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/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2016 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
*
* 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 .
*
*/
package com.actelion.research.orbit.beans;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
public class HCSContainer implements Serializable {
private static final long serialVersionUID = 1L;
public static final String HCSHeaderBase = "ContainerName\tWellName\tSiteX\tSiteY\tSiteZ\tObjectId\tObjectX\tObjectY\tTime";
public static final List HCSHeaderBaseList = new ArrayList() {{
add("ContainerName");
add("WellName");
add("SiteX");
add("SiteY");
add("SiteZ");
add("ObjectId");
add("ObjectX");
add("ObjectY");
add("Time");
}};
public static final int NumHeaderColumns = 9;
private String containerName = "";
private Date referenceDate = new Date();
private List data = new ArrayList();
private List header = new ArrayList();
private String plateFormat = "";
private int iPlateBatch = 0;
private String sConcentration = "";
private String sPipelineName = "";
public HCSContainer() {
}
public HCSContainer(String containerName, Date referenceDate, List data, List header, String plateFormat, int iPlateBatch, String sConcentration, String sPipelineName) {
this.containerName = containerName;
this.referenceDate = referenceDate;
if (data != null)
this.data = data;
this.header = header;
this.plateFormat = plateFormat;
this.iPlateBatch = iPlateBatch;
this.sConcentration = sConcentration;
this.sPipelineName = sPipelineName;
}
public HCSContainer(String containerName, Date referenceDate, List data, List header, String plateFormat, int iPlateBatch) {
this.containerName = containerName;
this.referenceDate = referenceDate;
if (data != null)
this.data = data;
this.header = header;
this.plateFormat = plateFormat;
this.iPlateBatch = iPlateBatch;
}
public HCSContainer(String containerName, Date referenceDate, List data, List header, String plateFormat) {
this.containerName = containerName;
this.referenceDate = referenceDate;
if (data != null)
this.data = data;
this.header = header;
this.plateFormat = plateFormat;
}
public HCSContainer(String containerName, Date referenceDate, List data, List header) {
this.containerName = containerName;
this.referenceDate = referenceDate;
if (data != null)
this.data = data;
this.header = header;
}
@Override
public String toString() {
return "HCSContainer [containerName=" + containerName + ", referenceDate=" + referenceDate + ", dataNumRows=" + (data == null ? null : data.size()) + ", plateFormat=" + plateFormat + ", plateBatch=" + iPlateBatch + "s]";
}
public List getValueNames() {
return header.subList(HCSContainer.HCSHeaderBase.split(String.valueOf(HCSRow.HCSSeparator)).length, header.size());
}
/**
* returns the header + datarows as a string
*
* @return
*/
public String getDataAsString() {
StringBuilder sb = new StringBuilder();
if (header != null && header.size() > 0) {
for (int i = 0; i < header.size(); i++) {
String colName = header.get(i);
sb.append(colName);
if (i < header.size() - 1) sb.append(HCSRow.HCSSeparator);
}
sb.append("\n");
}
if (data != null && data.size() > 0) {
for (HCSRow row : data) {
sb.append(row.toString() + "\n");
}
}
return sb.toString();
}
public byte[] toByteArray() {
if (data == null) return null;
ByteArrayOutputStream outStream = new ByteArrayOutputStream();
OutputStreamWriter osw = new OutputStreamWriter(outStream);
try {
osw.write(getDataAsString());
osw.flush();
} catch (IOException e) {
System.out.println("Error writing to outputstream: " + e.getMessage());
}
return outStream.toByteArray();
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
HCSContainer that = (HCSContainer) o;
if (iPlateBatch != that.iPlateBatch) return false;
if (containerName != null ? !containerName.equals(that.containerName) : that.containerName != null)
return false;
if (data != null ? !data.equals(that.data) : that.data != null) return false;
if (header != null ? !header.equals(that.header) : that.header != null) return false;
if (plateFormat != null ? !plateFormat.equals(that.plateFormat) : that.plateFormat != null) return false;
return referenceDate != null ? referenceDate.equals(that.referenceDate) : that.referenceDate == null;
}
@Override
public int hashCode() {
int result = containerName != null ? containerName.hashCode() : 0;
result = 31 * result + (referenceDate != null ? referenceDate.hashCode() : 0);
result = 31 * result + (data != null ? data.hashCode() : 0);
result = 31 * result + (header != null ? header.hashCode() : 0);
result = 31 * result + (plateFormat != null ? plateFormat.hashCode() : 0);
result = 31 * result + iPlateBatch;
return result;
}
public String getContainerName() {
return containerName;
}
public void setContainerName(String containerName) {
this.containerName = containerName;
}
public Date getReferenceDate() {
return referenceDate;
}
public void setReferenceDate(Date referenceDate) {
this.referenceDate = referenceDate;
}
public List getData() {
return data;
}
public void setData(List data) {
this.data = data;
}
public List getHeader() {
return header;
}
public void setHeader(List header) {
this.header = header;
}
public String getPlateFormat() {
return plateFormat;
}
public void setPlateFormat(String plateFormat) {
this.plateFormat = plateFormat;
}
public int getiPlateBatch() {
return iPlateBatch;
}
public void setiPlateBatch(int iPlateBatch) {
this.iPlateBatch = iPlateBatch;
}
public String getsConcentration() {
return sConcentration;
}
public void setsConcentration(String sConcentration) {
this.sConcentration = sConcentration;
}
public String getsPipelineName() {
return sPipelineName;
}
public void setsPipelineName(String sPipelineName) {
this.sPipelineName = sPipelineName;
}
}
