\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
-but selected region} option in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region} option. In the alignment window menu, {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
@@ -1240,7+1242,7 @@ columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
right of the selected residue.
-\exercise{Editing Alignments}
+\exercise{Editing Alignments Homework Exercise}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{
@@ -1320,7+1322,7 @@ backwards and replay the edits you have made.}
}
}
-\exercise{Keyboard Edits}
+\exercise{Keyboard Edits Homework Exercise}
{
\label{keyboardsex}
This continues on from the previous exercise, and recreates the final part of the example ferredoxin
{
\label{keyboardsex}
This continues on from the previous exercise, and recreates the final part of the example ferredoxin
@@ -1596,7+1598,7 @@ assigned colours (left). The profile is saved (center) and can then be accessed
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
-To All Groups} flag is not selected in {\sl Colour} menu in the alignment window.
+To All Groups} flag is not selected (ie unticked) in {\sl Colour} menu in the alignment window.
% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
% by default.
% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
% by default.
@@ -1605,7+1607,7 @@ seed database. Select the alignment menu option {\sl Colour $\Rightarrow$
Clustalx} and 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 score}. Select a group
Clustalx} and 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 score}. Select a group
-of around 4 similar sequences. Use the context menu (right click on the group)
+of around 4 similar sequences. Use the context menu (right click on the residues in the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
@@ -1617,7+1619,7 @@ the group using {\sl Colour $\Rightarrow$ Taylor}.
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
-Note: Feature colours overlay residue colouring. The features colours can be
+Note: Feature colours overlay residue colouring and this may mask residue colouring. If this is an issue, he features colours can be
toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
@@ -1645,7+1647,9 @@ Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu.
Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
sequence ID format and so on. }
\exstep{Hide all the annotation rows by toggling {\sl Annotations $\Rightarrow$
Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement,
sequence ID format and so on. }
\exstep{Hide all the annotation rows by toggling {\sl Annotations $\Rightarrow$
-Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} \exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
+Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.}
+\exstep{Deselect {\sl Format $\Rightarrow$ Wrap}.}
+\exstep{Right click on the
annotation row labels to bring up the context menu, then select {\sl
Hide This Row}. Bring up the context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
annotation row labels to bring up the context menu, then select {\sl
Hide This Row}. Bring up the context menu again and select {\sl
Show All Hidden Rows} to reveal them.}
@@ -1653,7+1657,7 @@ Show All Hidden Rows} to reveal them.}
dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}.
The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
\exstep{Move the mouse to the top left hand corner of the annotation labels -
dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}.
The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot}.}
\exstep{Move the mouse to the top left hand corner of the annotation labels -
-a up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed
+a up/down arrow symbol should appear - click on the icon, the height of the {\sl Annotation Area} can be changed