Problems could occur when trying to parse large CDF files > 1 GB. The current implementation shall be optimized to parse the data in forced nominal modus.

This is useful for simple scenarios where no special identification is performed.

Sorting the Peak/Scan List by clicking on the column header does not work propertly for the column Width and Name.
The latter only works as aspected if all names are filled.

The ion signals extractor crashes, when the extracted chromatogram range contains empty scans. Empty scans means, that no m/z value is stored, e.g. when the detector is turned to off.

A filter is available "Remove Empty Scans". This should be used in case one assumes that empty scans are contained.

Anyways, the signal extractor shall be fixed.

Selecting a reference chromatogram is done by its filename.
The resulting entries in the drop down menu in the Chromatogram Editor are showing the data name. This is a bit confusing.

Interestingly, the data name is not present in OpenChrom anywhere else as far I can see.
Looking in the header data by toggling the overview mode shows the Data Name in raw files from Chemstation files, but not in .odb files.
Also the date (of measurement) is the date of creating the file in .odb header data.

The X and Y axis is not updated correctly after setting a peak manually.

The SOPA https://www.ebi.ac.uk/seqdb/confluence/display/WEBSERVICES/EMBL-EBI+Web+Services might be promising. The API seems to be a bit more modern compared to the traditional queued NCBI web blast. I hope for better feedback of remaining time and structured data as return, which would make crafting good UI easier.

It appears that processing steps fail after the "Chromatogram Baseline Subtract Filter" has been applied.

Everything appears to run OK connecting with the NIST DB as I have highlighted peaks in my peak list and run the identifier command. I get a message with a green status bar that it may take a few minutes. No errors are thrown. However the targets view doesn't get populated with any compound ids.

Also it looks like some .HLM files are generated in the NIST directory when I run the program.

I'm using OpenChrom Community Edition OpenChrom Community Edition (Dalton) 1.3.0.201808081331

And NIST version 2.3

Any ideas what I am missing?

currently only VV and BB are supported with one fixed algorithm. It would be good if the user could select more or even alternative Detector Types for different Use-Cases.

It is a very nice feature to combine peaks with the same name or CAS.

But this does not seems to be for peaks with close retention times only.
It also combines peaks with the same name, retention time difference of more than 4 minutes and with other peaks in between.
This leads to loosing peaks, since all peaks with sooner retention time are not present in the exported list.

A profile PDF report to list the substances and Area% values shall be added.

The template peak detector is broken under Linux currently. The service is null:

` public static Collection<TemplatePeakDetector<?>> getDetectors() {

	ProcessorFactory service = serviceTracker.getService();
	if(service != null) {
		return service.getProcessors(ProcessorFactory.genericClass(TemplatePeakDetector.class), (always, ever) -> true);
	}
	return Collections.emptyList();
}`

Some errors occur on the comand line:

`!ENTRY org.apache.felix.scr 4 0 2020-02-10 14:16:40.931
!MESSAGE Circular reference detected trying to get service {org.eclipse.chemclipse.processing.ProcessorFactory}={service.id=218, service.bundleid=422, service.scope=bundle, component.name=org.eclipse.chemclipse.processing.internal.OSGiFilterFactory, component.id=171}
stack of references: ServiceReference: {org.eclipse.chemclipse.processing.ProcessorFactory}={service.id=218, service.bundleid=422, service.scope=bundle, component.name=org.eclipse.chemclipse.processing.internal.OSGiFilterFactory, component.id=171}
ServiceReference: {org.eclipse.chemclipse.msd.model.detector.TemplatePeakDetector, org.eclipse.chemclipse.processing.detector.Detector, org.eclipse.chemclipse.processing.Processor}={service.id=71, service.bundleid=177, service.scope=bundle, component.name=net.openchrom.xxd.process.supplier.templates.detector.DefaultTemplatePeakDetector, component.id=22}

!STACK 0
java.lang.Exception: stack trace
at org.apache.felix.scr.impl.ComponentRegistry.enterCreate(ComponentRegistry.java:467)
at org.apache.felix.scr.impl.BundleComponentActivator.enterCreate(BundleComponentActivator.java:809)
at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:806)
at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse$1.run(ServiceFactoryUse.java:212)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse.factoryGetService(ServiceFactoryUse.java:210)
at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse.getService(ServiceFactoryUse.java:111)
at org.eclipse.osgi.internal.serviceregistry.ServiceConsumer$2.getService(ServiceConsumer.java:45)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.getService(ServiceRegistrationImpl.java:524)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.getService(ServiceRegistry.java:461)
at org.eclipse.osgi.internal.framework.BundleContextImpl.getService(BundleContextImpl.java:624)
at org.osgi.util.tracker.ServiceTracker.addingService(ServiceTracker.java:416)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:943)
at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:1)
at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
at org.osgi.util.tracker.AbstractTracked.trackInitial(AbstractTracked.java:183)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:321)
at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:264)
at net.openchrom.xxd.process.supplier.templates.Activator.start(Activator.java:43)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:779)
at org.eclipse.osgi.internal.framework.BundleContextImpl$3.run(BundleContextImpl.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:772)
at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:729)
at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1002)
at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:354)
at org.eclipse.osgi.container.Module.doStart(Module.java:581)
at org.eclipse.osgi.container.Module.start(Module.java:449)
at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:468)
at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:114)
at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:505)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:328)
at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:392)
at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:470)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:419)
at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:411)
at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:150)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:609)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.initDependencyManagers(AbstractComponentManager.java:992)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.collectDependencies(AbstractComponentManager.java:1019)
at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:860)
at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:824)
at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse$1.run(ServiceFactoryUse.java:212)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse.factoryGetService(ServiceFactoryUse.java:210)
at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse.getService(ServiceFactoryUse.java:111)
at org.eclipse.osgi.internal.serviceregistry.ServiceConsumer$2.getService(ServiceConsumer.java:45)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.getService(ServiceRegistrationImpl.java:524)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.getService(ServiceRegistry.java:461)
at org.eclipse.osgi.internal.framework.BundleContextImpl.getService(BundleContextImpl.java:624)
at org.apache.felix.scr.impl.manager.SingleRefPair.getServiceObject(SingleRefPair.java:72)
at org.apache.felix.scr.impl.inject.BindMethod.getServiceObject(BindMethod.java:651)
at org.apache.felix.scr.impl.manager.DependencyManager.getServiceObject(DependencyManager.java:2206)
at org.apache.felix.scr.impl.manager.DependencyManager$MultipleDynamicCustomizer.prebind(DependencyManager.java:403)
at org.apache.felix.scr.impl.manager.DependencyManager.prebind(DependencyManager.java:1520)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.collectDependencies(AbstractComponentManager.java:1022)
at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:860)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:755)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.enableInternal(AbstractComponentManager.java:675)
at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:430)
at org.apache.felix.scr.impl.manager.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:657)
at org.apache.felix.scr.impl.BundleComponentActivator.initialEnable(BundleComponentActivator.java:341)
at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:387)
at org.apache.felix.scr.impl.Activator.access$200(Activator.java:52)
at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:262)
at org.apache.felix.scr.impl.AbstractExtender.createExtension(AbstractExtender.java:196)
at org.apache.felix.scr.impl.AbstractExtender.modifiedBundle(AbstractExtender.java:169)
at org.apache.felix.scr.impl.AbstractExtender.addingBundle(AbstractExtender.java:139)
at org.apache.felix.scr.impl.AbstractExtender.addingBundle(AbstractExtender.java:49)
at org.osgi.util.tracker.BundleTracker$Tracked.customizerAdding(BundleTracker.java:475)
at org.osgi.util.tracker.BundleTracker$Tracked.customizerAdding(BundleTracker.java:1)
at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:256)
at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:229)
at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:450)
at org.eclipse.osgi.internal.framework.BundleContextImpl.dispatchEvent(BundleContextImpl.java:908)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
at org.eclipse.osgi.internal.framework.EquinoxEventPublisher.publishBundleEventPrivileged(EquinoxEventPublisher.java:230)
at org.eclipse.osgi.internal.framework.EquinoxEventPublisher.publishBundleEvent(EquinoxEventPublisher.java:137)
at org.eclipse.osgi.internal.framework.EquinoxEventPublisher.publishBundleEvent(EquinoxEventPublisher.java:129)
at org.eclipse.osgi.internal.framework.EquinoxContainerAdaptor.publishModuleEvent(EquinoxContainerAdaptor.java:191)
at org.eclipse.osgi.container.Module.publishEvent(Module.java:476)
at org.eclipse.osgi.container.Module.start(Module.java:467)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1682)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.incStartLevel(ModuleContainer.java:1661)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.doContainerStartLevel(ModuleContainer.java:1624)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1555)
at org.eclipse.osgi.container.ModuleContainer$ContainerStartLevel.dispatchEvent(ModuleContainer.java:1)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:340)`

The MoleculeView is not updated by selecting a Peak in the Chromatogram Editor.

Should be easy with BioJava.

Add a UI method to review peaks and identifications.

Due to the following bug
https://bugs.eclipse.org/bugs/show_bug.cgi?id=559148
OpenChrom must currently stick to 1.5.1 Tycho version. As soon as a new Tycho version is available, the workaround could be removed.

The created file with filename {chromatogram_name}{extension} misses the . between name und fileextension.

Other exports with this kind of filename creation contain the .

A new EJML version with package version 0.38.x is available we should check if we can upgrade the NMR module to use this version as it includes some bugfixes and improvements.

@alexstark4 please have a look at this @lorenzgerber might can help with question regarding changed class/package names.

Create a template report. The template defines, which peaks shall be reported.

Feature request for options to

• classify peaks only if they donot have a classifier yet
• override existing classifiers
• classify peaks only if they have a name

Since in the current version .* leads to the behaviour of the latter request, these are all minor issues.

After peak identification via NIST14, entries in the Targets View does not contain the Mol Weight which would be usefull with respect to the parent ion.

Also in some cases the CAS number is 0-00-0.
I guess this leads to no creation of SMILES code and therefore no molecule structure is shown.
Examples are:

• Heneicosyl trifluoroacetate
• E-15-Heptadecenal
• Oxime-, methoxy-phenyl-_

Saving MSL files after modification does not lead to updated files.

"Save as" works.

and the original repository https://github.com/OpenChrom/GeneIdent is archived so I can't work with the issues as well.

I tried to export the OpenChrom .product file and I get:

 Cannot complete the install because one or more required items could not be found.
 Software being installed: OpenChrom Analytics Edition (Lawrence) 1.4.0.201910161021 (net.openchrom.rcp.compilation.community.product.id 1.4.0.201910161021)
 Missing requirement: CDK Support 1.4.0.201909170105 (net.openchrom.chromatogram.msd.identifier.supplier.cdk.feature.feature.group 1.4.0.201909170105) requires 'net.openchrom.thirdpartylibraries.cdk.feature.feature.group 0.0.0' but it could not be found
 Cannot satisfy dependency:
 Cannot satisfy dependency:

I follow the QuickStart in developer manual，but there's still appear many compile error .
Does any where I got wrong about the configuration？
@laeubi

Show the results in a table similar to the NCBI BLAST web interface.

I asked a question on stackoverflow but don't have the reputation yet to create a new tag for openchrom. Would someone who does have enough reputation do this?

Put the DNA one letter code above the peak including quality metrics. Should be possible with the greatly enhanced SWT Chart library from the Eclipse Advanced Visualization Project.

Zooming into m/z specta in the Comparison Scan Mode window may lead to loss of single mass bars.
It occures when the zoom does not include the maximum value of the mass bar. Then, the m/z value does not exist in the zoomed view anymore.

Currently the User is only presented with a single textfield and some basic regex-validation.
Due to the complex setup with many values this is not very User-Friendly as it is hard to guess correct settings if something gas gone wrong in-between.

Large molecule structures are cut-off.

Maximising the window loads to total crash of the Molecule View. No structures are printed until restart of the software.

This leads to a wrong molecular structure in the Molecule View window.

The correct one would be: C1=CC=C2C(=C1)C=CC3=CC=CC=C3N2

Hello, I have been trying to get openchrom running in Eclipse by following your DEV guidelines with no success. Latest issue I have is that it "Unable to locate installable unit net.openchrom.rcp.compilation.community.converter.feature.feature.group 0.0.0".
I'm really looking for the code that opens and converts an Agilent Data.Ms file - can you point me in right direction please.
Tx.

The three ticks for selection of data types are shuffling sometimes.

It also would be nice if the last selection e.g. (MSD) could be remembert for the session.

When opening a Chromatogram directly from the .D folder, I do not have the option to select a reference chromatogram.

If I save this chromatogram to ocb and reload this file, I can choose to display a reference chromatogram.

It is not possible to save a copy via "Save as" of process methods.
By clicking nothing happens.

The only way is to rename the process method in the file explorer.
Afterwards OpenChrom asks for a new saving location.

Improve the SMILES generator by letting the user define the settings.

There still seems to be some errors in plotting the molecule structures.

This is chemically unlikely:

This is wrong:

Maybe this is liked to #9

Importing a TXT file and then exporting it again does not yields the same result.
This is because of the implementation of the DetectorSetting equals method that only takes the start/stop rt into account.

Views, like the Molecule View, have to be activated every time starting the software.
Saveing properties like order and width of columns in tables would be smooth, too.

A hierarchical view of the identified organisms with links to https://www.ncbi.nlm.nih.gov/taxonomy might be helpful to get a better overview.

Similar to #26 we should provide a user friendly way to edit the Identifier settings.

The peak filter "Disable classified peaks" does not alter active peaks in peak/scan list.

currently one can supply start/stop and traces, bu especially with the UI- Part is would be very useful to have an optional "comment" that a user can provide and that is displayed, so it is easier to identify the peak that is currently reviewed

I do not get sufficient results by subtracting ms spectra. I'm going to show you with some screen shots, maybe it is just me...

This is what the advanced MCR-AR detector finds (but with no good matches):

This is what the first derivative detector finds:

Now, trying to subtract a background spectra just from the beginning of the peak.

selecting the spectra for subtraction:

And the result is:

It seems to me that the relevant m/z are subtracted rather than the background. Of cause, the peak identifier does not show up matches.

Just for comparison with Chemstation the same peak looks like this:

Selecting the background for subtraction:

And subtractiting the spectra leads to this with a quite good match:

What am I doing wrong or how can be subtract result be improved in OpenChrom?

Applying the TPD to a file I see a lots of the following messages in the log:
WARN ModalContext support.PeakSupport.extractPeakByScanRange (PeakSupport.java:111) org.eclipse.chemclipse.model.exceptions.PeakException: There must be at least one intensity value stored with a relative intensity of IPeakIntensityValues.MAX_INTENSITY.

If the Window for the comparison scan modus is activated it is refreshed every time when clicking in the peak list table or the targets table.
In case of right click in these tables the context menu disappears due to refreshing the comparison scan modus window.
Therefore, the context menu of right clicks are not available.