patches from Dundee Tutorial on Feb 2011

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index d3d523d..eab478e 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -97,9 +97,9 @@ Dundee, Scotland DD1 5EH, UK
 
 \vspace{2in}
 
 
 \vspace{2in}
 

-Manual version 1.2.1
+Manual version 1.2.2

 
 

-11th October 2010
+4th March 2011

 
 
 \end{center}
 
 
 \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{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}
 
 \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{
 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}
 
 \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{ 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. } }

 \r\r\section{Selecting and editing sequences}
 \label{selectingandediting} \rJalview makes extensive use of selections - most of the commands available from
 its menus operate on the currently selected region of the alignment, either to
 \r\r\section{Selecting and editing sequences}
 \label{selectingandediting} \rJalview 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.
 \r\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.
  
 \r\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.
 
 
 To clear (unselect)  the selection press the [ESC] (escape) key.
 

@@ -522,7 +530,10 @@ selection. }
 
 \subsubsection{Making selections in Cursor mode}
 
 
 \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.
 
 
 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.}
 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.}

-\r\r\subsection{Creating groups}\rSelections 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. 
+\r\r\subsection{Creating groups}\rSelections 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}
 
 \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}
 % 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
 \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
  }
 
 \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]}
 \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.}
 \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}
 \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}
 
  \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
 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.
 
 leaves will still be displayed, and can be highlighted using the {\sl View
 $\Rightarrow$ Show Unlinked Leaves} menu option.