From: gmungoc Date: Thu, 4 Jul 2019 12:09:13 +0000 (+0100) Subject: JAL-3111 help pages minor corrections X-Git-Tag: Release_2_11_0~1^2~5 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=dd193c9ceff22f721c53814fd9c37f269a9edfde 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 --- a/help/help/html/features/featureschemes.html +++ b/help/help/html/features/featureschemes.html @@ -80,7 +80,7 @@
  • Numeric - specify a threshold above, equal to or below which a feature will be selected or ignored.
  • String - select or ignore features based on - presence, absence, equivalence, or containment of a string.
    • + presence, absence, equivalence, or containment of a string (not case sensitive).

    The filters and colour schemes active for a particular feature type @@ -109,21 +109,21 @@ Graduated colour thresholded (less than) by - feature Score + feature Score (or other attribute) Graduated colour thresholded (greater than) by - feature Score + feature Score (or other attribute) - Colour by Feature Label (may also be thresholded) + Colour by Feature Label The - current threshold and attribute is given in the icon's tooltip. + current threshold and attribute is shown in the icon's tooltip. diff --git a/help/help/html/features/featuresettings.html b/help/help/html/features/featuresettings.html index d94e2a6..555e2ba 100755 --- a/help/help/html/features/featuresettings.html +++ b/help/help/html/features/featuresettings.html @@ -29,7 +29,7 @@

    Select View→Feature Settings... 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.

    @@ -39,7 +39,7 @@

    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.

    Feature colour schemes and filters

    diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html index bbc9f78..e013472 100755 --- 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.

  • Look at ensembl.org to identify the species' short name, - and the assembly's unique.
    • + and the assembly's unique id.
  • Add mappings to the VCF_SPECIES and VCF_ASSEMBLY properties in your .jalview_properties file. For example:
     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
--- a/help/help/html/menus/alignmentMenu.html
+++ b/help/help/html/menus/alignmentMenu.html
@@ -547,7 +547,7 @@
     
  • Calculate Tree or PCA ... 
     Opens the 
     calculations dialog for
         for calculating trees or
-         principle component analysis 
+         principal component analysis 
          plots on the alignment or the currently selected
         region. 
       
    • 
diff --git a/help/help/html/menus/alwcalculate.html b/help/help/html/menus/alwcalculate.html
index 8862955..3804538 100755
--- a/help/help/html/menus/alwcalculate.html
+++ b/help/help/html/menus/alwcalculate.html
@@ -56,7 +56,7 @@
     
  • Calculate Tree or PCA ... 
     Opens the 
     calculations dialog for
         for calculating trees or
-         principle component analysis 
+         principal component analysis 
          plots on the alignment or the currently selected
         region. 
       
    
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 07ed6e8..0a20650 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -75,7 +75,7 @@ li:before {
           
    • 
 					
  • 
 						File type associations for
-						formats supported by jalview (including .jvp project files)
+						formats supported by Jalview (including .jvp project files)
 					
    • 
 					
  • 
 						Jalview launch files (.jvl) to pass command line
@@ -100,7 +100,6 @@ li:before {
             IntervalStoreJ (NCList
             implementation that allows updates) used for Sequence Feature collections
    • 
           
  • 
-							
  • 
                 Sequence
                 features can be filtered and shaded according to any
                 associated attributes (e.g. variant attributes from VCF
@@ -176,7 +175,7 @@ li:before {
 							
    • 
 							
  • 
 								Alignment Overview now WYSIWIS (What you see is
-								what is shown)
    Only visible region of alignment is shown by
+								what is shown)
    Only visible regions of alignment are shown by
 								default (can be changed in user preferences)
 							
    • 
 							
  • 
@@ -232,59 +231,55 @@ li:before {
 				
         Deprecations
         
      
-          
    • 
-            DAS sequence retrieval and annotation
+          
    • DAS sequence retrieval and annotation
             capabilities removed from the Jalview Desktop
           
      • 
-          
    • 
-            Castor library for XML marshalling and
+          
    • Castor library for XML marshalling and
             unmarshalling has been replaced by JAXB for Jalview projects
             and XML based data retrieval clients
      • 
           
    • Disable VAMSAS menu in preparation for removal
      •  
           
    • Jalview Desktop no longer distributed via Java Web Start
      • 
         
     Documentation
 				
      
-					
    • 
-						Added remarks about transparent rendering effects
+					
    • Added remarks about transparent rendering effects
 						not supported in EPS figure export
 					
      • 
 					
    • Typos in documentation for Preferences dialog
      • 
 				
     Development and Release Processes
         
      
         	
    • 
-						Build system migrated from Ant to Gradle
+        	Build system migrated from Ant to Gradle
 					
      • 
-					
    • Enhanced checks for missing and duplicated keys in Message bundles
      • 
+			
    • 
+			Enhanced checks for missing and duplicated keys in Message bundles
      • 
           
    • 
-            Eclipse project configuration managed with
+          Eclipse project configuration managed with
             gradle-eclipse
           
      • 
           
    • 
-             Atlassian
+          Atlassian
             Bamboo continuous integration for unattended Test Suite
             execution
           
      • 
           
    • 
-            Memory test suite to detect leaks in common
+          Memory test suite to detect leaks in common
             operations
           
      • 
           
    • 
-            More unit test coverage, and minor
-            issues resolved.
+          More unit test coverage, and minor
+            issues resolved
           
      • 
           
    • 
-            Developer documentation migrated to
+          Developer documentation migrated to
             markdown (with HTML rendering)
           
      • 
           
    • 
-            HelpLinksChecker runs on Windows
+          HelpLinksChecker runs on Windows
           
      • 
           
    • 
-            New URLs for publishing development
+          New URLs for publishing development
             versions of Jalview
           
      • 
-          
    • 
-          
    • 
         
    
       
 			
@@ -327,8 +322,8 @@ li:before {
 						Settings and Jalview Preferences panels
 					
    • 
 					
  • 
-						Jalview hangs when closing windows or the
-						overview updates with large alignments
+						Jalview hangs when closing windows, or redrawing the
+						overview with large alignments
 					
    • 
 					
  • 
 						Tree and PCA calculation fails for selected
@@ -358,7 +353,7 @@ li:before {
           
    • 
 					
  • 
 						'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)
 					
    • 
 					
  • 
 						Blank extra columns drawn or printed
@@ -488,7 +483,8 @@ li:before {
           
    • 
          New Known Defects
         
      
-				
    • Select columns containing feature by double clicking ignores bounds of an existing selected region
+				
    • 
+				Select columns containing feature by double clicking ignores bounds of an existing selected region
 				
      • 
 					
    • 
 						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.
 					
      • 
-					
    • Cancel on Feature Settings dialog doesn't reset group visibility
      •  
+					
    • 
+					Cancel on Feature Settings dialog doesn't reset group visibility
      •  
 					
    • 
 					F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
 					
      • 
@@ -552,7 +549,7 @@ li:before {
               Hidden sequence markers and representative
               sequence bolding included when exporting alignment as EPS,
               SVG, PNG or HTML. 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.
             
             
    • 
@@ -626,7 +623,7 @@ li:before {
             
      • 
             
    • 
               .jvp should be used as default extension
-              (not .jar) when saving a jalview project file.
+              (not .jar) when saving a Jalview project file.
             
      • 
             
    • 
               Mac Users: closing a window correctly
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index eb318f0..4b406be 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -64,7 +64,7 @@
       also been improved.
      • 
     
    • Backup files. 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 Backups tab in
       Jalview's preferences dialog allows the number and format of