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group/annotation association, logos, autocalc group annotation and sequence id tooltip
author
jprocter
<Jim Procter>
Wed, 28 Apr 2010 10:21:05 +0000
(10:21 +0000)
committer
jprocter
<Jim Procter>
Wed, 28 Apr 2010 10:21:05 +0000
(10:21 +0000)
help/html/features/preferences.html
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a/help/html/features/preferences.html
b/help/html/features/preferences.html
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--- a/
help/html/features/preferences.html
+++ b/
help/html/features/preferences.html
@@
-6,7
+6,7
@@
<body>
<p><strong>Preferences</strong></p>
<body>
<p><strong>Preferences</strong></p>
-<p>There are four tabs in the Preferences dialog box:
+<p>There are four tabs in the Preferences dialog box:
<ul>
<li>The <a href="#visual"><strong>"Visual"</strong>
Preferences</a> tab allows you to configure the default display for a new
<ul>
<li>The <a href="#visual"><strong>"Visual"</strong>
Preferences</a> tab allows you to configure the default display for a new
@@
-20,7
+20,7
@@
<li>The <a href="#editing"><strong>"Editing"</strong>
Preferences</a> tab contains settings affecting the export of sequence
alignments and EPS files.</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
Preferences</a> tab contains settings affecting the export of sequence
alignments and EPS files.</li>
- <li>The <a href="#editing"><strong>"DAS
+ <li>The <a href="dassettings.html"><strong>"DAS
Settings"</strong> Preferences</a> tab allows you to select which DAS sources
to use when fetching DAS Features.</li>
</ul>
Settings"</strong> Preferences</a> tab allows you to select which DAS sources
to use when fetching DAS Features.</li>
</ul>
@@
-35,7
+35,13
@@
for a new alignment window.</p>
will display an annotation panel below the sequences. This annotation
panel may have several rows describing the whole alignment. The 3
standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
will display an annotation panel below the sequences. This annotation
panel may have several rows describing the whole alignment. The 3
standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
- may be shown or hidden by default.</p>
+for the alignment may be shown or hidden by default using the checkboxes
+below.</p>
+<p><em>Show group: Conservation and Consensus</em> controls the
+display of per-group automatic annotation.</p>
+<p><em>Consensus: Histogram and Logo</em> checkboxes control the
+display of the consensus histogram and sequence logo for consensus
+annotation rows.</p>
<p><em>Full Sequence ID</em> - If selected the ID panel will display
the name of a sequence plus the start and end residues in the format
name/start-end. If not selected, the displayed ID will be the name of
<p><em>Full Sequence ID</em> - If selected the ID panel will display
the name of a sequence plus the start and end residues in the format
name/start-end. If not selected, the displayed ID will be the name of
@@
-45,6
+51,9
@@
the left-hand edge of the sequence alignment, rather than the left-hand
edge of the alignment display window.</p>
<p><em>Font</em> - The default font name, size and style can be set
for a new alignment window.</p>
edge of the alignment display window.</p>
<p><em>Font</em> - The default font name, size and style can be set
for a new alignment window.</p>
+<p><em>Sequence ID Tooltip</em>: Control the display of Database
+References and Non-positional annotation in the tooltip displayed when
+the mouse is over a sequence's ID.</p>
<p><em>Sequence Name Italics</em> - select to apply the italicised
vbersion of the font to sequence labels.</p>
<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
<p><em>Sequence Name Italics</em> - select to apply the italicised
vbersion of the font to sequence labels.</p>
<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
@@
-108,8
+117,7
@@
style for EPS export:
<p><em>Sequence//Start-End Numbering</em><br>
The output tab also has a group of checkboxes for each file format. If
these are ticked, then Jalview will write files with the start and end
<p><em>Sequence//Start-End Numbering</em><br>
The output tab also has a group of checkboxes for each file format. If
these are ticked, then Jalview will write files with the start and end
-sequence positions appended to each sequence id:
-<pre>
+sequence positions appended to each sequence id: <pre>
>ID/1-10
AACDEAAFEA
</pre>
>ID/1-10
AACDEAAFEA
</pre>
@@
-134,8
+142,6
@@
sequence edit. New alignment windows will have their "Autocalculate
Consensus" option set according to this setting.</p>
<p><em>Pad gaps when editing</em> - New alignment windows will
"Pad Gaps" according to this setting.</p>
Consensus" option set according to this setting.</p>
<p><em>Pad gaps when editing</em> - New alignment windows will
"Pad Gaps" according to this setting.</p>
-<p><a name="editing"><strong>DAS Settings </strong></a></p>
-<p>See <a href="dassettings.html">DAS Settings</a></p>
<p> </p>
<p> </p>
</body>
<p> </p>
<p> </p>
</body>