From c5c9e76a2b6d39b0834791b244e04348d59f5d75 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 4 Mar 2011 14:20:15 +0000 Subject: [PATCH] patches from Dundee Tutorial on Feb 2011 --- TheJalviewTutorial.tex | 75 ++++++++++++++++++++++++++++++++---------------- 1 file changed, 50 insertions(+), 25 deletions(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index d3d523d..eab478e 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -97,9 +97,9 @@ Dundee, Scotland DD1 5EH, UK \vspace{2in} -Manual version 1.2.1 +Manual version 1.2.2 -11th October 2010 +4th March 2011 \end{center} @@ -269,10 +269,13 @@ from the Jalview 2.4 manual). \exstep{Open the Jalview Desktop's user preferences dialog (from the Tools menu), and untick the checkbox adjacent to the 'Open file' entry in the 'Visual' preferences tab.} -\exstep{Click OK to save the preferences, then close Jalview and launch it -again. The example alignment should not be loaded when Jalview starts up.} -} - +\exstep{Click OK to save the preferences, then \em{launch another Jalview +instance from the web site}. The example alignment should not be +loaded when the new Jalview instance starts up.} +{\sl Note: Should you want to reload the example alignment, then select the +{\em File$\Rightarrow$ From URL} entry from the Desktop menu, and click on the +URL history button on the right hand side of the dialog box that opens to +recover the example file's URL, followed by OK, to open the file. } } \subsection{Getting Help} \label{gettinghelp} @@ -408,9 +411,13 @@ Drag the alignment.fa file from the desktop onto the Jalview window. The alignme \exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s).. } from the main menu. Select the {\sl PFAM (seed)} database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. } -\exstep{Open the URL \textsf{http://www.jalview.org/tutorial/alignment.fa} in a web browser. Select and copy the entire text to the clipboard (usually via the browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} . Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$ Paste} text box menu option. Click {\sl Close} and the alignment will be loaded. -} -} +\exstep{Open the URL \textsf{http://www.jalview.org/tutorial/alignment.fa} in a +web browser. Select and copy the entire text to the clipboard (usually via the +browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running +and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} . +Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$ +Paste} text box menu option. Click {\sl New Window} and the alignment will be +loaded. } } \subsection{Memory Limits} \label{memorylimits} @@ -471,9 +478,10 @@ Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a \exstep{ Repeat the previous step trying different file formats.} \exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}. You can select and copy this alignment to the clipboard using the textbox menu options {\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}. The alignment can then be pasted into any application of choice, e.g. a word processor or web form. } -\exstep{Ensure at least one alignment window is shown in Jalview. Open the overview window and scroll to any part of the alignment. Select {\sl File $\Rightarrow$ Save Project} from the main menu and save in a suitable place. Close all windows and then load the project via the {\sl File $\Rightarrow$ Save Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. -} -} +\exstep{Ensure at least one alignment window is shown in Jalview. Open the +overview window and scroll to any part of the alignment. Select {\sl File +$\Rightarrow$ Save Project} from the main menu and save in a suitable place. +Close all windows and then load the project via the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } } \section{Selecting and editing sequences} \label{selectingandediting} Jalview makes extensive use of selections - most of the commands available from its menus operate on the currently selected region of the alignment, either to @@ -482,7 +490,7 @@ illustrates how to make and use selections and groups. \subsection{Selecting parts of an alignment} Selections can be of arbitrary regions in an alignment, one or more complete columns, or one or more complete sequences. -A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ As New Alignment} alignment window menu options. +A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ New Alignment} alignment window menu options. To clear (unselect) the selection press the [ESC] (escape) key. @@ -522,7 +530,10 @@ selection. } \subsubsection{Making selections in Cursor mode} -To define a selection in cursor mode, navigate to the top left corner of the proposed selection. Pressing the [Q] key marks this as the corner. A red outline appears around the cursor (Figure \ref{cselect}) +To define a selection in cursor mode (which is enabled by pressing [F2]), +navigate to the top left corner of the proposed selection (using keystroke +commands, the arrow keys or the mouse). Pressing the [Q] key marks this as the +corner. A red outline appears around the cursor (Figure \ref{cselect}) Navigate to the bottom right corner of the proposed selection and press the [M] key. This marks the bottom right corner of the selection. The selection can then be treated in the same way as if it had been created in normal mode. @@ -547,7 +558,14 @@ and rows that are to be hidden, simply select the region that is to be kept visible, and then invert the selection.\footnote{It is also possible to hide everything but the selected region using the {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region } menu entry.} - \subsection{Creating groups} Selections are lost as soon as a different region is selected. Groups can be created which are labeled regions of the alignment. To create a group, first select the region which is to comprise the group. Then click the right mouse button on the selection to bring up a context menu. Select {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group} then enter a name for the group in the dialogue box which appears. + \subsection{Creating groups} Selections are lost as soon as a different region is selected. Groups can be +created which are labeled regions of the alignment. To create a group, first +select the region which is to comprise the group. Then click the right mouse +button on the selection to bring up a context menu. Select {\sl Selection +$\Rightarrow$ Group $\Rightarrow$ Edit Group Name}\footnote{In earlier versions +of Jalview, this entry was variously 'Group' or 'JGroupXXXXX' (Where XXXXX was +some serial number).} then enter a name for the group in the dialogue box which +appears. \begin{figure} \begin{center} @@ -694,14 +712,16 @@ Jalview supports the undoing of edits via the {\sl Edit $\Rightarrow$ Undo Edit} % others, to simplify manual alignment construction \exercise{Editing alignments}{ \label{mousealedit} +% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF + \exstep{ Load the URL \textsf{http://www.jalview.org/tutorial/unaligned.fa} which contains part of the ferredoxin alignment from PF03460. You are going to manually reconstruct the alignment that jalview loads by - default. Remember to use [CTRL]+Z to undo an edit, or the {\tr File $\LeftArrow$ - Reload } function to revert the alignment back to the original version if you - want to start again. + default. Remember to use [CTRL]+Z to undo an edit, or the {\tr File + $\Rightarrow$ Reload } function to revert the alignment back to the original + version if you want to start again. } \exstep{ Select the first 7 sequences, and press H to hide them (or right click @@ -783,6 +803,7 @@ Gaps can be removed in cursor mode by pressing [BACKSPACE]. The gap under the cu \exstep{Load the sequence alignment at \textsf{http://www.jalview.org/tutorial/unaligned.fa}, or continue using the edited alignment from exercise \ref{mousealedit}. If you continue from the previous exercise, then first right click on the sequence ID panel and select {\tr Reveal All}. Now, enter cursor mode by pressing [F2]} +%TODO: BACKSPACE or DELETE WHEN SEQS ARE SELECTED WILL DELETE ALL SEQS JAL-783 \exstep{Insert 58 gaps at the start of the first sequence (FER\_CAPAA). Press {\sl 58} then {\sl [SPACE]}. } \exstep{Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER\_CAPAN). Hold down shift and click on the fifth (FER1\_PEA). } \exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing {\sl 1,2} then pressing {\sl [RETURN]}. Now insert 6 gaps. Type {\sl 6} then hold down [CTRL] and press the space bar.} @@ -831,7 +852,12 @@ The second method is to use the {\sl Selection $\Rightarrow$ Group $\Rightarrow \end{figure} \subsection{Shading by conservation} -For many colour schemes, the intensity of the colour in a column can be scaled by the degree of amino acid property conservation. Selecting {\sl Colour $\Rightarrow$ By Conservation} brings up a selection box (the {\sl Conservation Threshold dialog box}) allowing the alignment colouring to be modified. Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}). +For many colour schemes, the intensity of the colour in a column can be scaled +by the degree of amino acid property conservation. Selecting {\sl Colour +$\Rightarrow$ By Conservation} enables this mode, and {\sl Modify +conservation threshold} brings up a selection box (the {\sl Conservation +Threshold dialog box}) allowing the alignment colouring to be modified. +Selecting a higher value limits colouring to more highly conserved columns (Figure \ref{colcons}). \begin{figure}[htbp] \begin{center} @@ -1275,12 +1301,11 @@ Click on the tree window. Careful selection of the tree partition location will Jalview can calculate and display trees, providing interactive tree-based grouping of sequences though a tree viewer. All trees are calculated via the {\sl Calculate $\Rightarrow$ Calculate Tree $\Rightarrow$ \ldots} submenu. Trees can be calculated from distance matrices determined from \% identity or aggregate BLOSUM 62 score using either average distance (UPGMA) or Neighbour joining algorithms. The input data for a tree calculation is either the visible portions of the current selection, or the whole alignment if no selection is present. On calculating a tree, a new window opens (Figure \ref{trees1}) which contains -the tree. Various display options can be found in the tree window {\sl View} -menu, and export options in the {\sl File $\Rightarrow$ Save As} submenu. -Newick format is a standard file format for trees which allows them to be -exported to other programs. Jalview can also read in external trees in Newick -format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf -names on imported trees will be matched to the associated alignment - unmatched +the tree. Various display settings can be found in the tree window {\sl View} +menu, including font, scaling and label display options, and the {\sl File +$\Rightarrow$ Save As} submenu contains options for image and Newick file +export. Newick format is a standard file format for trees which allows them to +be exported to other programs. Jalview can also read in external trees in Newick format via the {\sl File $\Rightarrow$ Load Associated Tree} menu option. Leaf names on imported trees will be matched to the associated alignment - unmatched leaves will still be displayed, and can be highlighted using the {\sl View $\Rightarrow$ Show Unlinked Leaves} menu option. -- 1.7.10.2