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common objects for orbit image analysis
/*
* 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 {
public static final char DoseResponseSeparator = '\t';
private static final long serialVersionUID = 1L;
public enum wellTypes {p0, p100, dose, doseAndP0, doseAndP100}
public enum compoundTypes {compound, agonist, antagonist}
private String containerName = "";
private String wellName = "";
private String wellType = "";
private String compoundName = "";
private String tubeId = "";
private int compoundId = 0;
private String compoundType = "";
private double concentrationFactor = 0d;
private double concentration = 1d;
private String group = "";
private String measurementName = "";
private double measurementValue = Double.NaN;
private int substanceNo = -1;
private int replicateNo = 0;
public DoseResponseRow() {
}
public DoseResponseRow(String containerName, String wellName, String wellType, String compoundName, String tubeId, int compoundId, String compoundType, int substanceNo, int replicateNo, double concentration, double concentrationFactor, String group, String measurementName, double measurementValue) {
this.containerName = containerName;
this.wellName = wellName;
this.wellType = wellType;
this.compoundName = compoundName;
this.tubeId = tubeId;
this.compoundId = compoundId;
this.compoundType = compoundType;
this.substanceNo = substanceNo;
this.replicateNo = replicateNo;
this.concentration = concentration;
this.concentrationFactor = concentrationFactor;
this.group = group;
this.measurementName = measurementName;
this.measurementValue = measurementValue;
}
/**
* Parses a DoseResponseRow.toString() string and create a DoseResponseRow instance.
* compundId can be missing, then it will be set to 0.
* measurementValue can be missing, then it will be set to Double.NaN.
* Returns null if s is null.
*
* @param s
* @return
* @throws ParseException
*/
public static DoseResponseRow parseDoseResponseRow(String s) throws ParseException {
if (s == null) return null;
String[] split = s.split(String.valueOf(DoseResponseSeparator), -1);
if (split == null || split.length < 13)
throw new ParseException("argument is not a valid DoseResponseRow (null or length<12)", 0);
double mValue = Double.NaN;
try {
mValue = Double.parseDouble(split[13]);
} catch (Exception e) {
mValue = Double.NaN;
}
int cId;
try {
cId = Integer.parseInt(split[5]);
} catch (Exception e) {
cId = 0;
}
int substanceNo;
try {
substanceNo = Integer.parseInt(split[7]);
} catch (Exception e) {
substanceNo = -1;
}
int replicateNo;
try {
replicateNo = Integer.parseInt(split[8]);
} catch (Exception e) {
replicateNo = 0;
}
return new DoseResponseRow(split[0], split[1], split[2], split[3], split[4], cId, split[6], substanceNo, replicateNo, Double.parseDouble(split[9]), Double.parseDouble(split[10]), split[11], split[12], mValue);
}
/**
* Returns one data line as a string with respect to DoseResponseSeparator.
*/
@Override
public String toString() {
String s = containerName + DoseResponseSeparator +
wellName + DoseResponseSeparator +
wellType + DoseResponseSeparator +
compoundName + DoseResponseSeparator +
tubeId + DoseResponseSeparator +
compoundId + DoseResponseSeparator +
compoundType + DoseResponseSeparator +
substanceNo + DoseResponseSeparator +
replicateNo + DoseResponseSeparator +
concentration + DoseResponseSeparator +
concentrationFactor + DoseResponseSeparator +
group + DoseResponseSeparator +
measurementName + DoseResponseSeparator +
measurementValue;
return s;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
DoseResponseRow that = (DoseResponseRow) o;
if (compoundId != that.compoundId) return false;
if (Double.compare(that.substanceNo, substanceNo) != 0) return false;
if (Double.compare(that.replicateNo, replicateNo) != 0) return false;
if (Double.compare(that.concentration, concentration) != 0) return false;
if (Double.compare(that.concentrationFactor, concentrationFactor) != 0) return false;
if (Double.compare(that.measurementValue, measurementValue) != 0) return false;
if (compoundType != null ? !compoundType.equals(that.compoundType) : that.compoundType != null) return false;
if (containerName != null ? !containerName.equals(that.containerName) : that.containerName != null)
return false;
if (group != null ? !group.equals(that.group) : that.group != null)
return false;
if (measurementName != null ? !measurementName.equals(that.measurementName) : that.measurementName != null)
return false;
if (compoundName != null ? !compoundName.equals(that.compoundName) : that.compoundName != null) return false;
if (tubeId != null ? !tubeId.equals(that.tubeId) : that.tubeId != null) return false;
if (wellName != null ? !wellName.equals(that.wellName) : that.wellName != null) return false;
return wellType != null ? wellType.equals(that.wellType) : that.wellType == null;
}
@Override
public int hashCode() {
int result;
long temp;
result = containerName != null ? containerName.hashCode() : 0;
result = 31 * result + (wellName != null ? wellName.hashCode() : 0);
result = 31 * result + (wellType != null ? wellType.hashCode() : 0);
result = 31 * result + (compoundName != null ? compoundName.hashCode() : 0);
result = 31 * result + (tubeId != null ? tubeId.hashCode() : 0);
result = 31 * result + compoundId;
result = 31 * result + (compoundType != null ? compoundType.hashCode() : 0);
result = 31 * result + substanceNo;
result = 31 * result + replicateNo;
temp = Double.doubleToLongBits(concentration);
result = 31 * result + (int) (temp ^ (temp >>> 32));
temp = Double.doubleToLongBits(concentrationFactor);
result = 31 * result + (int) (temp ^ (temp >>> 32));
result = 31 * result + (group != null ? group.hashCode() : 0);
result = 31 * result + (measurementName != null ? measurementName.hashCode() : 0);
temp = Double.doubleToLongBits(measurementValue);
result = 31 * result + (int) (temp ^ (temp >>> 32));
return result;
}
@Override
public int compareTo(DoseResponseRow that) {
if (this.containerName.compareTo(that.containerName) < 0) {
return -1;
} else if (this.containerName.compareTo(that.containerName) > 0) {
return 1;
}
if (this.wellName.compareTo(that.wellName) < 0) {
return -1;
} else if (this.wellName.compareTo(that.wellName) > 0) {
return 1;
}
if (this.wellType.compareTo(that.wellType) < 0) {
return -1;
} else if (this.wellType.compareTo(that.wellType) > 0) {
return 1;
}
if (this.compoundType.compareTo(that.compoundType) < 0) {
return -1;
} else if (this.compoundType.compareTo(that.compoundType) > 0) {
return 1;
}
if (this.group.compareTo(that.group) < 0) {
return -1;
} else if (this.group.compareTo(that.group) > 0) {
return 1;
}
if (this.measurementName.compareTo(that.measurementName) < 0) {
return -1;
} else if (this.measurementName.compareTo(that.measurementName) > 0) {
return 1;
}
return 0;
}
public String getContainerName() {
return containerName;
}
public void setContainerName(String containerName) {
this.containerName = containerName;
}
public String getWellName() {
return wellName;
}
public void setWellName(String wellName) {
this.wellName = wellName;
}
public String getWellType() {
return wellType;
}
public void setWellType(String wellType) {
this.wellType = wellType;
}
public String getCompoundName() {
return compoundName;
}
public void setCompoundName(String compoundName) {
this.compoundName = compoundName;
}
public String getTubeId() {
return tubeId;
}
public void setTubeId(String tubeId) {
this.tubeId = tubeId;
}
public int getCompoundId() {
return compoundId;
}
public void setCompoundId(int compoundId) {
this.compoundId = compoundId;
}
public String getCompoundType() {
return compoundType;
}
public void setCompoundType(String compoundType) {
this.compoundType = compoundType;
}
public double getConcentration() {
return concentration;
}
public void setConcentration(double concentration) {
this.concentration = concentration;
}
public double getConcentrationFactor() {
return concentrationFactor;
}
public void setConcentrationFactor(double concentrationFactor) {
this.concentrationFactor = concentrationFactor;
}
public String getMeasurementName() {
return measurementName;
}
public void setMeasurementName(String measurementName) {
this.measurementName = measurementName;
}
public double getMeasurementValue() {
return measurementValue;
}
public void setMeasurementValue(double measurementValue) {
this.measurementValue = measurementValue;
}
public int getReplicateNo() {
return replicateNo;
}
public void setReplicateNo(int replicateNo) {
this.replicateNo = replicateNo;
}
public int getSubstanceNo() {
return substanceNo;
}
public void setSubstanceNo(int substanceNo) {
this.substanceNo = substanceNo;
}
public String getGroup() {
return group;
}
public void setGroup(String group) {
this.group = group;
}
}