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gmaj_news.html

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import galaxy-central

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1	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
2	"http://www.w3.org/TR/html4/loose.dtd">
3	<html>
4	<head>
5	<title>What's New in Gmaj</title>
6	<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
7	<meta http-equiv="Content-Style-Type" content="text/css">
8	<link rel="stylesheet" type="text/css" href="gmaj.css">
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10	<body>
11	<p class=vvlarge>
12	<h2>What's New in Gmaj</h2>
13	<p class=vvlarge>
14	<dl>
15	<dt><b>2008-Jun-30</b><br>
16	<dd> <ul>
17	<li> Gmaj can display several MAF files simultaneously on the same plots,
18	e.g. for comparing output from different alignment programs.
19	<li> A new Tags menu allows the user to tag particular blocks for special
20	treatment. Tagged blocks are conceptually separated from their MAFs
21	and can be displayed, hidden, or exported as a group.
22	<li> There are many new Export options, including MAF format and exporting
23	only the tagged blocks. Export is now possible in applet mode, by
24	posting the blocks to an administrator-designated URL (MAF format only).
25	The Export dialog remembers previous selections if you use it repeatedly.
26	<li> The parameters file has a new option <code>skipotherseq</code>, which
27	causes MAF sequences that aren't mentioned to be ignored (handy for
28	reducing the number of pips and saving memory).
29	<li> Aliases can be given for each <code>seqname</code> in the parameters
30	file, e.g. if two MAF files use different names for the same sequence.
31	<li> A new menu item Help - Sequence Summary reports the aligning extents
32	for all sequences (useful when fetching/trimming annotation files).
33	<li> The long-standing <i>Scrollbar obscures block buttons</i> bug has been
34	fixed, with additional usability enhancements such as remembering
35	manual divider placement (click divider to release).
36	<li> Minor fixes and improvements:
37	<ul>
38	<li> The <code>reconseq</code> field in the parameters file has been
39	renamed to <code>reconorg</code> (because it specifies an organism
40	rather than a single sequence); the old <code>reconseq</code>
41	keyword is deprecated but still supported for the time being.
42	The <code>seqfile</code> keyword from pre-MAF days is no longer
43	supported.
44	<li> Tiny mouse drags in plots are assumed to be accidental and treated
45	as clicks, to avoid the annoying message "Zoom region can't be
46	smaller than ... pixels".
47	<li> Options - Mark Always Red is now the default, due to the
48	<a href="gmaj_bugs.html#xor">rendering issue with XOR</a>.
49	<li> The text alignment omits rows below the % identity threshold.
50	<li> The row of block buttons and the position indicator's block list
51	only include blocks that are in visible categories (according to
52	the new MAF/Tagged checkboxes) and meet the % identity threshold.
53	<li> When self-alignments include the trivial block, it is typically
54	very slow to load and manipulate in the text panel due to its
55	huge size. Gmaj requests confirmation before moving the mark to
56	any block that covers the entire aligning extent of the reference
57	sequence, but then remembers if you say OK and only shows the
58	busy cursor thereafter.
59	<li> The bundle file can contain pre-compressed files.
60	<li> Several minor bug fixes and performance enhancements.
61	<!--
62	<li> Bugfix: some settings and state values were inappropriately shared
63	among applet invocations.
64	<li> Bugfix: opening an applet for a pairwise dataset no longer distorts
65	the initial multipip size for other applets.
66	<li> Bugfix: the text view must not be scrolled if it's not displayed.
67	<li> Bugfix: race condition when painting "Please wait" dialog is reduced.
68	-->
69	<li> Improved error checking and messages.
70	<li> Tweaks in wording, punctuation, spacing, dialog title, etc.
71	</ul>
72	</ul>
73	<p>
74	<dt><b>2008-Jan-08</b><br>
75	<dd> <ul>
76	<li> Special treatment for pairwise alignments:
77	<ul>
78	<li> The dotplot is displayed immediately.
79	<li> Self-alignments are allowed to use the same name for both sequences.
80	</ul>
81	<li> Filtering for underlays and highlights, based on score:
82	<ul>
83	<li> Scores are obtained from the annotation files.
84	<li> A new text box widget (with keyboard shortcuts) allows you to set the
85	display threshold.
86	<li> Pointing at an underlay/highlight displays its score on the location
87	status line.
88	</ul>
89	<li> The text alignment, headers, and status lines are now selectable for copying,
90	and for the text alignment the selection is rectangular.
91	<li> On a Mac, Gmaj uses standard key bindings (<code>Cmd-C</code>,
92	<code>Cmd-V</code>, etc.).
93	<li> Holding down the <code>Ctrl</code> key (on any platform) prevents the
94	position indicator from changing; this is useful for copying it and for
95	screenshots.
96	<li> Bugfixes:
97	<ul>
98	<li> Empty fields in annotation files were not accepted due to improper
99	handling.
100	<li> When loading a new dataset with File - Open, the old windows were not
101	closed properly.
102	<li> Descenders of pip header characters were clipped off.
103	</ul>
104	<li> Minor adjustments to behavior, appearance, and messages, including:
105	<ul>
106	<li> Sequence names in the MAF cannot end with <code>~</code> (which is used
107	internally for self-alignments).
108	<li> The first click in an inactive window just activates it.
109	</ul>
110	<li> Updated and enhanced documentation.
111	</ul>
112	<p>
113	<dt><b>2007-Jul-26</b><br>
114	<dd> <ul>
115	<li> Gmaj can now display dotplots in addition to the main multi-pip views,
116	with color underlays for both sequences.
117	<ul>
118	<li> Dotplots are opened by clicking on buttons in the pip headers.
119	<li> Each dotplot opens in a separate window, similar to the multi-pip
120	view except it has pip, dotplot, and text panels for two sequences
121	only.
122	<li> Dotplot windows share the same reference sequence and mark with
123	their parent multi-pip window but have independent zoom, and close
124	automatically when the parent does.
125	<li> There is only one mark for each reference sequence, so the circle
126	will not appear in dotplots having a different secondary sequence
127	than the mark.
128	</ul>
129	<li> Gmaj can now read annotation data in
130	<a href="http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml"
131	>GFF</a> (v1 & v2),
132	<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GTF"
133	>GTF</a>, and
134	<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED"
135	>BED</a> formats in addition to its previous PipMaker-style formats.
136	<ul>
137	<li> UCSC
138	<a href="http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks"
139	>custom track</a> headers are supported, with multiple tracks and
140	sequence names allowed in a single file.
141	<li> There is currently no way to use just one particular track from a
142	file, but lines in
143	<a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html"
144	>WIG</a> or other unrecognized formats are skipped.
145	<li> Files in these generic formats can be reused in multiple panels
146	(e.g. as both exons and underlays).
147	<li> A new <code>tabext</code> field and file specification modifiers
148	(seqname alias and type hint) in the parameters file facilitate
149	interpretation of these formats.
150	<li> Colors can be specified using UCSC-style RGB triplets (either
151	per-line or per-track), or Gmaj provides defaults.
152	<li> Currently there is no special support for multiple transcripts;
153	when inferring UTRs, the largest bounding range of given CDS data
154	is used.
155	</ul>
156	<li> A new control in the menu bar allows the user to limit the displayed
157	alignments by their average % identity.
158	<ul>
159	<li> Keyboard shortcuts make it easy to move the threshold up and down.
160	<li> The value for the current plot block is displayed with the mark
161	information when applicable.
162	</ul>
163	<li> If the alignment file contains per-nucleotide reconstruction scores
164	for an inferred ancestral sequence, they can be displayed as a pair of
165	bar graphs, binned according to the current zoom region and panel size.
166	<ul>
167	<li> The scores are transformed via simple linear scaling, and should
168	not be interpreted as probabilities.
169	<li> A new <code>reconseq</code> field in the parameters file
170	identifies the organism for the scores.
171	</ul>
172	<li> Miscellaneous:
173	<ul>
174	<li> "Unsupported MAF version" is now a warning instead of a fatal
175	error.
176	<li> A new <code>nowarn</code> field in the parameters file suppresses
177	certain warnings/errors using a keyword shown in the message.
178	<li> When opening a new window, the current zoom is translated to a
179	roughly equivalent one in the new sequence(s).
180	<li> Sequence choices in the Show dialog affect text rows and dotplots
181	in addition to pips.
182	<li> The default highlights built from exons now include the genes
183	(light yellow).
184	<li> The divider between the position indicator and the zoom indicator
185	is draggable.
186	<li> Plot segments are drawn thicker in Large Fonts mode.
187	<li> Plots that are completely empty have a gray background.
188	<li> The Set Zoom dialog accepts a blank box to mean "leave unchanged".
189	<li> Tabbing is easier in input dialogs: labels are skipped unless the
190	mouse is pointing at them.
191	<li> Note that "<code>=</code>" is now required for settings in the
192	parameters file (except <code>seq N:</code> lines), and
193	lines with empty values (e.g. unused template items) are allowed
194	and skipped.
195	</ul>
196	<!--
197	<li> Bug fixes:
198	<ul>
199	<li> Linkbar URLs are supposed to be optional; missing ones are now
200	handled gracefully.
201	<li> Entries in the parameters file for particular-pip underlays were
202	not recognized properly if the underlay file was bundled.
203	<li> Attempting to display a reference sequence that had no alignments
204	would cause a Java error.
205	<li> On some platforms, rebuilding all of the Gmaj windows (e.g. when
206	Options settings were changed) would leave the keyboard focus in
207	the wrong window.
208	</ul>
209	-->
210	<li> Various minor bug fixes, and improvements in appearance, behavior,
211	messages, efficiency, and robustness.
212	<li> Updated documentation.
213	<ul>
214	<li> Terminology: the optional colored clickable bars located above
215	the exons panel were formerly called "annotations", "annotation
216	links", or "hyperlink annotations", but are now referred to as
217	"linkbars" so that "annotation" can be used in the general sense.
218	</ul>
219	</ul>
220	<p>
221	<dt><b>2006-Jun-17</b><br>
222	<dd> <ul>
223	<li> Gmaj can now be deployed as a web-based applet, as an alternative to
224	the regular stand-alone mode.
225	<a href="http://globin.bx.psu.edu/java/gmaj/demo.html">Demo</a>
226	<ul>
227	<li> New parameters <code>bundle</code>, <code>initzoom</code>, and
228	<code>urlpause</code> facilitate applet use, but also work in
229	stand-alone mode.
230	<li> Clicking on hyperlinked annotations (colored bars) visits the
231	referenced site (or in stand-alone mode, displays the url).
232	<li> A new "Help - Manual" menu item visits a help page (or in
233	stand-alone mode, displays the file location).
234	<li> The "File - Export" feature does not work yet for applets.
235	</ul>
236	<li> Better conformance with the official UCSC specs for MAF format.
237	<li> A new <code>refseq</code> field in the parameters file can be used
238	to prevent selection of an inappropriate reference sequence when the
239	alignments are not sequence-symmetric (e.g. from <i>multiz</i>).
240	<li> Maximum zoom bounds are now the stated sequence length from the MAF
241	file (not just the extent of the blocks), but the default initial
242	view zooms to the aligned portion.
243	<li> Search rules for relative filenames have been simplified, and Windows
244	names starting with "<code>\</code>" are now handled better.
245	<li> The panel for hyperlinked annotations is now labeled, and it displays
246	the bars listed earliest in the file toward the top.
247	<li> Colors for underlays and other annotations have been adjusted slightly.
248	<li> The "Help - About" message now shows your current Java version and
249	vendor.
250	<li> Improved error reporting.
251	<li> Message dialogs have better line wrapping, and their contents can
252	be copied to the system clipboard (except in applets, due to a bug
253	in Java).
254	<li> Several minor bug fixes, tweaks, and internal improvements.
255	<li> Documentation has been reorganized.
256	</ul>
257	<p>
258	<dt><b>2006-Feb-08</b><br>
259	<dd> <ul>
260	<li> New arrow buttons slide the zoom region left or right by half a
261	screenful.
262	<li> The schematic diagrams for exons and repeats are now displayed in
263	separate, labeled panels.
264	<li> A new Show dialog on the Options menu allows individual panels
265	to be displayed or hidden.
266	<li> Users who have a one-button mouse can get crosshairs by using the
267	<code>Shift</code> key.
268	<li> Minor aesthetic tweaks.
269	</ul>
270	<p>
271	<dt><b>2005-Nov-20</b><br>
272	<dd> <ul>
273	<li> New export feature: Gmaj can now save the selected block (or all
274	blocks in the current zoom region) to files in FastA sequence format
275	for further processing by other programs. Options include clipping
276	the sequences to the current zoom region, and restoring those that
277	align in reverse complement to their original orientation.
278	<li> The zoom resolution limit has been reduced to 4 bp (or pixels),
279	instead of 10.
280	<li> When setting the zoom by dragging out a rectangle, Gmaj will display
281	an error message if the rectangle is too small (instead of beeping).
282	</ul>
283	<p>
284	<dt><b>2005-Sep-30</b><br>
285	<dd> <ul>
286	<li> Improved handling of <code>X</code>, <code>N</code>, and
287	unrecognized characters:
288	<ul>
289	<li> Bug fix: the percent identity computation now ignores these
290	characters (in both numerator and denominator).
291	<li> Bug fix: the text panel never shows dots for these characters.
292	<li> One warning is issued for each unrecognized character.
293	</ul>
294	<li> New zoom features:
295	<ul>
296	<li> Gmaj keeps track of your zoom history for each window, so you can
297	move back and forward through your previous zoom regions. A fresh
298	selection discards the history from the current point forward,
299	similar to a web browser.
300	<li> The Unzoom facility does not go back, it just puts the maximum
301	range into the history as a fresh selection.
302	<li> A new indicator box below the menu bar shows the current zoom
303	endpoints.
304	<li> A Set Zoom dialog allows you to enter zoom endpoints explicitly.
305	<li> When setting the zoom by dragging out a rectangle, a rectangle that
306	is too small will no longer be treated as a click; instead Gmaj
307	will beep (if possible).
308	</ul>
309	<li> Improved display of pip and text panels:
310	<ul>
311	<li> The divider between the pips and the text panel is now moveable, so
312	you can drag it to adjust the relative space they occupy.
313	<li> The text panel starts with an initial message to explain why it is
314	empty.
315	<li> After loading a file with many sequences, the pips will be scrolled
316	to start at the top.
317	<li> If the current mark can be transferred when selecting a new
318	reference sequence, the pip panel will scroll to it (though the red
319	circle may not be visible if the percent identity at that point is
320	below 50%).
321	<li> Vertical blue bars at the edges of the pips represent the
322	boundaries of the current zoom region.
323	</ul>
324	<li> Improved display of block buttons:
325	<ul>
326	<li> If there are too many block buttons to fit in their panel, a
327	scrollbar will appear so all of them can be accessed.
328	<li> The divider between the mark indicator and the block buttons is now
329	moveable, so you can drag it to adjust the relative space they
330	occupy (this will reset when a new block is selected, since the
331	number of block buttons will likely be different).
332	</ul>
333	<li> Miscellaneous:
334	<ul>
335	<li> The menus have been rearranged slightly, and Settings has been
336	renamed to Options.
337	<li> The keyboard shortcut for "Next Block" has been changed to
338	"<code>n</code>", so "<code>b</code>" can invoke "Zoom - Back".
339	<li> The cascade of RefSequence window positions wraps around the screen
340	(in both width and height) so they are never placed completely
341	offscreen.
342	<li> When opening a new RefSequence window, Gmaj will use the size of
343	the current window in case you have changed it.
344	<li> Window sizing no longer requires Java 1.4 (accidentally introduced
345	in the 2005-May-16 release).
346	<li> Bug fix: radio buttons for mark color now take effect immediately
347	in all windows.
348	<li> Improved behavior of dialog boxes: pressing Enter invokes "Ok",
349	Escape invokes "Cancel", and the cursor begins in the first text
350	box.
351	</ul>
352	</ul>
353	<p>
354	<dt><b>2005-Sep-13</b><br>
355	<dd> <ul>
356	<li> <i>IMPORTANT BUG FIX:</i>  Percent identities for the pip plots
357	were being computed in a case-sensitive fashion, which lowered the
358	scores when comparing soft-masked vs. unmasked sequences. (This bug
359	did not affect the text view, just the pips. Nor did it affect
360	<a href="http://globin.bx.psu.edu/dist/laj/">Laj</a>, which uses
361	pre-computed percent identity scores from the <code>lav</code> file.)
362	Note that hard masking and ambiguous nucleotides (<code>X</code>,
363	<code>N</code>, <code>W</code>, <code>R</code>, etc.) are still treated
364	literally.
365	</ul>
366	<p>
367	<dt><b>2005-Aug-26</b><br>
368	<dd> <ul>
369	<li> Improved support for working with overlapping blocks (e.g. those due to
370	genomic duplications):
371	<ul>
372	<li> A list of block numbers in the position indicator line shows the
373	blocks covering the mouse pointer's location.
374	<li> A row of buttons next to the mark indicator line shows the blocks
375	covering the marked location, and allows convenient selection of
376	a different block at the same position.
377	<li> The pip segments for the currently selected block are painted last,
378	so the red segments are not hidden by other blocks.
379	</ul>
380	<li> It is no longer required to list every sequence in the parameters file.
381	Any sequences that appear in the alignment but are not mentioned in the
382	parameters file will be displayed in the order they are encountered
383	(filling in around any sequence numbers explicitly assigned in the
384	parameters file).
385	<li> A new parameter <code>underlays</code> (plain, without a number) can be
386	used to specify a default underlay file for each reference sequence, so
387	it is no longer necessary to list underlays for each pip separately when
388	they are the same. The old <code>underlays.N</code> parameters are
389	still supported as well, and override these new ones.
390	<li> The <code>seqfile</code> parameter has been renamed to
391	<code>seqname</code>, in order to reflect MAF semantics (but
392	<code>seqfile</code> is still supported for backward compatibility).
393	<li> Sequence label widths are now computed dynamically, based on the longest
394	name and the current font.
395	<li> When the font size is changed, pip heights are also adjusted.
396	<li> A new option on the Settings menu makes the mark circle and selected
397	block's pip segments always red, instead of changing with the background.
398	<li> A new color <code>Clear</code> is provided, which is colorless and
399	transparent. It is intended for gene introns, so the same file can be
400	used for pip underlays (white background) and text highlights (gray
401	background).
402	<li> New colors <code>Brown</code> and <code>LightBrown</code> have also been
403	added, and <code>LightRed</code> and <code>Green</code> were tweaked.
404	<li> When a gap in the text view is clicked, the nearest gap-free position
405	is selected (up or down, instead of always down).
406	<li> Work-arounds for a few display problems in JRE 1.5 have been added.
407	<li> The RefSeq menu has been renamed to "RefSequence" in order to avoid
408	confusion with the NCBI database.
409	<li> The jar manifest and About information have been updated.
410	<li> Support for alignment files in <code>.bb</code> format (from the old
411	<i>blockbuilder</i> program) has been discontinued. The only alignment
412	format currently supported is MAF.
413	<li> Due to a new mechanism for registering keyboard shortcuts, Gmaj now
414	requires <b>Java 1.3 or higher</b>.
415	<li> This version should still be considered <b>beta quality</b>; please
416	report any bugs to
417	<img align=top alt="image of email address" src="cathy.gmaj.png">.
418	</ul>
419	<p>
420	<dt><b>2005-May-16</b><br>
421	<dd> <ul>
422	<li> Gmaj can now handle a wider variety of MAF files, including those
423	containing reverse-complement alignments.
424	<li> The "proper threading" requirement has been eliminated.
425	<li> Dynamic memory management for plot and underlay data allows larger files
426	to be viewed.
427	<li> The pip section is now scrollable when there are many sequences.
428	<li> Rows in the text alignment are sorted to match the order of pips.
429	<li> This release should be considered <b>beta quality</b>. In particular,
430	the numbering for reverse-complement alignments has not been thoroughly
431	tested.
432	</ul>
433	<p>
434	<dt><b>2004-Mar-12</b><br>
435	<dd> <ul>
436	<li> A new Settings menu allows the user to choose between two sizes of fonts
437	and associated settings.
438	<li> Initial window positions are cascaded according to reference sequence.
439	<li> The usage message has been adjusted to show the full command syntax,
440	instead of our local wrapper script shortcut.
441	<li> Empty alignment files are handled more gracefully.
442	<li> Minor aesthetic tweaks.
443	</ul>
444	<p>
445	<dt><b>2004-Jan-14</b><br>
446	<dd> <ul>
447	<li> Gmaj normally expects that the alignment data will be properly
448	<i>chained</i>, i.e., that for each sequence it is possible to order
449	the blocks so that every nucleotide from that sequence in the interval
450	<code>[1,length]</code> appears exactly once, and in the same order as
451	the original sequence. (Note that MAF files are 0-based, so
452	<code>+1</code> is added to all MAF coordinates to convert them to
453	Gmaj's 1-based system.)
454	However, sometimes you may want to use Gmaj to display a subset of such
455	data (e.g., output from the <i>slice_maf</i> program). Gmaj can now
456	handle input data where the chain starts after position <code>1</code>
457	and/or ends before position <code>length</code>, as long as it is still
458	contiguous. In this case Gmaj will issue a warning message, but will
459	proceed to use the actual interval it found in your file for threading
460	the blocks, instead of the usual <code>[1,length]</code>.
461	</ul>
462	<p>
463	<dt><b>2003-Sep-16</b><br>
464	<dd> <ul>
465	<li> Gmaj can now handle alignment files in the MAF format produced by
466	the <i>TBA</i> program, in addition to the <code>.bb</code> format
467	produced by <i>blockbuilder</i>.
468	<li> When using a MAF alignment, the semantics of the parameters file
469	are a bit different, and its rules are stricter. (See
470	<code><a href="sample.gmaj">sample.gmaj</a></code> for details.)
471	<li> Gmaj still doesn't support reverse complement alignments, or multiple
472	contigs per sequence.
473	</ul>
474	<p>
475	<dt><b>2003-Jul-14</b><br>
476	<dd> <ul>
477	<li> The "phantom repeats" phenomenon that was occurring with Java 1.4.x
478	has been greatly reduced, but not completely eliminated. It appears
479	to be due to a clipping problem involving integer overflow, so that
480	items which should be off-screen are drawn anyway. This (or a related
481	bug) may also manifest as the disappearance of items for certain zoom
482	windows. These problems can also occur with items other than repeats,
483	such as underlays and even pip segments, though this is less common.
484	Manual clipping seems to solve the problem, and this release of Gmaj
485	should always display pip segments, underlays, and annotation bars
486	correctly. Items in the "features" panel (exons, repeats, CpG islands,
487	etc.) are more difficult to clip manually, but a first approximation
488	has helped quite a bit. It is still possible to experience these
489	problems if you zoom in very closely on a long feature.
490	<p>
491	<li> If underlay labels are not provided but "kinds" (color meanings) are,
492	then Gmaj will use the kind as a default label, but only for the
493	underlay bands that are on top (i.e., not obscured by another band).
494	</ul>
495	<p>
496	<dt><b>2003-Apr-10</b><br>
497	<dd> <ul>
498	<li> Fixed keyboard shortcuts, and failure to exit upon closing last
499	window.
500	<li> New Help - Keys menu item lists keyboard shortcuts.
501	<li> Tweak appearance of the Unzoom button.
502	<li> Minor clarifications in documentation.
503	</ul>
504	<p>
505	<dt><b>2003-Apr-07</b><br>
506	<dd> <ul>
507	<li> Fixed several bugs in the text panel, including scrolling
508	behavior and cursor display.
509	<li> Added a comment in the <code>sample.gmaj</code> file regarding
510	the <code>#:gmaj</code> tag.
511	</ul>
512	<p>
513	<dt><b>2003-Mar-31</b><br>
514	<dd> <ul>
515	<li> Preliminary beta-quality release. Still has a few display
516	and behavior anomalies, and possibly other minor bugs.
517	</ul>
518	</dl>
519	<p>
520
521	<p class=vvlarge>
522	<hr>
523	<i>Cathy Riemer, June 2008</i>
524	</body>
525	</html>

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