figtree
figtree copied to clipboard
rambaut
Problems exporting big file to PDF
Here what I have in the console: bash-3.2$ java -jar /Users/David/Desktop/FigTree_v1.4.3/lib/figtree.jar javax.swing.UIManager$LookAndFeelInfo[Metal javax.swing.plaf.metal.MetalLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Nimbus com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[CDE/Motif com.sun.java.swing.plaf.motif.MotifLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Mac OS X com.apple.laf.AquaLookAndFeel] objc[14294]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff8c19eb68) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x11bf85cd8). One of the two will be used. Which one is undefined. Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException at java.util.AbstractList.add(AbstractList.java:131) at java.util.AbstractList.add(AbstractList.java:91) at figtree.treeviewer.decorators.DiscreteColourDecorator.setAttributes(Unknown Source) at figtree.treeviewer.AttributeColourController.getDecoratorForAttribute(Unknown Source) at figtree.treeviewer.AttributeColourController.setSettings(Unknown Source) at jam.controlpalettes.BasicControlPalette.setSettings(Unknown Source) at figtree.application.FigTreeFrame.readData(Unknown Source) at figtree.application.FigTreeFrame.readFromFile(Unknown Source) at jam.framework.DocumentFrame.openFile(Unknown Source) at figtree.application.FigTreeApplication.doOpenFile(Unknown Source) at jam.framework.Application.doOpen(Unknown Source) at jam.framework.Application$4.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95) at java.awt.MenuItem.processActionEvent(MenuItem.java:650) at java.awt.MenuItem.processEvent(MenuItem.java:609) at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343) at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:687) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) 2017-12-12 15:08:29.030 java[14294:418487] Persistent UI failed to open file file://localhost/Users/David/Library/Saved%20Application%20State/com.apple.javajdk16.cmd.savedState/window_1.data: Permission denied (13)
Thanks friend!
What OS is this on?
A.
On 12 Dec 2017, at 14:50, tapeda [email protected] wrote:
Here what I have in the console: bash-3.2$ java -jar /Users/David/Desktop/FigTree_v1.4.3/lib/figtree.jar javax.swing.UIManager$LookAndFeelInfo[Metal javax.swing.plaf.metal.MetalLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Nimbus com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[CDE/Motif com.sun.java.swing.plaf.motif.MotifLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Mac OS X com.apple.laf.AquaLookAndFeel] objc[14294]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff8c19eb68) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x11bf85cd8). One of the two will be used. Which one is undefined. Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException at java.util.AbstractList.add(AbstractList.java:131) at java.util.AbstractList.add(AbstractList.java:91) at figtree.treeviewer.decorators.DiscreteColourDecorator.setAttributes(Unknown Source) at figtree.treeviewer.AttributeColourController.getDecoratorForAttribute(Unknown Source) at figtree.treeviewer.AttributeColourController.setSettings(Unknown Source) at jam.controlpalettes.BasicControlPalette.setSettings(Unknown Source) at figtree.application.FigTreeFrame.readData(Unknown Source) at figtree.application.FigTreeFrame.readFromFile(Unknown Source) at jam.framework.DocumentFrame.openFile(Unknown Source) at figtree.application.FigTreeApplication.doOpenFile(Unknown Source) at jam.framework.Application.doOpen(Unknown Source) at jam.framework.Application$4.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95) at java.awt.MenuItem.processActionEvent(MenuItem.java:650) at java.awt.MenuItem.processEvent(MenuItem.java:609) at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343) at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:687) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) 2017-12-12 15:08:29.030 java[14294:418487] Persistent UI failed to open file file://localhost/Users/David/Library/Saved%20Application%20State/com.apple.javajdk16.cmd.savedState/window_1.data: Permission denied (13)
Thanks friend!
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120, or mute the thread https://github.com/notifications/unsubscribe-auth/AAp5RSXcruAV8fjbt0g5FLZsgwrCqK5Uks5s_pLGgaJpZM4Q_Fz0.
Mac OS High Sierra 10.13.2, If you want I can send you privately the file which is reporting me this problems…I cannot also see the name of my taxa. Thanks!
El 12 dic 2017, a las 15:53, rambaut [email protected] escribió:
What OS is this on?
A.
On 12 Dec 2017, at 14:50, tapeda [email protected] wrote:
Here what I have in the console: bash-3.2$ java -jar /Users/David/Desktop/FigTree_v1.4.3/lib/figtree.jar javax.swing.UIManager$LookAndFeelInfo[Metal javax.swing.plaf.metal.MetalLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Nimbus com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[CDE/Motif com.sun.java.swing.plaf.motif.MotifLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Mac OS X com.apple.laf.AquaLookAndFeel] objc[14294]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff8c19eb68) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x11bf85cd8). One of the two will be used. Which one is undefined. Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException at java.util.AbstractList.add(AbstractList.java:131) at java.util.AbstractList.add(AbstractList.java:91) at figtree.treeviewer.decorators.DiscreteColourDecorator.setAttributes(Unknown Source) at figtree.treeviewer.AttributeColourController.getDecoratorForAttribute(Unknown Source) at figtree.treeviewer.AttributeColourController.setSettings(Unknown Source) at jam.controlpalettes.BasicControlPalette.setSettings(Unknown Source) at figtree.application.FigTreeFrame.readData(Unknown Source) at figtree.application.FigTreeFrame.readFromFile(Unknown Source) at jam.framework.DocumentFrame.openFile(Unknown Source) at figtree.application.FigTreeApplication.doOpenFile(Unknown Source) at jam.framework.Application.doOpen(Unknown Source) at jam.framework.Application$4.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95) at java.awt.MenuItem.processActionEvent(MenuItem.java:650) at java.awt.MenuItem.processEvent(MenuItem.java:609) at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343) at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:687) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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) 2017-12-12 15:08:29.030 java[14294:418487] Persistent UI failed to open file file://localhost/Users/David/Library/Saved%20Application%20State/com.apple.javajdk16.cmd.savedState/window_1.data: Permission denied (13)
Thanks friend!
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120, or mute the thread https://github.com/notifications/unsubscribe-auth/AAp5RSXcruAV8fjbt0g5FLZsgwrCqK5Uks5s_pLGgaJpZM4Q_Fz0.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120#issuecomment-351074251, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ6qu6Iw5MI_VnxYJ8N2IKGo_pTYLXKBks5s_pNXgaJpZM4Q_Fz0.
In which case could you download and try the v1.4.4 pre-release:
https://github.com/rambaut/figtree/releases/tag/v1.4.4pre20171111 https://github.com/rambaut/figtree/releases/tag/v1.4.4pre20171111
I believe this is still not compatible with Java 1.9 on the Mac so do not upgrade from Java 1.8.
If there is still an issue, let me know.
Andrew
On 12 Dec 2017, at 14:55, tapeda [email protected] wrote:
Mac OS High Sierra 10.13.2, If you want I can send you privately the file which is reporting me this problems…I cannot also see the name of my taxa. Thanks!
El 12 dic 2017, a las 15:53, rambaut <[email protected] mailto:[email protected]> escribió:
What OS is this on?
A.
On 12 Dec 2017, at 14:50, tapeda <[email protected] mailto:[email protected]> wrote:
Here what I have in the console: bash-3.2$ java -jar /Users/David/Desktop/FigTree_v1.4.3/lib/figtree.jar javax.swing.UIManager$LookAndFeelInfo[Metal javax.swing.plaf.metal.MetalLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Nimbus com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[CDE/Motif com.sun.java.swing.plaf.motif.MotifLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Mac OS X com.apple.laf.AquaLookAndFeel] objc[14294]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff8c19eb68) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x11bf85cd8). One of the two will be used. Which one is undefined. Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException at java.util.AbstractList.add(AbstractList.java:131) at java.util.AbstractList.add(AbstractList.java:91) at figtree.treeviewer.decorators.DiscreteColourDecorator.setAttributes(Unknown Source) at figtree.treeviewer.AttributeColourController.getDecoratorForAttribute(Unknown Source) at figtree.treeviewer.AttributeColourController.setSettings(Unknown Source) at jam.controlpalettes.BasicControlPalette.setSettings(Unknown Source) at figtree.application.FigTreeFrame.readData(Unknown Source) at figtree.application.FigTreeFrame.readFromFile(Unknown Source) at jam.framework.DocumentFrame.openFile(Unknown Source) at figtree.application.FigTreeApplication.doOpenFile(Unknown Source) at jam.framework.Application.doOpen(Unknown Source) at jam.framework.Application$4.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95) at java.awt.MenuItem.processActionEvent(MenuItem.java:650) at java.awt.MenuItem.processEvent(MenuItem.java:609) at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343) at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:687) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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) 2017-12-12 15:08:29.030 java[14294:418487] Persistent UI failed to open file file://localhost/Users/David/Library/Saved%20Application%20State/com.apple.javajdk16.cmd.savedState/window_1.data: Permission denied (13)
Thanks friend!
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/rambaut/figtree/issues/120 https://github.com/rambaut/figtree/issues/120>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAp5RSXcruAV8fjbt0g5FLZsgwrCqK5Uks5s_pLGgaJpZM4Q_Fz0 https://github.com/notifications/unsubscribe-auth/AAp5RSXcruAV8fjbt0g5FLZsgwrCqK5Uks5s_pLGgaJpZM4Q_Fz0>.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/rambaut/figtree/issues/120#issuecomment-351074251 https://github.com/rambaut/figtree/issues/120#issuecomment-351074251>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJ6qu6Iw5MI_VnxYJ8N2IKGo_pTYLXKBks5s_pNXgaJpZM4Q_Fz0 https://github.com/notifications/unsubscribe-auth/AJ6qu6Iw5MI_VnxYJ8N2IKGo_pTYLXKBks5s_pNXgaJpZM4Q_Fz0>.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120#issuecomment-351074811, or mute the thread https://github.com/notifications/unsubscribe-auth/AAp5RfeQ4SPSolYXL_O8kw2WNRlhNEtPks5s_pPGgaJpZM4Q_Fz0.
Ok, I just download and tried, and I doesn’t work.
The tip labels also don’t appear, if you uncheck the option the screen shows the tree. Let me share with you the file, we are trying to extract the figure in PDF for our paper. I think that maybe there are too many number of taxa? Thanks for everythin, I would appreciate a lot your fast answer and your help. Thanks! Regards from Spain.
David
El 12 dic 2017, a las 15:57, rambaut [email protected] escribió:
In which case could you download and try the v1.4.4 pre-release:
https://github.com/rambaut/figtree/releases/tag/v1.4.4pre20171111 https://github.com/rambaut/figtree/releases/tag/v1.4.4pre20171111
I believe this is still not compatible with Java 1.9 on the Mac so do not upgrade from Java 1.8.
If there is still an issue, let me know.
Andrew
On 12 Dec 2017, at 14:55, tapeda [email protected] wrote:
Mac OS High Sierra 10.13.2, If you want I can send you privately the file which is reporting me this problems…I cannot also see the name of my taxa. Thanks!
El 12 dic 2017, a las 15:53, rambaut <[email protected] mailto:[email protected]> escribió:
What OS is this on?
A.
On 12 Dec 2017, at 14:50, tapeda <[email protected] mailto:[email protected]> wrote:
Here what I have in the console: bash-3.2$ java -jar /Users/David/Desktop/FigTree_v1.4.3/lib/figtree.jar javax.swing.UIManager$LookAndFeelInfo[Metal javax.swing.plaf.metal.MetalLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Nimbus com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[CDE/Motif com.sun.java.swing.plaf.motif.MotifLookAndFeel] javax.swing.UIManager$LookAndFeelInfo[Mac OS X com.apple.laf.AquaLookAndFeel] objc[14294]: Class FIFinderSyncExtensionHost is implemented in both /System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit (0x7fff8c19eb68) and /System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride (0x11bf85cd8). One of the two will be used. Which one is undefined. Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedOperationException at java.util.AbstractList.add(AbstractList.java:131) at java.util.AbstractList.add(AbstractList.java:91) at figtree.treeviewer.decorators.DiscreteColourDecorator.setAttributes(Unknown Source) at figtree.treeviewer.AttributeColourController.getDecoratorForAttribute(Unknown Source) at figtree.treeviewer.AttributeColourController.setSettings(Unknown Source) at jam.controlpalettes.BasicControlPalette.setSettings(Unknown Source) at figtree.application.FigTreeFrame.readData(Unknown Source) at figtree.application.FigTreeFrame.readFromFile(Unknown Source) at jam.framework.DocumentFrame.openFile(Unknown Source) at figtree.application.FigTreeApplication.doOpenFile(Unknown Source) at jam.framework.Application.doOpen(Unknown Source) at jam.framework.Application$4.actionPerformed(Unknown Source) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95) at java.awt.MenuItem.processActionEvent(MenuItem.java:650) at java.awt.MenuItem.processEvent(MenuItem.java:609) at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343) at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:720) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:687) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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.NullPointerException at figtree.treeviewer.TreePane.calibrate(Unknown Source) at figtree.treeviewer.TreePane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(JComponent.java:870) at javax.swing.JComponent.paint(JComponent.java:1046) at javax.swing.JViewport.paint(JViewport.java:795) at javax.swing.JComponent._paintImmediately(JComponent.java:5106) at javax.swing.JComponent.paintImmediately(JComponent.java:4890) at javax.swing.RepaintManager$3.run(RepaintManager.java:814) at javax.swing.RepaintManager$3.run(RepaintManager.java:802) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:802) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:745) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:725) at javax.swing.RepaintManager.access$1000(RepaintManager.java:46) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1680) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.awt.EventQueue.dispatchEvent(EventQueue.java:685) 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) 2017-12-12 15:08:29.030 java[14294:418487] Persistent UI failed to open file file://localhost/Users/David/Library/Saved%20Application%20State/com.apple.javajdk16.cmd.savedState/window_1.data: Permission denied (13)
Thanks friend!
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/rambaut/figtree/issues/120 https://github.com/rambaut/figtree/issues/120>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAp5RSXcruAV8fjbt0g5FLZsgwrCqK5Uks5s_pLGgaJpZM4Q_Fz0 https://github.com/notifications/unsubscribe-auth/AAp5RSXcruAV8fjbt0g5FLZsgwrCqK5Uks5s_pLGgaJpZM4Q_Fz0>.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/rambaut/figtree/issues/120#issuecomment-351074251 https://github.com/rambaut/figtree/issues/120#issuecomment-351074251>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJ6qu6Iw5MI_VnxYJ8N2IKGo_pTYLXKBks5s_pNXgaJpZM4Q_Fz0 https://github.com/notifications/unsubscribe-auth/AJ6qu6Iw5MI_VnxYJ8N2IKGo_pTYLXKBks5s_pNXgaJpZM4Q_Fz0>.
— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120#issuecomment-351074811, or mute the thread https://github.com/notifications/unsubscribe-auth/AAp5RfeQ4SPSolYXL_O8kw2WNRlhNEtPks5s_pPGgaJpZM4Q_Fz0.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120#issuecomment-351075576, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ6quzIyr215KMZnYhwJVD-NWjeSYuPRks5s_pRXgaJpZM4Q_Fz0.
Dear Andrew,
First of all my best wishes in the New Year 2018. I would like to know if you receive at the end my tree file in which I experimented problems during PDF export. Your software is being very useful to us in other to analyze and plot your results. We are very interested in obtain this plot because we are enrolled on the writing of a paper related with this data, It takes me a lot of time to group, contract and paint the different groups of data and I would like to show the results in the paper.
Thank you very much.
Sincerely yours
David
El 12 dic 2017, a las 16:11, rambaut [email protected] escribió:
Can you post the file here - or email it to me.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/rambaut/figtree/issues/120#issuecomment-351079880, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ6qu6tcj-eDp-KXJr4AySsSFVZZZml7ks5s_peRgaJpZM4Q_Fz0.
Dear Andrew,
I am still having problems with PDF export and my huge tree, even with the last version 1.4.4. In the last version I can't open the tree (it opens but I doesn't appear the image in the screen) and also is not able to export. Thanks!
I have the same problem. If there are additional information in the tree file, figtree cannot not export the figure to pdf. However, if the tree file was exported to a nexus format and re-open in Figtree, it can export PDF file. I think the additional information blocked the PDF export. Unfortunately, the additional information is the key point I need.
That’s the point...the additional information is the key point I need too...
Enviado desde mi iPad
El 18 sept 2019, a las 20:43, yzong [email protected] escribió:
I have the same problem. If there are additional information in the tree file, figtree cannot not export the figure to pdf. However, if the tree file was exported to a nexus format and re-open in Figtree, it can export PDF file. I think the additional information blocked the PDF export. Unfortunately, the additional information is the key point I need.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.
If its any help the following allowed me to save to pdf with annotations when I had the same problem:
- open the tree in figtree and show annotations
- export tree to a new nexus, making sure to tick the 'save as currently displayed', 'include figtree block', 'include annotations' options
- open the new nexus
- export to pdf
