From: Jim Procter Date: Fri, 4 Aug 2017 12:40:20 +0000 (+0100) Subject: JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation page and release notes X-Git-Tag: Release_2_10_3b1~132^2~15^2~11 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=80ac7d84002118186a11658f38abfa5c4fe3d8da;p=jalview.git JAL-2418 JAL-1632 JAL-2416 calculations dialog documentation page and release notes --- diff --git a/help/help.jhm b/help/help.jhm index 363f549..cb0c4c4 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -109,6 +109,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index a8aadf5..f3311a7 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -24,6 +24,7 @@ + @@ -109,8 +110,10 @@ - - + + + + diff --git a/help/html/calculations/calculatedialog.png b/help/html/calculations/calculatedialog.png new file mode 100644 index 0000000..fdc0c0d Binary files /dev/null and b/help/html/calculations/calculatedialog.png differ diff --git a/help/html/calculations/calculations.html b/help/html/calculations/calculations.html new file mode 100644 index 0000000..c194cd9 --- /dev/null +++ b/help/html/calculations/calculations.html @@ -0,0 +1,55 @@ + + + +The Alignment Calculations Dialog + + +

+ The Alignment Calculations Dialog +

+ Alignment Calculations dialog box - opened via Calculations->Tree or PCA... +

+ The Calculations Dialog (shown above) is opened via + the Calculations→Calculate Tree or PCA... + menu entry. +

+

+ It allows you to select the type of alignment analysis calculation (PCA or Tree), and the + sequence similarity score model that will be used to perform the + analysis. +

+

+ Adding additional score models
Jalview can + import substitution matrices in both AAindex + and NCBI format (see e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/). + In Jalview 2.10.2, the easiest way to import new models is to drag + the score model file onto any alignment window. See the Substitution Matrices Documentation + for more information. +

+ + diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index c38d9ac..7ffb160 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -26,16 +26,20 @@

Principal Component Analysis

+

A principal component analysis can be performed via the + calculations dialog which is accessed by selecting Calculate→Calculate + Tree or PCA....

This calculation creates a spatial representation of the similarities within a selected group, or all of the sequences in an alignment. After the calculation finishes, a 3D viewer displays the set of sequences as points in 'similarity space', and similar sequences tend to lie near each other in the space.

- Caveats
The calculation is computationally expensive, - and may fail for very large sets of sequences - usually because the - JVM has run out of memory. A future release of Jalview will be able - to avoid this by executing the calculation via a web service. + Caveats
The calculation can be computationally + expensive, and may fail for very large sets of sequences - usually + because the JVM has run out of memory. However, the PCA + implementation in Jalview 2.10.2 employs more memory efficient + matrix storage structures, allowing larger PCAs to be performed.

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 59736ca..95904b6 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -28,8 +28,8 @@

Trees are calculated on either the complete alignment, or just the - currently selected group of sequences, using the functions in the Calculate→Calculate - tree submenu. Once calculated, trees are displayed in a new calculations dialog opened from the Calculate→Calculate + Tree or PCA... menu entry. Once calculated, trees are displayed in a new tree viewing window. There are four different calculations, using one of two distance measures and constructing the tree from one of two diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index 51ad601..00a2ec4 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -244,7 +244,7 @@ Selects all the sequences and residues in the alignment.
Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all. - +

  • Deselect All (Escape)
    Removes the current selection box (red dashed box) from the alignment window. All selected sequences, residues and @@ -312,7 +312,7 @@ or hide sequence features on this alignment.
  • Sequence - Feature Settings...
    Opens the + Feature Settings...
    Opens the Sequence Feature Settings dialog box to control the colour and display of sequence features on the alignment, and configure and retrieve features from DAS annotation @@ -427,12 +427,12 @@ If this box is selected then the sequence names displayed in the sequence label area will be aligned against the left-hand edge of the alignment display, - rather than the left-hand edge of the alignment window. + rather than the left-hand edge of the alignment window.
  • Show Hidden Markers
    When this box is selected, positions in the alignment where rows and columns are hidden will be - marked by blue arrows.
    • + marked by blue arrows.
  • Boxes
    If this is selected the background of a residue will be coloured using the selected background colour. Useful if used in @@ -461,7 +461,6 @@ symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
    • - @@ -541,44 +540,26 @@ viewer window.
    -
  • Calculate Tree
    Functions - for calculating trees on the alignment or the currently - selected region. See calculating - trees. - -
      -
    • Neighbour Joining Using PAM250
      • -
    • Neighbour Joining Using Sequence - Feature Similarity
      • -
    • Neighbour Joining Using Blosum62
      • -
    • Neighbour Joining Using % Identity
      • -
    • Average Distance Using PAM250
      • -
    • Average Distance Using Sequence - Feature Similarity
      • -
    • Average Distance Using Blosum62
      • -
    • Average Distance Using % Identity
      • -
    Note: Since Version 2.8.1, a number of - additional similarity measures for tree calculation are - provided in this menu.
    • -
  • Pairwise Alignments
    Applies - Smith and Waterman algorithm to selected sequences. See pairwise - alignments. +
  • Calculate Tree or PCA ...
    Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region.
    • -
  • Principal Component Analysis
    Shows - a spatial clustering of the sequences based on similarity - scores calculated with the alignment. See Principal - Component Analysis. -
    • -
  • Extract Scores ... (optional)
    This - option is only visible if Jalview detects one or more - white-space separated values in the description line of the - alignment sequences.
    When selected, these numbers are - parsed into sequence associated annotation which can then be - used to sort the alignment via the Sort by→Score menu. -
    • -
  • Autocalculate Consensus
    For +
  • Pairwise Alignments
    Applies + Smith and Waterman algorithm to selected sequences. See pairwise + alignments. +
    • +
  • Extract Scores ... (optional)
    This + option is only visible if Jalview detects one or more + white-space separated values in the description line of the + alignment sequences.
    When selected, these numbers are + parsed into sequence associated annotation which can then be + used to sort the alignment via the Sort by→Score menu. +
    • +
  • Autocalculate Consensus
    For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents the sometimes lengthy calculations performed after @@ -614,7 +595,7 @@ in Jalview 2.8.1
  • 'Standard Databases' will check sequences against - the EBI databases plus any active DAS sequence sources<
    • + the EBI databases plus any active DAS sequence sources Other sub-menus allow you to pick a specific source to query - sources are listed alphabetically according to their nickname. diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html index 8032348..c7a1c87 100755 --- a/help/html/menus/alwcalculate.html +++ b/help/html/menus/alwcalculate.html @@ -53,37 +53,19 @@ window.
    -
  • Calculate Tree
    Functions - for calculating trees on the alignment or the currently selected - region. See calculating - trees. - -
      -
    • Neighbour Joining Using PAM250
      -
      • -
    • Neighbour Joining Using Sequence - Feature Similarity
      • -
    • Neighbour Joining Using Blosum62
      -
      • -
    • Neighbour Joining Using % Identity
      • -
    • Average Distance Using PAM250
      -
      • -
    • Average Distance Using Sequence - Feature Similarity
      • -
    • Average Distance Using Blosum62
      • -
    • Average Distance Using % Identity
      • -
    • +
  • Calculate Tree or PCA ...
    Opens the + calculations dialog for + for calculating trees or + principle component analysis + plots on the alignment or the currently selected + region. +
    +
  • Pairwise Alignments
    Applies Smith and Waterman algorithm to selected sequences. See pairwise alignments.
    • -
  • Principal Component Analysis
    Shows - a spatial clustering of the sequences based on similarity scores - calculated over the alignment.. See Principal Component - Analysis. -
  • Extract Scores ... (optional)
    This option is only visible if Jalview detects one or more white-space separated values in the description line of the diff --git a/help/html/releases.html b/help/html/releases.html index 10d5781..ec4f4ec 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -96,6 +96,10 @@ li:before {
  • + Tree/PCA calculation menu items merged to + a calculation dialog box +
    • +
  • More robust colours and shader model for alignments and groups