From 097286cf1aaa3767be06a2c99947265bc3417417 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 16 Jun 2005 17:39:14 +0000 Subject: [PATCH] lots of tidying in doco. --- help/help.jhm | 8 ++++++++ help/helpTOC.xml | 10 +++++++++- help/html/calculations/sorting.html | 4 ++-- help/html/calculations/tree.html | 7 ++++--- help/html/io/export.html | 2 +- help/html/io/index.html | 5 +++-- help/html/menus/alignmentMenu.html | 2 +- help/html/webServices/clwqueued.gif | Bin 7783 -> 5619 bytes help/html/webServices/index.html | 11 ++++++++--- 9 files changed, 36 insertions(+), 13 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index e387045..91eba83 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -11,8 +11,11 @@ + + + @@ -42,6 +45,11 @@ + + + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index e441033..c2221ac 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -9,9 +9,12 @@ + + + @@ -38,7 +41,12 @@ - + + + + + + diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index adc44c9..47522ee 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -6,7 +6,7 @@

Sorting Sequences

Any group of selected sequences may be reordered by pressing the up or down arrow keys. The whole alignment may also be reordered by -the use of the functions in the Sort menu (Calculate->Sort): +the use of the functions in the Sort menu (Calculate→Sort):

  • Sort by ID

    @@ -26,7 +26,7 @@ fraction of conserved residues. order the sequences corresponding to those leaves in the alignment.
    If a tree has been calculated from or associated with the current -alignment, its name will appear in the submenu Sort->By Tree Order.

    +alignment, its name will appear in the submenu Sort→By Tree Order.

  • Sort by alignment ordering

    Multiple alignment methods often order the sequences in their diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index c579677..c546497 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -3,9 +3,10 @@

    Calculation of trees from alignments

    Trees are calculated on either the complete alignment, or just the -currently selected group of sequences. There are four different -calculations, using one of two distance measures and constructing the -tree from one of two algorithms : +currently selected group of sequences, using the functions in the +Calculate→Calculate tree submenu. There are +four different calculations, using one of two distance measures and +constructing the tree from one of two algorithms :

    Distance Measures

    Trees are calculated on the basis of a measure of similarity diff --git a/help/html/io/export.html b/help/html/io/export.html index f559c1a..771ccba 100755 --- a/help/html/io/export.html +++ b/help/html/io/export.html @@ -3,7 +3,7 @@ Exporting alignments as artwork -

    Export

    +

    Exporting alignments as graphics and lineart

    The alignment view can be printed using File→Print, or exported in a number of ways via the File→Export menu: diff --git a/help/html/io/index.html b/help/html/io/index.html index c521747..332cdca 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -7,8 +7,9 @@

    The EBI has examples of these file formats.

    Additionally, annotated whole sets of alignments and trees can be -read from a Jalview -(jar) format file using Desktop→Load Project.

    +read from a Jalview (jar) +format file using Desktop→Load +Project.

    Use the Desktop→Input Alignment menu to read in files from:

    • From File: the local file system
    • diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 3538d0b..c935bd2 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -341,7 +341,7 @@ NAME START_RES END_RES SEQUENCE Submits all, or jut the currently selected sequences for alignment using Muscle. Do not use this if you are working with nucleic acid sequences.
      -
    • JPred
      +
    • JNet
      Secondary structure prediction by network consensus. The behaviour of this calculation depends on the current selection:
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        Web services

        A variety of web services are available from the Alignment window's - Calculations→Web Service→ menu. + Calculations→Web Service menu.

        Jalview's distributed computations are SOAP based services exposing protein sequence alignment and secondary structure prediction programs. These services actually run @@ -11,9 +11,14 @@ Dundee, and are maintained by the Barton group.

        Web Service Dialog Box

        - +

        - This dialog box is displayed when a web service job is submitted. + This dialog box is displayed when a web service job + is submitted. It gives the name of the service and + any method citation information, and monitors the + progress of the calculation. The cancel button will + permanently cancel the job, but this is only + possible for some services.

        Current services:

          -- 1.7.10.2