From 3f73b03257d72cbdd8cbe8889a6fc4fcab747dd3 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 3 Jun 2014 17:49:28 +0100 Subject: [PATCH] JAL-1503 documentation and release notes --- help/html/calculations/pca.html | 39 +++++++------- help/html/releases.html | 109 ++++++++++++++++++++++++--------------- help/html/whatsNew.html | 57 +++++++++++++------- 3 files changed, 125 insertions(+), 80 deletions(-) diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 49019a7..ba9dc30 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -32,7 +32,8 @@ 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.

-

About PCAPrincipal components analysis is a technique for examining the +

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 component is the one with the greatest magnitude, or length. The sets of @@ -52,26 +53,26 @@ of variation in the data set.

href="scorematrices.html#simplenucleotide">simple single nucleotide substitution matrix. The options available for calculation are given in the - Change Parameters menu.
Jalview allows - two types of PCA calculation. The default - Jalview PCA Calculation mode (indicated when - that option is ticked in the - Change Parameters menu) of the viewer - performs PCA on a matrix where elements in the upper diagonal give the - sum of scores for mutating in one direction, and the lower diagonal is - the sum of scores for mutating in the other. For protein substitution - models like BLOSUM62, this gives an asymmetric matrix, and a different - PCA to one produced with the method described in the paper by G. - Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, - February 1995 (Change Parameters menu.

+

+ PCA Calculation modes
+ The default Jalview calculation mode + (indicated when Jalview PCA Calculation is + ticked in the Change Parameters menu) is to + perform a PCA on a matrix where elements in the upper diagonal give + the sum of scores for mutating in one direction, and the lower + diagonal is the sum of scores for mutating in the other. For protein + substitution models like BLOSUM62, this gives an asymmetric matrix, + and a different PCA to a matrix produced with the method described in the + paper by G. Casari, C. Sander and A. Valencia. Structural Biology + volume 2, no. 2, February 1995 (pubmed) - and implemented at the SeqSpace server at the EBI. The original method - preconditions the matrix by multiplying it with its transpose, and - this mode is enabled by unchecking the - Jalview PCA Calculation option in the - Change Parameters menu. + and implemented at the SeqSpace server at the EBI. This method + preconditions the matrix by multiplying it with its transpose, and can be employed in the PCA viewer by unchecking the Jalview + PCA Calculation option in the Change + Parameters menu.

- +

The PCA Viewer

This is an interactive display of the sequences positioned within the similarity space, as points in a rotateable 3D scatterplot. The diff --git a/help/html/releases.html b/help/html/releases.html index a240a49..1eb7abf 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -34,85 +34,106 @@

Issues Resolved
- +
- 2.8.1
- 20/5/2014 + 2.8.1
3/6/2014
Application -