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  5<title>Known Bugs in Gmaj</title>
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 11<p class=vvlarge>
 12<h2>Known Bugs in Gmaj</h2>
 13<p class=vvlarge>
 14The following anomalies in Gmaj's display and behavior have been
 15observed, but not yet resolved.  Some of these are intermittent,
 16and some may depend on your computer platform and/or version of
 19If you experience any of these (or similar) problems, it may help
 20to switch to a different version of Java.  For example, the first
 21bug listed below (phantom repeats) seems to have been introduced
 22with Sun's J2SE 1.4.x series, so you may be better off with 1.3.x
 23or 1.5.x.  You can also try switching to a different vendor's
 24implementation, but then you are on your own, as we develop and
 25test Gmaj using Sun's official API and SDK.  Currently Gmaj does
 26not rely on any features beyond Java 1.3, in order to preserve
 27version flexibility for our users.
 29Note that anomalies that depend on the Java version could be due
 30to bugs in Java itself, but could also be bugs in Gmaj that only
 31"matter" with certain implementations of Java.  In either case,
 32however, with further investigation it may be possible to work
 33around the problem in future releases of Gmaj.
 34<p class=vlarge>
 36<li>	<a name="phantom"><i>Phantom repeats.</i></a>&nbsp;
 37	After zooming in on a small region, the "repeats" panel
 38	sometimes shows a spurious extra bar superimposed on the
 39	legitimate features across the entire width of the window,
 40	or the features may disappear entirely.
 42<li>	<a name="zoombox"><i>Missing zoom box and crosshairs.</i></a>&nbsp;
 43	With some datasets (large ones especially) the lines for the
 44	zoom rectangle and crosshairs may not display.  It still
 45	zooms OK though, if you just pretend the lines are there.
 46	<b>Update:</b> This appears to have been fixed in Java 1.5.
 48<!-- [fixed 02/19/08]
 49<li>	<a name="buttonscroll"><i>Scrollbar obscures block buttons.</i></a>&nbsp;
 50	If there is not enough room for all of the block buttons
 51	corresponding to the marked position, a scrollbar will
 52	appear.  However, the extra vertical space required for
 53	the scrollbar may not be calculated properly, so that the
 54	scrollbar partially obscures the button labels.  To read
 55	the labels, drag the partition between the mark indicator
 56	box and the button panel toward the left, to create more
 57	space for the buttons.
 60<li>	<a name="dialogcopy"><i>Can't copy text from dialog messages in applet.</i></a>&nbsp;
 61	In applet mode, you may not be able to select and copy text
 62	from pop-up message boxes to the system clipboard for
 63	pasting elsewhere.  This is apparently due to a bug in Java;
 64	hopefully Sun will fix it eventually.
 66<li>	<a name="xor"><i>Patchy rendering of mark circle and/or red segments.</i></a>&nbsp;
 67	When using the Large Fonts option with Mark Color Varies,
 68	the red circle and plot segments may not appear as solid
 69	as they should.  This is because Mark Color Varies is
 70	implemented using Java's XOR drawing mode, and the thick
 71	lines are built up from several thin ones, so whenever two
 72	red pixels overlap they turn white again.  Fixing this will
 73	likely involve a custom implementation of Mark Color Varies
 74	that doesn't use XOR.  In the meantime, switching to Mark
 75	Always Red when using Large Fonts should solve the problem
 76	(except that it will be invisible against red underlays).
 78<!-- [fixed 07/16/07]
 79<li>	<a name="buildfocus"><i>GUI rebuild breaks keyboard shortcuts.</i></a>&nbsp;
 80	The items on the Options menu generally require all of the
 81	open windows to be rebuilt, and although the window that was
 82	active may still be in front, on some systems it might not
 83	actually have the keyboard focus.  So when you press a key,
 84	say "<code>b</code>" for "Zoom - Back", one of the other
 85	windows changes instead of the one you wanted.  Even the
 86	Escape key doesn't help, because it goes to the wrong
 87	window too.  Investigation of how best to prevent this is
 88	underway; in the meantime you can fix it by clicking on a
 89	different window and then returning to the one you want.
 92<li>	<a name="leak"><i>Memory leak when closing or rebuilding windows.</i></a>&nbsp;
 93	When windows are closed or rebuilt (e.g. when loading data
 94	via File - Open, switching to Large Fonts, or even just
 95	displaying dialog boxes), not all of the memory they were
 96	using is being reclaimed, so Gmaj will gradually run out
 97	and have to be restarted.  How quickly this happens will
 98	depend on how much memory you have allocated to Java with
 99	the <code><a href="gmaj_help.html#memory">-Xmx</a></code>
100	switch, and the size of your dataset.
103<li>	<a name=" "><i>Name.</i></a>&nbsp;
104	Description.
108<p class=vlarge>
109If you encounter any bugs not listed here, please report them to
110<img align=top alt="[image of email address]" src="cathy.gmaj.png">.
111It would be helpful if you can include the version of Gmaj you
112are using (i.e., the JarDate line from the Help - About message),
113your computer platform and version of Java, copies of the data
114files you were trying to view, and a description of exactly what
115you were doing when the problem occurred.  This will help us to
116reproduce the problem so we can track it down and fix it.
117Non-bug suggestions and feedback are also welcome.
119Thank you for using Gmaj, and helping us to make it better.
122<p class=vvlarge>
124<i>Cathy Riemer, June 2008</i>
126<p class=scrollspace>