From b5edbd2a03d16372bc3e8019ddbf3840dcfe38ed Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 8 Dec 2005 10:57:52 +0000 Subject: [PATCH] Updated help --- help/help.jhm | 6 +- help/helpTOC.xml | 9 +- help/html/editing/index.html | 6 +- help/html/features/pdbviewer.html | 4 + help/html/menus/alignmentMenu.html | 18 +++- help/html/menus/alwfile.html | 7 +- help/html/menus/alwview.html | 67 +++++++------- help/html/menus/desktopMenu.html | 7 +- help/html/whatsNew.html | 173 +++++------------------------------- 9 files changed, 100 insertions(+), 197 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index ed877d8..4820b6f 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -4,11 +4,9 @@ - - - - + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 6a8fe72..7e5ed95 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -3,9 +3,11 @@ + + @@ -40,9 +42,8 @@ - - - + + @@ -52,7 +53,7 @@ - + diff --git a/help/html/editing/index.html b/help/html/editing/index.html index bb43c37..734a662 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -5,9 +5,9 @@

Inserting / removing gaps - hold down the "Shift" key. Click a residue with the mouse and drag the residue to the right to insert gaps or to the left to remove gaps.
- If the residue selected is within a defined group, hold down either "Alt" - or "Control" key and drag the residue left or right to edit all sequences - in the defined group at once.

+ If the residue selected is within a defined group, hold down either "Control" + key and drag the residue left or right to edit all sequences in the defined + group at once.

Copy/paste/cut/delete - any sequences which are in the current selection box (indicated in red) may be cut and / or copied to a new alignment or deleted.

diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index a35fe5f..a7e2c10 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -26,6 +26,9 @@ -> View Mapping" from the structure viewer window.

Moving the mouse over the structure will highlight the residue in the alignment window, and vice versa.

+

"Colour by Charge/Cysteine" will colour all Aspartate and Glutamate + residues red, Lysine and Arginine will be blue and Cysteine residues will be + coloured yellow.

Tips for Viewing Structures

  • Colour By Sequence follows the exact colours of the alignment window, including @@ -36,6 +39,7 @@
  • Use Wireframe, without depthcue, and without Z Buffering in order to accelerate the rendering of the structure.
  • You can save an image of your structure as a PNG or EPS file.
    • +
  • Use the cursor keys Up and Down arrow to zoom in and zoom out
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index d6b69a3..a514412 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -6,6 +6,11 @@
  • File
      +
    • Fetch Sequence
      + Shows a dialog window in which you can select known ids from Uniprot, + EMBL, EMBLCDS or PDB database using Web Services provided by the European + Bioinformatics Institute. See Sequence + Fetcher.
    • Save As
      Save the alignment to local file. A file selection window will open, use the "Files of type:" selection box to determine @@ -201,6 +206,11 @@
      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.
    • 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 @@ -270,7 +280,11 @@
    • Principal Component Analysis
      Shows a spatial clustering of the sequences based on the BLOSUM62 scores in the alignment. See Principal - Component Analysis.
      + Component Analysis.
      • +
    • Translate cDNA
      + If you are viewing a cDNA alignment a very simple translation service + is available. The translation ignores all gaps in the cDNA sequences. +
    • @@ -294,7 +308,7 @@ sequences.
-
  • Secondary Structure Prediction +
  • Secondary Structure Prediction
    • JPred Secondary Structure Prediction
      Secondary structure prediction by network consensus. The behaviour diff --git a/help/html/menus/alwfile.html b/help/html/menus/alwfile.html index 4aca47e..f262679 100755 --- a/help/html/menus/alwfile.html +++ b/help/html/menus/alwfile.html @@ -4,7 +4,12 @@

      Alignment Window File Menu

        -
      • File
        • +
      • File
        +
        • +
      • Fetch Sequence
        + Shows a dialog window in which you can select known ids from Uniprot, + EMBL, EMBLCDS or PDB database using Web Services provided by the European + Bioinformatics Institute. See Sequence Fetcher.
      • Save As
        diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index 66f4284..6088546 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -6,65 +6,68 @@
        • View
        -
        +
        • Font
          -           Change the font of the display from the - "Choose Font" dialog box, which is shown when this - item is selected.
          +           Change the font of the display from the "Choose Font" + dialog box, which is shown when this item is selected.
        • Wrap
          -           When ticked, the alignment display is - "wrapped" to the - width of the alignment window. This is useful if your alignment - has only a few sequences to view its full width at once.
          - Options are available to show the residue numbering at the start and/or - end of an alignment as well as showing the alignment position above each + When ticked, the alignment display is "wrapped" + to the width of the alignment window. This is useful if your alignment has + only a few sequences to view its full width at once.
          + Options are available to show the residue numbering at the start and/or + end of an alignment as well as showing the alignment position above each sequence row.
          - NOTE: When in wrapped alignment view, the - alignment cannot be edited or have regions selected on it.
          + NOTE: When in wrapped alignment view, the alignment cannot + be edited or have regions selected on it.
        • Show Full Sequence ID
          -           If this box is selected the sequence name will have the start + If this box is selected the sequence name will have the start and end position of the sequence appended to the name, in the format NAME/START-END
        • Boxes
          - If this is selected the background of a residue will be coloured using the - selected background colour. Useful if used in conjunction with "Colour + If this is selected the background of a residue will be coloured using the + selected background colour. Useful if used in conjunction with "Colour Text."
        • Text
          -           If this is selected the residues will be displayed using the + If this is selected the residues will be displayed using the standard 1 character amino acid alphabet.
        • Colour Text
          -           If this is selected the residues will be coloured according - to the background colour associated with that residue. The colour is slightly + If this is selected the residues will be coloured according + to the background colour associated with that residue. The colour is slightly darker than background so the amino acid symbol remains visible.
        • Show Gaps
          -           When this is selected, gap characters will be displayed as "." - or "-". If unselected, then gap characters will appear as blank spaces. -
          + When this is selected, gap characters will be displayed as + "." or "-". If unselected, then gap characters will + appear as blank spaces.
          You may set the default gap character in preferences.
        • Show Annotations
          -           If this is selected the "Annotation Panel" will be - displayed below the alignment. The default setting is to display the conservation + If this is selected the "Annotation Panel" will be + displayed below the alignment. The default setting is to display the conservation calculation, quality calculation and consensus values as bar charts.
        • 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 longer than 1 residue are - coloured blue. Move the mouse over a coloured feature to display the details - of the feature.
          - Note: The retrieved information will update the sequence start and end labels - if they are incorrect.
          + 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 + longer than 1 residue are coloured blue. Move the mouse over a coloured + feature to display the details of the feature.
          + 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.
        • 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 alignment. + A scaled version of the alignment will be displayed in a small + window. A red box will indicate the currently visible area of the alignment. Move the visible region using the mouse.
        diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html index 1fa861a..c99b64c 100755 --- a/help/html/menus/desktopMenu.html +++ b/help/html/menus/desktopMenu.html @@ -17,9 +17,14 @@ copy and paste an alignment into a text window
      • +
    • Fetch Sequence
      +       Shows a dialog window in which you can select known ids from + Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by + the European Bioinformatics Institute.
    • Save Project
      Saves all currently open alignment windows with their current view - settings and any associated trees, as a Jalview Archive (which has a .jar extension).
      • + settings and any associated trees, as a Jalview + Archive (which has a .jar extension).
    • Load Project
      Loads Jalview archives only.
    • Quit
      diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 31b3f1f..bd57b81 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -2,156 +2,29 @@ What's new ?

      What's new ?

      -

      If you are reading this then you will already have seen some of the recent changes - made to Jalview.
      - Jalview takes advantage of some of the more recent user interface developments - in the Java programming language. For instance Jalview is now a multi windowed - application, this keeps all your Jalview windows neatly together in one main - application window.

      -

      If you were familiar with the original Jalview, here is a list of important - features you should know about the current development:

      -
        -
      • Editing sequences is no longer the default when mouse clicking the alignment. - Instead, mouse clicking on the alignment creates a "selection region" - which may be full sequences or groups of residues.
        • -
      • To insert or edit the gaps in one sequence in alignment, the "Shift" - key must be held down when dragging the mouse.
        • -
      • To insert or edit gaps for a group of sequences, the "Alt" key - (or in X windows the "Control" key) must be held down.
        • -
      • Selecting colour schemes in the colour menu either sets just the "background" - colourscheme for the alignment, or - when the tickbox "Apply colour to - all groups" is ticked, applies the scheme to the background and all groups - defined on the alignment.
        • -
      • Use the right mouse button (apple and click on the Mac) whilst the pointer - is within the selection area to access the "define" region menu - to define a new region, give it a name, and change its colourscheme and display - properties.
        • -
      • Conservation is automatically updated whenever the alignment is edited
        • -
      • There is no "quick draw" option
        • -
      • Edits can be undone, and redone!
        • -
      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      Release
      New Features
      Issues Resolved
      2.07
      - 7 /12/05
        -
      • PDB Structure Viewer enhanced
        • -
      • Sequence Feature retrieval and display enhanced
        • -
      • Choose to output sequence start-end after sequence name for file output
        • -
      • Sequence Fetcher WSDBFetch@EBI
        • -
        -
      • HTML output writes groups and features
        • -
      • Group editing is Control and mouse click
        • -
      • Applet can read feature files, PDB files and can be used for HTML - form input
        • -
      2.06
      - 28/9/05
        -
      • View annotations in wrapped mode
        • -
      • More options for PCA viewer
        • -
        -
      • GUI bugs resolved
        • -
      • Runs with -nodisplay from command line
        • -
      2.05b
      - 15/9/05
        -
      • Choose EPS export as lineart or text
        • -
      • Jar files are executable
        • -
      • Can read in Uracil - maps to unknown residue
        • -
        -
      • Known OutOfMemory errors give warning message
        • -
      • Overview window calculated more efficiently
        • -
      • Several GUI bugs resolved
        • -
      2.05
      - 30/8/05
        -
      • Edit and annotate in "Wrapped" view
        • -
        -
      • Several GUI bugs resolved
        • -
      2.04
      - 24/8/05
        -
      • Hold down mouse wheel & scroll to change font size
        • -
        -
      • Improved JPred client reliability
        • -
      • Improved loading of Jalview files
        • -
      2.03
      - 18/8/05
        -
      • Set Proxy server name and port in preferences
        • -
      • Multiple URL links from sequence ids
        • -
      • User Defined Colours can have a scheme name and added to Colour Menu
        • -
      • Choose to ignore gaps in consensus calculation
        • -
      • Unix users can set default web browser
        • -
      • Runs without GUI for batch processing
        • -
      • Dynamically generated Web Service Menus
        • -
        -
      • InstallAnywhere download for Sparc Solaris
        • -
      2.02
      - 18/7/05
      		 
        -
      • Copy & Paste order of sequences maintains alignment order.
        • -
      2.01
      - 12/7/05
        -
      • Use delete key for deleting selection.
        • -
      • Use Mouse wheel to scroll sequences.
        • -
      • Help file updated to describe how to add alignment annotations.
        • -
      • Version and build date written to build properties file.
        • -
      • InstallAnywhere installation will check for updates at launch of Jalview.
        • -
        -
      • Delete gaps bug fixed.
        • -
      • FileChooser sorts columns.
        • -
      • Can remove groups one by one.
        • -
      • Filechooser icons installed.
        • -
      • Finder ignores return character when searching. Return key will initiate - a search.
        -
        • -
      2.0
      - 20/6/05
        -
      • New codebase
        • -
      		 
      +

      Jalview Version 2.07

      +

      Sequence Fetcher has been added to quickly + retrieve sequences with known ids from several databases.

      +

      Sequence Features enhanced to allow + the user to display all features of a Uniprot file on the alignment and subsequently + colour, hide or show overlapping features.

      +

      Choose to omit /start-end from sequences when + saving files. This is important for saving files to be used by some programs + which cannot read the original Jalview sequence output with the appended /start-end.

      +

      PDB structure viewer enhanced. Mapping + between sequence and structure has been enhanced, colours on the alignment are + reflected in the structure viewer.

      +

      Jalview Applet can read + in feature files, PDB files be used as input to HTML form See the website + to find out the new parameters available for the Applet Version of Jalview.

       

      +

      Issues Resolved

      +

      Group Editing is possible with Control and mouse click. Alt key and mouse press + does not work as this translates as the middle mouse button, which since 2.04 + is now used to scroll the alignment and change the font size.

      +

      HTML export now writes groups and features which were previously missing.

      +

       

      +

      See the Release History page for details of all + new features and resolved issues.

      -- 1.7.10.2