From: jprocter Date: Mon, 27 Nov 2006 11:57:47 +0000 (+0000) Subject: *** keyword substitution change *** X-Git-Tag: Release_2_2~28 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1ae8526d5e831567aeae02d85751ecaeb6cf9178;p=jalview.git *** keyword substitution change *** --- diff --git a/help/html/menus/alwFormat.html b/help/html/menus/alwFormat.html index fc1fd58..0c45d46 100644 --- a/help/html/menus/alwFormat.html +++ b/help/html/menus/alwFormat.html @@ -1,56 +1,56 @@ - - -Alignment Window Menus - - -

Alignment Window Format Menu

Font...
- Opens the "Choose Font" dialog box, in order to - change the font of the display and enable or disable 'smooth fonts' - (anti-aliasing) for faster alignment rendering.
Wrap
- When ticked, the alignment display is "wrapped" to the width of the - alignment window. This is useful if your alignment has only a few - sequences to view its full width at once.
- Additional options for display of sequence numbering and scales are - also visible in wrapped layout mode:
-
- Show Sequence Limits
  - If this box is selected the sequence name will have the start - and end position of the sequence appended to the name, in the format - NAME/START-END
- Right Align Sequence ID
  - If this box is selected then the sequence names displayed in - the sequence label area will be aligned against the left-hand edge of - the alignment display, rather than the left-hand edge of the alignment - window.
- - + + +Alignment Window Menus + + +
Alignment Window Format Menu
+
+
Font...
+ Opens the "Choose Font" dialog box, in order to + change the font of the display and enable or disable 'smooth fonts' + (anti-aliasing) for faster alignment rendering.
+
Wrap
+ When ticked, the alignment display is "wrapped" to the width of the + alignment window. This is useful if your alignment has only a few + sequences to view its full width at once.
+ Additional options for display of sequence numbering and scales are + also visible in wrapped layout mode:
+
+
Scale Above
Show the alignment column position scale.
+
Scale Left
Show the sequence position for the first aligned residue in each row in the left column of the alignment.
+
Scale Right
Show the sequence position for the last aligned residue in each row in the right-most column of the alignment.
+ +
Show Sequence Limits
+ If this box is selected the sequence name will have the start + and end position of the sequence appended to the name, in the format + NAME/START-END
+
Right Align Sequence ID
+ If this box is selected then the sequence names displayed in + the sequence label area will be aligned against the left-hand edge of + the alignment display, rather than the left-hand edge of the alignment + window.
+
Show Hidden Markers
+ When this box is selected, positions in the alignment where + rows and columns are hidden will be marked by blue arrows.
+
Boxes
+ If this is selected the background of a residue will be coloured using + the selected background colour. Useful if used in conjunction with + "Colour Text."
+
Text
+ If this is selected the residues will be displayed using the + standard 1 character amino acid alphabet.
+
Colour Text
+ If this is selected the residues will be coloured according to + the background colour associated with that residue. The colour is + slightly darker than background so the amino acid symbol remains + visible.
+
Show Gaps
+ When this is selected, gap characters will be displayed as + "." or "-". If unselected, then gap characters will + appear as blank spaces.
+ You may set the default gap character in preferences.
+
+ + diff --git a/help/html/menus/alwSelect.html b/help/html/menus/alwSelect.html index 2c66fc5..87b0a49 100644 --- a/help/html/menus/alwSelect.html +++ b/help/html/menus/alwSelect.html @@ -1,31 +1,31 @@ - - -Alignment Window Menus - - -
Alignment Window Select Menu
-
-
Find... - (Control F)
- Opens the Find dialog box to perform regular expression searches on the - aligned sequences and their IDs and create new features. -
Select All (Control A)
- Selects all the sequences and residues in the alignment.
- Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
-
Deselect All (Escape)
- Removes the current selection box (red dashed box) from the - alignment window. All selected sequences, residues and marked columns - will be deselected.
- Use <ESCAPE> to deselect all.
-
Invert Sequence Selection (Control I)
- Any sequence ids currently not selected will replace the - current selection.
-
Invert Column Selection (Control Alt I)
- Any columns currently not selected will replace the current - column selection.
-
Undefine Groups (Control U)
- The alignment will be reset with no defined groups.
- WARNING: This cannot be undone.
-
- - + + +Alignment Window Menus + + +
Alignment Window Select Menu
+
+
Find... + (Control F)
+ Opens the Find dialog box to perform regular expression searches on the + aligned sequences and their IDs and create new features. +
Select All (Control A)
+ Selects all the sequences and residues in the alignment.
+ Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.
+
Deselect All (Escape)
+ Removes the current selection box (red dashed box) from the + alignment window. All selected sequences, residues and marked columns + will be deselected.
+ Use <ESCAPE> to deselect all.
+
Invert Sequence Selection (Control I)
+ Any sequence ids currently not selected will replace the + current selection.
+
Invert Column Selection (Control Alt I)
+ Any columns currently not selected will replace the current + column selection.
+
Undefine Groups (Control U)
+ The alignment will be reset with no defined groups.
+ WARNING: This cannot be undone.
+
+ +