JAL-3111 TODOs for next workshop/revision

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 64885d6..d341447 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -690,10 +690,13 @@ parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
 \label{load}
 \exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
 close all windows.}
+%% TODO: omit or combine this exercise
+%% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
 \exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
 Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
 Click {\sl OK} to load the alignment.}
 
+%%TODO: omit or combine
 \exstep{{\bf Loading sequences from a file:} Close all windows using the
 {\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
 Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
@@ -1102,6 +1105,8 @@ of the hidden groups function. The remaining representative sequence can be visu
 Note, any alignment edits that affect the sequence will also affect the whole
 sequence group.
 
+%% TODO introduce select/hide by annotation here
+%% favor coverage of these core interactions (hide, show, select, reorder, multiple view)
 \exercise{Hiding and Revealing Regions}{
 \label{hidingex}
 \exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
@@ -1698,6 +1703,8 @@ Annotations} menu (left) or individually from the context menu opened by right c
 \end{center}
 \end{figure}
 
+%%TODO: multiple views - simple edits - observe changes in other views.
+
 \exercise{Alignment Layout}{
 \label{exscreen}
 \exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jvp}. 
@@ -2019,7 +2026,7 @@ Sequence features are annotation associated with a specific sequence - often mar
 Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence. 
 Each feature remains associated with its own sequence.
 
-
+%%TODO: change EMBL to ENA in Jalview and the Manual !
 
 \section{Importing Features from Databases}
 \label{featuresfromdb}
@@ -2470,6 +2477,7 @@ same way as a custom alignment colourscheme, so when Jalview is launched again,
 it will show your custom preset amongst the options available for running the
 JABA service.
 
+%% TODO - reinstate this exercise about reinstating presets
 % 
 % \exercise{Creating and using user defined presets}{\label{createandusepreseex}
 % \exstep{Import the file at