java.lang.ArrayIndexOutOfBoundsException: No such child: 4

Google Groups | Dani | 7 years ago
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    Google Groups | 7 years ago | Dani
    java.lang.ArrayIndexOutOfBoundsException: No such child: 4
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    Hi, I'm a regular user of Jalview and have used over 1.5 year and currently using anywhere installed version 2.8. I am not able to access web services and gets error message when open the program. I use Mac OS X 10.8.3 and Win7 64bit in parallel and tried to run jalview on both the OS. I have upgraded my java version but still does't help! Kindly let me know how to fix this issue. Thank you! Error message: "Failed to submit sequences for alignment. Just close the window" Java console (Mac) Jalview Desktop 2.8 Build Date: 12 November 2012 Java version: 1.7.0_21 x86_64 Mac OS X 10.8.3 WARN - Exception when discovering One Way services: WARN - Exception when discovering One Way services: INFO - Not enabling Google Tracking. INFO - Constructing news reader. INFO - Completed construction of reader. INFO - Saved last read date as Apr 18, 2013 1:02:08 PM INFO - Saved last read date as Apr 18, 2013 1:02:08 PM INFO - Saved last read date as Apr 18, 2013 1:02:08 PM Java console windows (opens by default on startup) Jalview Desktop 2.8 Build Date: 12 November 2012 Java version: 1.6.0_01 x86 Windows Vista 6.1 WARN - Exception when discovering One Way services: WARN - Exception when discovering One Way services: May 3, 2013 8:53:11 PM compbio.ws.client.Jws2Client connectToRegistry INFO: Connected to RegistryWS successfully! Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service JronnWS: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl the server is down? java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl the server is down? at compbio.ws.client.Jws2Client.connect(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150) at java.lang.Thread.run(Unknown Source) Connecting to JABAWS version 2 service Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service DisemblWS: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl the server is down? java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl the server is down? at compbio.ws.client.Jws2Client.connect(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150) at java.lang.Thread.run(Unknown Source) Connecting to JABAWS version 2 service Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service GlobPlotWS: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl the server is down? java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl the server is down? at compbio.ws.client.Jws2Client.connect(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150) at java.lang.Thread.run(Unknown Source) Warning - overwriting a sequenceSetId for a viewport! Building ws menu again Thread[Thread-19,5,main] Connecting to JABAWS version 2 service WARN - Exception when discovering Jws2 services. Connecting to JABAWS version 2 service Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service IUPredWS: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl the server is down? java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl the server is down? at compbio.ws.client.Jws2Client.connect(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150) at java.lang.Thread.run(Unknown Source) Connecting to JABAWS version 2 service Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service AAConWS: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl the server is down? java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl the server is down? at compbio.ws.client.Jws2Client.connect(Unknown Source) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150) at java.lang.Thread.run(Unknown Source) 1822 script command tokens (C) 2009 Jmol Development Jmol Version: 12.2.4 2011-10-11 21:29 java.vendor: Sun Microsystems Inc. java.version: 1.6.0_01 os.name: Windows Vista memory: 22.3/33.8 processors available: 2 useCommandThread: false May 3, 2013 8:53:13 PM compbio.ws.client.Jws2Client connect INFO: Connected successfully! FileManager.getAtomSetCollectionFromFile(C:\\Users\\GANESH~1\\AppData\\Local\\Temp\\jalview_pdb24017.txt) Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@640f1a FileManager opening C:\Users\GANESH~1\AppData\Local\Temp\jalview_pdb24017.txt The Resolver thinks Pdb java.lang.NullPointerException at jalview.ws.jws2.Jws2Discoverer.addService(Jws2Discoverer.java:253) at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:181) at java.lang.Thread.run(Unknown Source) Setting space group name to P 21 21 21 openFile(C:\\Users\\GANESH~1\\AppData\\Local\\Temp\\jalview_pdb24017.txt): 116 ms reading 817 atoms ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Jmol 817 atoms created Time to autoBond: 13 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically Rebuild WS Menu for service change Building ws menu again Thread[Thread-26,6,main] ColorManager: color "roygb" range 0.0 0.0 measurement[0] = [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm] Unhandled callback MEASURE [[FES]1602.S1 #736, [THR]89.OG1 #665, 1.328 nm] History on; Warning - overwriting a sequenceSetId for a viewport! Building ws menu again Thread[Thread-32,5,main] header key X-DAS-Server=[regrest/1.5] header key Content-Type=[application/xml] header key Date=[Fri, 03 May 2013 18:53:12 GMT] header key Access-Control-Allow-Origin=[*] header key X-DAS-Status=[200] header key Transfer-Encoding=[chunked] header key X-OSSProxy=[OSSProxy 1.3.335.337 (Build 335.337 Win32 en-us)(Apr 4 2013 16:51:42)] header key Connection=[keep-alive] Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Contig 2.0) (DAS)) Added another sequence DB source for Anolis_carolinensis.AnoCar2.0.reference (Anolis_carolinensis.AnoCar2.0.reference (AnoCar Scaffold 2.0) (DAS)) Added another sequence DB source for Bos_taurus.UMD3.1.reference (Bos_taurus.UMD3.1.reference (UMD Scaffold 3.1) (DAS)) Added another sequence DB source for Callithrix_jacchus.C_jacchus3.2.1.reference (Callithrix_jacchus.C_jacchus3.2.1.reference (C_jacchus Chromosome 3.2.1) (DAS)) Added another sequence DB source for Choloepus_hoffmanni.choHof1.reference (Choloepus_hoffmanni.choHof1.reference (choHof Gene Scaffold 1) (DAS)) Added another sequence DB source for Danio_rerio.Zv9.reference (Danio_rerio.Zv9.reference (Zv Scaffold 9) (DAS)) Added another sequence DB source for Dasypus_novemcinctus.dasNov2.reference (Dasypus_novemcinctus.dasNov2.reference (dasNov Scaffold 2) (DAS)) Added another sequence DB source for Dipodomys_ordii.dipOrd1.reference (Dipodomys_ordii.dipOrd1.reference (dipOrd Scaffold 1) (DAS)) Building ws menu again Thread[Thread-41,5,main] Warning - overwriting a sequenceSetId for a viewport! Added another sequence DB source for Echinops_telfairi.TENREC.reference (Echinops_telfairi.TENREC.reference (TENREC Scaffold) (DAS)) Added another sequence DB source for Erinaceus_europaeus.HEDGEHOG.reference (Erinaceus_europaeus.HEDGEHOG.reference (HEDGEHOG Scaffold) (DAS)) Added another sequence DB source for Felis_catus.CAT.reference (Felis_catus.CAT.reference (CAT Gene Scaffold) (DAS)) Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Gene Scaffold 1) (DAS)) Added another sequence DB source for Gadus_morhua.gadMor1.reference (Gadus_morhua.gadMor1.reference (gadMor Scaffold 1) (DAS)) Added another sequence DB source for Gasterosteus_aculeatus.BROADS1.reference (Gasterosteus_aculeatus.BROADS1.reference (BROADS Scaffold 1) (DAS)) Added another sequence DB source for Homo_sapiens.GRCh37.reference (Homo_sapiens.GRCh37.reference (GRCh Chromosome 37) (DAS)) Building ws menu again Thread[Thread-52,5,main] Warning - overwriting a sequenceSetId for a viewport! Added another sequence DB source for Macaca_mulatta.MMUL_1.reference (Macaca_mulatta.MMUL_1.reference (MMUL Chromosome 1) (DAS)) Added another sequence DB source for Macropus_eugenii.Meug_1.0.reference (Macropus_eugenii.Meug_1.0.reference (Meug Scaffold 1.0) (DAS)) Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Scaffold 2) (DAS)) Added another sequence DB source for Meleagris_gallopavo.UMD2.reference (Meleagris_gallopavo.UMD2.reference (UMD Contig 2) (DAS)) Added another sequence DB source for Microcebus_murinus.micMur1.reference (Microcebus_murinus.micMur1.reference (micMur Scaffold 1) (DAS)) Added another sequence DB source for Mus_musculus.NCBIM37.reference (Mus_musculus.NCBIM37.reference (NCBIM Supercontig 37) (DAS)) Added anotheINFO - Not enabling Google Tracking. r sequence DB source for Nomascus_leucogenys.Nleu1.0.reference (Nomascus_leucogenys.Nleu1.0.reference (Nleu Contig 1.0) (DAS)) Added another sequence DB source for Ochotona_princeps.pika.reference (Ochotona_princeps.pika.reference (pika Gene Scaffold) (DAS)) Building ws menu again Thread[Thread-66,5,main] Warning - overwriting a sequenceSetId for a viewport! Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Ultracontig 5) (DAS)) Added another sequence DB source for Ornithorhynchus_anatinus.OANA5.reference (Ornithorhynchus_anatinus.OANA5.reference (OANA Supercontig 5) (DAS)) Added another sequence DB source for Oryctolagus_cuniculus.oryCun2.reference (Oryctolagus_cuniculus.oryCun2.reference (oryCun Chromosome 2) (DAS)) Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (Oryzias_latipes.MEDAKA1.reference (MEDAKA Scaffold 1) (DAS)) Added another sequence DB source for Oryzias_latipes.MEDAKA1.reference (OryziasINFO - Constructing news reader. INFO - Completed construction of reader. deregistering discoverer listener deregistering discoverer listener deregistering discoverer listener deregistering discoverer listener _latipes.MEDAKA1.reference (MEDAKA Chromosome 1) (DAS)) Exception occurred during event dispatching: java.lang.ArrayIndexOutOfBoundsException: No such child: 4 at java.awt.Container.getComponent(Unknown Source) at javax.swing.JComponent.rectangleIsObscured(Unknown Source) at javax.swing.JComponent.paint(Unknown Source) at javax.swing.JLayeredPane.paint(Unknown Source) at javax.swing.JComponent.paintToOffscreen(Unknown Source) at javax.swing.BufferStrategyPaintManager.paint(Unknown Source) at javax.swing.RepaintManager.paint(Unknown Source) at javax.swing.JComponent._paintImmediately(Unknown Source) at javax.swing.JComponent.paintImmediately(Unknown Source) at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source) at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.Dialog$1.run(Unknown Source) at java.awt.Dialog$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Dialog.show(Unknown Source) at javax.swing.JOptionPane.showOptionDialog(Unknown Source) at javax.swing.JOptionPane.showConfirmDialog(Unknown Source) at javax.swing.JOptionPane.showConfirmDialog(Unknown Source) at jalview.gui.Desktop$20.run(Desktop.java:2550) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Added another sequence DB source for Pan_troglodytes.CHIMP2.1.4.reference (Pan_troglodytes.CHIMP2.1.4.reference (CHIMP Chromosome 2.1.4) (DAS)) Added another sequence DB source for Procavia_capensis.proCap1.reference (Procavia_capensis.proCap1.reference (proCap Gene Scaffold 1) (DAS)) Added another sequence DB source for Pteropus_vampyrus.pteVam1.reference (Pteropus_vampyrus.pteVam1.reference (pteVam Gene Scaffold 1) (DAS)) Added another sequence DB source for Sorex_araneus.COMMON_SHREW1.reference (Sorex_araneus.COMMON_SHREW1.reference (COMMON_SHREW Gene Scaffold 1) (DAS)) Added another sequence DB source for Spermophilus_tridecemlineatus.SQUIRREL.reference (Spermophilus_tridecemlineatus.SQUIRREL.reference (SQUIRREL Gene Scaffold) (DAS)) Added another sequence DB source for Tarsius_syrichta.tarSyr1.reference (Tarsius_syrichta.tarSyr1.reference (tarSyr Scaffold 1) (DAS)) Added another sequence DB source for Tupaia_belangeri.TREESHREW.reference (Tupaia_belangeri.TREESHREW.reference (TREESHREW Scaffold) (DAS)) Added another sequence DB source for Tursiops_truncatus.turTru1.reference (Tursiops_truncatus.turTru1.reference (turTru Gene Scaffold 1) (DAS)) Added another sequence DB source for Vicugna_pacos.vicPac1.reference (Vicugna_pacos.vicPac1.reference (vicPac Gene Scaffold 1) (DAS)) Added another sequence DB source for Ciona_intestinalis.JGI2.reference (Ciona_intestinalis.JGI2.reference (JGI Chromosome 2) (DAS)) Added another sequence DB source for Bos_taurus.Btau_4.0.reference (Bos_taurus.Btau_4.0.reference (Btau Contig 4.0) (DAS)) Added another sequence DB source for Otolemur_garnettii.BUSHBABY1.reference (Otolemur_garnettii.BUSHBABY1.reference (BUSHBABY Scaffold 1) (DAS)) Added another sequence DB source for Myotis_lucifugus.MICROBAT1.reference (Myotis_lucifugus.MICROBAT1.reference (MICROBAT Scaffold 1) (DAS)) Added another sequence DB source for Danio_rerio.Zv8.reference (Danio_rerio.Zv8.reference (Zv Scaffold 8) (DAS)) Added another sequence DB source for Gorilla_gorilla.gorGor1.reference (Gorilla_gorilla.gorGor1.reference (gorGor Gene Scaffold 1) (DAS)) Added another sequence DB source for Loxodonta_africana.loxAfr2.reference (Loxodonta_africana.loxAfr2.reference (loxAfr Scaffold 2) (DAS)) Added another sequence DB source for Oryctolagus_cuniculus.RABBIT.reference (Oryctolagus_cuniculus.RABBIT.reference (RABBIT Scaffold) (DAS)) Added another sequence DB source for Homo_sapiens.NCBI36.reference (Homo_sapiens.NCBI36.reference (NCBI Supercontig 36) (DAS)) Added another sequence DB source for Danio_rerio.ZFISH7.reference (Danio_rerio.ZFISH7.reference (ZFISH Scaffold 7) (DAS)) INFO - Saved last read date as Apr 18, 2013 1:02:08 PM INFO - Saved last read date as Apr 18, 2013 1:02:08 PM INFO - Saved last read date as Apr 18, 2013 1:02:08 PM Best, Ganesh Karolinska institutet, Stockholm

    JIRA | 4 years ago | Ganesh Phad
    java.lang.ArrayIndexOutOfBoundsException: No such child: 4
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    java.lang.ArrayIndexOutOfBoundsException: No such child: 0
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    java.lang.ArrayIndexOutOfBoundsException: No such child: 2

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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      No such child: 4

      at java.awt.Container.getComponent()
    2. Java RT
      JMenu.getMenuComponent
      1. java.awt.Container.getComponent(Unknown Source)
      2. javax.swing.JMenu.getMenuComponent(Unknown Source)
      2 frames