/static/gmaj/docs/gmaj_bugs.html

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  5. <title>Known Bugs in Gmaj</title>
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  11. <p class=vvlarge>
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  12. <h2>Known Bugs in Gmaj</h2>
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  13. <p class=vvlarge>
    14. 

  14. The following anomalies in Gmaj's display and behavior have been
    15. 

  15. observed, but not yet resolved.  Some of these are intermittent,
    16. 

  16. and some may depend on your computer platform and/or version of
    17. 

  17. Java.
    18. 

  18. <p>
    19. 

  19. If you experience any of these (or similar) problems, it may help
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  20. to switch to a different version of Java.  For example, the first
    21. 

  21. bug listed below (phantom repeats) seems to have been introduced
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  22. with Sun's J2SE 1.4.x series, so you may be better off with 1.3.x
    23. 

  23. or 1.5.x.  You can also try switching to a different vendor's
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  24. implementation, but then you are on your own, as we develop and
    25. 

  25. test Gmaj using Sun's official API and SDK.  Currently Gmaj does
    26. 

  26. not rely on any features beyond Java 1.3, in order to preserve
    27. 

  27. version flexibility for our users.
    28. 

  28. <p>
    29. 

  29. Note that anomalies that depend on the Java version could be due
    30. 

  30. to bugs in Java itself, but could also be bugs in Gmaj that only
    31. 

  31. "matter" with certain implementations of Java.  In either case,
    32. 

  32. however, with further investigation it may be possible to work
    33. 

  33. around the problem in future releases of Gmaj.
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  34. <p class=vlarge>
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  35. <ul>
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  36. <li>	<a name="phantom"><i>Phantom repeats.</i></a>&nbsp;
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  37. 	After zooming in on a small region, the "repeats" panel
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  38. 	sometimes shows a spurious extra bar superimposed on the
    39. 

  39. 	legitimate features across the entire width of the window,
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  40. 	or the features may disappear entirely.
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  41. <p>
    42. 

  42. <li>	<a name="zoombox"><i>Missing zoom box and crosshairs.</i></a>&nbsp;
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  43. 	With some datasets (large ones especially) the lines for the
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  44. 	zoom rectangle and crosshairs may not display.  It still
    45. 

  45. 	zooms OK though, if you just pretend the lines are there.
    46. 

  46. 	<b>Update:</b> This appears to have been fixed in Java 1.5.
    47. 

  47. <p>
    48. 

  48. <!-- [fixed 02/19/08]
    49. 

  49. <li>	<a name="buttonscroll"><i>Scrollbar obscures block buttons.</i></a>&nbsp;
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  50. 	If there is not enough room for all of the block buttons
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  51. 	corresponding to the marked position, a scrollbar will
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  52. 	appear.  However, the extra vertical space required for
    53. 

  53. 	the scrollbar may not be calculated properly, so that the
    54. 

  54. 	scrollbar partially obscures the button labels.  To read
    55. 

  55. 	the labels, drag the partition between the mark indicator
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  56. 	box and the button panel toward the left, to create more
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  57. 	space for the buttons.
    58. 

  58. <p>
    59. 

  59. -->
    60. 

  60. <li>	<a name="dialogcopy"><i>Can't copy text from dialog messages in applet.</i></a>&nbsp;
    61. 

  61. 	In applet mode, you may not be able to select and copy text
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  62. 	from pop-up message boxes to the system clipboard for
    63. 

  63. 	pasting elsewhere.  This is apparently due to a bug in Java;
    64. 

  64. 	hopefully Sun will fix it eventually.
    65. 

  65. <p>
    66. 

  66. <li>	<a name="xor"><i>Patchy rendering of mark circle and/or red segments.</i></a>&nbsp;
    67. 

  67. 	When using the Large Fonts option with Mark Color Varies,
    68. 

  68. 	the red circle and plot segments may not appear as solid
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  69. 	as they should.  This is because Mark Color Varies is
    70. 

  70. 	implemented using Java's XOR drawing mode, and the thick
    71. 

  71. 	lines are built up from several thin ones, so whenever two
    72. 

  72. 	red pixels overlap they turn white again.  Fixing this will
    73. 

  73. 	likely involve a custom implementation of Mark Color Varies
    74. 

  74. 	that doesn't use XOR.  In the meantime, switching to Mark
    75. 

  75. 	Always Red when using Large Fonts should solve the problem
    76. 

  76. 	(except that it will be invisible against red underlays).
    77. 

  77. <p>
    78. 

  78. <!-- [fixed 07/16/07]
    79. 

  79. <li>	<a name="buildfocus"><i>GUI rebuild breaks keyboard shortcuts.</i></a>&nbsp;
    80. 

  80. 	The items on the Options menu generally require all of the
    81. 

  81. 	open windows to be rebuilt, and although the window that was
    82. 

  82. 	active may still be in front, on some systems it might not
    83. 

  83. 	actually have the keyboard focus.  So when you press a key,
    84. 

  84. 	say "<code>b</code>" for "Zoom - Back", one of the other
    85. 

  85. 	windows changes instead of the one you wanted.  Even the
    86. 

  86. 	Escape key doesn't help, because it goes to the wrong
    87. 

  87. 	window too.  Investigation of how best to prevent this is
    88. 

  88. 	underway; in the meantime you can fix it by clicking on a
    89. 

  89. 	different window and then returning to the one you want.
    90. 

  90. <p>
    91. 

  91. -->
    92. 

  92. <li>	<a name="leak"><i>Memory leak when closing or rebuilding windows.</i></a>&nbsp;
    93. 

  93. 	When windows are closed or rebuilt (e.g. when loading data
    94. 

  94. 	via File - Open, switching to Large Fonts, or even just
    95. 

  95. 	displaying dialog boxes), not all of the memory they were
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  96. 	using is being reclaimed, so Gmaj will gradually run out
    97. 

  97. 	and have to be restarted.  How quickly this happens will
    98. 

  98. 	depend on how much memory you have allocated to Java with
    99. 

  99. 	the <code><a href="gmaj_help.html#memory">-Xmx</a></code>
    100. 

  100. 	switch, and the size of your dataset.
    101. 

  101. <p>
    102. 

  102. <!--
    103. 

  103. <li>	<a name=" "><i>Name.</i></a>&nbsp;
    104. 

  104. 	Description.
    105. 

  105. <p>
    106. 

  106. -->
    107. 

  107. </ul>
    108. 

  108. <p class=vlarge>
    109. 

  109. If you encounter any bugs not listed here, please report them to
    110. 

  110. <img align=top alt="[image of email address]" src="cathy.gmaj.png">.
    111. 

  111. It would be helpful if you can include the version of Gmaj you
    112. 

  112. are using (i.e., the JarDate line from the Help - About message),
    113. 

  113. your computer platform and version of Java, copies of the data
    114. 

  114. files you were trying to view, and a description of exactly what
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  115. you were doing when the problem occurred.  This will help us to
    116. 

  116. reproduce the problem so we can track it down and fix it.
    117. 

  117. Non-bug suggestions and feedback are also welcome.
    118. 

  118. <p>
    119. 

  119. Thank you for using Gmaj, and helping us to make it better.
    120. 

  120. <p>
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  121. 

  122. <p class=vvlarge>
    123. 

  123. <hr>
    124. 

  124. <i>Cathy Riemer, June 2008</i>
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