From e143a4bd499db90ed40cec0ac3626efb5937983b Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 30 May 2005 17:02:34 +0000 Subject: [PATCH] added the sorting entry to calculations, and corrected the PID ordering and the redundancy calculation help description. --- help/help.jhm | 3 ++- help/helpTOC.xml | 3 ++- help/html/calculations/redundancy.html | 10 +++++++--- help/html/calculations/sorting.html | 15 ++++++--------- 4 files changed, 17 insertions(+), 14 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index 44f072b..36a54e4 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -14,9 +14,10 @@ - + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index ca759ee..c0b0adc 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -30,7 +30,8 @@ - + + diff --git a/help/html/calculations/redundancy.html b/help/html/calculations/redundancy.html index 1f3d464..e97e3b0 100755 --- a/help/html/calculations/redundancy.html +++ b/help/html/calculations/redundancy.html @@ -3,9 +3,13 @@

Removing redundancy

Selecting this option brings up a window asking you to select a threshold. - If the percentage identity between two sequences exceeds this value one of the + If the percentage identity between two sequences (based on the + current alignment) exceeds this value one of the sequences (the shorter) is discarded. The redundancy calculation is done when - the Apply button is pressed. For large numbers of sequences this can take a - long time as all pairs have to be compared.

+ the Apply button is pressed, and the undo button recovers the + original set or any previously calculated subset. The detection of + redundant sequences involves a pairwise comparison of all the + sequences, so you may have to wait a few moments when applying this to + large sequence sets.

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index c61481f..a432824 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -17,8 +17,8 @@ precedence of their names.

Places sequences in the same group adjacent to eachother.

  • Sort by Pairwise Identity

    -

    Places pairs of sequences together that align with the greatest -fraction of conserved residues. +

    Sequences are ordered by decreasing fraction of conserved residues +with respect to the first sequence in the alignment.

  • Sort by Tree Order

    @@ -33,15 +33,12 @@ alignment, its name will appear in the submenu Sort->By Tree Order.< alignments by some measure of sequence identity.
    If the current alignment has been generated by one of Jalview's alignment web services, the alignment ordering can be recovered by -its corresponding entry in the Sort menu. -

    +its corresponding entry in the Sort menu:

    • -

    Reversing the Order

    -

    Selecting any item from the Sort menu will sort sequences in an -ascending order according to the property defining the sort. If the -same sort is re-applied, the sequences will be sorted in the inverse -order. In the case of trees and alignment orderings, Jalview will +Reversing the Order +

    If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse +order for that property. In the case of trees and alignment orderings, Jalview will remember your last choice for sorting the alignment and only apply the inverse ordering if you select the same tree or alignment ordering item again.

    -- 1.7.10.2