improve the reporting of NEXUS reading failures in BEAUti

[GoogleCodeExporter]

Sent by Scott Edwards. I assume the file is legit.

dr.evolution.io.Importer$BadFormatException: Expecting ';' after sequences
data, has 'C' in line 409
    at dr.evolution.io.NexusImporter.readSequenceData(NexusImporter.java:666)
    at dr.evolution.io.NexusImporter.readDataBlock(NexusImporter.java:737)
    at dr.evolution.io.NexusImporter.parseDataBlock(NexusImporter.java:167)
    at dr.app.beauti.BeautiFrame.importNexusFile(BeautiFrame.java:467)
    at dr.app.beauti.BeautiFrame.importFromFile(BeautiFrame.java:364)
    at dr.app.beauti.BeautiFrame.doImport(BeautiFrame.java:337)
    at dr.app.beauti.BeautiFrame$4.actionPerformed(BeautiFrame.java:1101)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
    at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)
    at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1051)
    at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuIt
emUI.java:1155)
    at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:578)
    at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:475)
    at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:422)
    at
javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:283
)
    at
javax.swing.plaf.basic.BasicPopupMenuUI$MouseGrabber.eventDispatched(BasicPopupM
enuUI.java:783)
    at
java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Toolkit.java:2206)
    at java.awt.Toolkit$ToolkitEventMulticaster.eventDispatched(Toolkit.java:2100)
    at java.awt.Toolkit.notifyAWTEventListeners(Toolkit.java:2058)
    at java.awt.Component.dispatchEventImpl(Component.java:3883)
    at java.awt.Container.dispatchEventImpl(Container.java:2024)
    at java.awt.Component.dispatchEvent(Component.java:3819)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
    at java.awt.Container.dispatchEventImpl(Container.java:2010)
    at java.awt.Window.dispatchEventImpl(Window.java:1791)
    at java.awt.Component.dispatchEvent(Component.java:3819)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
    at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:2
42)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163
)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

Original issue reported on code.google.com by jhe...@gmail.com on 16 Aug 2009 at 11:10

Attachments:

• manakinconcat2.nex

[GoogleCodeExporter]

After removing the !\n in lines Beauti parsed the MR block, but incorrectly I 
think.

nrodc reports 1 site while, charset nrodc = 1500 - 1985;

Pmentalis1084, which is part of the (deleted) outgroup is in the alignment

(there might be other problems as well)

Original comment by jhe...@gmail.com on 16 Aug 2009 at 11:36

Attachments:

• mana.png

[GoogleCodeExporter]

nr reports 386 sites while

charset nr = 1-386 387-1045 
1500-1985 1986-2300 2301-2414;

Original comment by jhe...@gmail.com on 16 Aug 2009 at 11:37

[GoogleCodeExporter]

Had chat with Joseph. He made file to import successfully, but not sure it was 
a new
format or just a mistake. 

Need either Andrew or Alexei to verify this issue, and decide whether to close 
or
continue.

Original comment by dong.w.xie@gmail.com on 18 Aug 2009 at 12:23

[GoogleCodeExporter]

Still MrBayes import is totally off.

Original comment by jhe...@gmail.com on 18 Aug 2009 at 12:31

[GoogleCodeExporter]

The file as uploaded here is corrupted with '!' at the end of some lines. I 
believe these to have been added by an 
email program where it has wrapped the lines. However they were put there, they 
contravene the NEXUS format 
and thus means this is not a failure on BEAST's part. There is some room for 
improvement in the reporting of 
NEXUS reading failures but I am closing this issue. 

If there is an issue with the reading of the 'charset' commands, we should 
start a new issue using a cleaned-up 
version of the file (and then close this issue).

Original comment by ramb...@gmail.com on 2 Oct 2009 at 12:51

[GoogleCodeExporter]

change tittle as Andrew's comment

Original comment by dong.w.xie@gmail.com on 17 Aug 2010 at 10:36

• Changed title: improve the reporting of NEXUS reading failures in BEAUti
• Added labels: 1.6, BEAUti, Type-Enhancement
• Removed labels: Type-Defect