Java tutorial
/* This file is part of RUbioSeq-GUI. RUbioSeq-GUI is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. RUbioSeq-GUI 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 General Public License for more details. You should have received a copy of the GNU General Public License along with RUbioSeq-GUI. If not, see <http://www.gnu.org/licenses/>. */ package es.uvigo.ei.sing.rubioseq.gui.view.models.configuration; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.util.Arrays; import java.util.List; import java.util.Map; import org.jdom2.Comment; import org.jdom2.Document; import org.jdom2.Element; import org.jdom2.JDOMException; import org.jdom2.input.SAXBuilder; import org.jdom2.output.Format; import org.jdom2.output.XMLOutputter; import es.uvigo.ei.sing.rubioseq.gui.macros.RUbioSeqFile; import es.uvigo.ei.sing.rubioseq.gui.util.Utils; /** * * @author hlfernandez * */ public class ConfigProgramPathsCNV { private static final String COMMENT_VARIANT_CALLER = "RUbioSeq variantCaller CONFIG FILE"; private static final String TEMPLATE_CNV = "template_configProgramPaths.txt"; public static final String CONFIG_DATA = "configData"; public static final String BWA_PATH = "bwaPath"; public static final String SAMTOOLS_PATH = "samtoolsPath"; public static final String GATK_PATH = "gatkpath"; public static final String PICARD_PATH = "picardPath"; public static final String BFAST_PATH = "BFASTPath"; public static final String BED_TOOLS_PATH = "BEDToolsPath"; public static final String CONTRA_PATH = "CONTRAPath"; public static final String FASTQC_PATH = "fastqcPath"; public static final String NTHR = "nthr"; public static final String JAVA_RAM = "javaRam"; public static final String QUEUE_SYSTEM = "queueSystem"; public static final String QUEUE_NAME = "queueName"; public static final String MULTICORE_NAME = "multicoreName"; public static final String MULTICORE_NUMBER = "multicoreNumber"; private RUbioSeqFile bwaPath; private RUbioSeqFile samtoolsPath; private RUbioSeqFile gatkpath; private RUbioSeqFile picardPath; private RUbioSeqFile bfastPath; private RUbioSeqFile bedtoolsPath; private RUbioSeqFile contraPath; private RUbioSeqFile fastqcPath; private Integer nthr = 1; private Integer nthr_DV = 1; private String javaRam = "-Xmx16G"; private String javaRam_DV = "-Xmx16G"; private QueueSystem queueSystem; private String queueName = ""; private String queueName_DV = ""; private String multicoreName = ""; private String multicoreName_DV = ""; private Integer multicoreNumber = -1; private Integer multicoreNumber_DV = -1; public enum QueueSystem { SGE("SGE"), PBS("PBS"), NONE("none"); private final String displayName; private QueueSystem(String displayName) { this.displayName = displayName; } public String getDisplayName() { return displayName; } } public List<QueueSystem> getQueueSystemValues() { return Arrays.asList(QueueSystem.values()); } public RUbioSeqFile getBwaPath() { return bwaPath; } public void setBwaPath(RUbioSeqFile bwaPath) { this.bwaPath = bwaPath; } public RUbioSeqFile getSamtoolsPath() { return samtoolsPath; } public void setSamtoolsPath(RUbioSeqFile samtoolsPath) { this.samtoolsPath = samtoolsPath; } public RUbioSeqFile getBfastPath() { return bfastPath; } public void setBfastPath(RUbioSeqFile bfastPath) { this.bfastPath = bfastPath; } public RUbioSeqFile getGatkpath() { return gatkpath; } public void setGatkpath(RUbioSeqFile gatkpath) { this.gatkpath = gatkpath; } public RUbioSeqFile getPicardPath() { return picardPath; } public void setPicardPath(RUbioSeqFile picardPath) { this.picardPath = picardPath; } public RUbioSeqFile getBedtoolsPath() { return bedtoolsPath; } public void setBedtoolsPath(RUbioSeqFile bedtoolsPath) { this.bedtoolsPath = bedtoolsPath; } public RUbioSeqFile getContraPath() { return contraPath; } public void setContraPath(RUbioSeqFile contraPath) { this.contraPath = contraPath; } public RUbioSeqFile getFastqcPath() { return fastqcPath; } public void setFastqcPath(RUbioSeqFile fastqcPath) { this.fastqcPath = fastqcPath; } public Integer getNthr() { return nthr; } public void setNthr(Integer nthr) { this.nthr = nthr; } public String getJavaRam() { return javaRam; } public void setJavaRam(String javaRam) { this.javaRam = javaRam; } public QueueSystem getQueueSystem() { return queueSystem; } public void setQueueSystem(QueueSystem queueSystem) { this.queueSystem = queueSystem; } public String getQueueName() { return queueName; } public void setQueueName(String queueName) { this.queueName = queueName; } public String getMulticoreName() { return multicoreName; } public void setMulticoreName(String multicoreName) { this.multicoreName = multicoreName; } public Integer getMulticoreNumber() { return multicoreNumber; } public void setMulticoreNumber(Integer multicoreNumber) { this.multicoreNumber = multicoreNumber; } public Integer getNthr_DV() { return nthr_DV; } public String getJavaRam_DV() { return javaRam_DV; } public String getQueueName_DV() { return queueName_DV; } public String getMulticoreName_DV() { return multicoreName_DV; } public Integer getMulticoreNumber_DV() { return multicoreNumber_DV; } public boolean validElement(Element e) { return e != null && e.getValue() != null && !e.getValue().equals(""); } private void loadDefaultParameters(File configFile) { File defaultParametersFile = new File(configFile.getParentFile(), TEMPLATE_CNV); Map<String, String> paramNameToValue = Utils.loadTemplateParametersFile(defaultParametersFile); for (String parameterName : paramNameToValue.keySet()) { String parameterValue = paramNameToValue.get(parameterName); if (parameterName.equals(NTHR)) { try { this.nthr_DV = Integer.valueOf(parameterValue); this.nthr = this.nthr_DV; } catch (Exception ex) { } } else if (parameterName.equals(JAVA_RAM)) { this.javaRam_DV = parameterValue; this.javaRam = parameterValue; } else if (parameterName.equals(QUEUE_NAME)) { this.queueName_DV = parameterValue; this.queueName = parameterValue; } else if (parameterName.equals(MULTICORE_NAME)) { this.multicoreName_DV = parameterValue; this.multicoreName = parameterValue; } else if (parameterName.equals(MULTICORE_NUMBER)) { try { this.multicoreNumber_DV = Integer.valueOf(parameterValue); this.multicoreNumber = this.multicoreNumber_DV; } catch (Exception ex) { } } } } public void loadDataFromFile(File editFile) { loadDefaultParameters(editFile); SAXBuilder saxBuilder = new SAXBuilder(); try { Document document = saxBuilder.build(editFile); Element configData = document.getRootElement(); Element bwaPath = configData.getChild(BWA_PATH); if (validElement(bwaPath)) { this.setBwaPath(Utils.getRUbioSeqFile(bwaPath.getValue())); } Element samtoolsPath = configData.getChild(SAMTOOLS_PATH); if (validElement(samtoolsPath)) { this.setSamtoolsPath(Utils.getRUbioSeqFile(samtoolsPath.getValue())); } Element gatkpath = configData.getChild(GATK_PATH); if (validElement(gatkpath)) { this.setGatkpath(Utils.getRUbioSeqFile(gatkpath.getValue())); } Element picardPath = configData.getChild(PICARD_PATH); if (validElement(picardPath)) { this.setPicardPath(Utils.getRUbioSeqFile(picardPath.getValue())); } Element BFASTPath = configData.getChild(BFAST_PATH); if (validElement(BFASTPath)) { this.setBfastPath(Utils.getRUbioSeqFile(BFASTPath.getValue())); } Element fastqcPath = configData.getChild(FASTQC_PATH); if (validElement(fastqcPath)) { this.setFastqcPath(Utils.getRUbioSeqFile(fastqcPath.getValue())); } Element BEDToolsPath = configData.getChild(BED_TOOLS_PATH); if (validElement(BEDToolsPath)) { this.setBedtoolsPath(Utils.getRUbioSeqFile(BEDToolsPath.getValue())); } Element CONTRAPath = configData.getChild(CONTRA_PATH); if (validElement(CONTRAPath)) { this.setContraPath(Utils.getRUbioSeqFile(CONTRAPath.getValue())); } Element nthr = configData.getChild(NTHR); if (validElement(nthr)) { try { this.setNthr(Integer.valueOf(nthr.getValue())); } catch (Exception e) { } } Element javaRam = configData.getChild(JAVA_RAM); if (validElement(javaRam)) { this.setJavaRam(javaRam.getValue()); } Element queueSystem = configData.getChild(QUEUE_SYSTEM); if (validElement(queueSystem)) { String queueSystemValue = queueSystem.getValue().toUpperCase(); if (queueSystemValue.equals("SGE")) { this.setQueueSystem(QueueSystem.SGE); } else if (queueSystemValue.equals("PBS")) { this.setQueueSystem(QueueSystem.PBS); } else if (queueSystemValue.equals("NONE")) { this.setQueueSystem(QueueSystem.NONE); } } Element queueName = configData.getChild(QUEUE_NAME); if (validElement(queueName)) { this.setQueueName(queueName.getValue()); } Element multicoreName = configData.getChild(MULTICORE_NAME); if (validElement(multicoreName)) { this.setMulticoreName(multicoreName.getValue()); } Element multicoreNumber = configData.getChild(MULTICORE_NUMBER); if (validElement(multicoreNumber)) { try { this.setMulticoreNumber(Integer.valueOf(multicoreNumber.getValue())); } catch (Exception e) { } } } catch (JDOMException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } public void exportToXML(File output) throws IOException { Document configurationFile = new Document(); Comment comment = new Comment(COMMENT_VARIANT_CALLER); configurationFile.addContent(comment); Element configData = new Element(CONFIG_DATA); configurationFile.setRootElement(configData); Element bwaPath = new Element(BWA_PATH); bwaPath.addContent(this.getBwaPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(bwaPath); Element samtoolsPath = new Element(SAMTOOLS_PATH); samtoolsPath.addContent(this.getSamtoolsPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(samtoolsPath); Element gatkpath = new Element(GATK_PATH); gatkpath.addContent(this.getGatkpath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(gatkpath); Element picardPath = new Element(PICARD_PATH); picardPath.addContent(this.getPicardPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(picardPath); Element BFASTPath = new Element(BFAST_PATH); BFASTPath.addContent(this.getBfastPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(BFASTPath); Element BEDToolsPath = new Element(BED_TOOLS_PATH); BEDToolsPath.addContent(this.getBedtoolsPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(BEDToolsPath); Element CONTRAPath = new Element(CONTRA_PATH); CONTRAPath.addContent(this.getContraPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(CONTRAPath); Element fastqcPath = new Element(FASTQC_PATH); fastqcPath.addContent(this.getFastqcPath().getFile().getAbsolutePath()); configurationFile.getRootElement().addContent(fastqcPath); if (!this.getNthr().equals(nthr_DV)) { Element nthr = new Element(NTHR); nthr.addContent(String.valueOf(this.getNthr())); configurationFile.getRootElement().addContent(nthr); } if (!this.getJavaRam().equals(javaRam_DV)) { Element javaRam = new Element(JAVA_RAM); javaRam.addContent(this.getJavaRam()); configurationFile.getRootElement().addContent(javaRam); } Element queueSystem = new Element(QUEUE_SYSTEM); queueSystem.addContent(this.getQueueSystem().getDisplayName()); configurationFile.getRootElement().addContent(queueSystem); if (!this.getQueueName().equals(queueName_DV)) { Element queueName = new Element(QUEUE_NAME); queueName.addContent(this.getQueueName()); configurationFile.getRootElement().addContent(queueName); } if (!this.getMulticoreName().equals(multicoreName_DV)) { Element multicoreName = new Element(MULTICORE_NAME); multicoreName.addContent(this.getMulticoreName()); configurationFile.getRootElement().addContent(multicoreName); } if (!this.getMulticoreNumber().equals(multicoreNumber_DV)) { Element multicoreNumber = new Element(MULTICORE_NUMBER); multicoreNumber.addContent(String.valueOf(this.getMulticoreNumber())); configurationFile.getRootElement().addContent(multicoreNumber); } XMLOutputter xmlOutput = new XMLOutputter(); xmlOutput.setFormat(Format.getPrettyFormat()); xmlOutput.output(configurationFile, new FileWriter(output)); } }