From: Jim Procter Date: Fri, 6 May 2011 14:42:05 +0000 (+0000) Subject: rude typo fixed X-Git-Tag: Version_1.9.2~87 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=d9cf8d7121858b024c2b54d5f763acd555b3ffea;hp=b69407127255feddf4c50f6df04e4220c9c6ed3c rude typo fixed --- diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index eab478e..39732d0 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -28,7 +28,7 @@ \title{Jalview 2.5: A manual and introductory tutorial } \author{David Martin, James Procter, Andrew Waterhouse and Geoff Barton} -\date{Manual version 1.2.1 11th October 2010} +\date{Manual version 1.2.3 6th May 2011} \newcommand{\clearemptydoublepage}{\newpage{\pagestyle{empty}}\cleardoublepage} @@ -97,9 +97,9 @@ Dundee, Scotland DD1 5EH, UK \vspace{2in} -Manual version 1.2.2 +Manual version 1.2.3 -4th March 2011 +6th May 2011 \end{center} @@ -686,7 +686,8 @@ The alignment view provides an interactive editing interface, allowing gaps to b \subsubsection{Locked Editing} \label{lockededits} -The Jalview alignment editing model is different to that used in other alignment editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, editing has the effect of shiting the rest of the sequence(s) being edited down or up-stream with respect to the rest of alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, but does not avoid the `knock-on' effect which is sometimes undesirable. However, its effect can be limited by performing the edit within a selected region. In this case, gaps will only be removed or inserted within the selected region. Edits are similarly constrained when they occur adjacent to a hidden column. +The Jalview alignment editing model is different to that used in other alignment +editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, but does not avoid the `knock-on' effect which is sometimes undesirable. However, its effect can be limited by performing the edit within a selected region. In this case, gaps will only be removed or inserted within the selected region. Edits are similarly constrained when they occur adjacent to a hidden column. \subsubsection{Introducing gaps in a single sequence} @@ -702,7 +703,11 @@ Gaps can be removed by dragging the residue to the immediate right of the gap leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences). \subsubsection{Sliding Sequences} -Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more sequences are selected will ``slide'' the selected sequences to the left or right (respectively). +Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more +sequences are selected will ``slide'' the selected sequences to the left or +right (respectively). Slides occur regardless of the region selection - +which, for example, allows you to easily reposition misaligned subfamilies +within a larger alignment. \subsubsection{Undoing edits} Jalview supports the undoing of edits via the {\sl Edit $\Rightarrow$ Undo Edit} alignment window menu option. Each editing action is stored and can be reversed in sequence. Colouring of the alignment is not reversible via the {\sl Undo} option. diff --git a/latest/TheJalviewTutorial.pdf b/latest/TheJalviewTutorial.pdf index 43b98ca..de578b7 100644 Binary files a/latest/TheJalviewTutorial.pdf and b/latest/TheJalviewTutorial.pdf differ diff --git a/latest/TheJalviewTutorial_screen.pdf b/latest/TheJalviewTutorial_screen.pdf index 983d590..2a996c2 100644 Binary files a/latest/TheJalviewTutorial_screen.pdf and b/latest/TheJalviewTutorial_screen.pdf differ