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JAL-3111 help pages minor corrections
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 4 Jul 2019 12:09:13 +0000
(13:09 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 4 Jul 2019 12:09:13 +0000
(13:09 +0100)
help/help/html/features/featureschemes.html
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help/help/html/features/featuresettings.html
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help/help/html/features/importvcf.html
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help/help/html/menus/alignmentMenu.html
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help/help/html/menus/alwcalculate.html
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help/help/html/releases.html
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help/help/html/whatsNew.html
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diff --git
a/help/help/html/features/featureschemes.html
b/help/help/html/features/featureschemes.html
index
688e492
..
63dd0e5
100644
(file)
--- a/
help/help/html/features/featureschemes.html
+++ b/
help/help/html/features/featureschemes.html
@@
-80,7
+80,7
@@
<li><strong>Numeric</strong> - specify a threshold above, equal
to or below which a feature will be selected or ignored.</li>
<li><strong>String</strong> - select or ignore features based on
<li><strong>Numeric</strong> - specify a threshold above, equal
to or below which a feature will be selected or ignored.</li>
<li><strong>String</strong> - select or ignore features based on
- presence, absence, equivalence, or containment of a string.</li>
+ presence, absence, equivalence, or containment of a string (not case sensitive).</li>
</ul>
<p>
The filters and colour schemes active for a particular feature type
</ul>
<p>
The filters and colour schemes active for a particular feature type
@@
-109,21
+109,21
@@
</tr>
<tr>
<td><em>Graduated colour thresholded (less than) by
</tr>
<tr>
<td><em>Graduated colour thresholded (less than) by
- feature Score</em></td>
+ feature Score (or other attribute)</em></td>
<td><img src="fcsltthan.gif" /></td>
</tr>
<tr>
<td><em>Graduated colour thresholded (greater than) by
<td><img src="fcsltthan.gif" /></td>
</tr>
<tr>
<td><em>Graduated colour thresholded (greater than) by
- feature Score</em></td>
+ feature Score (or other attribute)</em></td>
<td><img src="fcsgtthan.gif" /></td>
</tr>
<tr>
<td><img src="fcsgtthan.gif" /></td>
</tr>
<tr>
- <td><em>Colour by Feature Label (may also be thresholded)</em></td>
+ <td><em>Colour by Feature Label</em></td>
<td><img src="fcsntlabel.gif" /></td>
</tr>
<tr>
<td align="center" colspan="2"><em> <strong>The
<td><img src="fcsntlabel.gif" /></td>
</tr>
<tr>
<td align="center" colspan="2"><em> <strong>The
- current threshold and attribute is given in the icon's tooltip.</strong>
+ current threshold and attribute is shown in the icon's tooltip.</strong>
</em></td>
</tr>
</table>
</em></td>
</tr>
</table>
diff --git
a/help/help/html/features/featuresettings.html
b/help/help/html/features/featuresettings.html
index
d94e2a6
..
555e2ba
100755
(executable)
--- a/
help/help/html/features/featuresettings.html
+++ b/
help/help/html/features/featuresettings.html
@@
-29,7
+29,7
@@
<p>
Select <strong>View→Feature Settings...</strong> in an alignment
window to open the feature settings dialog box, which allows
<p>
Select <strong>View→Feature Settings...</strong> in an alignment
window to open the feature settings dialog box, which allows
- precise control the visibility and appearance of sequence features for
+ precise control of the visibility and appearance of sequence features for
an alignment view.
</p>
<div align="center">
an alignment view.
</p>
<div align="center">
@@
-39,7
+39,7
@@
<p>The top section of the dialog box lists all the sequence feature
groups, along with a tickbox for each that controls whether its
features are displayed. When many groups are present, their names may
<p>The top section of the dialog box lists all the sequence feature
groups, along with a tickbox for each that controls whether its
features are displayed. When many groups are present, their names may
- be truncated, but the full name be shown in a tooltip when the mouse
+ be truncated, but the full name is shown in a tooltip when the mouse
hovers over their checkbox.</p>
<p><em>Feature colour schemes and filters</em>
<p>
hovers over their checkbox.</p>
<p><em>Feature colour schemes and filters</em>
<p>
diff --git
a/help/help/html/features/importvcf.html
b/help/help/html/features/importvcf.html
index
bbc9f78
..
e013472
100755
(executable)
--- a/
help/help/html/features/importvcf.html
+++ b/
help/help/html/features/importvcf.html
@@
-57,7
+57,7
@@
##reference header that define what species and assembly name the
VCF was generated against.</li>
<li>Look at ensembl.org to identify the species' short name,
##reference header that define what species and assembly name the
VCF was generated against.</li>
<li>Look at ensembl.org to identify the species' short name,
- and the assembly's unique.</li>
+ and the assembly's unique id.</li>
<li>Add mappings to the <strong>VCF_SPECIES</strong> and <strong>VCF_ASSEMBLY</strong>
properties in your .jalview_properties file. For example:<pre>
VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans
<li>Add mappings to the <strong>VCF_SPECIES</strong> and <strong>VCF_ASSEMBLY</strong>
properties in your .jalview_properties file. For example:<pre>
VCF_SPECIES=1000genomes=homo_sapiens,c_elegans=celegans
diff --git
a/help/help/html/menus/alignmentMenu.html
b/help/help/html/menus/alignmentMenu.html
index
3a057a8
..
e26707f
100755
(executable)
--- a/
help/help/html/menus/alignmentMenu.html
+++ b/
help/help/html/menus/alignmentMenu.html
@@
-547,7
+547,7
@@
<li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
<a href="../calculations/calculations.html">calculations dialog</a> for
for calculating <a href="../calculations/tree.html">trees</a> or
<li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
<a href="../calculations/calculations.html">calculations dialog</a> for
for calculating <a href="../calculations/tree.html">trees</a> or
- <a href="../calculations/pca.html">principle component analysis
+ <a href="../calculations/pca.html">principal component analysis
plots</a> on the alignment or the currently selected
region.
</em><br></li>
plots</a> on the alignment or the currently selected
region.
</em><br></li>
diff --git
a/help/help/html/menus/alwcalculate.html
b/help/help/html/menus/alwcalculate.html
index
8862955
..
3804538
100755
(executable)
--- a/
help/help/html/menus/alwcalculate.html
+++ b/
help/help/html/menus/alwcalculate.html
@@
-56,7
+56,7
@@
<li><strong>Calculate Tree or PCA ...</strong> <br> <em>Opens the
<a href="../calculations/calculations.html">calculations dialog</a> for
for calculating <a href="../calculations/tree.html">trees</a> or
<li><strong>Calculate Tree or PCA ...</strong> <br> <em>Opens the
<a href="../calculations/calculations.html">calculations dialog</a> for
for calculating <a href="../calculations/tree.html">trees</a> or
- <a href="../calculations/pca.html">principle component analysis
+ <a href="../calculations/pca.html">principal component analysis
plots</a> on the alignment or the currently selected
region.
</em><br>
plots</a> on the alignment or the currently selected
region.
</em><br>
diff --git
a/help/help/html/releases.html
b/help/help/html/releases.html
index
07ed6e8
..
0a20650
100755
(executable)
--- a/
help/help/html/releases.html
+++ b/
help/help/html/releases.html
@@
-75,7
+75,7
@@
li:before {
</li>
<li>
<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
</li>
<li>
<!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
- formats supported by jalview (including .jvp project files)
+ formats supported by Jalview (including .jvp project files)
</li>
<li>
<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
</li>
<li>
<!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
@@
-100,7
+100,6
@@
li:before {
<!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
implementation that allows updates) used for Sequence Feature collections</li>
<li>
<!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
implementation that allows updates) used for Sequence Feature collections</li>
<li>
- <li>
<!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
features can be filtered and shaded according to any
associated attributes (e.g. variant attributes from VCF
<!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
features can be filtered and shaded according to any
associated attributes (e.g. variant attributes from VCF
@@
-176,7
+175,7
@@
li:before {
</li>
<li>
<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
</li>
<li>
<!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
- what is shown)<br />Only visible region of alignment is shown by
+ what is shown)<br />Only visible regions of alignment are shown by
default (can be changed in user preferences)
</li>
<li>
default (can be changed in user preferences)
</li>
<li>
@@
-232,59
+231,55
@@
li:before {
</ul>
<em>Deprecations</em>
<ul>
</ul>
<em>Deprecations</em>
<ul>
- <li>
- <!-- JAL-3035 -->DAS sequence retrieval and annotation
+ <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
capabilities removed from the Jalview Desktop
</li>
capabilities removed from the Jalview Desktop
</li>
- <li>
- <!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
+ <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
unmarshalling has been replaced by JAXB for Jalview projects
and XML based data retrieval clients</li>
<li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
<li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
</ul> <em>Documentation</em>
<ul>
unmarshalling has been replaced by JAXB for Jalview projects
and XML based data retrieval clients</li>
<li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
<li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
</ul> <em>Documentation</em>
<ul>
- <li>
- <!-- JAL-3003 -->Added remarks about transparent rendering effects
+ <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
not supported in EPS figure export
</li>
<li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
</ul> <em>Development and Release Processes</em>
<ul>
<li>
not supported in EPS figure export
</li>
<li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
</ul> <em>Development and Release Processes</em>
<ul>
<li>
- <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
+ <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
</li>
</li>
- <li><!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
+ <li>
+ <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
<li>
<li>
- <!-- JAL-3225 -->Eclipse project configuration managed with
+ <!-- JAL-3225 -->Eclipse project configuration managed with
gradle-eclipse
</li>
<li>
gradle-eclipse
</li>
<li>
- <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 --> Atlassian
+ <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
Bamboo continuous integration for unattended Test Suite
execution
</li>
<li>
Bamboo continuous integration for unattended Test Suite
execution
</li>
<li>
- <!-- JAL-2864 -->Memory test suite to detect leaks in common
+ <!-- JAL-2864 -->Memory test suite to detect leaks in common
operations
</li>
<li>
operations
</li>
<li>
- <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
- issues resolved.
+ <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
+ issues resolved
</li>
<li>
</li>
<li>
- <!-- JAL-3248 -->Developer documentation migrated to
+ <!-- JAL-3248 -->Developer documentation migrated to
markdown (with HTML rendering)
</li>
<li>
markdown (with HTML rendering)
</li>
<li>
- <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+ <!-- JAL-3287 -->HelpLinksChecker runs on Windows
</li>
<li>
</li>
<li>
- <!-- JAL-3289 -->New URLs for publishing development
+ <!-- JAL-3289 -->New URLs for publishing development
versions of Jalview
</li>
versions of Jalview
</li>
- <li>
- <li>
</ul>
</td>
<td align="left" valign="top">
</ul>
</td>
<td align="left" valign="top">
@@
-327,8
+322,8
@@
li:before {
Settings and Jalview Preferences panels
</li>
<li>
Settings and Jalview Preferences panels
</li>
<li>
- <!-- JAL-2865 -->Jalview hangs when closing windows or the
- overview updates with large alignments
+ <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
+ overview with large alignments
</li>
<li>
<!-- JAL-2750 -->Tree and PCA calculation fails for selected
</li>
<li>
<!-- JAL-2750 -->Tree and PCA calculation fails for selected
@@
-358,7
+353,7
@@
li:before {
</li>
<li>
<!-- JAL-2060 -->'Graduated colour' option not offered for
</li>
<li>
<!-- JAL-2060 -->'Graduated colour' option not offered for
- manually created features (where if feature score is Float.NaN)
+ manually created features (where feature score is Float.NaN)
</li>
<li>
<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
</li>
<li>
<!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
@@
-488,7
+483,8
@@
li:before {
</li>
</ul> <em>New Known Defects</em>
<ul>
</li>
</ul> <em>New Known Defects</em>
<ul>
- <li><!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
+ <li>
+ <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
</li>
<li>
<!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
</li>
<li>
<!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
@@
-517,7
+513,8
@@
li:before {
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
</li>
not shown as thresholded features in 2.11. To workaround please
create a Score filter instead.
</li>
- <li><!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
+ <li>
+ <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
<li>
<!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
</li>
<li>
<!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
</li>
@@
-552,7
+549,7
@@
li:before {
<!-- JAL-247 -->Hidden sequence markers and representative
sequence bolding included when exporting alignment as EPS,
SVG, PNG or HTML. <em>Display is configured via the
<!-- JAL-247 -->Hidden sequence markers and representative
sequence bolding included when exporting alignment as EPS,
SVG, PNG or HTML. <em>Display is configured via the
- Format menu, or for command-line use via a jalview
+ Format menu, or for command-line use via a Jalview
properties file.</em>
</li>
<li>
properties file.</em>
</li>
<li>
@@
-626,7
+623,7
@@
li:before {
</li>
<li>
<!-- JAL-3106 -->.jvp should be used as default extension
</li>
<li>
<!-- JAL-3106 -->.jvp should be used as default extension
- (not .jar) when saving a jalview project file.
+ (not .jar) when saving a Jalview project file.
</li>
<li>
<!-- JAL-3105 -->Mac Users: closing a window correctly
</li>
<li>
<!-- JAL-3105 -->Mac Users: closing a window correctly
diff --git
a/help/help/html/whatsNew.html
b/help/help/html/whatsNew.html
index
eb318f0
..
4b406be
100755
(executable)
--- a/
help/help/html/whatsNew.html
+++ b/
help/help/html/whatsNew.html
@@
-64,7
+64,7
@@
also been improved.</li>
<li><strong>Backup files</strong>. Jalview will automatically
create backups when overwriting existing files, and - unlike with
also been improved.</li>
<li><strong>Backup files</strong>. Jalview will automatically
create backups when overwriting existing files, and - unlike with
- earlier versions, should Jalview crash during a save, the original
+ earlier versions - should Jalview crash during a save, the original
file will be unaffected. The <a
href="features/preferences.html#backups">Backups tab</a> in
Jalview's preferences dialog allows the number and format of
file will be unaffected. The <a
href="features/preferences.html#backups">Backups tab</a> in
Jalview's preferences dialog allows the number and format of