Skip to content

Simplify calibration file wizard #2754

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
eselmeister merged 1 commit into from
Feb 27, 2026
Merged

Simplify calibration file wizard #2754

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
58 changes: 42 additions & 16 deletions ...ipse/chromatogram/xxd/calculator/supplier/amdiscalri/ui/wizards/PageCalibrationTable.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2016, 2025 Lablicate GmbH.
* Copyright (c) 2016, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,9 +12,12 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.ui.wizards;

import java.io.File;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;

import org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.impl.CalibrationFile;
import org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.impl.RetentionIndexExtractor;
import org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.io.StandardsReader;
import org.eclipse.chemclipse.model.columns.IRetentionIndexEntry;
Expand All @@ -35,14 +38,17 @@
import org.eclipse.swt.layout.GridLayout;
import org.eclipse.swt.widgets.Button;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.FileDialog;
import org.eclipse.swt.widgets.Label;
import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Table;
import org.eclipse.swt.widgets.TableItem;
import org.eclipse.swt.widgets.Text;

public class PageCalibrationTable extends AbstractExtendedWizardPage {

private RetentionIndexWizardElements wizardElements;

private Button checkBoxValidateRetentionIndices;
private ChromatogramPeakChart chromatogramPeakChart;
private ExtendedRetentionIndexListUI extendedRetentionIndexTableViewerUI;

Expand All @@ -57,7 +63,7 @@ public PageCalibrationTable(RetentionIndexWizardElements wizardElements) {
@Override
public boolean canFinish() {

return wizardElements.isRetentionIndexDataValidated();
return wizardElements.getExportFilePath() != null;
}

@Override
Expand Down Expand Up @@ -90,31 +96,50 @@ public void createControl(Composite parent) {
composite.setBackgroundMode(SWT.INHERIT_DEFAULT);
composite.setLayout(new GridLayout(1, false));

createCheckBoxField(composite);
createChromatogramField(composite);
createTableField(composite);
createCalibrationFileField(composite);

validateSelection();
setControl(composite);
}

private void createCheckBoxField(Composite composite) {
private void createCalibrationFileField(Composite composite) {

checkBoxValidateRetentionIndices = new Button(composite, SWT.CHECK);
checkBoxValidateRetentionIndices.setText("Retention indices are valid.");
checkBoxValidateRetentionIndices.setSelection(false);
checkBoxValidateRetentionIndices.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));
checkBoxValidateRetentionIndices.addSelectionListener(new SelectionAdapter() {
Composite parent = new Composite(composite, SWT.NONE);
parent.setLayoutData(new GridData(GridData.FILL_BOTH));
parent.setLayout(new GridLayout(3, false));

@Override
public void widgetSelected(SelectionEvent e) {
Label labelFile = new Label(parent, SWT.NONE);
labelFile.setText("Save as:");

Text fileText = new Text(parent, SWT.BORDER);
fileText.setLayoutData(new GridData(GridData.FILL_HORIZONTAL));

wizardElements.setRetentionIndexDataIsValidated(checkBoxValidateRetentionIndices.getSelection());
validateSelection();
Button buttonBrowse = new Button(parent, SWT.PUSH);
buttonBrowse.setText("Browse...");

buttonBrowse.addListener(SWT.Selection, e -> {
String selected = openFileDialog(getShell());
if(selected != null) {
fileText.setText(selected);
wizardElements.setExportFilePath(new File(selected));
}
validateSelection();
});
}

private String openFileDialog(Shell shell) {

FileDialog fileDialog = new FileDialog(shell, SWT.SAVE);
fileDialog.setOverwrite(true);
fileDialog.setText("Retention Index");
fileDialog.setFileName("RetentionIndices_" + new Date().getTime() + CalibrationFile.FILTER_EXTENSION);
fileDialog.setFilterExtensions(CalibrationFile.FILTER_EXTENSION);
fileDialog.setFilterNames(CalibrationFile.FILTER_NAME);
return fileDialog.open();
}

private void createChromatogramField(Composite composite) {

Composite parent = new Composite(composite, SWT.NONE);
Expand Down Expand Up @@ -177,8 +202,9 @@ private IPeak getSelectedPeak(IChromatogram chromatogram, int retentionTime) {
private void validateSelection() {

String message = null;
if(!checkBoxValidateRetentionIndices.getSelection()) {
message = "Please verify the data and activate the check box.";
File file = wizardElements.getExportFilePath();
if(file == null) {
message = "Please select a file location.";
}
/*
* Updates the status
Expand Down
14 changes: 7 additions & 7 deletions ...omatogram/xxd/calculator/supplier/amdiscalri/ui/wizards/RetentionIndexWizardElements.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2016, 2025 Lablicate GmbH.
* Copyright (c) 2016, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -12,6 +12,7 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.ui.wizards;

import java.io.File;
import java.util.ArrayList;
import java.util.List;

Expand All @@ -31,12 +32,11 @@ public class RetentionIndexWizardElements extends ChromatogramWizardElements {
private String startIndexName = "";
private String stopIndexName = "";
private boolean useAlreadyDetectedPeaks = false;
private File calibrationFile;

private IChromatogramSelection chromatogramSelection;
private ISeparationColumnIndices separationColumnIndices = new SeparationColumnIndices();

private boolean retentionIndexDataIsValidated = false;

public List<String> getSelectedIndices() {

List<String> selectedIndices = new ArrayList<>();
Expand Down Expand Up @@ -161,13 +161,13 @@ public void setSeparationColumnIndices(ISeparationColumnIndices separationColumn
this.separationColumnIndices = separationColumnIndices;
}

public boolean isRetentionIndexDataValidated() {
public File getExportFilePath() {

return retentionIndexDataIsValidated;
return calibrationFile;
}

public void setRetentionIndexDataIsValidated(boolean retentionIndexDataIsValidated) {
public void setExportFilePath(File calibrationFile) {

this.retentionIndexDataIsValidated = retentionIndexDataIsValidated;
this.calibrationFile = calibrationFile;
}
}
47 changes: 27 additions & 20 deletions ...atogram/xxd/calculator/supplier/amdiscalri/ui/wizards/WizardCreateRetentionIndexFile.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2016, 2025 Lablicate GmbH.
* Copyright (c) 2016, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand All @@ -14,25 +14,28 @@
package org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.ui.wizards;

import java.io.File;
import java.util.Date;

import org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.impl.CalibrationFile;
import org.eclipse.chemclipse.chromatogram.xxd.calculator.supplier.amdiscalri.io.CalibrationFileWriter;
import org.eclipse.chemclipse.csd.converter.chromatogram.ChromatogramConverterCSD;
import org.eclipse.chemclipse.csd.model.core.IChromatogramCSD;
import org.eclipse.chemclipse.csd.model.core.selection.IChromatogramSelectionCSD;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
import org.eclipse.chemclipse.model.types.DataType;
import org.eclipse.chemclipse.msd.converter.chromatogram.ChromatogramConverterMSD;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.selection.IChromatogramSelectionMSD;
import org.eclipse.chemclipse.support.ui.wizards.AbstractFileWizard;
import org.eclipse.chemclipse.support.l10n.SupportMessages;
import org.eclipse.chemclipse.support.ui.wizards.AbstractWizard;
import org.eclipse.chemclipse.ux.extension.xxd.ui.Activator;
import org.eclipse.chemclipse.ux.extension.xxd.ui.part.support.SupplierEditorSupport;
import org.eclipse.chemclipse.xxd.converter.supplier.ocx.versions.VersionConstants;
import org.eclipse.core.resources.IFile;
import org.eclipse.core.runtime.CoreException;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.jface.wizard.IWizardPage;

public class WizardCreateRetentionIndexFile extends AbstractFileWizard {
public class WizardCreateRetentionIndexFile extends AbstractWizard {

/**
* Preferred size of the wizard.
Expand All @@ -42,9 +45,7 @@ public class WizardCreateRetentionIndexFile extends AbstractFileWizard {

private static final Logger logger = Logger.getLogger(WizardCreateRetentionIndexFile.class);

private RetentionIndexWizardElements wizardElements = new RetentionIndexWizardElements();

private static final String CALIBRATION_FILE_EXTENSION = ".cal";
private RetentionIndexWizardElements wizardElements;

private PageCalibrationSettings pageCalibrationSettings;
private PagePeakSelection pagePeakSelection;
Expand All @@ -53,7 +54,8 @@ public class WizardCreateRetentionIndexFile extends AbstractFileWizard {

public WizardCreateRetentionIndexFile() {

super("RetentionIndices_" + new Date().getTime(), CALIBRATION_FILE_EXTENSION);
super(new RetentionIndexWizardElements());
this.wizardElements = (RetentionIndexWizardElements)getWizardElements();
}

@Override
Expand Down Expand Up @@ -107,23 +109,23 @@ public boolean canFinish() {
canFinish = pagePeakAssignment.canFinish();
}
if(canFinish) {
canFinish = wizardElements.isRetentionIndexDataValidated();
canFinish = wizardElements.getExportFilePath() != null;
}
return canFinish;
}

@Override
public void doFinish(IProgressMonitor monitor) throws CoreException {

File calibrationFile = wizardElements.getExportFilePath();

monitor.beginTask("Create Chromatogram Evaluation", IProgressMonitor.UNKNOWN);
final IFile file = super.prepareProject(monitor);
try {
/*
* Calibration File.
*/
File calibrationFile = file.getLocation().toFile();
if(!calibrationFile.getAbsolutePath().endsWith(CALIBRATION_FILE_EXTENSION)) {
calibrationFile = new File(calibrationFile.getAbsolutePath() + CALIBRATION_FILE_EXTENSION);
if(!calibrationFile.getAbsolutePath().endsWith(CalibrationFile.FILTER_EXTENSION)) {
calibrationFile = new File(calibrationFile.getAbsolutePath() + CalibrationFile.FILTER_EXTENSION);
}
CalibrationFileWriter calibrationFileWriter = new CalibrationFileWriter();
calibrationFileWriter.write(calibrationFile, wizardElements.getSeparationColumnIndices());
Expand All @@ -132,7 +134,7 @@ public void doFinish(IProgressMonitor monitor) throws CoreException {
* Export the chromatogram.
*/
String path = calibrationFile.getAbsolutePath();
File chromatogramFile = new File(path.substring(0, path.length() - CALIBRATION_FILE_EXTENSION.length()) + VersionConstants.FILE_EXTENSION_CHROMATOGRAM);
File chromatogramFile = new File(path.substring(0, path.length() - CalibrationFile.FILTER_EXTENSION.length()) + VersionConstants.FILE_EXTENSION_CHROMATOGRAM);
IChromatogramSelection chromatogramSelection = wizardElements.getChromatogramSelection();
if(wizardElements.isUseMassSpectrometryData()) {
if(chromatogramSelection instanceof IChromatogramSelectionMSD chromatogramSelectionMSD) {
Expand All @@ -148,10 +150,15 @@ public void doFinish(IProgressMonitor monitor) throws CoreException {
} catch(Exception e) {
logger.warn(e);
}
/*
* Refresh
*/
super.refreshWorkspace(monitor);
super.runOpenEditor(file, monitor);
runOpenEditor(calibrationFile, monitor);
}

private void runOpenEditor(File file, IProgressMonitor monitor) {

monitor.subTask(SupportMessages.taskOpenEditor);
SupplierEditorSupport supplierEditorSupport = new SupplierEditorSupport(DataType.CAL, () -> Activator.getDefault().getEclipseContext());
if(!supplierEditorSupport.openEditor(file)) {
logger.warn("Failed to open editor.");
}
}
}
4 changes: 2 additions & 2 deletions ...e.chemclipse.support.ui/src/org/eclipse/chemclipse/support/ui/wizards/AbstractWizard.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2015, 2025 Lablicate GmbH.
* Copyright (c) 2015, 2026 Lablicate GmbH.
*
* This program and the accompanying materials are made
* available under the terms of the Eclipse Public License 2.0
Expand Down Expand Up @@ -35,7 +35,7 @@ public abstract class AbstractWizard extends Wizard implements IFileWizard {
private IWizardElements wizardElements;
private Set<IExtendedWizardPage> wizardPages;

public AbstractWizard(IWizardElements wizardElements) {
protected AbstractWizard(IWizardElements wizardElements) {

super();
setNeedsProgressMonitor(true);
Expand Down