From 89adba2efdf80de92e3a39eddefbc6b01ce9cd3c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 8 May 2019 15:37:36 +0100 Subject: [PATCH] JAL-3111 TODOs for next workshop/revision --- TheJalviewTutorial.tex | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 64885d6..d341447 100644 --- 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 -- 1.7.10.2