From f5770876d43b028ccedc7cd30a13e44d8c3b2836 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 24 Sep 2020 14:55:45 +0100 Subject: [PATCH] TODOs from the Jalview 2.11.1.1 course --- TheJalviewTutorial.tex | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 19156b0..a51692f 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -728,6 +728,8 @@ $\Rightarrow$ Fetch Sequences...} from the Jalview desktop menu. The {\sl Select Database Retrieval Source} dialog will open listing all the database sources. Select the {\bf PFAM seed} database and click {\sl OK}. +%TODO fix ss appearing as RNA ss issue with secondary structure from pfam when downloading the Full alignment. + (ii) The {\sl New Sequence Fetcher} window will open. Enter the accession number {\bf PF03460} and click {\sl OK}. @@ -1135,6 +1137,8 @@ group is dragged to the right with [CTRL] pressed.} %% TODO introduce select/hide by annotation here %% favor coverage of these core interactions (hide, show, select, reorder, multiple view) +%% TODO - if columns are selected, then View->hide selected region hides *all* sequences, but it should leave the unselected columns visible ! + \exercise{Hiding and Revealing Regions}{ \label{hidingex} \exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}). @@ -2559,6 +2563,8 @@ JABA service. % } % } +%%TODO just typing a value into parameter slider doesn't actually modify value, return needs to be hit. This is not intuitive (these days) - loss of focus should update values of parameters (e.g. when the run/start job button is hit) + \section{Protein Alignment Conservation Analysis} \label{aacons} The {\sl Web Service $\Rightarrow$ Conservation} menu controls the computation @@ -3267,6 +3273,8 @@ If you would prefer to use Jmol to manage structure colours, then select the automatic application of colour schemes when new structure data is added, or when associated alignment views are modified. +%%TODO: no mapping when using N&W alg. + \exercise{Viewing Structures with the integrated Jmol Viewer}{ \label{viewingstructex} \exstep{Load the alignment at -- 1.7.10.2