urmi-21/metaomgraph

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Hi there 👋

🔭 I’m a Bioinformatics Scientist at Illumina.

metaomgraph's Issues

Previous issues

Previous issues are listed here
https://github.com/urmi-21/MOG-debugging/issues

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.updateTable(MetadataTableDisplayPanel.java:1595)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.addExtInfoTab(MetaOmTablePanel.java:2329)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.<init>(MetaOmTablePanel.java:676)
edu.iastate.metnet.metaomgraph.MetaOmGraph.projectOpened(MetaOmGraph.java:1867)
edu.iastate.metnet.metaomgraph.MetaOmGraph.access$2(MetaOmGraph.java:1856)
edu.iastate.metnet.metaomgraph.MetaOmGraph$OpenProjectWorker.finished(MetaOmGraph.java:2339)
edu.iastate.metnet.metaomgraph.AnimatedSwingWorker$1.run(AnimatedSwingWorker.java:93)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117)
java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
Testing token, Ignore this
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.actionPerformed(MetadataTableDisplayPanel.java:2479)
java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279)
java.desktop/java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:297)
java.desktop/java.awt.Component.processMouseEvent(Component.java:6632)
java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342)
java.desktop/java.awt.Component.processEvent(Component.java:6397)
java.desktop/java.awt.Container.processEvent(Container.java:2263)
java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5008)
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
java.desktop/java.awt.Component.dispatchEvent(Component.java:4840)
java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918)
java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547)
java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488)
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307)
java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2762)
java.desktop/java.awt.Component.dispatchEvent(Component.java:4840)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
color chooser bug
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.ClassCastException: edu.iastate.metnet.metaomgraph.ui.ColorChooseButton$1 cannot be cast to javax.swing.AbstractButton
javax.swing.plaf.basic.BasicButtonListener.stateChanged(BasicButtonListener.java:158)
edu.iastate.metnet.metaomgraph.ui.ColorChooseButton$1.actionPerformed(ColorChooseButton.java:46)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Error shown after Sample metadata table is filtered/updated

Occasionally this error message is shown after the sample metadata table is updated. It is harmless, after closing error dialog things seem normal.

Describe the dataset used
The human dataset from here: http://metnetweb.gdcb.iastate.edu/MetNet_MetaOmGraph.htm

To Reproduce
Steps to reproduce the behavior:

1. Go to sample metadata table
2. Click on Edit->Filter rows
3. Perform query
4. See error

Expected behavior
After the search, the metadata table should be updated and display the retained rows.

Desktop (please complete the following information):

• OS: Windows10
• Java version: 1.8
• Total available memory: 8GB
• CPU and number of cores: Intel i5/4 cores

MOG Error Report

java.lang.ArrayIndexOutOfBoundsException: 4 >= 4 java.base/java.util.Vector.elementAt(Vector.java:463) java.desktop/javax.swing.table.DefaultTableColumnModel.getColumn(DefaultTableColumnModel.java:295) java.desktop/javax.swing.plaf.basic.BasicTableHeaderUI.paint(BasicTableHeaderUI.java:671) java.desktop/javax.swing.plaf.ComponentUI.update(ComponentUI.java:161) java.desktop/javax.swing.JComponent.paintComponent(JComponent.java:797) java.desktop/javax.swing.JComponent.paint(JComponent.java:1074) java.desktop/javax.swing.JComponent.paintToOffscreen(JComponent.java:5255) java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBufferedImpl(RepaintManager.java:1643) java.desktop/javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1618) java.desktop/javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1556) java.desktop/javax.swing.RepaintManager.paint(RepaintManager.java:1323) java.desktop/javax.swing.JComponent._paintImmediately(JComponent.java:5203) java.desktop/javax.swing.JComponent.paintImmediately(JComponent.java:5013) java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:865) java.desktop/javax.swing.RepaintManager$4.run(RepaintManager.java:848) java.base/java.security.AccessController.doPrivileged(AccessController.java:391) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:848) java.desktop/javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:823) java.desktop/javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:772) java.desktop/javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1884) java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313) java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770) java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721) java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715) java.base/java.security.AccessController.doPrivileged(AccessController.java:391) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740) java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117) java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190) java.desktop/java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:235) java.desktop/java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:233) java.base/java.security.AccessController.doPrivileged(AccessController.java:312) java.desktop/java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:233) java.desktop/java.awt.Dialog.show(Dialog.java:1070) java.desktop/java.awt.Component.show(Component.java:1716) java.desktop/java.awt.Component.setVisible(Component.java:1663) java.desktop/java.awt.Window.setVisible(Window.java:1021) java.desktop/java.awt.Dialog.setVisible(Dialog.java:1005) edu.iastate.metnet.metaomgraph.AnimatedSwingWorker.start(AnimatedSwingWorker.java:166) edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.updateTable(MetadataTableDisplayPanel.java:1203) edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.updateTable(MetadataTableDisplayPanel.java:1126) edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.updateMetadataTable(MetaOmTablePanel.java:3781) edu.iastate.metnet.metaomgraph.ui.MetadataTreeDisplayPanel.updateTree(MetadataTreeDisplayPanel.java:666) edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.updateMetadataTree(MetaOmTablePanel.java:3788) edu.iastate.metnet.metaomgraph.ui.MetadataFilter$2.actionPerformed(MetadataFilter.java:170) java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967) java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308) java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) java.desktop/java.awt.Component.processMouseEvent(Component.java:6636) java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342) java.desktop/java.awt.Component.processEvent(Component.java:6401) java.desktop/java.awt.Container.processEvent(Container.java:2263) java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5012) java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321) java.desktop/java.awt.Component.dispatchEvent(Component.java:4844) java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918) java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547) java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488) java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307) java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2762) java.desktop/java.awt.Component.dispatchEvent(Component.java:4844) java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772) java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721) java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715) java.base/java.security.AccessController.doPrivileged(AccessController.java:391) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95) java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745) java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743) java.base/java.security.AccessController.doPrivileged(AccessController.java:391) java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85) java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742) java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MOG will not export more than 250 columns to xls.

MOG will not export more than 250 columns to xls from the import to xls box on the line chart

. (250 used to be the column limit for xls >10 years ago when this was implemented, but it is far greater now.)

Improve MOG tooltips

Is your feature request related to a problem? Please describe.
Many buttons and fields lack tooltip.

Describe the solution you'd like
Add tooltips to MOG interface objects.

add "NOT" as user option to search and selection functions.

add "NOT" as user option to search and selection functions.

Implement a taskbar to track MOG's internal windows

Many windows tend to hide behind others. Implement a taskbar to track MOG's internal windows.

Improve interface to save plots; show file-type options

MOG can export charts as .png and .svg graphics. Write now interface relies on the user's provided file-type extension to choose the file-type. The interface should display the options to the user to choose the file type e.g. .png, .svg, .jpg.

sorting problem in project data and chart

From @lijing28101 on June 29, 2018 15:37

When sorting in project data, it cannot distinguish the number and string.
Hope to add a function to sort the x-axis name in the chart.

Copied from original issue: urmi-21/MOG-debugging#14

allow to check for the latest version

From @urmi-21 on October 27, 2018 23:31

Let MOG check for the latest version and update if required.

Copied from original issue: urmi-21/MOG-debugging#16

doesnt ID number of columns with study metadata correctly

From @evewurtele on April 23, 2018 14:50

(using maize study metadata .cvs file)

Copied from original issue: urmi-21/MOG-debugging#9

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
for testing
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.updateTable(MetadataTableDisplayPanel.java:1595)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.addExtInfoTab(MetaOmTablePanel.java:2329)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.<init>(MetaOmTablePanel.java:676)
edu.iastate.metnet.metaomgraph.MetaOmGraph.projectOpened(MetaOmGraph.java:1867)
edu.iastate.metnet.metaomgraph.MetaOmGraph.access$2(MetaOmGraph.java:1856)
edu.iastate.metnet.metaomgraph.MetaOmGraph$OpenProjectWorker.finished(MetaOmGraph.java:2339)
edu.iastate.metnet.metaomgraph.AnimatedSwingWorker$1.run(AnimatedSwingWorker.java:93)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117)
java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments: I chnaged themes a couple times, then changed color properties, then reverted to blue color theme. then I clicked "color" tab at bottom left. this is result
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.TaskbarPanel$1.actionPerformed(TaskbarPanel.java:211)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.AbstractButton.doClick(AbstractButton.java:376)
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

quitting MOG

Every place that says "Quit MOG" should actually function.

shared project

When a project is shared, it does not open automatically. rather, as a user, I am asked to find the correct data and metadata txt files. When this happens, correct files are greyed out.

If I select "see all files", then then can see and chose correct data and metadata files, and make the project. But a first time user would not know that.

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.updateTable(MetadataTableDisplayPanel.java:1595)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.addExtInfoTab(MetaOmTablePanel.java:2329)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.<init>(MetaOmTablePanel.java:676)
edu.iastate.metnet.metaomgraph.MetaOmGraph.projectOpened(MetaOmGraph.java:1867)
edu.iastate.metnet.metaomgraph.MetaOmGraph.access$2(MetaOmGraph.java:1856)
edu.iastate.metnet.metaomgraph.MetaOmGraph$OpenProjectWorker.finished(MetaOmGraph.java:2339)
edu.iastate.metnet.metaomgraph.AnimatedSwingWorker$1.run(AnimatedSwingWorker.java:93)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117)
java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.actionPerformed(MetadataTableDisplayPanel.java:2479)
java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279)
java.desktop/java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:297)
java.desktop/java.awt.Component.processMouseEvent(Component.java:6632)
java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3342)
java.desktop/java.awt.Component.processEvent(Component.java:6397)
java.desktop/java.awt.Container.processEvent(Container.java:2263)
java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5008)
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2321)
java.desktop/java.awt.Component.dispatchEvent(Component.java:4840)
java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4918)
java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4547)
java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4488)
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2307)
java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2762)
java.desktop/java.awt.Component.dispatchEvent(Component.java:4840)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:772)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:95)
java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
java.desktop/java.awt.EventQueue$5.run(EventQueue.java:743)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Add a button to close the Import Meta Data frame after data is imported.

Implement the same for all the frames changed as part of issue #23

Subsets/lists for samples

MOG can search and subset the samples but there should be a way to store the subset lists and switch to the selected subset with just a click, just like feature lists.

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.MetaOmProject.getAllDefaultRowNames(MetaOmProject.java:2409)
edu.iastate.metnet.metaomgraph.MetaOmProject.getRowIndexbyName(MetaOmProject.java:2347)
edu.iastate.metnet.metaomgraph.ui.StripedTable.getToolTipText(StripedTable.java:75)
javax.swing.ToolTipManager$insideTimerAction.actionPerformed(ToolTipManager.java:675)
javax.swing.Timer.fireActionPerformed(Timer.java:313)
javax.swing.Timer$DoPostEvent.run(Timer.java:245)
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Enable hypothesis testing in boxplot charts

When two or more features are plotted as boxplot, perform hypothesis test on the distribution and display the results in the box plot. User can choose U test or t test. For more than two categories perform anova.

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.MetadataTableDisplayPanel.updateTable(MetadataTableDisplayPanel.java:1595)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.addExtInfoTab(MetaOmTablePanel.java:2329)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.<init>(MetaOmTablePanel.java:676)
edu.iastate.metnet.metaomgraph.MetaOmGraph.projectOpened(MetaOmGraph.java:1867)
edu.iastate.metnet.metaomgraph.MetaOmGraph.access$2(MetaOmGraph.java:1856)
edu.iastate.metnet.metaomgraph.MetaOmGraph$OpenProjectWorker.finished(MetaOmGraph.java:2339)
edu.iastate.metnet.metaomgraph.AnimatedSwingWorker$1.run(AnimatedSwingWorker.java:93)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117)
java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:190)
java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email: urmi-21
Comments:
Cosine similarity histogram from matrix table
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.IllegalArgumentException: Identifier not found
javax.swing.table.DefaultTableColumnModel.getColumnIndex(DefaultTableColumnModel.java:282)
javax.swing.JTable.getColumn(JTable.java:2564)
edu.iastate.metnet.metaomgraph.ui.SimilarityDisplayFrame$5.actionPerformed(SimilarityDisplayFrame.java:132)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.AbstractButton.doClick(AbstractButton.java:376)
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

filter didn't work in linux

From @lijing28101 on February 27, 2018 21:33

The filter function for metadata didn't work in linux

Copied from original issue: urmi-21/MOG-debugging#7

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.MetaOmProject.getAllDefaultRowNames(MetaOmProject.java:2409)
edu.iastate.metnet.metaomgraph.MetaOmProject.getRowIndexbyName(MetaOmProject.java:2347)
edu.iastate.metnet.metaomgraph.ui.StripedTable.getToolTipText(StripedTable.java:75)
javax.swing.ToolTipManager$insideTimerAction.actionPerformed(ToolTipManager.java:675)
javax.swing.Timer.fireActionPerformed(Timer.java:313)
javax.swing.Timer$DoPostEvent.run(Timer.java:245)
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Show tips while MOG is busy

While doing some complex operations like loading projects, it would be great if MOG displays tips to user while waiting.

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
here, I clicked on the star.
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.ClassCastException: java.lang.String cannot be cast to edu.iastate.metnet.metaomgraph.playback.LoggingTreeNode
edu.iastate.metnet.metaomgraph.ui.ReproducibilityDashboardPanel.markActionsAsFavorite(ReproducibilityDashboardPanel.java:1054)
edu.iastate.metnet.metaomgraph.ui.ReproducibilityDashboardPanel$8.actionPerformed(ReproducibilityDashboardPanel.java:447)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Implement a new tab to display results of DEA

Implement a new tab to display results of DEA, Differential correlation, etc.

MOG can't handle files which don't follow the required format.

From @urmi-21 on February 9, 2018 22:28

MOG will crash when a file is in weired format. e.g. load a non-tab delimited file in the metadata as a metadata file. Need to handle these exceptions.

Copied from original issue: urmi-21/MOG-debugging#3

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
I tried to open a previous session. the default is logging set to permanently off. yet I seem to have choices of previous sessions.
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.playback.PlaybackAction.playActions(PlaybackAction.java:58)
edu.iastate.metnet.metaomgraph.ui.ReproducibilityDashboardPanel$7.actionPerformed(ReproducibilityDashboardPanel.java:425)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Feature request: Preload the test dataset on the jar file and provide it as an option in the "Welcome to MetaOmGraph" window

From @aseetharam on February 9, 2018 15:1

Like the title says, it is useful to just play around without downloading anything other than the MOG jar file. I think it will be useful for getting started really quickly for beginners!

Copied from original issue: urmi-21/MOG-debugging#2

Implement import metadata window as an internal frame

Is your feature request related to a problem? Please describe.
Importing metadata into a project opens a new window outside of MOG. It would be better if it opes a new internal frame.
This also goes for editing samples window from Edit-->Manage samples.

Describe the solution you'd like
Reimplement import metadata window to be an internal frame.

allow to check for the latest version

From @urmi-21 on October 27, 2018 23:31

Let MOG check for the latest version and update if required.

Copied from original issue: urmi-21/MOG-debugging#16

Implement heatmap visualisation

Heatmaps are great for visualizing gene expression datasets. MOG doesn't have interactive heatmaps yet.

Add sorting options for box plot

Is your feature request related to a problem? Please describe.
Add sorting options to box plot. E.g. sort by median value, sort by groups, etc.

Describe the solution you'd like
Implement an interface to allow the sorting of boxplots. Currently, a triple-click allows reordering the box plot but an automated sorting method is needed.

Mog doesn't update the sample meta data table when editing metadata structure.

Cannot open the most recent project directly (clear unwanted recent projects)

From @lijing28101 on February 12, 2018 19:5

In linux, when open MOG, and the mouse cannot click on the most two recent project under "Open an existing project". The mouse is always flash.

Copied from original issue: urmi-21/MOG-debugging#5

Crash reported from user

MetaOmGraph Error:
Email: [email protected]
Comments:
This is a test exception generated by MOG
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Windows 10
Error log:

java.lang.ArithmeticException: / by zero
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.makeBoxPlot(MetaOmTablePanel.java:1429)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.actionPerformed(MetaOmTablePanel.java:2572)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.AbstractButton.doClick(AbstractButton.java:376)
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Clicking the external web applications button in line chart crashes the window

Clicking the external web applications button in line chart crashes the window.

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.ui.TaskbarPanel$1.actionPerformed(TaskbarPanel.java:211)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.AbstractButton.doClick(AbstractButton.java:376)
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

often wont sort columns, select lines, even though I click

From @evewurtele on August 6, 2018 19:47

often won't sort columns - this is new issue.
I am using the human dat, regular file.

With any dataset, in the graph view, it is hard to get MOG to change a line to make it thicker, or sometimes to change the color of the line.

I piut these together because they may be related.

Copied from original issue: urmi-21/MOG-debugging#15

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.ClassCastException: java.lang.String cannot be cast to edu.iastate.metnet.metaomgraph.playback.LoggingTreeNode
edu.iastate.metnet.metaomgraph.playback.PlaybackAction.playActions(PlaybackAction.java:61)
edu.iastate.metnet.metaomgraph.ui.ReproducibilityDashboardPanel$7.actionPerformed(ReproducibilityDashboardPanel.java:425)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException
edu.iastate.metnet.metaomgraph.MetaOmProject.getAllDefaultRowNames(MetaOmProject.java:2409)
edu.iastate.metnet.metaomgraph.MetaOmProject.getRowIndexbyName(MetaOmProject.java:2347)
edu.iastate.metnet.metaomgraph.ui.StripedTable.getToolTipText(StripedTable.java:75)
javax.swing.ToolTipManager$insideTimerAction.actionPerformed(ToolTipManager.java:675)
javax.swing.Timer.fireActionPerformed(Timer.java:313)
javax.swing.Timer$DoPostEvent.run(Timer.java:245)
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

MetaOmBot: Bug report from user

MetaOmGraph Error:
Email:
Comments:
MOG version: v. 1.8.1
MOG date: February 20, 2020
OS: Mac OS X
Error log:

java.lang.NullPointerException: No last correlation to save
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.keepLastCorrelation(MetaOmTablePanel.java:5331)
edu.iastate.metnet.metaomgraph.ui.MetaOmTablePanel.actionPerformed(MetaOmTablePanel.java:4263)
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
javax.swing.AbstractButton.doClick(AbstractButton.java:376)
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
java.awt.Component.processMouseEvent(Component.java:6539)
javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
java.awt.Component.processEvent(Component.java:6304)
java.awt.Container.processEvent(Container.java:2239)
java.awt.Component.dispatchEventImpl(Component.java:4889)
java.awt.Container.dispatchEventImpl(Container.java:2297)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
java.awt.Container.dispatchEventImpl(Container.java:2283)
java.awt.Window.dispatchEventImpl(Window.java:2746)
java.awt.Component.dispatchEvent(Component.java:4711)
java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
java.awt.EventQueue.access$500(EventQueue.java:97)
java.awt.EventQueue$3.run(EventQueue.java:709)
java.awt.EventQueue$3.run(EventQueue.java:703)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
java.awt.EventQueue$4.run(EventQueue.java:733)
java.awt.EventQueue$4.run(EventQueue.java:731)
java.security.AccessController.doPrivileged(Native Method)
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Re-implent MOG error reporting

From @urmi-21 on February 9, 2018 22:30

The code which is responsible for sending out emails should be encrypted.

Copied from original issue: urmi-21/MOG-debugging#4

allow to check for the latest version

From @urmi-21 on October 27, 2018 23:31

Let MOG check for the latest version and update if required.

Copied from original issue: urmi-21/MOG-debugging#16

Is-it--possible-to-reorient-labels-in-box-plots-so-that-they-are-vertical,-underneath-each-box?--would-be-very-helpful-if-possible

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

Add density histogram

Is your feature request related to a problem? Please describe.
Currently, the histogram plot shows the frequency of data. There should be an option to create normalized by sum histogram that would correspond to density.

Describe the solution you'd like
Add an option to the histogram plot to normalize histogram by total count.