/*
*------------------------------------------------------------------------------
* Copyright (C) 2006-2008 University of Dundee. All rights reserved.
*
*
* 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 2 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, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
*------------------------------------------------------------------------------
*/
package omero.gateway.model;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import static omero.rtypes.*;
import omero.RInt;
import omero.RString;
import omero.model.Well;
import omero.model.WellI;
import omero.model.WellSample;
/**
* The data that makes up an <i>OME</i> Well and the Experimenter that owns
* this Well.
*
* @author Jean-Marie Burel <a
* href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @author Donald MacDonald <a
* href="mailto:donald@lifesci.dundee.ac.uk">donald@lifesci.dundee.ac.uk</a>
* @version 3.0
* @since 3.0-Beta3
*/
public class WellData extends DataObject {
/**
* All the well samples that are linked to this Well. The elements of this
* set are {@link WellSampleData} objects. If this Well is not linked to any
* Well Sample. then this set will be empty — but never
* <code>null</code>.
*/
private List<WellSampleData> wellSamples;
/** The {@link PlateData plate} containing this well. */
private PlateData plate;
/** Creates a new instance. */
public WellData() {
setDirty(true);
setValue(new WellI());
}
/**
* Creates a new instance.
*
* @param well
* Back pointer to the {@link Well} model object. Mustn't be
* <code>null</code>.
* @throws IllegalArgumentException
* If the object is <code>null</code>.
*/
public WellData(Well well) {
if (well == null) {
throw new IllegalArgumentException("Object cannot be null.");
}
setValue(well);
}
/**
* Returns the external description of the well.
*
* @return See above.
*/
public String getExternalDescription() {
RString d = asWell().getExternalDescription();
return d == null ? null : d.getValue();
}
/**
* Returns the status of the well.
*
* @return See above.
*/
public String getStatus() {
RString d = asWell().getStatus();
return d == null ? null : d.getValue();
}
/**
* Returns a human readable identifier for the screening status e.g. empty,
* positive control, etc.
*
* @return See above.
*/
public String getWellType() {
RString t = asWell().getType();
return t == null ? null : t.getValue();
}
/**
* Sets a human readable identifier for the screening status e.g. empty,
* positive control, etc.
*
* @param type The value to set.
*/
public void setWellType(String type)
{
setDirty(true);
asWell().setType(type == null ? null : rstring(type));
}
/**
* Returns the red component of the color associated to the well,
* or <code>-1</code>.
*
* @return See above.
*/
public int getRed()
{
RInt value = asWell().getRed();
if (value == null) return -1;
return value.getValue();
}
/**
* Sets the red component of the color associated to the well.
*
* @param red The value to set.
*/
public void setRed(Integer red)
{
setDirty(true);
if (red == null) {//reset the color
asWell().setRed(null);
asWell().setGreen(null);
asWell().setBlue(null);
asWell().setAlpha(null);
} else {
if (red < 0) red = 0;
if (red > 255) red = 255;
asWell().setRed(rint(red));
}
}
/**
* Returns the green component of the color associated to the well,
* or <code>-1</code>.
*
* @return See above.
*/
public int getGreen()
{
RInt value = asWell().getGreen();
if (value == null) return -1;
return value.getValue();
}
/**
* Sets the green component of the color associated to the well.
*
* @param green The value to set.
*/
public void setGreen(Integer green)
{
setDirty(true);
if (green == null) {
asWell().setRed(null);
asWell().setGreen(null);
asWell().setBlue(null);
asWell().setAlpha(null);
} else {
if (green < 0) green = 0;
if (green > 255) green = 255;
asWell().setGreen(rint(green));
}
}
/**
* Returns the blue component of the color associated to the well,
* or <code>-1</code>.
*
* @return See above.
*/
public int getBlue()
{
RInt value = asWell().getBlue();
if (value == null) return -1;
return value.getValue();
}
/**
* Sets the blue component of the color associated to the well.
*
* @param blue The value to set.
*/
public void setBlue(Integer blue)
{
setDirty(true);
if (blue == null) {
asWell().setRed(null);
asWell().setGreen(null);
asWell().setBlue(null);
asWell().setAlpha(null);
} else {
if (blue < 0) blue = 0;
if (blue > 255) blue = 255;
asWell().setBlue(rint(blue));
}
}
/**
* Returns the alpha component of the color associated to the well,
* or <code>-1</code>.
*
* @return See above.
*/
public int getAlpha()
{
RInt value = asWell().getAlpha();
if (value == null) return -1;
return value.getValue();
}
/**
* Sets the alpha component of the color associated to the well.
*
* @param alpha The value to set.
*/
public void setAlpha(Integer alpha)
{
setDirty(true);
if (alpha == null) {
asWell().setRed(null);
asWell().setGreen(null);
asWell().setBlue(null);
asWell().setAlpha(null);
} else {
if (alpha < 0) alpha = 0;
if (alpha > 255) alpha = 255;
asWell().setAlpha(rint(alpha));
}
}
/**
* Sets the external description of the well.
*
* @param description
* The description of the well.
*/
public void setExternalDescription(String description) {
setDirty(true);
asWell().setExternalDescription(
description == null ? null : rstring(description));
}
/**
* Sets the status of the well.
*
* @param status The status of the well.
*/
public void setStatus(String status) {
setDirty(true);
asWell().setStatus(
status == null ? null : rstring(status));
}
/**
* Returns the number of annotations linked to the object, key: id of the
* user, value: number of annotation. The map may be <code>null</code> if
* no annotation.
*
* @return See above.
*/
public Map<Long, Long> getAnnotationsCounts() {
return asWell().getAnnotationLinksCountPerOwner();
}
/**
* Returns the number of reagents linked to the object, key: id of the user,
* value: number of annotation. The map may be <code>null</code> if no
* annotation.
*
* @return See above.
*/
public Map<Long, Long> getReagentsCounts() {
return asWell().getReagentLinksCountPerOwner();
}
/**
* Returns the column used to indicate the location of the well on the grid.
*
* @return See above.
*/
public Integer getColumn() {
RInt c = asWell().getColumn();
return c == null ? null : c.getValue();
}
/**
* Returns the row used to indicate the location of the well on the grid.
*
* @return See above.
*/
public Integer getRow() {
RInt r = asWell().getRow();
return r == null ? null : r.getValue();
}
/**
* Returns the plate containing this Well.
*
* @return See above.
*/
public PlateData getPlate() {
if (plate == null) {
plate = new PlateData(asWell().getPlate());
}
return plate;
}
// Lazy loaded Links
/**
* Returns the well samples linked to the well.
*
* @return See above.
*/
public List<WellSampleData> getWellSamples() {
if (wellSamples == null && asWell().sizeOfWellSamples() >= 0) {
wellSamples = new ArrayList<WellSampleData>();
List<WellSample> samples = asWell().copyWellSamples();
for (WellSample sample : samples) {
if (sample != null)
wellSamples.add(new WellSampleData(sample));
}
}
return wellSamples == null ? null : new ArrayList<WellSampleData>(
wellSamples);
}
// Link mutations
/**
* Sets the well samples linked to the well.
*
* @param value
* The set of well samples.
*/
public void setWellSamples(List<WellSampleData> value) {
List<WellSampleData> currentValue = getWellSamples();
SetMutator<WellSampleData> m = new SetMutator<WellSampleData>(
currentValue, value);
while (m.moreDeletions()) {
setDirty(true);
asWell().removeWellSample(m.nextDeletion().asWellSample());
}
while (m.moreAdditions()) {
setDirty(true);
asWell().addWellSample(m.nextAddition().asWellSample());
}
wellSamples = m.result();
}
}