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Merge pull request #886 from Mailaender/undo
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Added undo/redo for peak/scan deletion
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@eselmeister
eselmeister authored Jan 28, 2022
2 parents 6588eda + 8789077 commit a555d71
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Showing 42 changed files with 359 additions and 1,792 deletions.
4 changes: 2 additions & 2 deletions ...am.filter/src/org/eclipse/chemclipse/chromatogram/filter/impl/AbstractTransferFilter.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2019 Lablicate GmbH.
* Copyright (c) 2019, 2022 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -43,7 +43,7 @@ protected List<IScan> extractIdentifiedScans(IChromatogramSelection chromatogram
List<IScan> identifiedScans = new ArrayList<>();
for(int i = startScan; i <= stopScan; i++) {
IScan scan = chromatogram.getScan(i);
if(scan.getTargets().size() > 0) {
if(!scan.getTargets().isEmpty()) {
identifiedScans.add(scan);
}
}
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8 changes: 4 additions & 4 deletions ...s/src/org/eclipse/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/Activator.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2008, 2018 Lablicate GmbH.
* Copyright (c) 2008, 2022 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -11,7 +11,6 @@
*******************************************************************************/
package org.eclipse.chemclipse.chromatogram.msd.peak.detector.supplier.amdis;

import org.eclipse.chemclipse.model.versioning.PathHelper;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;

Expand All @@ -28,6 +27,7 @@ public static BundleContext getContext() {
* (non-Javadoc)
* @see org.osgi.framework.BundleActivator#start(org.osgi.framework.BundleContext)
*/
@Override
public void start(BundleContext bundleContext) throws Exception {

Activator.context = bundleContext;
Expand All @@ -37,9 +37,9 @@ public void start(BundleContext bundleContext) throws Exception {
* (non-Javadoc)
* @see org.osgi.framework.BundleActivator#stop(org.osgi.framework.BundleContext)
*/
@Override
public void stop(BundleContext bundleContext) throws Exception {

PathHelper.cleanStoragePath();
Activator.context = null;
}
}
}
3 changes: 1 addition & 2 deletions chemclipse/plugins/org.eclipse.chemclipse.model/META-INF/MANIFEST.MF
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Expand Up @@ -52,8 +52,7 @@ Export-Package: org.eclipse.chemclipse.model.baseline,
org.eclipse.chemclipse.model.targets,
org.eclipse.chemclipse.model.traces,
org.eclipse.chemclipse.model.types,
org.eclipse.chemclipse.model.updates,
org.eclipse.chemclipse.model.versioning
org.eclipse.chemclipse.model.updates
Import-Package: org.osgi.service.component.annotations;version="1.2.0"
Service-Component: OSGI-INF/org.eclipse.chemclipse.model.supplier.IMeasurementFilterProcessTypeSupplier.xml,
OSGI-INF/org.eclipse.chemclipse.model.supplier.IPeakFilterProcessTypeSupplier.xml
259 changes: 0 additions & 259 deletions ....eclipse.chemclipse.model/src/org/eclipse/chemclipse/model/core/AbstractChromatogram.java
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Expand Up @@ -12,15 +12,7 @@
*******************************************************************************/
package org.eclipse.chemclipse.model.core;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
Expand All @@ -43,21 +35,14 @@
import org.eclipse.chemclipse.model.implementation.TripleQuadMethod;
import org.eclipse.chemclipse.model.notifier.IChromatogramSelectionUpdateNotifier;
import org.eclipse.chemclipse.model.preferences.PreferenceSupplier;
import org.eclipse.chemclipse.model.processor.IChromatogramProcessor;
import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
import org.eclipse.chemclipse.model.signals.ITotalScanSignalExtractor;
import org.eclipse.chemclipse.model.signals.ITotalScanSignals;
import org.eclipse.chemclipse.model.signals.TotalScanSignalExtractor;
import org.eclipse.chemclipse.model.support.IAnalysisSegment;
import org.eclipse.chemclipse.model.support.IScanRange;
import org.eclipse.chemclipse.model.updates.IChromatogramUpdateListener;
import org.eclipse.chemclipse.model.versioning.IVersionManagement;
import org.eclipse.chemclipse.model.versioning.VersionManagement;
import org.eclipse.chemclipse.support.history.EditHistory;
import org.eclipse.chemclipse.support.history.EditInformation;
import org.eclipse.chemclipse.support.history.IEditHistory;
import org.eclipse.chemclipse.support.preferences.SupportPreferences;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.ISafeRunnable;
import org.eclipse.core.runtime.Platform;
import org.eclipse.core.runtime.SafeRunner;
Expand Down Expand Up @@ -85,10 +70,6 @@ public abstract class AbstractChromatogram<T extends IPeak> extends AbstractMeas
* has to update itself.
*/
private final List<IChromatogramUpdateListener> updateSupport;
/*
* The version management handles the temporary files and revision names.
*/
private final IVersionManagement versionManagement;
/*
* EditHistory stores all information about the edit operations processed on
* the chromatogram.
Expand Down Expand Up @@ -133,7 +114,6 @@ public abstract class AbstractChromatogram<T extends IPeak> extends AbstractMeas
public AbstractChromatogram() {

updateSupport = new ArrayList<IChromatogramUpdateListener>(5);
versionManagement = new VersionManagement();
editHistory = new EditHistory();
baselineModelMap.put(DEFAULT_BASELINE_ID, new BaselineModel(this));
referencedChromatograms = new ArrayList<IChromatogram<?>>();
Expand Down Expand Up @@ -206,18 +186,6 @@ public void setScanInterval(float scansPerSecond) {
}
}

@Override
public String getIdentifier() {

return versionManagement.getChromatogramIdentifier();
}

@Override
public File getStorageDirectory() {

return versionManagement.getStorageDirectory();
}

@Override
public File getFile() {

Expand Down Expand Up @@ -495,125 +463,13 @@ public void replaceAllScans(List<IScan> scans) {
list.addAll(scans);
}

@Override
public boolean isUndoable() {

return SupportPreferences.isUndoable();
}

// TODO Junit
@Override
public boolean canUndo() {

boolean result = false;
if(isUndoable() && versionManagement.getRevision() > 0) {
result = true;
}
return result;
}

// TODO Junit
@Override
public boolean canRedo() {

boolean result = false;
if(isUndoable() && versionManagement.getNextScanRevision().exists()) {
result = true;
}
return result;
}

@Override
public void hibernate() {

if(!isUndoable()) {
return;
}
File file = versionManagement.getActualScanRevision();
writeSerializedChromatogram(file);
// TODO set scans = null;
}

@Override
public void wakeUp() {

if(!isUndoable()) {
return;
}
File file = versionManagement.getActualScanRevision();
if(file.exists()) {
readSerializedChromatogram(file);
}
}

@Override
public void writeSerializedChromatogram(File file) {

assert file != null : getClass().getName() + " writeSerializedFile: The file must not be null.";
ObjectOutputStream outputStream = null;
try {
outputStream = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(file)));
outputStream.writeObject(getScans());
} catch(FileNotFoundException e) {
logger.warn(e);
} catch(IOException e) {
logger.warn(e);
} finally {
if(outputStream != null) {
try {
outputStream.close();
} catch(IOException e) {
logger.warn(e);
}
}
}
}

@SuppressWarnings("unchecked")
@Override
public void readSerializedChromatogram(File file) {

assert file != null : getClass().getName() + " readSerializedFile: The file must not be null.";
ObjectInputStream inputStream = null;
Object inputObject;
try {
inputStream = new ObjectInputStream(new BufferedInputStream(new FileInputStream(file)));
inputObject = inputStream.readObject();
if(inputObject instanceof ArrayList) {
List<IScan> scans = getScans();
scans.clear();
scans.addAll((ArrayList<IScan>)inputObject);
}
} catch(FileNotFoundException e) {
logger.warn(e);
} catch(IOException e) {
logger.warn(e);
} catch(ClassNotFoundException e) {
logger.warn(e);
} finally {
if(inputStream != null) {
try {
inputStream.close();
} catch(IOException e) {
logger.warn(e);
}
}
}
}

@Override
@SuppressWarnings({"rawtypes", "unchecked"})
public Object getAdapter(Class adapter) {

return Platform.getAdapterManager().getAdapter(this, adapter);
}

@Override
public IVersionManagement getVersionManagement() {

return versionManagement;
}

@Override
public IEditHistory getEditHistory() {

Expand Down Expand Up @@ -884,121 +740,6 @@ public void removeAllChromatogramIntegrationEntries() {
chromatogramIntegrationEntries.clear();
}

@Override
public void doOperation(IChromatogramProcessor chromatogramProcessor, IProgressMonitor monitor) {

boolean isUndoable = isUndoable();
doOperation(chromatogramProcessor, isUndoable, true, monitor);
}

@Override
public void doOperation(IChromatogramProcessor chromatogramProcessor, boolean isUndoable, boolean isDataModifying, IProgressMonitor monitor) {

/*
* Return if the chromatogram modifier instance is null.<br/> Set the
* monitor to the state done.
*/
if(chromatogramProcessor == null) {
return;
}
/*
* Test, that chromatogram selection is != null and the given
* chromatogram is == this chromatogram.
*/
@SuppressWarnings("rawtypes")
final IChromatogramSelection chromatogramSelection = chromatogramProcessor.getChromatogramSelection();
if(chromatogramSelection != null && chromatogramSelection.getChromatogram() == this) {
File file;
/*
* Save the first revision if neccessary.
*/
if(isUndoable) {
if(getVersionManagement().isBaseRevision()) {
monitor.subTask("Save the actual state.");
file = getVersionManagement().getActualScanRevision();
writeSerializedChromatogram(file);
}
}
/*
* Remove all detected peaks and targets and the baseline.
*/
if(isDataModifying) {
removeAllPeaks();
getTargets().clear();
removeAllMeasurementResults();
IBaselineModel baselineModel = getBaselineModel();
if(baselineModel != null) {
baselineModel.removeBaseline();
}
}
/*
* Perform the operation.
*/
chromatogramProcessor.execute(monitor);
/*
* Save the actual state.
*/
if(isUndoable) {
monitor.subTask("Save the undoable state.");
getVersionManagement().doOperation();
file = getVersionManagement().getActualScanRevision();
writeSerializedChromatogram(file);
}
monitor.subTask("Edit the history entries.");
getEditHistory().add(new EditInformation(chromatogramProcessor.getDescription()));
/*
* Set the S/N recalculate flag.
*/
chromatogramSelection.getChromatogram().recalculateTheNoiseFactor();
//
fireUpdate(chromatogramSelection);
}
}

// TODO Junit
@SuppressWarnings("rawtypes")
@Override
public void redoOperation(IChromatogramSelection chromatogramSelection) {

if(chromatogramSelection != null && chromatogramSelection.getChromatogram() == this) {
/*
* Redo
*/
if(isUndoable()) {
File file = getVersionManagement().getNextScanRevision();
if(file.exists()) {
readSerializedChromatogram(file);
getVersionManagement().redoOperation();
getEditHistory().add(new EditInformation("redo operation performed"));
}
//
fireUpdate(chromatogramSelection);
}
}
}

// TODO Junit
@SuppressWarnings("rawtypes")
@Override
public void undoOperation(IChromatogramSelection chromatogramSelection) {

if(chromatogramSelection != null && chromatogramSelection.getChromatogram() == this) {
/*
* Undo
*/
if(isUndoable()) {
File file = getVersionManagement().getPreviousScanRevision();
if(file.exists()) {
readSerializedChromatogram(file);
getVersionManagement().undoOperation();
getEditHistory().add(new EditInformation("undo operation performed"));
}
//
fireUpdate(chromatogramSelection);
}
}
}

@Override
public void setUnloaded() {

Expand Down
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