JAL-3111 help pages minor corrections

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
-                       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
@@ -109,21 +109,21 @@
                        </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
-                                               feature Score</em></td>
+                                               feature Score (or other attribute)</em></td>
                                <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
-                                                       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>

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&#8594;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">
@@ -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
-               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>

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,
-      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

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
-         <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>

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
-         <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>

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
-                                               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
@@ -100,7 +100,6 @@ li:before {
             <!-- 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
@@ -176,7 +175,7 @@ li:before {
                                                        </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>
@@ -232,59 +231,55 @@ li:before {
                                </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>
-          <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>
-                                       <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>
-                                               <!-- 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><!-- 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>
-            <!-- JAL-3225 -->Eclipse project configuration managed with
+          <!-- JAL-3225 -->Eclipse project configuration managed with
             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>
-            <!-- JAL-2864 -->Memory test suite to detect leaks in common
+          <!-- JAL-2864 -->Memory test suite to detect leaks in common
             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>
-            <!-- JAL-3248 -->Developer documentation migrated to
+          <!-- JAL-3248 -->Developer documentation migrated to
             markdown (with HTML rendering)
           </li>
           <li>
-            <!-- JAL-3287 -->HelpLinksChecker runs on Windows
+          <!-- JAL-3287 -->HelpLinksChecker runs on Windows
           </li>
           <li>
-            <!-- JAL-3289 -->New URLs for publishing development
+          <!-- JAL-3289 -->New URLs for publishing development
             versions of Jalview
           </li>
-          <li>
-          <li>
         </ul>
       </td>
                        <td align="left" valign="top">
@@ -327,8 +322,8 @@ li:before {
                                                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
@@ -358,7 +353,7 @@ li:before {
           </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
@@ -488,7 +483,8 @@ li:before {
           </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
@@ -517,7 +513,8 @@ li:before {
                                                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>
@@ -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
-                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>
@@ -626,7 +623,7 @@ li:before {
             </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

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
-      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