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4<head>
5<title>Known Bugs in Gmaj</title>
6<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
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8<link rel="stylesheet" type="text/css" href="gmaj.css">
9</head>
10<body>
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
17Java.
18<p>
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.
28<p>
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>
35<ul>
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.
41<p>
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.
47<p>
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.
58<p>
59-->
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.
65<p>
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).
77<p>
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.
90<p>
91-->
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.
101<p>
102<!--
103<li>    <a name=" "><i>Name.</i></a>&nbsp;
104        Description.
105<p>
106-->
107</ul>
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.
118<p>
119Thank you for using Gmaj, and helping us to make it better.
120<p>
121
122<p class=vvlarge>
123<hr>
124<i>Cathy Riemer, June 2008</i>
125
126<p class=scrollspace>
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