From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 24 Sep 2020 13:55:45 +0000 (+0100)
Subject: TODOs from the Jalview 2.11.1.1 course
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f5770876d43b028ccedc7cd30a13e44d8c3b2836;p=jalview-manual.git

TODOs from the Jalview 2.11.1.1 course
---

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