writeToHapmap(inputAlignment, true, saveFile(), '\t', includeTaxaAnnotations(), this);
} else if (fileType() == FileLoadPlugin.TasselFileType.Plink) {
resultFile = ExportUtils.writeToPlink(inputAlignment, saveFile(), '\t');
} else if (fileType() == FileLoadPlugin.TasselFileType.Flapjack) {
resultFile = FlapjackUtils.writeToFlapjack(inputAlignment, saveFile(), '\t');
} else if (fileType() == FileLoadPlugin.TasselFileType.Phylip_Seq) {
resultFile = Utils.addSuffixIfNeeded(saveFile(), ".phy");
try (PrintWriter out = new PrintWriter(new FileWriter(resultFile))) {
ExportUtils.printSequential(inputAlignment, out);
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("ExportPlugin: performFunction: Problem writing file: " + resultFile);
}
} else if (fileType() == FileLoadPlugin.TasselFileType.Phylip_Inter) {
resultFile = Utils.addSuffixIfNeeded(saveFile(), ".phy");
try (PrintWriter out = new PrintWriter(new FileWriter(resultFile))) {
ExportUtils.printInterleaved(inputAlignment, out);
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("ExportPlugin: performFunction: Problem writing file: " + resultFile);
}
} else if (fileType() == FileLoadPlugin.TasselFileType.Table) {
resultFile = ExportUtils.saveDelimitedAlignment(inputAlignment, "\t", saveFile());
} else if (fileType() == FileLoadPlugin.TasselFileType.Serial) {
resultFile = ExportUtils.writeAlignmentToSerialGZ(inputAlignment, saveFile());
} else if (fileType() == FileLoadPlugin.TasselFileType.HDF5) {
resultFile = ExportUtils.writeGenotypeHDF5(inputAlignment, saveFile(), keepDepth());
} else if (fileType() == FileLoadPlugin.TasselFileType.VCF) {
resultFile = ExportUtils.writeToVCF(inputAlignment, saveFile(), keepDepth(), this);
} else if (fileType() == FileLoadPlugin.TasselFileType.Avro) {
resultFile = ExportAvro.write(inputAlignment, saveFile());
} else {
throw new IllegalStateException("ExportPlugin: performFunction: Unknown Genotype File Format: " + fileType());
}
return resultFile;
}
public String performFunctionForSimpleTree(SimpleTree input) {
String resultFile = null;
if (fileType() == FileLoadPlugin.TasselFileType.Newick) {
resultFile = Utils.addSuffixIfNeeded(saveFile(), FileLoadPlugin.FILE_EXT_NEWICK);
NewickUtils.write(resultFile, input, includeBranchLengths());
} else {
resultFile = Utils.addSuffixIfNeeded(saveFile(), ".txt");
try (PrintWriter writer = new PrintWriter(resultFile)) {
input.report(writer);
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("ExportPlugin: performFunctionForReport: Problem writing file: " + resultFile);
}
}
return resultFile;
}
public String performFunctionForTaxaList(TaxaList input) {
if (fileType() == FileLoadPlugin.TasselFileType.TaxaList) {
return JSONUtils.exportTaxaListToJSON(input, saveFile());
} else if (fileType() == FileLoadPlugin.TasselFileType.Table) {
File theFile = new File(Utils.addSuffixIfNeeded(saveFile(), ".txt"));
TableReportUtils.saveDelimitedTableReport(new TaxaListTableReport(input), "\t", theFile);
return theFile.getAbsolutePath();
} else {
throw new IllegalStateException("ExportPlugin: performFunctionForTaxaList: Can't export TaxaList as: " + fileType());
}
}
public String performFunctionForPositionList(PositionList input) {
if (fileType() == FileLoadPlugin.TasselFileType.PositionList) {
return JSONUtils.exportPositionListToJSON(input, saveFile());
} else if (fileType() == FileLoadPlugin.TasselFileType.Table) {
File theFile = new File(Utils.addSuffixIfNeeded(saveFile(), ".txt"));
TableReportUtils.saveDelimitedTableReport(new PositionListTableReport(input), "\t", theFile);
return theFile.getAbsolutePath();
} else {
throw new IllegalStateException("ExportPlugin: performFunctionForPositionList: Can't export PositionList as: " + fileType());
}
}
/**
* Icon for this plugin to be used in buttons, etc.
*
* @return ImageIcon
*/
@Override
public ImageIcon getIcon() {
URL imageURL = ExportPlugin.class.getResource("/net/maizegenetics/analysis/images/Export16.gif");
if (imageURL == null) {
return null;
} else {
return new ImageIcon(imageURL);
}
}
/**
* Button name for this plugin to be used in buttons, etc.
*
* @return String
*/
@Override
public String getButtonName() {
return "Save As...";
}
/**
* Tool Tip Text for this plugin
*
* @return String
*/
@Override
public String getToolTipText() {
return "Save data to files.";
}
@Override
public String pluginUserManualURL() {
return "https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/Export/Export";
}
/**
* Save file as...
*
* @return Save As
*/
public String saveFile() {
return mySaveFile.value();
}
/**
* Save file as...
*
* @param value filename
*
* @return this plugin
*/
public ExportPlugin saveFile(String value) {
mySaveFile = new PluginParameter<>(mySaveFile, value);
return this;
}
@Deprecated
/**
* Deprecated use saveFile(value)
*/
public ExportPlugin setSaveFile(String saveFile) {
mySaveFile = new PluginParameter<>(mySaveFile, saveFile);
return this;
}
/**
* Export file format
*
* @return Format
*/
public FileLoadPlugin.TasselFileType fileType() {
return myFileType.value();
}
/**
* Set Format. Export file format
*
* @param value Format
*
* @return this plugin
*/
public ExportPlugin fileType(FileLoadPlugin.TasselFileType value) {
myFileType = new PluginParameter<>(myFileType, value);
return this;
}
@Deprecated
/**
* Deprecated use fileType(value)
*/
public ExportPlugin setAlignmentFileType(FileLoadPlugin.TasselFileType type) {
fileType(type);
return this;
}
/**
* Whether to keep depth if format supports depth.
*
* @return Keep Depth
*/
public Boolean keepDepth() {
return myKeepDepth.value();
}
/**
* Set Keep Depth. Whether to keep depth if format supports depth.
*
* @param value Keep Depth
*
* @return this plugin
*/
public ExportPlugin keepDepth(Boolean value) {
myKeepDepth = new PluginParameter<>(myKeepDepth, value);
return this;
}
/**
* Whether to include taxa annotations if format supports taxa annotations.
*
* @return Include Taxa Annotations
*/
public Boolean includeTaxaAnnotations() {
return myIncludeTaxaAnnotations.value();
}
/**
* Set Include Taxa Annotations. Whether to include taxa annotations if
* format supports taxa annotations.
*
* @param value Include Taxa Annotations
*
* @return this plugin
*/
public ExportPlugin includeTaxaAnnotations(Boolean value) {
myIncludeTaxaAnnotations = new PluginParameter<>(myIncludeTaxaAnnotations, value);
return this;
}
/**
* Whether to include branch lengths for Newick formatted
* files.
*
* @return Include Branch Lengths
*/
public Boolean includeBranchLengths() {
return myIncludeBranchLengths.value();
}
/**
* Set Include Branch Lengths. Whether to include branch
* lengths for Newick formatted files.
*
* @param value Include Branch Lengths
*
* @return this plugin
*/
public ExportPlugin includeBranchLengths(Boolean value) {
myIncludeBranchLengths = new PluginParameter<>(myIncludeBranchLengths, value);
return this;
}
}
