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Update AlignmentTrack.java #1245

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Update AlignmentTrack.java #1245

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CJ-Chen
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@CJ-Chen CJ-Chen commented Oct 25, 2022

"insertionRect" needs to be initialized though not displayed.
It might cause a null pointer exception in Line 709 "Rectangle iRect = new Rectangle(inputRect.x, insertionRect.y, inputRect.width, insertionRect.height);"
when some alignment tracks are displaying insertion markers while others do not.

@CJ-Chen
Update AlignmentTrack.java
1530cc6 
"insertionRect" needs to be initialized though not displayed.
It might cause a null pointer exception in Line 709 "Rectangle iRect = new Rectangle(inputRect.x, insertionRect.y, inputRect.width, insertionRect.height);"
when some alignment tracks are displaying insertion markers while others do not.
@CJ-Chen
Merge pull request #1 from CJ-Chen/CJ-Chen-patch-insertionRect
9426af0 
Update AlignmentTrack.java
@CJ-Chen
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CJ-Chen commented Oct 25, 2022

Sorry for this PR.
It seems that this modification will consume much more time for graph rendering.
I don't know why.

@CJ-Chen
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CJ-Chen commented Oct 25, 2022

Maybe we can use "insertionRect.setBounds(rect);" to replace "insertionRect = new Rectangle(rect);" around line 523?

@jrobinso
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I'll investigate when I can find time, but do you have steps to reproduce an issue? In what situation did an error occur?

@CJ-Chen
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CJ-Chen commented Oct 27, 2022

I'll investigate when I can find time, but do you have steps to reproduce an issue? In what situation did an error occur?

Here is a genome with two alignment track. One is displaying with “Show Insertion Mark” and the other without selected this option.

And when i click this the insertion mark. It will report a null pointer exception that mention above.

igv.log:
SEVERE [10月 27,2022 14:00] [DataPanel] Error painting DataPanel
SEVERE [10月 27,2022 14:00] [DataPanel] java.lang.NullPointerException
	at org.igv/org.broad.igv.sam.AlignmentTrack.renderExpandedInsertion(AlignmentTrack.java:679)
	at org.igv/org.broad.igv.ui.panel.DataPanelPainter.paintExpandedInsertion(DataPanelPainter.java:214)
	at org.igv/org.broad.igv.ui.panel.DataPanelPainter.paint(DataPanelPainter.java:89)
	at org.igv/org.broad.igv.ui.panel.DataPanel.paintComponent(DataPanel.java:154)

Sorry for the inconvenience.

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jrobinso commented Nov 7, 2022

I can't reproduce the error just loading tracks, only after loading tracks via a session. So I think this is the same error as reported here: #1252. I will close this PR as a duplicate bug report.

@jrobinso jrobinso closed this Nov 7, 2022
jrobinso added a commit that referenced this pull request Nov 7, 2022
@jrobinso
Fixes #1252, #1245
b7da8e5
archlinux-github referenced this pull request in archlinux/aur Nov 8, 2022
Update to 2.15.2-1
ad9ac8e 
* Upstream changelog: Fixes [https://github.com/igvteam/igv/issues/1252](#1252), [https://github.com/igvteam/igv/pull/1245](#1245)
jrobinso added a commit that referenced this pull request Dec 14, 2022
@jrobinso
Fixes #1252, #1245
c9f483c
jrobinso added a commit that referenced this pull request Dec 15, 2022
@jrobinso
Fixes #1252, #1245
32e5f82
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@CJ-Chen @jrobinso