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.}
 \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.}
 
 \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
 \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.
 
 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)}).
 \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}
 
 \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}. 
 \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.
 
 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}
 
 \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.
 
 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
 % 
 % \exercise{Creating and using user defined presets}{\label{createandusepreseex}
 % \exstep{Import the file at