Fix NullPointerException in motif finder

[sjl]

Hello, got another NullPointerException fix for you. A while back my coworker noticed the motif finder had stopped working (we're both still living on main IGV, so I'm unsure if this ever made it into a release). Running the motif finder produces a null pointer exception and a stack trace:

SEVERE [Apr 01,2026 10:14] [DefaultExceptionHandler] Unhandled exception
SEVERE [Apr 01,2026 10:14] [DefaultExceptionHandler] java.lang.NullPointerException: Cannot invoke "org.igv.util.ResourceLocator.getPath()" because the return value of "org.igv.track.Track.getResourceLocator()" is null
        at org.igv.ui.IGV.lambda$addTracks$5(IGV.java:1217)
        at java.base/java.util.stream.Collectors.lambda$groupingBy$53(Collectors.java:1105)
        at java.base/java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
        at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1708)
        at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
        at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
        at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
        at org.igv.ui.IGV.addTracks(IGV.java:1217)
        at org.igv.tools.motiffinder.MotifFinderPlugin.addTracksForPatterns(MotifFinderPlugin.java:58)
        at org.igv.tools.motiffinder.MotifFinderPlugin.handleDialogResult(MotifFinderPlugin.java:44)
        at org.igv.tools.motiffinder.MotifFinderPlugin.lambda$getMenuItem$0(MotifFinderPlugin.java:33)
        at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
        at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
        at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
        at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
        at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
        at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029)
        at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073)
        at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
        at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
        at java.desktop/java.awt.Component.processEvent(Component.java:6386)
        at java.desktop/java.awt.Container.processEvent(Container.java:2266)
        at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
        at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
        at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
        at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
        at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
        at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
        at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
        at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
        at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
        at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
        at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
        at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
        at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
        at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
        at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
        at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
        at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
        at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
        at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
        at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
        at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

The problem seems to be that when adding the result tracks it uses addTracks(), which uses .getResourceLocator() on each track to figure out where to put it, and MotifTrack doesn't implement that function or pass any kind of resource locator to the FeatureTrack superclass constructor.

This commit fixes the NPE by adding the motif tracks one by one with addTrack and explicitly telling them to go to the annotation panel. Another way to fix it might be to give MotifTracks a resource locator, either by overriding getResourceLocator or by passing along some kind of ResourceLocator in the constructor instead of null. I'm happy to take a crack at doing either of those instead if the current solution is too much of a hack (though I'm still a little fuzzy on what exactly a ResourceLocator is).

Thanks!

[jrobinso]

Thanks for the PR. I'm going to put it on hold for now because I think this is fixed in a branch I am working on, but I will test it.

[sjl]

Sounds good, feel free to close if it's already fixed!