@SuppressWarnings("deprecation")
private Form getRemoveForm(final String admin) {
removeExperimentForm = new Form();
removeExperimentForm.setCaption("Remove Existing Experiment");
removeExperimentForm.setWidth("50%");
expList = eh.getExperiments(null);
List<String> strExpList = new ArrayList<String>();
for (ExperimentBean exp : expList.values()) {
if (user.getEmail().equalsIgnoreCase("*****@*****.**")
|| exp.getEmail().equalsIgnoreCase(user.getEmail())) {
String str = exp.getExpId() + " " + exp.getName() + " ( " + exp.getUploadedByName() + " )";
strExpList.add(str);
}
}
final Select selectExp = new Select("Experiment ID", strExpList);
selectExp.setWidth("100%");
removeExperimentForm.addField(Integer.valueOf(1), selectExp);
Button removeExpButton = new Button("Remove Experiment");
removeExpButton.setStyle(Reindeer.BUTTON_SMALL);
removeExperimentForm.addField(Integer.valueOf(2), removeExpButton);
removeExpButton.addListener(
new ClickListener() {
/** */
private static final long serialVersionUID = 1L;
@Override
public void buttonClick(ClickEvent event) {
String str = selectExp.getValue().toString();
String[] strArr = str.split("\t");
Integer expId = (Integer.valueOf(strArr[0]));
if (expId != null) {
boolean test = auth.removeExp(expId);
if (test) {
updateComponents(user);
} else {
getWindow().showNotification("Failed to Remove The Experiment! ");
}
} else {
}
}
});
return removeExperimentForm;
}
public SelectWindow(
float width,
int units,
Collection<T> items,
T selectedItem,
Resource icon,
String caption,
String message,
String okButtonText,
String cancelButtonText) {
super();
if (caption != null) {
setCaption(caption);
}
if (icon != null) {
setIcon(icon);
}
setWidth(width, units);
setModal(true);
setClosable(false);
setResizable(false);
setDraggable(false);
VerticalLayout verticalLayout = new VerticalLayout();
verticalLayout.setMargin(true);
verticalLayout.setSpacing(true);
setContent(verticalLayout);
Label label = new Label(message);
addComponent(label);
mySelect = new Select(null, items);
mySelect.setNullSelectionAllowed(false);
mySelect.setValue(selectedItem != null ? selectedItem : items.iterator().next());
mySelect.setWidth(100, Sizeable.UNITS_PERCENTAGE);
addComponent(mySelect);
Panel panel = new Panel();
addComponent(panel);
verticalLayout.setComponentAlignment(panel, Alignment.MIDDLE_RIGHT);
panel.addStyleName("light");
HorizontalLayout horizontalLayout = new HorizontalLayout();
panel.setContent(horizontalLayout);
horizontalLayout.setSpacing(true);
verticalLayout.setComponentAlignment(panel, Alignment.MIDDLE_RIGHT);
myCancelButton = new Button(cancelButtonText, this);
panel.addComponent(myCancelButton);
myOkButton = new Button(okButtonText, this);
panel.addComponent(myOkButton);
}
@SuppressWarnings("serial")
@Override
public void afterPropertiesSet() throws Exception {
setHeight("200px");
setWidth("700px");
crossNameOptionGroup = new OptionGroup();
sequenceNumCheckBox = new CheckBox();
sequenceNumCheckBox.setImmediate(true);
sequenceNumCheckBox.addListener(
new Property.ValueChangeListener() {
@Override
public void valueChange(ValueChangeEvent event) {
enableSpecifyLeadingZerosComponents(sequenceNumCheckBox.booleanValue());
}
});
specifyPrefixLabel = new Label();
prefixTextField = new TextField();
prefixTextField.setWidth("500px");
howManyDigitsLabel = new Label();
leadingZerosSelect = new Select();
for (int i = 1; i <= MAX_LEADING_ZEROS; i++) {
leadingZerosSelect.addItem(Integer.valueOf(i));
}
leadingZerosSelect.setNullSelectionAllowed(false);
leadingZerosSelect.select(Integer.valueOf(1));
leadingZerosSelect.setWidth("50px");
specifySuffixLabel = new Label();
suffixTextField = new TextField();
suffixTextField.setWidth("500px");
nextNameInSequenceLabel = new Label();
generatedNameLabel = new Label();
generateButton = new Button();
generateButton.setData(GENERATE_BUTTON_ID);
generateButton.addListener(new CrossingManagerImportButtonClickListener(this));
layoutComponents();
initializeToggableComponents();
}
@SuppressWarnings({"deprecation", "serial"})
private void updateComponents(final User user) {
if (container != null) {
container.removeAllComponents();
}
container = new Panel();
root = new Panel();
root.setStyle(Reindeer.PANEL_LIGHT);
container.setHeight("100%");
container.setStyle(Reindeer.PANEL_LIGHT);
setCompositionRoot(container);
// Create the Form
newExpForm = new Form();
newExpForm.setCaption("New Experiment");
newExpForm.setWriteThrough(false); // we want explicit 'apply'
newExpForm.setInvalidCommitted(false); // no invalid values in data model
// Determines which properties are shown, and in which order:
expNameField = new TextField("Experiment Name:");
expNameField.setStyle(Reindeer.TEXTFIELD_SMALL);
expNameField.setRequired(true);
expNameField.setRequiredError("EXPERIMENT NAME CAN NOT BE EMPTY!");
expNameField.setWidth("350px");
expNameField.setMaxLength(70);
speciesField = new TextField("Species:");
speciesField.setStyle(Reindeer.TEXTFIELD_SMALL);
speciesField.setRequired(true);
speciesField.setRequiredError("EXPERIMENT SPECIES CAN NOT BE EMPTY!");
speciesField.setWidth("350px");
speciesField.setMaxLength(70);
sampleTypeField = new TextField("Sample Type:");
sampleTypeField.setStyle(Reindeer.TEXTFIELD_SMALL);
sampleTypeField.setRequired(true);
sampleTypeField.setRequiredError("EXPERIMENT SAMPLE TYPE CAN NOT BE EMPTY!");
sampleTypeField.setWidth("350px");
sampleTypeField.setMaxLength(70);
sampleProcessingField = new TextField("Sample Processing:");
sampleProcessingField.setStyle(Reindeer.TEXTFIELD_SMALL);
sampleProcessingField.setRequired(true);
sampleProcessingField.setRequiredError("EXPERIMENT SAMPLE PROCESSING CAN NOT BE EMPTY!");
sampleProcessingField.setWidth("350px");
sampleProcessingField.setMaxLength(70);
instrumentTypeField = new TextField("Instrument Type:");
instrumentTypeField.setStyle(Reindeer.TEXTFIELD_SMALL);
instrumentTypeField.setRequired(true);
instrumentTypeField.setRequiredError("EXPERIMENT INSTURMENT TYPE CAN NOT BE EMPTY!");
instrumentTypeField.setWidth("350px");
instrumentTypeField.setMaxLength(70);
fragModeField = new TextField("Frag Mode:");
fragModeField.setStyle(Reindeer.TEXTFIELD_SMALL);
fragModeField.setRequired(true);
fragModeField.setRequiredError("EXPERIMENT FRAG MODE CAN NOT BE EMPTY!");
fragModeField.setWidth("350px");
fragModeField.setMaxLength(70);
UploadedByNameField = new TextField("Uploaded By:");
UploadedByNameField.setStyle(Reindeer.TEXTFIELD_SMALL);
UploadedByNameField.setRequired(true);
UploadedByNameField.setRequiredError("EXPERIMENT UPLOADED BY CAN NOT BE EMPTY!");
UploadedByNameField.setValue(user.getUsername());
UploadedByNameField.setEnabled(false);
UploadedByNameField.setWidth("350px");
UploadedByNameField.setMaxLength(70);
emailField = new TextField("Email:");
emailField.setStyle(Reindeer.TEXTFIELD_SMALL);
emailField.setRequired(true);
emailField.setValue(user.getEmail());
emailField.setEnabled(false);
emailField.setRequiredError("EXPERIMENT EMAIL CAN NOT BE EMPTY!");
emailField.setWidth("350px");
emailField.setMaxLength(70);
descriptionField = new TextArea("Description:");
descriptionField.setStyle(Reindeer.TEXTFIELD_SMALL);
descriptionField.setRequired(true);
descriptionField.setRequiredError("EXPERIMENT Description CAN NOT BE EMPTY!");
descriptionField.setWidth("350px");
descriptionField.setMaxLength(950);
publicationLinkField = new TextField("Publication Link:");
publicationLinkField.setStyle(Reindeer.TEXTFIELD_SMALL);
publicationLinkField.setWidth("350px");
publicationLinkField.setMaxLength(300);
newExpForm.addField(Integer.valueOf(1), expNameField);
newExpForm.addField(Integer.valueOf(2), descriptionField);
newExpForm.addField(Integer.valueOf(3), speciesField);
newExpForm.addField(Integer.valueOf(4), sampleTypeField);
newExpForm.addField(Integer.valueOf(5), sampleProcessingField);
newExpForm.addField(Integer.valueOf(6), instrumentTypeField);
newExpForm.addField(Integer.valueOf(7), fragModeField);
newExpForm.addField(Integer.valueOf(8), UploadedByNameField);
newExpForm.addField(Integer.valueOf(9), emailField);
newExpForm.addField(Integer.valueOf(10), publicationLinkField);
// Add form to layout
container.addComponent(newExpForm);
Panel p = new Panel();
Label l =
new Label(
"<h4 style='color:blue'>Or Update Existing Experiments !</h4><h4 style='color:blue'>For New Experiment Please Leave Experiment ID Blank!</h4><h4 style='color:blue'><strong style='color:red'>* </strong> For New Experiment Please Remember to Upload Protein file first!</h4>");
l.setContentMode(Label.CONTENT_XHTML);
p.addComponent(l);
container.addComponent(p);
// Create the Form
Form existExpForm = new Form();
existExpForm.setCaption("Exist Experiments");
expList = eh.getExperiments(null);
List<String> strExpList = new ArrayList<String>();
for (ExperimentBean exp : expList.values()) {
if (user.getEmail().equalsIgnoreCase("*****@*****.**")
|| exp.getEmail().equalsIgnoreCase(user.getEmail())) {
String str = exp.getExpId() + " " + exp.getName() + " ( " + exp.getUploadedByName() + " )";
strExpList.add(str);
}
}
select = new Select("Experiment ID", strExpList);
select.setImmediate(true);
select.addListener(
new Property.ValueChangeListener() {
@Override
public void valueChange(ValueChangeEvent event) {
Object o = select.getValue();
if (o != null) {
String str = select.getValue().toString();
String[] strArr = str.split("\t");
int id = (Integer.valueOf(strArr[0]));
ExperimentBean expDet = expList.get(id);
if (expDetails != null) {
expDetails.removeAllComponents();
if (expDet.getProteinsNumber() == 0) {
Label l = new Label("<h4 style='color:red'>1) Protein File is Missing</h4>");
l.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(l);
} else {
Label l = new Label("<h4 style='color:blue'>1) Protein File is Uploaded</h4>");
l.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(l);
}
if (expDet.getFractionsNumber() == 0) {
Label l = new Label("<h4 style='color:red'>2) Fraction File is Missing</h4>");
l.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(l);
} else {
Label l = new Label("<h4 style='color:blue'>2) Fraction File Uploaded</h4>");
l.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(l);
}
// if (expDet.getFractionRange() == 0) {
// Label l = new Label("<h4 style='color:red'>3) Fraction
// Range File is Missing</h4>");
// l.setContentMode(Label.CONTENT_XHTML);
// expDetails.addComponent(l);
// } else {
// Label l = new Label("<h4 style='color:blue'>3)
// Fraction Range File Uploaded</h4>");
// l.setContentMode(Label.CONTENT_XHTML);
// expDetails.addComponent(l);
// }
if (expDet.getPeptidesNumber() == 0) {
Label l = new Label("<h4 style='color:red'>3) Peptides File is Missing</h4>");
l.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(l);
} else {
Label l = new Label("<h4 style='color:blue'>3) Peptides File Uploaded</h4>");
l.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(l);
}
}
} else {
expDetails.removeAllComponents();
Label labelDetails =
new Label(
"<h4 style='color:red;'>Please Select Experiment To Show the Details.</h4>");
labelDetails.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(labelDetails);
}
}
});
select.setWidth("60%");
existExpForm.addField(Integer.valueOf(1), select);
// Add form to layout
VerticalLayout vlo = new VerticalLayout();
if (hslo != null) {
vlo.removeComponent(hslo);
}
hslo = new HorizontalLayout();
hslo.setSizeFull();
hslo.addComponent(existExpForm);
vlo.addComponent(hslo);
if (removeExperimentLayout != null) {
hslo.removeComponent(removeExperimentLayout);
}
removeExperimentLayout = this.getRemoveForm(user.getEmail());
hslo.addComponent(removeExperimentLayout);
hslo.setComponentAlignment(removeExperimentForm, Alignment.MIDDLE_CENTER);
vlo.addComponent(hslo);
container.addComponent(vlo);
// Create the Upload component.
upload = new Upload(null, this);
upload.setStyleName("small");
upload.setVisible(true);
upload.setHeight("30px");
upload.setButtonCaption("ADD / EDIT EXPERIMENT !");
// *****************************************************
upload.addListener(
new Upload.StartedListener() {
@SuppressWarnings("static-access")
@Override
public void uploadStarted(StartedEvent event) {
try {
Thread.currentThread().sleep(1000);
Thread t =
new Thread(
new Runnable() {
@Override
public void run() {
pi.setVisible(true);
}
});
t.start();
t.join();
} catch (InterruptedException e) {
}
mainTabs.setReadOnly(true);
subTabs.setReadOnly(true);
}
});
upload.addListener(
new Upload.FinishedListener() {
@Override
public void uploadFinished(FinishedEvent event) {
pi.setVisible(false);
mainTabs.setReadOnly(false);
subTabs.setReadOnly(false);
file = new File(event.getFilename());
}
});
// ***********************************
upload.addListener((Upload.SucceededListener) this);
upload.addListener((Upload.FailedListener) this);
if (helpNote != null) {
vlo.removeComponent(helpNote);
}
Label label =
new Label(
"<h4 style='color:red;'>Please upload proteins file first</h4><h4 style='color:red;'>Please upload proteins files in (.txt) format.</h4><h4 style='color:red;'>Upload fraction range file after upload protein fraction file.</h4><h4 style='color:red;'>Upload fraction range file in (.xlsx) format.</h4>");
label.setContentMode(Label.CONTENT_XHTML);
helpNote = help.getHelpNote(label);
helpNote.setMargin(false, true, true, true);
vlo.addComponent(upload);
vlo.addComponent(pi);
vlo.addComponent(helpNote);
vlo.setComponentAlignment(helpNote, Alignment.MIDDLE_RIGHT);
expDetails = new Panel("Experiment Details");
Label labelDetails =
new Label("<h4 style='color:red;'>Please Select Experiment To Show the Details.</h4>");
labelDetails.setContentMode(Label.CONTENT_XHTML);
expDetails.addComponent(labelDetails);
vlo.addComponent(expDetails);
root.addComponent(vlo);
container.addComponent(root);
}