\label{hidingregions}
It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create the several different views in the example alignment file that is loaded when Jalview is first started (See Figure \ref{startpage}).
-To hide a set of sequences, select them and right-click the mouse on the selected sequence IDs to bring up the context menu. Select {\sl Hide Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
+To hide a set of sequences, select them and right-click the mouse on the
+selected sequence IDs to bring up the context pop-up menu. Select {\sl Hide
+Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
\begin{figure}[htbp]
\end{center}
\end{figure}
-A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns (indicated by a red marker) can be hidden and revealed in the same way {\sl via} the context menu by right clicking on the ruler bar. The hidden column selection is indicated by a small blue triangle in the ruler bar.
+A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns
+(indicated by a red marker) can be hidden and revealed in the same way {\sl via}
+the context pop-up menu by right clicking on the ruler bar. The hidden column
+selection is indicated by a small blue triangle in the ruler bar.
\begin{figure}[htbp]
\begin{center}
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
\exercise{Hiding and revealing regions}{
-\exstep{Close all windows then open the PFAM accession PF03460. Select a contiguous set of sequences by clicking and dragging on the sequence ID panel. Right click on the selected sequence IDs and select {\sl Hide Sequences}.
+\exstep{Close all windows, open the PFAM accession PF03460. Select a
+contiguous set of sequences by clicking and dragging on the sequence ID panel.
+Right click on the selected sequence IDs to bring up the selection pop-up menu, select {\sl Hide Sequences}.
}
\exstep{
-Right click on the blue triangle indicating hidden sequences and select {\sl Reveal Sequences}. (If you have hidden all sequences then you will need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.})
-}
+Right click on the blue triangle indicating hidden sequences and select {\sl
+Reveal Sequences} in the panel. (If you have hidden all sequences then you will
+need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.}) }
\exstep{
-Repeat but using a non-contiguous set of sequences. Note that when multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
-}
-\exstep{Repeat the above but hiding and revealing columns instead of sequences.
+Repeat the process but use a non-contiguous set of sequences. Note that when
+multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
}
-\exstep{Select a region of the alignment, add in some additional columns to the
-selection, and experiment with the `Hide all but selected region' function. }
-\exstep{Select some sequences and pick one to represent the rest. Bring up the sequence ID pop-up menu for that sequence and select the {\sl Represent group with $<$Sequence ID$>$ } option. Use the pop-up menu again to reveal the hidden sequences that you just picked a representative for.}
+\exstep{Repeat the above using columns to hide and reveale columns
+instead of sequences.
}
+\exstep{Select a region of the alignment, then add in some additional columns to
+the selection, and experiment with the `Hide all but selected region' function
+in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
+\exstep{Select some sequences and pick one to represent the rest by hoovering
+the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
+clicking and then seelct {\sl (Sequence ID name) $\Rightarrow$ Represent group
+with (Sequence ID name )}. To reveal these hidden sequences, right click on the
+Sequence ID and in the the pop-up menu select Reveal All.}}
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}
+\subsubsection{Introducing Gaps in a Single equence}
-To introduce a gap, place the cursor on the residue to the immediate right of where the gap should appear. Hold down the SHIFT key and the left mouse button, then drag the sequence to the right till the required number of gaps has been inserted.
+To introduce a gap, place the cursor on the residue to the immediate right of
+where the gap should appear. Hold down the SHIFT key and the left mouse button,
+then drag the sequence to the right untill the required number of gaps has been inserted.
One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
-\subsubsection{Introducing gaps in all sequences of a group}
+\subsubsection{Introducing Gaps in all Sequences of a Group}
To insert gaps in all sequences in a selection or group, place the mouse cursor on any residue in the selection or group to the immediate right of the position in which a gap should appear. Hold down the CTRL key and the left mouse button, then drag the sequences to the right until the required number of gaps has appeared.
which, for example, allows you to easily reposition misaligned subfamilies
within a larger alignment.
-\subsubsection{Undoing edits}
+\subsubsection{Undoing Edits}
Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
% % better idea to introduce hiding sequences, and use the invert selection, hide
% others, to simplify manual alignment construction
-\exercise{Editing alignments}{
+\exercise{Editing Alignments}{
\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{You are going to manually reconstruct part of the example Jalview alignment
the left so the initial {\bf A} lies at column 57 using the $\Rightarrow$ key.}
\exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
-O80429\_MAIZE (Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
+O80429\_MAIZE
+
+(Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
deselect FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they
begin at column 5 of the alignment view.}
\exstep{ Select all the visible
-sequences in the block by pressing [CTRL]-A. Insert a single gap in all selected
-sequences at column 38 by holding [CTRL] and clicking on the R in FER1\_SPIOL and
-dragging one column to right. Insert another gap at column 47 in all sequences in
-the same way.}
+sequences (those not hidden) in the block by pressing [CTRL]-A.
+
+Insert a single
+gap in all selected sequences at column 38 of the alignment by holding [CTRL]
+and clicking on the R at column 38 in the FER1\_SPIOL, then drag one
+column to right.
+Insert another gap at column 47 in all sequences in the same way.}
\exstep{ Correct the ferredoxin domain alignment for FER1\_SPIOL by
inserting two additional gaps after the gap at column 47: First press [ESC] to
\exstep{ Now complete the
alignment of FER1\_SPIOL with a {\bf locked edit} by pressing [ESC] and select
columns 47 to 57 of the FER1\_SPIOL row. Move the mouse onto the G at column 50,
-hold [SHIFT] and drag the G to the left by one column to insert a gap at column
-57.}
+hold [SHIFT] and drag the G in column 47 of FER1\_SPIOL to the left by one
+column to insert a gap at column 57.}
\exstep{ In the next two steps you will complete the alignment of the last two sequences.
Select the last two sequences (FER1\_MAIZE and O80429\_MAIZE), then press [SHIFT]
and click and drag the initial methionine of O80429\_MAIZE 5 columns to the right
-so it lies at column 10. Keep holding [SHIFT] and click and drag to insert
+so it lies at column 10.
+
+Keep holding [SHIFT] and click and drag to insert
another gap at the proline at column 25 (25C in cursor mode). Remove the gap at
column 44, and insert 4 gaps at column 47 (after AAPM).}
columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
-\exercise{Keyboard edits}{ \item{This continues on from exercise
+\exercise{Keyboard Edits}{ \item{This continues on from exercise
\ref{mousealedit}, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
% 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 {\sl [CTRL]} and press {\sl [SPACE]}.}
-\exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
+\exstep{Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing
+{\sl 1,2} then press {\sl [RETURN]}. Now insert 6 gaps in all the sequences.
+Type {\sl 6} then hold down {\sl [CTRL]} and press {\sl [SPACE]}.} \exstep{Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47.
Press {\sl 34C} then {\sl [CTRL]-[SPACE]}. Press {\sl 38C} then [CTRL]-[SPACE].
Press {\sl 47C} then {\sl 3 [CTRL-SPACE]} the first through fourth sequences are
now aligned.}
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Features} option before you can see your colourscheme.
-There are two main types of colouring styles: simple static residue colourschemes and dynamic schemes which use conservation and consensus analysis to control colouring. A hybrid colouring is also possible, where static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
+There are two main types of colouring styles: {\bfsimple static residue}
+colourschemes and {\bfdynamic schemes} which use conservation and consensus
+analysis to control colouring. A {\bfhybrid colouring} is also possible, where
+static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
\subsection{Colouring the Whole Alignment}
\subsection{Colouring a Group or Selection}
-Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above, after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected. This must be turned {\sl off} specifically as it is {\sl on} by default. When unticked, selections from the Colours menu will only change the colour for residues in the current selection, or the alignment view's ''background colourscheme'' when no selection exists.
+Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above,
+ after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected.
+ This must be turned {\sl off} specifically as it is {\sl on} by default.
+ When unticked, selections from the Colours menu will only change the colour for residues in the current selection,
+ or the alignment view's ``background colourscheme'' when no selection exists.
-The second method is to use the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour} context menu option obtained by right clicking on the group (Figure \ref{colgrp}). This only changes the colour of the current selection or group.
+The second method is to select sequences and right click mouse to open pop-up
+menu and seelct {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group
+Colour} from context menu options
+(Figure \ref{colgrp}). This only changes the colour of the current selection or group.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=2.75in]{images/col_rnahelix.pdf} }
\exercise{Colouring Alignments}{
+\exstep{Ensuring that the {\sl Apply Colour To All Groups} flag is not selected
+in View sequence alignment menu.
+ This must be turned {\sl off} specifically as it is {\sl on} by default.}
\exstep{
-Open a sequence alignment, for example the PFAM domain PF03460. Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
+Open a sequence alignment, for example the PFAM domain PF03460 in PFAM seed.
+Select the alignment menu option {\sl Colour $\Rightarrow$ ClustalX}. Note the colour change. Now try all the other colour schemes in the {\sl Colour} menu. Note that some colour schemes do not colour all residues.
}
\exstep{
Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62}. Select a group of around 4 similar sequences. Use the context menu (right click on the group) option {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62} to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the group being coloured, not the whole alignment (this also explains the colouring changes observed in exercise \ref{exselectgrpcolour} during the group selection step).
git://source.jalview.org / jalview-manual.git / blobdiff