From 2e2bc3fbb0231c705e5d019df9cb8e0e600ca12e Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 10 Apr 2006 14:16:55 +0000 Subject: [PATCH] updated menus and rearranged seqfeatures (again) --- help/help.jhm | 5 +++-- help/helpTOC.xml | 1 + help/html/menus/alignmentMenu.html | 37 +++++++++++++++++++++++++----------- help/html/menus/alwedit.html | 7 +++++-- help/html/menus/alwfile.html | 4 ++++ help/html/menus/alwview.html | 12 +++++++----- help/html/whatsNew.html | 4 ++-- 7 files changed, 48 insertions(+), 22 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index fcfc0a8..16e620f 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -19,7 +19,8 @@ - + + @@ -49,7 +50,7 @@ - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index bae82d4..6630a0a 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -11,6 +11,7 @@ + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index d0f1052..ee8661f 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -146,10 +146,14 @@ the current alignment) exceeds this value then one of the sequences (the shorter) is discarded. Press the "Apply" button to remove redundant sequences. The "Undo" button will undo the last redundancy deletion. -
  • Pad Gaps
    -     Adds gaps to the end of all the sequences so they are all - the same length. This is useful for making a tree using unaligned sequences.
    - You may set the default gap character in preferences. +
  • Pad Gaps
    +     When selected, the alignment will be kept at minimal + width (no empty columns before or after the first or last aligned + residue). This is useful when making a tree using unaligned + sequences and when working with alignment analysis programs which + require 'properly aligned sequences' to be all the same length.
    + You may set the default gap character in preferences. +

    • @@ -158,7 +162,8 @@
    • Find
      Select this to search - for residues, sequence name or residue position within the alignment. + for residues, sequence name or residue position within the + alignment and create new sequence features from the queries.
    @@ -168,6 +173,10 @@
  • Font
    Change the font of the display from the "Choose Font" dialog box, which is shown when this item is selected.
    • +
  • Smooth Fonts
    + If selected, the alignment will be drawn with anti-aliasing on which looks + better, but performace is reduced. +
  • Wrap
    When ticked, the alignment display is "wrapped" to the width of the alignment window. This is useful if your alignment @@ -201,7 +210,7 @@ be displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
    • -
  • Sequence Features
    +
  • Fetch Sequence Features
    If the sequence names are Swissprot entries Jalview will use the names to retrieve sequence features from the EBI. Features which are 1 residue in length are @@ -210,11 +219,13 @@
    Note: The retrieved information will update the sequence start and end labels if they are incorrect.
    • -
  • Seqence Settings
    - If features have been added to the alignment then the priority of - rendering the features can be altered so that overlapping features can - be displayed or hidden. See Sequence - Features.
    • +
  • Show Sequence Features
    Show or + hide sequence features on this alignment.
    • +
  • Seqence Feature Settings...
    + Control the colour and display of sequence features on the + alignment. See Sequence Feature Settings.
    +
  • Overview Window
    A scaled version of the alignment will be displayed in a small window. A red box will indicate the currently visible area of the @@ -245,6 +256,10 @@     Use this to set the threshold value for colouring above Identity. Useful if the window has been closed.
    • +
  • By Annotation
    + Colours the alignment on a per-column value from a specified annotation. + See Annotation Colouring.
    +
  • Calculate diff --git a/help/html/menus/alwedit.html b/help/html/menus/alwedit.html index 4e0c8b0..e3d1958 100755 --- a/help/html/menus/alwedit.html +++ b/help/html/menus/alwedit.html @@ -82,8 +82,11 @@ is discarded. Press the "Apply" button to remove redundant sequences. The "Undo" button will undo the last redundancy deletion.
  • Pad Gaps
    -     Adds gaps to the end of all the sequences so they are all the - same length. This is useful for making a tree using unaligned sequences.
    + When selected, the alignment will be kept at minimal + width (no empty columns before or after the first or last aligned + residue). This is useful when making a tree using unaligned + sequences and when working with alignment analysis programs which + require 'properly aligned sequences' to be all the same length.
    You may set the default gap character in preferences.
    • diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index f262679..53c7e6c 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -65,6 +65,10 @@ alignment. Note: the ids of the tree file and your alignment MUST be the same.
     +
  • Load Features / Annotations
    +     Jalview load precalculated sequence + features or alignment + annotations.
  • Close
    Close the alignment window. Make sure you have saved your alignment before you close - either as a Jalview diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 9be2775..d83d105 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -57,7 +57,7 @@ displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
    • -
  • Sequence Features
    +
  • Fetch Sequence Features
    If the sequence names are Swissprot entries Jalview will use the names to retrieve sequence features from the EBI. Features which are 1 residue in length are coloured red, sequences @@ -66,10 +66,12 @@ Note: The retrieved information will update the sequence start and end labels if they are incorrect.
    • -
  • Seqence Settings
    - If features have been added to the alignment then the priority of rendering - the features can be altered so that overlapping features can be displayed - or hidden. See Sequence Features.
    +
  • Show Sequence Features
    Show or + hide sequence features on this alignment.
    • +
  • Seqence Feature Settings...
    + Control the colour and display of sequence features on the + alignment. See Sequence Feature Settings.
  • Overview Window
    A scaled version of the alignment will be displayed in a small diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 9c13b59..7d88e7f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -46,8 +46,8 @@ and Gnome)
    • internal Jalview schema), and sequence description strings are now preserved in the archive.
  • Jalview can now correctly read and write MODELLER style -PIR description lines for proteins with a PDB reference. +href="io/modellerpir.html">MODELLER style +PIR files.

    • See the Release History page for details of all -- 1.7.10.2