/*****************************************************************************
* Copyright (c) 2008 Bioclipse Project
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
*****************************************************************************/
package net.bioclipse.spectrum.wizards;
import java.io.StringReader;
import java.util.HashMap;
import java.util.Iterator;
import nu.xom.Builder;
import nu.xom.Element;
import nu.xom.Elements;
import org.eclipse.jface.viewers.CellEditor;
import org.eclipse.jface.viewers.IStructuredSelection;
import org.eclipse.jface.viewers.TableViewer;
import org.eclipse.jface.viewers.TextCellEditor;
import org.eclipse.jface.wizard.WizardPage;
import org.eclipse.swt.SWT;
import org.eclipse.swt.events.SelectionAdapter;
import org.eclipse.swt.events.SelectionEvent;
import org.eclipse.swt.layout.GridData;
import org.eclipse.swt.layout.GridLayout;
import org.eclipse.swt.layout.RowData;
import org.eclipse.swt.layout.RowLayout;
import org.eclipse.swt.widgets.Button;
import org.eclipse.swt.widgets.Combo;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Dialog;
import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Event;
import org.eclipse.swt.widgets.Label;
import org.eclipse.swt.widgets.Listener;
import org.eclipse.swt.widgets.MessageBox;
import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Table;
import org.eclipse.swt.widgets.TableColumn;
import org.eclipse.swt.widgets.Text;
import org.xmlcml.cml.base.CMLElements;
import org.xmlcml.cml.element.CMLPeak;
import org.xmlcml.cml.element.CMLPeakList;
import au.com.bytecode.opencsv.CSVReader;
public class NewSpectrumDetailWizardPage extends WizardPage {
private Combo spectrumTypeCombo;
private TableViewer tableViewer;
public static final String MASS = "Mass Spectrum";
public static final String NMR = "NMR Spectrum";
public static final String IR = "IR Spectrum";
public static final String UV = "UV Spectrum";
HashMap<String, Element> spectypemap = new HashMap<String, Element>();
static Table table =null;
private boolean peakdone=false;
protected String separator;
protected NewSpectrumDetailWizardPage() {
super("SpectrumDetailWizardPage");
setTitle("New Spectrum Detail Wizard");
setDescription("This wizard lets you select the Spectrum type and gives you the possibiliy to add peaks");
}
public void createControl(Composite parent) {
try{
Builder builder = new nu.xom.Builder();
nu.xom.Document doc = builder.build(this
.getClass()
.getClassLoader()
.getResourceAsStream(
"net/bioclipse/spectrum/editor/spec.xml"));
Element docRoot = doc.getRootElement();
Elements specTypeElements = docRoot.getChildElements("spectrumtype");
for (int i=0; i<specTypeElements.size(); i++) {
Element specTypeElement = specTypeElements.get(i);
String name = specTypeElement.getAttribute("name").getValue();
spectypemap.put(name, specTypeElement);
}
}catch(Exception ex){
ex.printStackTrace();
//don't worry, only columns headers not working
}
Composite container = new Composite(parent, SWT.NULL);
GridLayout layout = new GridLayout();
container.setLayout(layout);
layout.numColumns = 2;
layout.verticalSpacing = 9;
Label spectrumTypeLabel = new Label(container, SWT.None);
spectrumTypeLabel.setText("Please select the Spectrum type:");
spectrumTypeCombo = new Combo(container, SWT.DROP_DOWN | SWT.READ_ONLY);
Object[] array = spectypemap.keySet().toArray();
String[] keyArray = new String[array.length];
for (int i=0; i<array.length; i++) {
keyArray[i] = (String) array[i];
}
spectrumTypeCombo.setItems(keyArray);
spectrumTypeCombo.addSelectionListener(new SelectionAdapter() {
public void widgetSelected(SelectionEvent e) {
try {
Element selection = spectypemap.get(((Combo) e.getSource()).getText());
Element xaxisNode = selection.getChildElements("xaxis").get(0);
Element yaxisNode = selection.getChildElements("yaxis").get(0);
table.getColumn(0).setText(xaxisNode.getAttributeValue("name"));
table.getColumn(1).setText(yaxisNode.getAttributeValue("name"));
dialogChanged();
} catch (Exception ex) {
//don't worry, only column headers not working
}
}
});
spectrumTypeCombo.select(0);
Label peakListLabel = new Label(container, SWT.NONE);
GridData gd = new GridData();
gd.horizontalSpan = 2;
peakListLabel.setLayoutData(gd);
peakListLabel.setText("Peak List:");
Composite comp = new Composite(container, SWT.None);
RowLayout innerLayout = new RowLayout(SWT.VERTICAL);
comp.setLayout(innerLayout);
String[] columnNames = new String[2];
columnNames[0] = spectypemap.get(spectrumTypeCombo.getText()).getChildElements("xaxis").get(0).getAttributeValue("name");
columnNames[1] = spectypemap.get(spectrumTypeCombo.getText()).getChildElements("yaxis").get(0).getAttributeValue("name");
table = createTable(comp, columnNames);
tableViewer = createTableViewer(table, columnNames);
tableViewer.setContentProvider(new PeakContentProvider());
tableViewer.setLabelProvider(new PeakLabelProvider());
CMLPeakList peakList = new CMLPeakList();
for (int i = 0; i < 5; i++) {
CMLPeak peak = new CMLPeak();
peak.setXValue(0);
peak.setYValue(0);
peakList.addPeak(peak);
}
tableViewer.setInput(peakList);
Composite buttonComp = new Composite(comp, SWT.NONE);
RowLayout buttonLayout = new RowLayout(SWT.HORIZONTAL);
buttonComp.setLayout(buttonLayout);
createButtons(buttonComp, tableViewer);
setControl(container);
dialogChanged();
}
private void createButtons(final Composite parent,
final TableViewer tableViewer) {
// Create and configure the "Add" button
Button add = new Button(parent, SWT.PUSH | SWT.CENTER);
add.setText("Add Peak");
add.addSelectionListener(new SelectionAdapter() {
// Add a peakvalue to the PeakTable and refresh the view
public void widgetSelected(SelectionEvent e) {
CMLPeak peak = new CMLPeak();
peak.setXValue(0);
peak.setYValue(0);
((CMLPeakList) tableViewer.getInput()).addPeak(peak);
int elements = tableViewer.getTable().getItemCount();
tableViewer.getTable().select(elements - 1);
tableViewer.setInput(tableViewer.getInput());
tableViewer.editElement(peak, 0);
}
});
// Create and configure the "Delete" button
Button delete = new Button(parent, SWT.PUSH | SWT.CENTER);
delete.setText("Delete Peak");
delete.addSelectionListener(new SelectionAdapter() {
// Remove the selection and refresh the view
public void widgetSelected(SelectionEvent e) {
CMLPeak task = (CMLPeak) ((IStructuredSelection) tableViewer
.getSelection()).getFirstElement();
if (task != null) {
tableViewer.remove(task);
((CMLPeakList) tableViewer.getInput()).removeChild(task);
}
}
});
// Create and configure the "Inser CSV" button
Button insertcsv = new Button(parent, SWT.PUSH | SWT.CENTER);
insertcsv.setText("Insert CSV list");
insertcsv.addSelectionListener(new SelectionAdapter() {
// Remove empty entries, add csv values and refresh the view
public void widgetSelected(SelectionEvent e) {
CMLPeakList peakList = getPeakList();
CMLElements<CMLPeak> peaks = peakList.getPeakElements();
Iterator<CMLPeak> it = peaks.iterator();
while (it.hasNext()) {
CMLPeak peak = it.next();
if (peak.getXValue() == 0 && peak.getYValue() == 0) {
peakList.removeChild(peak);
}
}
InputDialog dialog = new InputDialog(NewSpectrumDetailWizardPage.this.getShell());
String text = dialog.open(NewSpectrumDetailWizardPage.this);
//String text = new MyJOptionPane().showInputDialog( "Enter your CSV test here" );
CSVReader reader = new CSVReader(new StringReader(text),separator.charAt( 0 ));
String [] nextLine;
try {
while ((nextLine = reader.readNext()) != null) {
boolean first=true;
CMLPeak peak = new CMLPeak();
for(int i=0;i<nextLine.length;i++){
if(!nextLine[i].equals( "" )){
if(first){
peak.setXValue(Float.parseFloat( nextLine[i]));
first=false;
}else{
peak.setYValue(Float.parseFloat(nextLine[i]));
}
}
}
((CMLPeakList) tableViewer.getInput()).addPeak(peak);
}
tableViewer.refresh();
dialogChanged();
} catch ( Exception e1 ) {
MessageBox mb = new MessageBox(NewSpectrumDetailWizardPage.this.getShell(),SWT.ICON_ERROR | SWT.OK );
mb.setMessage( "There was some problem reading your input. Most likely, it was corrupt!");
mb.setText( "Problems reading input" );
mb.open();
e1.printStackTrace();
}
}
});
}
private TableViewer createTableViewer(final Table table,
String[] columnNames) {
final TableViewer tableViewer = new TableViewer(table);
tableViewer.setUseHashlookup(true);
tableViewer.setColumnProperties(columnNames);
CellEditor[] editors = new CellEditor[columnNames.length + 4];
// Column 2 : X_AXIS (Free text)
TextCellEditor xEditor = new TextCellEditor(table);
((Text) xEditor.getControl()).setTextLimit(60);
((Text) xEditor.getControl()).addListener(SWT.Traverse, new Listener() {
int highestColumn = 1;
public void handleEvent(Event event) {
if (event.detail == SWT.TRAVERSE_TAB_PREVIOUS
|| event.detail == SWT.TRAVERSE_ARROW_PREVIOUS) {
if (table.getSelectionIndex() > 0)
tableViewer.editElement(tableViewer.getElementAt(table
.getSelectionIndex() - 1), highestColumn);
}
if (event.detail == SWT.TRAVERSE_TAB_NEXT
|| event.detail == SWT.TRAVERSE_ARROW_NEXT) {
tableViewer.editElement(tableViewer.getElementAt(table
.getSelectionIndex()), 1);
}
dialogChanged();
}
});
((Text) xEditor.getControl()).addListener(SWT.KeyDown, new Listener() {
public void handleEvent(Event event) {
peakdone=true;
dialogChanged();
}
});
editors[0] = xEditor;
// Column 3 : Y_AXIS ;
TextCellEditor yEditor = new TextCellEditor(table);
((Text) yEditor.getControl()).setTextLimit(60);
((Text) yEditor.getControl()).addListener(SWT.Traverse, new Listener() {
int highestColumn = 1;
public void handleEvent(Event event) {
if (event.detail == SWT.TRAVERSE_TAB_PREVIOUS
|| event.detail == SWT.TRAVERSE_ARROW_PREVIOUS) {
tableViewer.editElement(tableViewer.getElementAt(table
.getSelectionIndex()), 0);
}
if (event.detail == SWT.TRAVERSE_TAB_NEXT
|| event.detail == SWT.TRAVERSE_ARROW_NEXT) {
if (highestColumn == 1
&& table.getSelectionIndex() < ((CMLPeakList) tableViewer
.getInput()).getChildCount() - 1)
tableViewer.editElement(tableViewer.getElementAt(table
.getSelectionIndex() + 1), 0);
if (highestColumn > 1)
tableViewer.editElement(tableViewer.getElementAt(table
.getSelectionIndex()), 2);
}
}
});
editors[1] = yEditor;
for (int i = 0; i < 1; i++) {
TextCellEditor cellEditor = new TextCellEditor(table);
((Text) cellEditor.getControl()).setTextLimit(60);
((Text) cellEditor.getControl()).addListener(SWT.Traverse,
new PeakTableTabListener(2 + i, tableViewer));
editors[2 + i] = cellEditor;
}
tableViewer.setCellEditors(editors);
tableViewer.setCellModifier(new PeakCellModifier(columnNames,
tableViewer));
return tableViewer;
}
private Table createTable(Composite container, String[] columnNames) {
int style = SWT.SINGLE | SWT.BORDER | SWT.H_SCROLL | SWT.V_SCROLL
| SWT.FULL_SELECTION | SWT.HIDE_SELECTION | SWT.LEFT;
Table table = new Table(container, style);
RowData rowData = new RowData();
rowData.height = 100;
table.setLayoutData(rowData);
table.setLinesVisible(true);
table.setHeaderVisible(true);
TableColumn[] column = new TableColumn[columnNames.length];
for (int i = 0; i < columnNames.length; i++) {
column[i] = new TableColumn(table, SWT.CENTER, i);
column[i].setText(columnNames[i]);
column[i].setWidth(100);
}
return table;
}
public String getSpectrumType() {
return this.spectypemap.get(spectrumTypeCombo
.getText()).getAttributeValue("name");
}
public CMLPeakList getPeakList() {
return (CMLPeakList) tableViewer.getInput();
}
private void updateStatus(String message) {
setErrorMessage(message);
setPageComplete(message == null);
}
/**
* Ensures that spectrum type and peaks are given.
*/
private void dialogChanged() {
CMLPeakList peaks = getPeakList();
String spectype = getSpectrumType();
if (spectype==null || spectype.length() == 0 || spectype.equals( "unknown" )) {
updateStatus("Spectrum type must be specified");
return;
}
if(peakdone){
updateStatus( null );
return;
}
if (peaks == null) {
updateStatus("At least one peak must be given");
return;
}else{
int realpeakcount=0;
Iterator<CMLPeak> it = peaks.getPeakElements().iterator();
while (it.hasNext()) {
CMLPeak peak = it.next();
if (peak.getXValue() != 0) {
realpeakcount++;
}
}
if(realpeakcount==0){
updateStatus("At least one peak must be given");
return;
}
}
updateStatus(null);
}
/**
* This class demonstrates how to create your own dialog classes. It allows users
* to input a String
*/
public class InputDialog extends Dialog {
private String message;
private String input;
private Text septext=null;
private NewSpectrumDetailWizardPage wizardpage;
/**
* InputDialog constructor
*
* @param parent the parent
*/
public InputDialog(Shell parent) {
// Let users override the default styles
super(parent, SWT.DIALOG_TRIM | SWT.APPLICATION_MODAL);
setText("Input CSV");
setMessage("Please enter CSV text:");
}
/**
* Gets the message
*
* @return String
*/
public String getMessage() {
return message;
}
/**
* Sets the message
*
* @param message the new message
*/
public void setMessage(String message) {
this.message = message;
}
/**
* Gets the input
*
* @return String
*/
public String getInput() {
return input;
}
/**
* Sets the input
*
* @param input the new input
*/
public void setInput(String input) {
this.input = input;
}
/**
* Opens the dialog and returns the input
*
* @return String
*/
public String open(NewSpectrumDetailWizardPage wizardpage) {
// Create the dialog window
this.wizardpage = wizardpage;
Shell shell = new Shell(getParent(), getStyle());
shell.setText(getText());
createContents(shell);
shell.pack();
shell.open();
Display display = getParent().getDisplay();
while (!shell.isDisposed()) {
if (!display.readAndDispatch()) {
display.sleep();
}
}
// Return the entered value, or null
return input;
}
/**
* Creates the dialog's contents
*
* @param shell the dialog window
*/
private void createContents(final Shell shell) {
shell.setLayout(new GridLayout(2, true));
// Show the message
Label label = new Label(shell, SWT.NONE);
label.setText(message);
GridData data = new GridData();
data.horizontalSpan = 2;
label.setLayoutData(data);
// Display the input box
final Text text = new Text(shell, SWT.BORDER | SWT.MULTI | SWT.V_SCROLL);
text.setSize( 100,200 );
data = new GridData(GridData.FILL_HORIZONTAL);
data.horizontalSpan = 2;
data.minimumHeight=200;
data.heightHint=200;
text.setLayoutData(data);
final Label seplabel = new Label(shell, SWT.NONE);
seplabel.setText( "Enter your separator:" );
data = new GridData();
data.horizontalSpan = 2;
seplabel.setLayoutData(data);
// Display the input box
septext = new Text(shell, SWT.BORDER | SWT.MULTI);
septext.setText( "," );
data = new GridData(GridData.FILL_HORIZONTAL);
data.horizontalSpan = 2;
septext.setLayoutData(data);
// Create the cancel button and add a handler
// so that pressing it will set input to null
Button cancel = new Button(shell, SWT.PUSH);
cancel.setText("Cancel");
data = new GridData(GridData.FILL_HORIZONTAL);
cancel.setLayoutData(data);
cancel.addSelectionListener(new SelectionAdapter() {
public void widgetSelected(SelectionEvent event) {
input = null;
shell.close();
}
});
// Create the OK button and add a handler
// so that pressing it will set input
// to the entered value
Button ok = new Button(shell, SWT.PUSH);
ok.setText("OK");
data = new GridData(GridData.FILL_HORIZONTAL);
ok.setLayoutData(data);
ok.addSelectionListener(new SelectionAdapter() {
public void widgetSelected(SelectionEvent event) {
input = text.getText();
wizardpage.separator=septext.getText();
shell.close();
}
});
// Set the OK button as the default, so
// user can type input and press Enter
// to dismiss
shell.setDefaultButton(ok);
}
}
}