/**
* Creates a default project and returns it.
*
* @return See above.
*/
public PlateData simplePlateData() {
PlateData data = new PlateData();
data.setName("plate name");
data.setDescription("plate name");
data.setStatus("done");
data.setExternalIdentifier("External Identifier");
return data;
}
/**
* Views the selected field.
*
* @param index The index of the field to view.
*/
void viewField(int index) {
if (index < 0 || index >= fieldsNumber) return;
selectedField = index;
Set<ImageDisplay> samples = new HashSet<ImageDisplay>();
List<ImageDisplay> l = getNodes();
Iterator<ImageDisplay> i = l.iterator();
WellImageSet well;
int row = -1;
int col = -1;
Collection<ImageDisplay> c = browser.getSelectedDisplays();
Map<Integer, Integer> location = new HashMap<Integer, Integer>();
WellSampleNode selected;
if (c != null && c.size() > 0) {
Iterator<ImageDisplay> j = c.iterator();
Object object;
while (j.hasNext()) {
object = j.next();
if (object instanceof WellSampleNode) {
selected = (WellSampleNode) object;
location.put(selected.getRow(), selected.getColumn());
}
}
}
List<ImageDisplay> nodes = new ArrayList<ImageDisplay>();
while (i.hasNext()) {
well = (WellImageSet) i.next();
well.setSelectedWellSample(index);
selected = (WellSampleNode) well.getSelectedWellSample();
row = selected.getRow();
if (location.containsKey(row)) {
col = location.get(row);
if (selected.getColumn() == col) nodes.add(selected);
}
samples.add(selected);
}
samples.addAll(cells);
browser.refresh(samples, nodes);
layoutBrowser(LayoutFactory.PLATE_LAYOUT);
// quietly save the field.
PlateData plate = (PlateData) parent;
long userID = DataBrowserAgent.getUserDetails().getId();
if (plate.getOwner().getId() == userID) {
plate.setDefaultSample(selectedField);
List<DataObject> list = new ArrayList<DataObject>();
list.add(plate);
DataBrowserLoader loader = new PlateSaver(component, ctx, list);
loader.load();
}
}
/**
* Creates a new instance.
*
* @param ctx The security context.
* @param parent The parent of the wells.
* @param wells The collection to wells the model is for.
* @param withThumbnails Pass <code>true</code> to load the thumbnails, <code>false</code>
* otherwise.
*/
WellsModel(SecurityContext ctx, Object parent, Set<WellData> wells, boolean withThumbnails) {
super(ctx);
if (wells == null) throw new IllegalArgumentException("No wells.");
this.withThumbnails = withThumbnails;
selectedNodes = new ArrayList<WellImageSet>();
wellDimension = null;
this.parent = parent;
wellNodes = sortByRow(DataBrowserTranslator.transformHierarchy(wells));
PlateData plate = (PlateData) parent;
columnSequenceIndex = plate.getColumnSequenceIndex();
rowSequenceIndex = plate.getRowSequenceIndex();
selectedField = plate.getDefaultSample();
if (selectedField < 0) selectedField = 0;
Set<ImageDisplay> samples = new HashSet<ImageDisplay>();
cells = new HashSet<CellDisplay>();
rows = -1;
columns = -1;
int row, column;
Iterator<ImageDisplay> j = wellNodes.iterator();
WellImageSet node;
ImageNode selected;
int f;
String columnSequence;
String rowSequence;
Map<Integer, ColourObject> cMap = new HashMap<Integer, ColourObject>();
Map<Integer, ColourObject> rMap = new HashMap<Integer, ColourObject>();
WellData data;
String type;
ColourObject co;
Color color;
boolean b;
validWells = new ArrayList<WellGridElement>();
int minRow = -1;
int minColumn = -1;
while (j.hasNext()) {
node = (WellImageSet) j.next();
row = node.getRow();
column = node.getColumn();
data = (WellData) node.getHierarchyObject();
type = data.getWellType();
if (cMap.containsKey(column)) {
co = cMap.get(column);
color = createColor(data);
if (!UIUtilities.isSameColors(co.getColor(), color, true)
|| !isSameDescription(co.getDescription(), type)) {
co.setColor(null);
co.setDescription(null);
cMap.put(column, co);
}
} else {
cMap.put(column, new ColourObject(createColor(data), type));
}
if (rMap.containsKey(row)) {
co = rMap.get(row);
color = createColor(data);
if (!UIUtilities.isSameColors(co.getColor(), color, true)
|| !isSameDescription(co.getDescription(), type)) {
co.setColor(null);
co.setDescription(null);
rMap.put(row, co);
}
} else {
rMap.put(row, new ColourObject(createColor(data), type));
}
if (row > rows) rows = row;
if (column > columns) columns = column;
if (minRow < 0 || minRow > row) {
minRow = row;
}
if (minColumn < 0 || minColumn > column) {
minColumn = column;
}
columnSequence = "";
if (columnSequenceIndex == PlateData.ASCENDING_LETTER)
columnSequence = UIUtilities.LETTERS.get(column + 1);
else if (columnSequenceIndex == PlateData.ASCENDING_NUMBER)
columnSequence = "" + (column + 1);
rowSequence = "";
if (rowSequenceIndex == PlateData.ASCENDING_LETTER)
rowSequence = UIUtilities.LETTERS.get(row + 1);
else if (rowSequenceIndex == PlateData.ASCENDING_NUMBER) rowSequence = "" + (row + 1);
node.setCellDisplay(columnSequence, rowSequence);
f = node.getNumberOfSamples();
if (fieldsNumber < f) fieldsNumber = f;
node.setSelectedWellSample(selectedField);
selected = node.getSelectedWellSample();
// set the title to Row/Column
node.formatWellSampleTitle();
samples.add(selected);
b = false;
if (node.isSampleValid()) {
wellDimension = selected.getThumbnail().getOriginalSize();
b = true;
}
validWells.add(new WellGridElement(row, column, b));
}
//
if (minRow >= 0 || minColumn >= 0) {
j = wellNodes.iterator();
while (j.hasNext()) {
node = (WellImageSet) j.next();
if (minRow > 0) node.setIndentRow(minRow);
if (minColumn > 0) node.setIndentColumn(minColumn);
if (node.getRow() == minRow || node.getColumn() == minColumn) node.formatWellSampleTitle();
}
}
columns++;
rows++;
CellDisplay cell;
for (int k = 1; k <= columns; k++) {
columnSequence = "";
if (columnSequenceIndex == PlateData.ASCENDING_LETTER)
columnSequence = UIUtilities.LETTERS.get(k + 1);
else if (columnSequenceIndex == PlateData.ASCENDING_NUMBER) columnSequence = "" + k;
cell = new CellDisplay(k - 1, columnSequence);
co = cMap.get(k - 1);
if (co != null) {
cell.setHighlight(co.getColor());
cell.setDescription(co.getDescription());
}
// if (!isMac)
// samples.add(cell);
// cells.add(cell);
}
for (int k = 1; k <= rows; k++) {
rowSequence = "";
if (rowSequenceIndex == PlateData.ASCENDING_LETTER) rowSequence = UIUtilities.LETTERS.get(k);
else if (rowSequenceIndex == PlateData.ASCENDING_NUMBER) rowSequence = "" + k;
cell = new CellDisplay(k - 1, rowSequence, CellDisplay.TYPE_VERTICAL);
co = rMap.get(k - 1);
if (co != null) {
cell.setHighlight(co.getColor());
cell.setDescription(co.getDescription());
}
// if (!isMac)
// samples.add(cell);
// cells.add(cell);
}
browser = BrowserFactory.createBrowser(samples);
browser.accept(new DecoratorVisitor(getCurrentUser().getId()));
layoutBrowser(LayoutFactory.PLATE_LAYOUT);
if (wellDimension == null)
wellDimension =
new Dimension(ThumbnailProvider.THUMB_MAX_WIDTH, ThumbnailProvider.THUMB_MAX_HEIGHT);
}