public Component getListCellRendererComponent(
JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
if (value instanceof WSIBox) {
value = ((WSIBox) value).getTitle();
}
if (value instanceof TridasMeasurementSeries) {
TridasMeasurementSeries ms = (TridasMeasurementSeries) value;
TridasGenericField f = GenericFieldUtils.findField(ms, "tellervo.internal.labcodeText");
value = (f != null) ? f.getValue() : ms.getTitle();
}
if (value instanceof TridasRadius) {
TridasRadius r = (TridasRadius) value;
TridasGenericField f = GenericFieldUtils.findField(r, "tellervo.internal.labcodeText");
value = (f != null) ? f.getValue() : r.getTitle();
}
if (value instanceof TridasSample) {
TridasSample s = (TridasSample) value;
LabCode labcode = new LabCode();
boolean set = false;
if (GenericFieldUtils.findField(s, "tellervo.objectLabCode") != null) {
labcode.appendSiteCode(GenericFieldUtils.findField(s, "tellervo.objectLabCode").getValue());
if (GenericFieldUtils.findField(s, "tellervo.elementLabCode") != null) {
labcode.setElementCode(
GenericFieldUtils.findField(s, "tellervo.elementLabCode").getValue());
labcode.setSampleCode(s.getTitle());
set = true;
}
}
if (set) {
value = LabCodeFormatter.getRadiusPrefixFormatter().format(labcode);
} else {
TridasGenericField f = GenericFieldUtils.findField(s, "tellervo.internal.labcodeText");
value = (f != null) ? f.getValue() : s.getTitle();
}
}
if (value instanceof TridasElement) {
TridasElement e = (TridasElement) value;
TridasGenericField f = GenericFieldUtils.findField(e, "tellervo.internal.labcodeText");
value = (f != null) ? f.getValue() : e.getTitle();
}
/*else
{
System.out.println("The object type "+ value.getClass().toString()+" is unsupported in TridasListCellRenderer");
}*/
return super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
}
@Override
public String getTaxon() {
ControlledVoc voc;
if (have(element) && (voc = element.getTaxon()) != null) {
if (voc.isSetNormal()) return voc.getNormal();
else if (voc.isSetValue() && voc.getValue().length() > 0) return voc.getValue();
}
return null;
}
private TridasProject getProject() {
TridasProject project = null;
try {
project = defaults.getProjectWithDefaults(true);
TridasObject o = project.getObjects().get(0);
TridasElement e = o.getElements().get(0);
TridasSample s = e.getSamples().get(0);
if (mseriesList.size() > 0) {
TridasRadius r = s.getRadiuses().get(0);
r.setMeasurementSeries(mseriesList);
}
} catch (NullPointerException e) {
} catch (IndexOutOfBoundsException e2) {
}
return project;
}
/**
* Parse the specified legacy data file for series
*
* @param file
* @param fileType
*/
private void parseFile(File file, AbstractDendroFormat format) {
ArrayList<Sample> sampleList = new ArrayList<Sample>();
// Create a reader based on the file type supplied
AbstractDendroFileReader reader = TridasIO.getFileReaderFromFormat(format);
if (reader == null) {
Alert.error(containerFrame, "Error", "Unknown file type");
return;
}
// Try and load the file
try {
reader.loadFile(file.getAbsolutePath());
} catch (IOException e) {
Alert.errorLoading(file.getAbsolutePath(), e);
return;
} catch (InvalidDendroFileException e) {
Alert.error(
containerFrame,
"Error",
"The selected file is not a valid "
+ format.getShortName()
+ " file.\nPlease check and try again");
return;
} catch (NullPointerException e) {
Alert.error(containerFrame, "Invalid File", e.getLocalizedMessage());
}
TridasTridas tc = reader.getTridasContainer();
log.debug("Project count: " + tc.getProjects().size());
Boolean hideWarningsFlag = false;
for (TridasProject p : tc.getProjects()) {
for (TridasObject o : p.getObjects()) {
for (TridasElement e : TridasUtils.getElementList(o)) {
log.debug("Element count: " + o.getElements().size());
for (TridasSample s : e.getSamples()) {
for (TridasRadius r : s.getRadiuses()) {
for (TridasMeasurementSeries ms : r.getMeasurementSeries()) {
Sample sample =
EditorFactory.createSampleFromSeries(ms, e, file, format, hideWarningsFlag);
if (sample == null) {
hideWarningsFlag = true;
} else {
sampleList.add(sample);
}
}
}
}
}
}
for (TridasDerivedSeries ds : p.getDerivedSeries()) {
Sample sample =
EditorFactory.createSampleFromSeries(ds, null, file, format, hideWarningsFlag);
if (sample == null) {
hideWarningsFlag = true;
} else {
sampleList.add(sample);
}
}
}
Boolean unitsSet = false;
for (ITridasSeries ser : getSeries(sampleList)) {
for (TridasValues tv : ser.getValues()) {
if (tv.isSetUnit()) {
if (tv.getUnit().isSetNormalTridas()) {
unitsSet = true;
}
}
}
}
if (unitsSet == false && sampleList.size() > 0 && unitsIfNotSpecified == null) {
Object[] possibilities = {"1/1000th mm", "1/100th mm", "1/50th mm", "1/20th mm", "1/10th mm"};
Object s =
JOptionPane.showInputDialog(
containerFrame,
"One or more series has no units defined.\n" + "Please specify units below:",
"Set Units",
JOptionPane.PLAIN_MESSAGE,
null,
possibilities,
"1/1000th mm");
if (s.equals("1/1000th mm")) {
unitsIfNotSpecified = NormalTridasUnit.MICROMETRES;
} else if (s.equals("1/100th mm")) {
unitsIfNotSpecified = NormalTridasUnit.HUNDREDTH_MM;
} else if (s.equals("1/50th mm")) {
unitsIfNotSpecified = NormalTridasUnit.FIFTIETH_MM;
} else if (s.equals("1/20th mm")) {
unitsIfNotSpecified = NormalTridasUnit.TWENTIETH_MM;
} else if (s.equals("1/10th mm")) {
unitsIfNotSpecified = NormalTridasUnit.TENTH_MM;
} else {
Alert.error(containerFrame, "Error", "Invalid measurement units specified");
return;
}
}
for (Sample sample : sampleList) {
ITridasSeries series = sample.getSeries();
try {
for (int i = 0; i < series.getValues().size(); i++) {
TridasValues tv = series.getValues().get(i);
if (tv.isSetUnit()) {
if (!tv.getUnit().isSetNormalTridas()) {
tv.getUnit().setNormalTridas(unitsIfNotSpecified);
}
} else {
TridasUnit unit = new TridasUnit();
unit.setNormalTridas(unitsIfNotSpecified);
tv.setUnit(unit);
tv.setUnitless(null);
}
tv = UnitUtils.convertTridasValues(NormalTridasUnit.MICROMETRES, tv, true);
TridasUnit unit = new TridasUnit();
unit.setNormalTridas(NormalTridasUnit.MICROMETRES);
tv.setUnit(unit);
series.getValues().set(i, tv);
}
} catch (NumberFormatException e) {
Alert.error("Error", "One or more data values are not numbers.");
return;
} catch (ConversionWarningException e) {
Alert.error("Error", "Error converting units");
return;
}
}
for (Sample s : sampleList) {
SeriesIdentity id = new SeriesIdentity(file, format, s);
model.addItem(id);
}
}