From cb56d532a3b7cc50d724b0761cc7c49ed2d081cd Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 1 Dec 2014 16:14:50 +0000 Subject: [PATCH] JAL-1544 typos/formatting in help (and Phylip added) --- help/html/calculations/consensus.html | 4 ++-- help/html/calculations/pca.html | 4 ++-- help/html/colourSchemes/pid.html | 2 ++ help/html/features/annotation.html | 2 +- help/html/features/clarguments.html | 2 +- help/html/features/dassettings.html | 2 +- help/html/features/featuresFormat.html | 2 +- help/html/features/featuresettings.html | 6 +++--- help/html/features/hiddenRegions.html | 2 +- help/html/features/multipleViews.html | 4 ++-- help/html/features/seqfetch.html | 2 +- help/html/features/varna.html | 4 ++-- help/html/io/export.html | 2 +- help/html/io/fileformats.html | 2 +- help/html/menus/alignmentMenu.html | 26 ++++++++++++-------------- help/html/menus/alwedit.html | 4 ++-- help/html/menus/alwfile.html | 4 ++++ help/html/privacy.html | 6 +++--- help/html/vamsas/index.html | 2 +- help/html/webServices/RNAalifold.html | 2 +- help/html/webServices/dbreffetcher.html | 2 +- 21 files changed, 45 insertions(+), 41 deletions(-) diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index bc42278..d5ce720 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -23,7 +23,7 @@

Alignment Consensus Annotation

The consensus displayed below the alignment is the percentage of the modal - residue per column. By default this calculation takes includes gaps in column. + residue per column. By default this calculation includes gaps in columns. You can choose to ignore gaps in the calculation by right clicking on the label "Consensus" to the left of the consensus bar chart.

If the modal value is shared by more than 1 residue, a "+" symbol @@ -38,7 +38,7 @@ clipboard. By clicking on the label you can also activate the sequence logo. It indicates the relative amount of residues per column which can be estimated by its size in the logo. The tooltip of a column gives the - exact numbers for all occuring residues. + exact numbers for all occurring residues.
If columns of the alignment are very diverse, then it can sometimes be difficult to see the sequence logo - in this case, right click on the annotation row label and select diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 8d6f329..66dbabd 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -37,10 +37,10 @@ executing the calculation via a web service.

About PCA

Principal components analysis is a technique for examining the structure of complex data sets. The components are a set of dimensions -formed from the measured values in the data set, and the principle +formed from the measured values in the data set, and the principal component is the one with the greatest magnitude, or length. The sets of measurements that differ the most should lie at either end of this -principle axis, and the other axes correspond to less extreme patterns +principal axis, and the other axes correspond to less extreme patterns of variation in the data set.

diff --git a/help/html/colourSchemes/pid.html b/help/html/colourSchemes/pid.html index 47b992a..d4e70fb 100755 --- a/help/html/colourSchemes/pid.html +++ b/help/html/colourSchemes/pid.html @@ -35,6 +35,7 @@ td { The PID option colours the residues (boxes and/or text) according to the percentage of the residues in each column that agree with the consensus sequence. Only the residues that agree with the consensus residue for each column are coloured.

+
@@ -49,5 +50,6 @@ td {
> 80 %< 40%
+
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index a036bd5..01d9f64 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -132,7 +132,7 @@ href="../features/jalarchive.html">Jalview Archives.

Current Limitations

As of version 2.5, the Jalview user interface does not support the -creation and editing quantitative annotation (histograms and line graphs), or +creation and editing of quantitative annotation (histograms and line graphs), or to create annotation associated with a specific sequence. It is also incapable of annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an Annotation file.
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html index dc28e03..2a040fe 100644 --- a/help/html/features/clarguments.html +++ b/help/html/features/clarguments.html @@ -53,7 +53,7 @@ Set the colourscheme for the alignment. This can be any of the built-in colourschemes, a name of a predefined colourscheme - (defined in the jalview properties file), or an 'inline' colourscheme + (defined in the Jalview properties file), or an 'inline' colourscheme (see the applet's colour parameter for more information). diff --git a/help/html/features/dassettings.html b/help/html/features/dassettings.html index 9676ed7..86162dc 100644 --- a/help/html/features/dassettings.html +++ b/help/html/features/dassettings.html @@ -45,7 +45,7 @@ more about these values.

When the DAS Settings panel is first opened, and when the 'Refresh source' buton is pressed, a list of DAS sources is retrieved from the DAS registry URL (set by default to the DAS registration server at -http://das.sanger.ac.uk/registry/das1/sources/).

+http://www.dasregistry.org/das/).

Adding your own DAS Sources

You can add your own DAS source to the list by clicking the "Add Local Source" button. Enter the URL and nickname of your diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html index 8665e66..32b4ccb 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -163,7 +163,7 @@ Specify the start and end for a feature to be 0 in order to attach it to the whole sequence. 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
+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). The score field is optional, and malformed scores will be diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 63217ee..3830302 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -76,8 +76,8 @@ alignment based on the average score or total number of currently active features and groups on each sequence. To order the alignment using a specific feature type, use the sort by .. entries in the pop-up menu for that type.
-Feature sorting and graduated feature colouring was introduced -in jalview 2.5

+Feature sorting and graduated feature colouring were introduced +in Jalview 2.5

Transparency and Feature Ordering

It is important to realise that sequence features are often not @@ -85,7 +85,7 @@ distinct and often overlap (for example, a metal binding site feature may be attached to one position along a stretch of sequence marked with a secondary structure feature).

The ordering of the sequence features in the dialog box list is -the order used by jalview for rendering sequence features. A feature at +the order used by Jalview for rendering sequence features. A feature at the bottom of the list is rendered below a feature higher up in the list.
You can change the order of a feature by diff --git a/help/html/features/hiddenRegions.html b/help/html/features/hiddenRegions.html index 9b85cf9..63920f5 100644 --- a/help/html/features/hiddenRegions.html +++ b/help/html/features/hiddenRegions.html @@ -41,7 +41,7 @@ web service alignments performed on visible sequences.

A more advanced hide involves a right-mouse click on a sequence, then selecting "SequenceID -> Represent Group with SequenceId". Using this method of hiding sequences, any edits -performed on the visible group representative will be propogated to all +performed on the visible group representative will be propagated to all the sequences in that group.
The hidden representative sequences will not be used in any calculations or web service alignments (nb. this may change in the future). diff --git a/help/html/features/multipleViews.html b/help/html/features/multipleViews.html index 209aba4..b1ccf4b 100644 --- a/help/html/features/multipleViews.html +++ b/help/html/features/multipleViews.html @@ -24,10 +24,10 @@

Multiple Alignment Views

-

Multiple alignment views allows the same alignment to be viewed +

Multiple alignment views allow the same alignment to be viewed independently in many different ways simultaneously. Each view is an independent visualization of the same alignment, so each may have a -different ordering, colouring, row and column hiding and seuqence +different ordering, colouring, row and column hiding and sequence feature and annotation display setting, but alignment, feature and annotation edits are common to all, since this affects the underlying data.

diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index 6f4363b..5f0744d 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -25,7 +25,7 @@

Sequence Fetcher

Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).

+WSDBFetch service provided by the European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).

The Jalview Sequence Fetcher Dialog Box

The Sequence Fetcher dialog box can be opened via the "File" diff --git a/help/html/features/varna.html b/help/html/features/varna.html index ffc582b..290135c 100644 --- a/help/html/features/varna.html +++ b/help/html/features/varna.html @@ -30,7 +30,7 @@ selecting the "Structure→View Structure:" option in the sequence id pop-up menu (if you can't see this, then no RNA structure is associated with your -sequence or alignment. In the pop-up menu all structures that +sequence or alignment). In the pop-up menu all structures that are associated with this sequence and all sequences that are associated with the alignment are available. @@ -52,7 +52,7 @@ associated with the alignment are available. Individual structures: this is a structure associated with the individual sequence and therefore not related to the alignment - +

Controls
  • Page Setup ...
    diff --git a/help/html/privacy.html b/help/html/privacy.html index be5cf56..e19122c 100644 --- a/help/html/privacy.html +++ b/help/html/privacy.html @@ -25,7 +25,7 @@

    Privacy for Jalview Users

    The Jalview Desktop application which is available from the -www.jalview.org site does not contain code designed collect personal or +www.jalview.org site does not contain code designed to collect personal or private information without your consent. However, we do collect usage statistics to work out who is using Jalview, so we can apply for funding to support Jalview development, and make it better for our users.

    @@ -51,7 +51,7 @@ These are described below:


  • Google Analytics
    - Since jalview 2.4.0b2, the Jalview Desktop records usage data with + Since Jalview 2.4.0b2, the Jalview Desktop records usage data with Google Analytics via the JGoogleAnalytics class.
    @@ -68,7 +68,7 @@ program shouldn't try to contact any of the web servers mentioned above href="features/commandline.html">command line options to disable the questionnaire and usage statistics check. Finally, the Connections Tab of the -jalview preferences contains options for controlling the submission of +Jalview preferences contains options for controlling the submission of usage statistics.

    Other Web Clients in Jalview
    The Jalview desktop is intended to make it easier to interact with diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index b34289c..fcc9b0c 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -94,7 +94,7 @@ crashes or otherwise fails, the VAMSAS session it is connected to will whilst it is still connected to a session, that session can be recovered in a new Jalview instance using the Vamsas→"Existing session" sub menu.

    -A quick Demo +

    A quick Demo
    Jalview can talk to itself through VAMSAS. Simply start two copies of the application, create a new vamsas session in one, and connect to the diff --git a/help/html/webServices/RNAalifold.html b/help/html/webServices/RNAalifold.html index 55fe70c..6c3c6b5 100644 --- a/help/html/webServices/RNAalifold.html +++ b/help/html/webServices/RNAalifold.html @@ -62,7 +62,7 @@ Partition Function (-p)
    Calculate the Partition Function and base pairing probability matrix in addition to the mfe structure. A coarse representation of the pair probabilities in the - from of a pseudo bracket notation, as well as the centroid structure + form of a pseudo bracket notation, as well as the centroid structure derived from the pair probabilities are displayed. The most likely base pairings are stored in a separate file by RNAalifold and represented in Jalview by a bar graph annotation line labeled diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html index ad42153..b02f940 100644 --- a/help/html/webServices/dbreffetcher.html +++ b/help/html/webServices/dbreffetcher.html @@ -49,7 +49,7 @@ reference, and any cross-references that its records contain.

    The Sequence Identification Process
    The method of accession id discovery is derived from the method which earlier Jalview versions used for Uniprot sequence feature retrieval, -and was originally restricted to the identifaction of valid Uniprot +and was originally restricted to the identification of valid Uniprot accessions.
    Essentially, Jalview will try to retrieve records from a subset of the databases accessible by the sequence -- 1.7.10.2