From 0943de76f6a7435894e72479671642c05f2f3687 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 27 Aug 2015 12:00:37 +0100 Subject: [PATCH] JAL-1544 'Jalview' consistently capitalised --- help/html/features/commandline.html | 10 +++++----- help/html/features/featuresFormat.html | 2 +- help/html/features/groovy.html | 13 +++++-------- help/html/features/hiddenRegions.html | 2 +- help/html/features/jmol.html | 2 +- help/html/features/preferences.html | 4 ++-- help/html/features/seqfetch.html | 2 +- help/html/features/viewingpdbs.html | 2 +- help/html/io/export.html | 2 +- help/html/io/fileformats.html | 4 ++-- help/html/memory.html | 2 +- help/html/menus/alignmentMenu.html | 2 +- help/html/menus/desktopMenu.html | 2 +- help/html/privacy.html | 2 +- help/html/releases.html | 10 +++++----- 15 files changed, 29 insertions(+), 32 deletions(-) diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html index e393701..dd6c0de 100644 --- a/help/html/features/commandline.html +++ b/help/html/features/commandline.html @@ -24,24 +24,24 @@

Running Jalview from the command line

Jalview is most easily run from the command line if you have built it from source, or via the 'Jalview' executable created from the - InstallAnywhere jalview installation. Both of these mechanisms allow - true command line execution of jalview - allowing you to provide + InstallAnywhere Jalview installation. Both of these mechanisms allow + true command line execution of Jalview - allowing you to provide additional options.

The Java Webstart version of - jalview can be executed from the command line using something like + Jalview can be executed from the command line using something like : 

javaws http://www.jalview.org/webstart/jalview.jnlp -open
  yourFileName
But, this is not guaranteed to work on all versions of webstart on all operating systems, and doesn't let you execute Jalview with any additional parameters. -

Running jalview from the InstallAnywhere +

Running Jalview from the InstallAnywhere installation

If you install with InstallAnywhere you can use several more commands. However, if you call the application with the link provided by InstallAnywhere any output from the application will be sent to output.txt, not standard out.
- The jalview application also requires a number of additional + The Jalview application also requires a number of additional libraries on the class path. The command line below adds the Jalview installation's 'lib' directory to the list of directories that are searched for jars to be added to the classpath:

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 9e2be6a..82e46cb 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -165,7 +165,7 @@ Non-positional features are shown in a tooltip when the mouse hovers over the sequence ID panel, and any embedded links can be accessed from the popup menu.
Scores
Scores can be associated with sequence features, and used to sort -sequences or shade the alignment (this was added in jalview 2.5). +sequences or shade the alignment (this was added in Jalview 2.5). The score field is optional, and malformed scores will be ignored.

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html index b49fc17..6db1d1c 100644 --- a/help/html/features/groovy.html +++ b/help/html/features/groovy.html @@ -44,7 +44,7 @@ The jars are obtained from the embedded directory within the groovy distribution. The easiest way of adding them to the Jalview classpath - is to download and build jalview from its source distribution, and + is to download and build Jalview from its source distribution, and then add the groovy-all-*.jar to the lib directory whose path is given in the java.ext.dirs property.

@@ -59,13 +59,13 @@

Executing groovy scripts on Jalview startup
- The -groovy <script> option on the + The -groovy <script> option on the Jalview command line will execute the contents of <script>. <script> may be a file, a URL, or alternatively if it is "STDIN" then the standard input will be used.
Note: The groovy script will be executed after any data is loaded, and before images or any output - files are written. This allows you to perform customised jalview + files are written. This allows you to perform customised Jalview analysis workflows with groovy.

@@ -76,13 +76,12 @@ object defined in the groovy environent which corresponds to the 

jalview.gui.Desktop
object which manages all the Jalview windows. -

Here's an example to get you started:
-

- -

 

+If you have downloaded the InstallAnywhere version of Jalview, you can find additional groovy scripts in the examples/groovy subfolder of the installation directory. diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index b9e8382..48d205f 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -48,7 +48,7 @@ or web service alignments (nb. this may change in the future).

Hidden Sequence Representatives and Multiple Views
A word of warning: hidden representative sequence groups are -(still) only partly implemented in the jalview 2.5 release, and we hope +(still) only partly implemented in the Jalview 2.5 release, and we hope to deal with the following issues in the future.
Currently, represented hidden groups are only made correctly if there is just one alignment view. When multiple views on an alignment exist, then diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index c81fcc3..9d0ad11 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -221,7 +221,7 @@ labels, plotting surfaces, and display animation. The 'Set Picking' menu controls the behaviour of single and double mouse clicking on the structure, and the 'Console' option opens the Jmol scripting console.

The state of each Jmol display is stored within jalview archives as a Jmol state recovery + href="jalarchive.html">Jalview archives as a Jmol state recovery script file. This means that any Jmol visualization effects that you add beyond those provided by Jalview will be able to be stored and recovered along with the displayed alignments in Jalview.

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 928ea2c..c86abfa 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -142,7 +142,7 @@ details as necessary. Web Services will not work if you are using a proxy server and do not enter the settings here.

Usage statistics, Questionnaire and Version checks
Uncheck these options to prevent Jalview from submitting usage -statistics to google analytics, checking for jalview questionnaires or +statistics to google analytics, checking for Jalview questionnaires or retrieving details of the latest release version (at www.jalview.org). See the user privacy statement for more information.

@@ -163,7 +163,7 @@ style for EPS export: EPS files will be a mixture of text and lineart. This produces compact files that can be edited easily in programs like Microsoft Word and Adobe Illustrator, but can be problematic if the fonts available to - jalview are not accessible by the program reading the EPS file. + Jalview are not accessible by the program reading the EPS file.

Automatically set ID width
When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 2516f3f..2a7c429 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -49,7 +49,7 @@ WSDBFetch service provided by the European Bioinformatics Institute, or, since J one or more accession ids (as a semi-colon separated list), or press the "Example" button to paste the example accession for the currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.

-

Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - PDB Sequence Fetcher is used for discovering and retrieving the sequenec data.

+

Since Jalview 2.9 if PDB is selected as the sequence database, a specialised interface - PDB Sequence Fetcher is used for discovering and retrieving the sequence data.

Specifying chains for PDB IDs If you are retrieving sequences from the PDB, you can retrieve specific chains by appending a colon and the chain id to the PDB diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 506beef..44a07cc 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -124,7 +124,7 @@ associate PDB files with names like '1gaq.pdb' with sequences that have an ID like '1gaq'.
Note: This feature was added in Jalview 2.7

-

Note for jalview applet users:
+

Note for Jalview applet users:
Due to the applet security constraints, PDB Files can currently only be imported by cut and paste of the PDB file text into the text box opened by the 'From File' entry of the structure menu.

diff --git a/help/html/io/export.html b/help/html/io/export.html index e9726de..a7a5a1a 100755 --- a/help/html/io/export.html +++ b/help/html/io/export.html @@ -40,7 +40,7 @@ diagrams in publications and on the web.

Tips for working with EPS Files

-
  • The EPS file generated by jalview contains vector graphics which are directly +
  • The EPS file generated by Jalview contains vector graphics which are directly editable in graphics applications such as Adobe Illustrator.
  • EPS files can be produced as "Text" or "Lineart". Use "Text" if you want the final document to be MUCH smaller in diskspace diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html index b457adf..16e9cc6 100755 --- a/help/html/io/fileformats.html +++ b/help/html/io/fileformats.html @@ -34,7 +34,7 @@ td {

    Alignment File Formats

    Jalview understands a wide range of sequence alignment formats. In order to determine which format has been used for an alignment, -jalview tries to detect some text or formatting unique to one of the formats: +Jalview tries to detect some text or formatting unique to one of the formats:

    @@ -83,7 +83,7 @@ THISISASEQUENCE
    Format .json
    -

    The file extensions are used to associate jalview alignment icons +

    The file extensions are used to associate Jalview alignment icons with alignment files:

    diff --git a/help/html/memory.html b/help/html/memory.html index f35c457..664904f 100755 --- a/help/html/memory.html +++ b/help/html/memory.html @@ -67,7 +67,7 @@ The way you increase the memory settings for the JVM depends on which installati your Java installation's bin directory) with the file location as its argument. The file's url is something like :
     file://<full path to file>
-
    If jalview doesn't start up, see below. + If Jalview doesn't start up, see below. You'll have to edit the above settings in the JNLP file using a text editor, save it, and try starting Jalview with it once more.

    • diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 8b50d9e..5bf9e60 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -245,7 +245,7 @@ selected groups of the alignment will be subdivided according to the contents of the currently selected region.
    Use this to subdivide an alignment based on the different combinations of - residues observed at specific positions. (new in jalview 2.5) + residues observed at specific positions. (new in Jalview 2.5)
  • Undefine Groups (Control U)
    The alignment will be reset with no defined groups.
    WARNING: diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index 374aa9c..a650927 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -65,7 +65,7 @@
  • Show Memory Usage
     When ticked, the currently available memory will be displayed in the bottom right of the desktop background area.
    - See the help on jalview memory settings for more information.
    • + See the help on Jalview memory settings for more information.
  • Collect Garbage
     Selecting this will initiate the Java Virtual Machine garbage collector, which might help free up some memory... perhaps.
    • diff --git a/help/html/privacy.html b/help/html/privacy.html index 1635475..858aa32 100644 --- a/help/html/privacy.html +++ b/help/html/privacy.html @@ -46,7 +46,7 @@ These are described below:

    properties file.
  • The Jalview web services stack is contacted to retrieve the currently available web services. All interactions with - the public jalview web services are logged, but we delete all job data + the public Jalview web services are logged, but we delete all job data (input data and results) after about two weeks.

    • diff --git a/help/html/releases.html b/help/html/releases.html index 1df3bb9..19fa285 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -162,7 +162,7 @@
  • Hide sequence doesn't hide associated annotation
  • User defined colours dialog box too big to fit on screen and buttons not visible
    • -
  • author list isn't updated if already written to jalview +
  • author list isn't updated if already written to Jalview properties
  • Popup menu won't open after retrieving sequence from database
    • @@ -230,7 +230,7 @@
  • - out of memory errors are not raised when saving jalview project + out of memory errors are not raised when saving Jalview project from alignment window file menu
  • @@ -316,7 +316,7 @@
  • Newly created RNA secondary structure line doesn't have 'display all symbols' flag set
  • T-COFFEE alignment score shading scheme and other - annotation shading not saved in jalview project
    • + annotation shading not saved in Jalview project
  • Local file cannot be loaded in freshly downloaded Jalview
  • Jalview icon not shown on dock in Mountain Lion/Webstart
  • Load file from desktop file browser fails
    • @@ -341,7 +341,7 @@
  • Not all working JABAWS services are shown in Jalview's menu
    • -
  • JAVAWS version of jalview fails to launch with 'invalid +
  • JAVAWS version of Jalview fails to launch with 'invalid literal/length code'
  • Annotation/RNA Helix colourschemes cannot be applied to alignment with groups (actually fixed in 2.8.0b1)
    • @@ -403,7 +403,7 @@
  • Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works
    • -
  • Groovy scripting for headless jalview operation
    • +
  • Groovy scripting for headless Jalview operation
    • Other improvements