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  1. Jalview
  2. JAL-1010

putting fractional value into integer text box in alignment parameter dialog causes jalview to hang

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.7
    • Fix Version/s: 2.8
    • Component/s: JWS-GUI
    • Labels:
      None

      Description

      To repeat, open the 'ClustalW' parameter settings, and type '0.05' into the GAPDIST parameter. Then, press create (or update) to save the parameter settings.

      No error is raised in jalview, but the GUI locks up whilst Jalview tries to validate the value with the server. Exceptions thrown on the console are:
      java.lang.NumberFormatException: For input string: "0.05"
      at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
      at java.lang.Integer.parseInt(Integer.java:458)
      at java.lang.Integer.parseInt(Integer.java:499)
      at compbio.metadata.ValueConstrain.checkValue(Unknown Source)
      at compbio.metadata.Parameter.setDefaultValue(Unknown Source)
      at jalview.ws.jws2.dm.JabaOption.setValue(JabaOption.java:79)
      at jalview.gui.OptsAndParamsPage$ParamBox.getParameter(OptsAndParamsPage.java:494)
      at jalview.gui.OptsAndParamsPage.getCurrentSettings(OptsAndParamsPage.java:873)
      at jalview.gui.WsJobParameters.getJobParams(WsJobParameters.java:1076)
      at jalview.ws.jws2.MsaWSClient.<init>(MsaWSClient.java:166)
      at jalview.ws.jws2.MsaWSClient$2.actionPerformed(MsaWSClient.java:316)
      at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
      at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
      at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
      at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
      at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
      at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
      at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
      at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.Component.processMouseEvent(Component.java:6373)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
      at java.awt.Container.dispatchEventImpl(Container.java:2129)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      at java.awt.EventQueue.access$000(EventQueue.java:85)
      at java.awt.EventQueue$1.run(EventQueue.java:638)
      at java.awt.EventQueue$1.run(EventQueue.java:636)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$2.run(EventQueue.java:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
      Exception in thread "AWT-EventQueue-0" java.lang.Error: Implementation error: cannot set Jaba Option to a value outside its allowed value range!
      at jalview.ws.jws2.dm.JabaOption.setValue(JabaOption.java:83)
      at jalview.gui.OptsAndParamsPage$ParamBox.getParameter(OptsAndParamsPage.java:494)
      at jalview.gui.OptsAndParamsPage.getCurrentSettings(OptsAndParamsPage.java:873)
      at jalview.gui.WsJobParameters.getJobParams(WsJobParameters.java:1076)
      at jalview.ws.jws2.MsaWSClient.<init>(MsaWSClient.java:166)
      at jalview.ws.jws2.MsaWSClient$2.actionPerformed(MsaWSClient.java:316)
      at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
      at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
      at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
      at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
      at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
      at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
      at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
      at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
      at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
      at java.awt.Component.processMouseEvent(Component.java:6373)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
      at java.awt.Container.dispatchEventImpl(Container.java:2129)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      at java.awt.EventQueue.access$000(EventQueue.java:85)
      at java.awt.EventQueue$1.run(EventQueue.java:638)
      at java.awt.EventQueue$1.run(EventQueue.java:636)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$2.run(EventQueue.java:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated:
              Resolved: