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When using any java application in gnome-shell if the window is maximised the pointer position is way off; but only on the menu's, in the editor, or the side panel, the pointer is fine.

This only presents itself when the window is maximized, and it seems that the further away from 0x0 the window is when you maximise it, the bigger the pointer offset.

From what I have gathered it has to do with the window not updating it's size when it gets maximised.

The other issue is that when a gnome-shell notification appears, when clicking on it, I lose the ability to type in the editor, I can select text etc, but can't give it focus to type. I must bring up some other text input (e.g. right click on a file on the left, select rename, which brings up a rename dialog) after that I can type in the editor again.

So, how can I fix this?

Below is as much information as I can think to provide

Pointer position offset

enter image description here

$ gnome-shell --version
GNOME Shell 3.6.1

$ java -version
java version "1.7.0_09" Java(TM) SE Runtime
Environment (build 1.7.0_09-b05) Java HotSpot(TM) 64-Bit Server VM
(build 23.5-b02, mixed mode)

$ file /etc/alternatives/java /etc/alternatives/javac
/etc/alternatives/java: symbolic link to '/usr/lib/jvm/java-7-oracle/jre/bin/java'
/etc/alternatives/javac: symbolic link to '/usr/lib/jvm/java-7-oracle/bin/javac'

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if you get this problem fixed? i have the same problem. – turtledove Dec 18 '12 at 5:54
jetbrains have implemented a fix in the eap version – Hailwood Dec 18 '12 at 6:17
I think this is a bug. And if not I would just say "Wow!". (I've seen this problem on MATLAB some releases back.) So you should file it where appropriate. According to the answer here the bug is not reproducible in Java 6, try switching to Java 6 if possible. – edwin Jul 6 '13 at 0:41
up vote 0 down vote accepted

This bug was fixed in the EAP release of PHPstorm following this post, as far as I am aware a global fix was implemented with the upgraded java version.

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