From dd193c9ceff22f721c53814fd9c37f269a9edfde Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 4 Jul 2019 13:09:13 +0100 Subject: [PATCH] JAL-3111 help pages minor corrections --- help/help/html/features/featureschemes.html | 10 ++--- help/help/html/features/featuresettings.html | 4 +- help/help/html/features/importvcf.html | 2 +- help/help/html/menus/alignmentMenu.html | 2 +- help/help/html/menus/alwcalculate.html | 2 +- help/help/html/releases.html | 53 ++++++++++++-------------- help/help/html/whatsNew.html | 2 +- 7 files changed, 36 insertions(+), 39 deletions(-) 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 -- 1.7.10.2