does not recognize mzrt.csv

[lorenzgerber]

I try to import features as mzrt.csv files but they are not recognised. I'm on BatMass 201411181905, with Java 1.8.0_111 using a OSX 10.12.5

[rsalek]

Have same issue, with XCMS.CSV I created for ML. Followed your example.

[lorenzgerber]

@rsalek Reza, I just got it to work. I reinstalled from a recent download, fixed the permission issue and then after startup, the application updates the plugins. Then mzrt.csv import is available Cheers Lorenz

[rsalek]

Is that correcting file:/G:/projects/netbeans/BatMass/build/updates/updates.xml ? hmm, did that still not updated, could it be to /Dev updated center/ URL above?

[lorenzgerber]

For me it did. I got the exact same error. I think my issue was that because batmass didn't run with the install script (OSX, due to the permission issues), I started to run it out of the dowloaded directory, which somehow worked, but as such, the plugin update was broken. I removed the whole installation (hidden directory in home .batmass), downloaded a fresh tgz and finally it worked. I also tried on Linux (ubuntu 16.04), which also worked just fine.

[rsalek]

can you share your "mzrt.csv" pls I think it could be due to: https://www.dropbox.com/s/sndnmqvhkndp48q/Screenshot%202017-05-20%2021.57.15.png?dl=0

[lorenzgerber]

hmm, the mzrt.csv's are really as simple as it sounds. Here is an example that works for me: someTargets.mzrt.csv

[lorenzgerber]

@rsalek Here are my configurations settings, they are different to yours: configuration settings

[rsalek]

Thx, worked 👍, just now need to figure out how to overlay them :)

[chhh]

Hi guys, sorry, I missed the conversation. I guess you've seen this one tutorial: http://www.batmass.org/tutorial/custom-drawing/ To overlay:

• Select both the mzrt.csv file and the mzml/mzxml file (left click while holding Ctrl)
• With both files selected, right click any of the two
• In the dropdown menu select Feature Overlay

[rsalek]

Hi, got it working but can't see the boxes, question rt in second is ok or have to be in min? I also get Java error below ....sorry for the dump!

---

java.lang.ArrayIndexOutOfBoundsException: -4952 at umich.ms.batmass.gui.viewers.map2d.components.BaseMap2D.addPeakRaw(BaseMap2D.java:651) at umich.ms.batmass.gui.viewers.map2d.components.BaseMap2D.fillMapFromScans(BaseMap2D.java:289) at umich.ms.batmass.gui.viewers.map2d.components.Map2DZoomLevel.initMapAxesColors(Map2DZoomLevel.java:82) at umich.ms.batmass.gui.viewers.map2d.components.Map2DZoomLevel.(Map2DZoomLevel.java:71) at umich.ms.batmass.gui.viewers.map2d.components.Map2DPanel.zoom(Map2DPanel.java:802) at umich.ms.batmass.gui.viewers.map2d.components.Map2DPanel$BusHandler.eventbusHandlerFeatureClickEvent(Map2DPanel.java:1463) Caused: java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) [catch] at net.engio.mbassy.dispatch.ReflectiveHandlerInvocation.invokeHandler(ReflectiveHandlerInvocation.java:23) at net.engio.mbassy.dispatch.ReflectiveHandlerInvocation.invoke(ReflectiveHandlerInvocation.java:49) at net.engio.mbassy.dispatch.MessageDispatcher.dispatch(MessageDispatcher.java:30) at net.engio.mbassy.dispatch.FilteredMessageDispatcher.dispatch(FilteredMessageDispatcher.java:41) at net.engio.mbassy.subscription.Subscription.publish(Subscription.java:66) at net.engio.mbassy.bus.MessagePublication.execute(MessagePublication.java:46) at net.engio.mbassy.bus.MBassador.publish(MBassador.java:46) at umich.ms.batmass.gui.viewers.featuretable.components.FeatureTable$BusHandler.featureClicked(FeatureTable.java:116) at umich.ms.batmass.gui.viewers.featuretable.components.FeatureTable$1.mousePressed(FeatureTable.java:77) at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) at java.awt.Component.processMouseEvent(Component.java:6530) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:159) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

[chhh]

Has to be in minutes - there's no way to differentiate between time units. Everything in batmass and msftbx is in minutes.

[rsalek]

That explains it ... thx :) mine is: xmzLo mzHi rtLo rtHi color opacity 57.97554649 57.97562426 67.846 69.6165 R=255,G=127,B=80 0.1 61.98828098 61.98834594 53.5205 59.0379 R=255,G=127,B=81 0.1 63.61907023 63.62289588 346.002 352.352 R=255,G=127,B=82 0.1 70.94597034 70.94624015 52.0364 54.976 R=255,G=127,B=83 0.1 72.94260526 72.94320084 52.9876 54.976 R=255,G=127,B=84 0.1

[chhh]

@rsalek there's also an extra x in mzLo column name. If you're using color it has to be in hex starting with #. e.g. #FF7F50, I believe, for your color.

[rsalek]

just copied it from your tools it is: mzLo mzHi rtLo rtHi color opacity 57.97554649 57.97562426 67.846 69.6165 #ff7f50 0.1 61.98828098 61.98834594 53.5205 59.0379 #ff7f50 0.1 63.61907023 63.62289588 346.002 352.352 #ff7f50 0.1 70.94597034 70.94624015 52.0364 54.976 #ff7f50 0.1

[chhh]

@rsalek is that working now? Because the error in the dump that you've sent was related to something different, I believe.

[rsalek]

Seems working now @chhh with rt in min, thx ... all good