X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fediting%2Findex.html;h=fd8c5a3c017dc55463fe16ccd1d1c059a90ff5c3;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=70776af17846bf5b224fba047d7598fff3875f12;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/editing/index.html b/help/html/editing/index.html index 70776af..fd8c5a3 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -1,73 +1,107 @@ -Editing + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +Editing + -

Editing

-

There are two major ways to edit alignments - in 'Normal mode', -gaps are inserted and deleted at the mouse pointer in various ways by -clicking the left mouse button and pressing a combination of either -shift and control (or the apple key on Macs) and dragging the mouse. Pressing -F2 toggles the alternative 'Cursor -mode' keyboard editing facility, where the space bar and delete -keys add and remove gaps at the current editing position. The key -strokes for both these modes are summarised in the keystrokes table.

-

Tip: For large alignments, deselect "Calculate -> - Autocalculate Consensus" to prevent the alignment performing lengthy calculations - after every edit.

-

Inserting / removing gaps - hold down the - "Shift" key. Click on a residue with the mouse and drag it - to the left or right to insert gaps and remove gaps.
- If the current selection is a group over all sequences in the - alignment, or a group over some sequences or all columns in the - alignment, then hold down either "Control" - key and drag the residue left or right to edit all sequences in the defined - group at once.

-

Copy/paste/cut/delete - any sequences which are in the current selection - box (indicated in red) may be cut and / or copied to a new alignment or deleted. -

-

Undo / redo - editing of sequences (insertion/removal of gaps, removal - of sequences, trimming sequences etc) may be undone or redone at any time using - the appropriate menu items from the edit menu. The undo history list only allows - a maximum of 10 actions. -

Trimming alignment - First select a column by clicking the scale indicator - (above the sequences) The alignment may then be trimmed to the left or right - of this column. If multiple columns are selected, the alignment is trimmed to - the right of the rightmost selected column (or to the left of the leftmost selected - column)

-

Remove gapped columns - Removes columns within the alignment which - contain only space characters ("-" or "." or " ")

-

Removing gaps - Removes all gaps from the alignment. Gaps are "-" - or "." or " ".

-

Set gap character - Switches the gap character between "." - and "-". If the "Render Gaps" option from the "View" - menu is unticked all gaps will appear as blank spaces.

-

 

-

Editing In Selection Areas

-Editing can be restricted to the current selection area. -This allows the user to "Lock" the alignment either side of the selection -area. Any gap insertions or deletions will only affect the current selection area. -

-

In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, - the same number of gaps will be inserted at position 116, (between M and L). -

-

Locked selection area based editing was introduced in Jalview 2.08

-

 

+

+ Editing +

+

+ There are two major ways to edit alignments - in 'Normal mode', gaps + are inserted and deleted at the mouse pointer in various ways by + clicking the left mouse button and pressing a combination of either + shift and control (or the alt, option or apple key on Macs) and + dragging the mouse. Pressing F2 toggles the alternative 'Cursor mode' keyboard + editing facility, where the space bar and delete keys add and remove + gaps at the current editing position. The key strokes for both these + modes are summarised in the keystrokes + table. +

+

+ Tip: For large alignments, deselect "Calculate + -> Autocalculate Consensus" to prevent the alignment + performing lengthy calculations after every edit. +

+

+ Inserting / removing gaps - hold down the "Shift" + key. Click on a residue with the mouse and drag it to the left or + right to insert gaps and remove gaps.
If the current + selection is a group over all sequences in the alignment, or a group + over some sequences or all columns in the alignment, then hold down + "Control" key ("Cmd" key on OSX) and drag the residue + left or right to edit all sequences in the defined group at once. +

+

+ Copy/paste/cut/delete - any sequences which are in the + current selection box (indicated in red) may be cut and / or copied + to a new alignment or deleted. +

+

+ Undo / redo - editing of sequences (insertion/removal of + gaps, removal of sequences, trimming sequences etc) may be undone or + redone at any time using the appropriate menu items from the edit + menu. The undo history list only allows a maximum of 10 actions. +

+ Trimming alignment - First select a column by clicking the + scale indicator (above the sequences) The alignment may then be + trimmed to the left or right of this column. If multiple columns are + selected, the alignment is trimmed to the right of the rightmost + selected column (or to the left of the leftmost selected column) +

+

+ Remove gapped columns - Removes columns within the + alignment which contain only space characters ("-" or + "." or " ") +

+

+ Removing gaps - Removes all gaps from the alignment. Gaps + are "-" or "." or " ". +

+

+ Set gap character - Switches the gap character between + "." and "-". If the "Render Gaps" + option from the "View" menu is unticked all gaps will + appear as blank spaces. +

+

 

+

+ Editing In Selection Areas +

+ Editing can be restricted to the current selection area. This allows + the user to "Lock" the alignment either side of the + selection area. Any gap insertions or deletions will only affect the + current selection area. +

+ +

+

In this example, if Sequence IL2RA_MACMU has gaps removed from + position 98-104, the same number of gaps will be inserted at + position 116, (between M and L).

+

+ Locked selection area based editing was introduced in + Jalview 2.08 +

+