Java tutorial
/* * Copyright (C) 2013 SeqWare * * This program 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. * * This program 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 this program. If not, see <http://www.gnu.org/licenses/>. */ package net.sourceforge.seqware.pipeline.plugins.batchmetadatainjection; import java.io.IOException; import java.util.HashSet; import java.util.List; import java.util.Set; import net.sourceforge.seqware.common.metadata.Metadata; import net.sourceforge.seqware.common.model.*; import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.builder.EqualsBuilder; import org.apache.commons.lang.builder.HashCodeBuilder; import net.sourceforge.seqware.common.model.SequencerRunStatus; /** * * @author mtaschuk */ public class RunInfo { //study private String studyTitle; private String studyDescription; private String studyCenterName; private String studyCenterProject; //study and lane private String studyType; //Used for experiment and for sequencer run private String platformId; //sequencer_run private String runName; //experiment private String experimentName; private String workflowType; private String assayType; //samples, lanes, barcodes //private List<SampleInfo> samples = null; private Set<TagValueUnit> experimentAttributes; private Set<TagValueUnit> studyAttributes; private Set<TagValueUnit> runAttributes; private Set<LaneInfo> lanes; private boolean runSkip = false; private boolean pairedEnd = true; private String runDescription; private String runFilePath; private String experimentDescription; private SequencerRunStatus status = null; /** * Get the value of the sequencer run status * @return the status. Complete or if not complete, then null */ public SequencerRunStatus getStatus() { return status; } /** * Set the value of the sequencer run status * @param status the status */ public void setStatus(SequencerRunStatus status) { this.status = status; } /** * Get the value of runFilePath * * @return the value of runFilePath */ public String getRunFilePath() { return runFilePath; } /** * Set the value of runFilePath * * @param runFilePath new value of runFilePath */ public void setRunFilePath(String runFilePath) { this.runFilePath = runFilePath; } /** * Get the value of experimentDescription * * @return the value of experimentDescription */ public String getExperimentDescription() { return experimentDescription; } /** * Set the value of experimentDescription * * @param experimentDescription new value of experimentDescription */ public void setExperimentDescription(String experimentDescription) { this.experimentDescription = experimentDescription; } /** * Get the value of runDescription * * @return the value of runDescription */ public String getRunDescription() { return runDescription; } /** * Set the value of runDescription * * @param runDescription new value of runDescription */ public void setRunDescription(String runDescription) { this.runDescription = runDescription; } /** * Get the value of pairedEnd * * @return the value of pairedEnd */ public boolean isPairedEnd() { return pairedEnd; } /** * Set the value of pairedEnd * * @param pairedEnd new value of pairedEnd */ public void setPairedEnd(boolean pairedEnd) { this.pairedEnd = pairedEnd; } /** * Get the value of runSkip * * @return the value of runSkip */ public boolean getRunSkip() { return runSkip; } /** * Set the value of runSkip * * @param runSkip new value of runSkip */ public void setRunSkip(boolean runSkip) { this.runSkip = runSkip; } /** * Get the value of lanes * * @return the value of lanes */ public Set<LaneInfo> getLanes() { if (lanes == null) { lanes = new HashSet<>(); } return lanes; } /** * Set the value of lanes * * @param lanes new value of lanes */ public void setLanes(Set<LaneInfo> lanes) { this.lanes = lanes; } public String getPlatformId() { return platformId; } public void setPlatformId(int platformId) { this.platformId = String.valueOf(platformId); } public String getStudyType() { return studyType; } public void setStudyType(int studyType) { this.studyType = String.valueOf(studyType); } /** * Get the value of runAttributes * * @return the value of runAttributes */ public Set<TagValueUnit> getRunAttributes() { if (runAttributes == null) { runAttributes = new HashSet<TagValueUnit>(); } return runAttributes; } /** * Adds a new run attribute if the tag does not exist for this run, or changes the value of an existing run attribute. * * @param tag the key of the attribute * @param value the value of the attribute */ public void setRunAttribute(String tag, String value) { TagValueUnit sa = null; //look for the existing attribute for (TagValueUnit s : getRunAttributes()) { if (s.getTag().equals(tag.trim())) { sa = s; break; } } //if we are unsetting the run attribute, remove it from the list. if (value == null && sa != null) { getRunAttributes().remove(sa); return; } //create a new attribute if (sa == null) { sa = new TagValueUnit(); getRunAttributes().add(sa); } sa.setTag(tag.trim()); sa.setValue(value.trim()); } /** * Set the value of runAttributes * * @param runAttributes new value of runAttributes */ public void setRunAttributes(Set<TagValueUnit> runAttributes) { this.runAttributes = runAttributes; } /** * Get the value of studyAttributes * * @return the value of studyAttributes */ public Set<TagValueUnit> getStudyAttributes() { if (studyAttributes == null) { studyAttributes = new HashSet<TagValueUnit>(); } return studyAttributes; } /** * Adds a new study attribute if the tag does not exist for this study, or * changes the value of an existing study attribute. * * @param tag the key of the attribute * @param value the value of the attribute */ public void setStudyAttribute(String tag, String value) { TagValueUnit sa = null; //look for the existing attribute for (TagValueUnit s : getStudyAttributes()) { if (s.getTag().equals(tag.trim())) { sa = s; break; } } //if we are unsetting the study attribute, remove it from the list. if (value == null && sa != null) { getStudyAttributes().remove(sa); return; } //create a new attribute if (sa == null) { sa = new TagValueUnit(); getStudyAttributes().add(sa); } sa.setTag(tag.trim()); sa.setValue(value.trim()); } /** * Set the value of studyAttributes * * @param studyAttributes new value of studyAttributes */ public void setStudyAttributes(Set<TagValueUnit> studyAttributes) { this.studyAttributes = studyAttributes; } /** * Get the value of experimentAttributes * * @return the value of experimentAttributes */ public Set<TagValueUnit> getExperimentAttributes() { if (experimentAttributes == null) { experimentAttributes = new HashSet<TagValueUnit>(); } return experimentAttributes; } /** * Set the value of experimentAttributes * * @param experimentAttributes new value of experimentAttributes */ public void setExperimentAttributes(Set<TagValueUnit> experimentAttributes) { this.experimentAttributes = experimentAttributes; } /** * Get the value of studyCenterProject * * @return the value of studyCenterProject */ public String getStudyCenterProject() { return studyCenterProject; } /** * Set the value of studyCenterProject * * @param studyCenterProject new value of studyCenterProject */ public void setStudyCenterProject(String studyCenterProject) { this.studyCenterProject = studyCenterProject; } /** * Get the value of studyCenterName * * @return the value of studyCenterName */ public String getStudyCenterName() { return studyCenterName; } /** * Set the value of studyCenterName * * @param studyCenterName new value of studyCenterName */ public void setStudyCenterName(String studyCenterName) { this.studyCenterName = studyCenterName; } /** * Get the value of studyDescription * * @return the value of studyDescription */ public String getStudyDescription() { return studyDescription; } /** * Set the value of studyDescription * * @param studyDescription new value of studyDescription */ public void setStudyDescription(String studyDescription) { this.studyDescription = studyDescription; } /** * Get the value of assayType * * @return the value of assayType */ public String getAssayType() { return assayType; } /** * Set the value of assayType * * @param assayType new value of assayType */ public void setAssayType(String assayType) { this.assayType = assayType; } /** * Get the value of workflowType * * @return the value of workflowType */ public String getWorkflowType() { return workflowType; } /** * Set the value of workflowType * * @param workflowType new value of workflowType */ public void setWorkflowType(String workflowType) { this.workflowType = workflowType; } /** * Get the value of experimentName * * @return the value of experimentName */ public String getExperimentName() { return experimentName; } /** * Set the value of experimentName * * @param experimentName new value of experimentName */ public void setExperimentName(String experimentName) { this.experimentName = experimentName; } /** * Get the value of runName * * @return the value of runName */ public String getRunName() { return runName; } /** * Set the value of runName * * @param runName new value of runName */ public void setRunName(String runName) { this.runName = runName; } /** * Get the value of studyTitle * * @return the value of studyTitle */ public String getStudyTitle() { return studyTitle; } /** * Set the value of studyTitle * * @param studyTitle new value of studyTitle */ public void setStudyTitle(String studyTitle) { this.studyTitle = studyTitle; } // @Override // public String toString() { // String string = "RunInfo{" + "studyTitle=" + studyTitle+ "\n\t runName=" + runName; // for (SampleInfo sample : samples) { // string += sample.toString() + "\n"; // } // string += '}'; // return string; // } @Override public String toString() { return "RunInfo{" + "studyTitle=" + studyTitle + "\n\t studyDescription=" + studyDescription + "\n\t studyCenterName=" + studyCenterName + "\n\t studyCenterProject=" + studyCenterProject + "\n\t studyType=" + studyType + "\n\t platformId=" + platformId + "\n\t runName=" + runName + "\n\t experimentName=" + experimentName + "\n\t workflowType=" + workflowType + "\n\t assayType=" + assayType + "\n\t runSkip=" + runSkip + "\n\t pairedEnd=" + pairedEnd + "\n\t runDescription=" + runDescription + "\n\t runFilePath=" + runFilePath + "\n\t experimentDescription=" + experimentDescription + '}'; } public void print(Appendable writer, Metadata metadata) throws IOException { String platform = "<null>"; if (platformId != null && !platformId.trim().isEmpty() && StringUtils.isNumeric(platformId)) { for (Platform p : metadata.getPlatforms()) { if (p.getPlatformId().equals(Integer.parseInt(platformId))) { platform = p.getName(); } } } String studyTypeStr = "<null>"; if (studyType != null && !studyType.trim().isEmpty() && StringUtils.isNumeric(studyType)) { for (StudyType st : metadata.getStudyTypes()) { if (st.getStudyTypeId().equals(Integer.parseInt(studyType))) { studyTypeStr = st.getName(); } } } writer.append("RunInfo{"); writer.append("\n\tstudyTitle=").append(studyTitle); writer.append("\n\tstudyDescription=").append(studyDescription); writer.append("\n\tstudyCenterName=").append(studyCenterName); writer.append("\n\tstudyCenterProject=").append(studyCenterProject); writer.append("\n\trunName=").append(runName); writer.append("\n\trunDescription=").append(runDescription); writer.append("\n\trunFilePath=").append(runFilePath); writer.append("\n\texperimentName=").append(experimentName); writer.append("\n\texperimentDescription=").append(experimentDescription); writer.append("\n\tplatform=").append(platform); writer.append("\n\tstudyType=").append(studyTypeStr); writer.append("\n\tskipRun=").append(String.valueOf(runSkip)); if (lanes != null) for (LaneInfo lane : lanes) { lane.print(writer, metadata); } writer.append("\n\t}"); writer.append("\n}"); } @Override public boolean equals(Object obj) { return EqualsBuilder.reflectionEquals(this, obj); } @Override public int hashCode() { return HashCodeBuilder.reflectionHashCode(this); } }