From 478b64f84c3d35ecd7eea0b69ad0a38d54de4d65 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 10 Apr 2006 13:06:40 +0000 Subject: [PATCH] added annotationColouring to whats new and updated IO and cursorMode (mac os and backspace==delete) --- help/helpTOC.xml | 1 + help/html/features/cursorMode.html | 8 +++++--- help/html/io/index.html | 9 +++++++-- help/html/keys.html | 22 +++++++++++++--------- 4 files changed, 26 insertions(+), 14 deletions(-) diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 62cba6b..316b63d 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -11,6 +11,7 @@ + diff --git a/help/html/features/cursorMode.html b/help/html/features/cursorMode.html index 5172cfa..579d886 100755 --- a/help/html/features/cursorMode.html +++ b/help/html/features/cursorMode.html @@ -44,9 +44,11 @@ unavailable in cursor mode).

To group insert, hold control or shift together with space.
    -
  • Delete - Delete a gap at the cursor position.
    - To delete 12 spaces at the current cursor, type 12 before pressing Delete.
    - To group delete, hold down control or shift together with Delete.
    • +
  • Delete (or backspace) - Delete a gap at the cursor position.
    + To delete 12 spaces at the current cursor, type 12 before pressing + Delete (or backspace).
    + To group delete, hold down control or shift together with Delete + (or backspace).

diff --git a/help/html/io/index.html b/help/html/io/index.html index 063f329..79e7576 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -24,15 +24,20 @@ alignment file then you will be given an error message. If you think Jalview really should be able to read your file, then send an email containing the problem file to jalview@jalview.org.

+

Jalview can also read jalview specific files for sequence features +and alignment annotation.

Output

Each alignment, whether it is the original or an edited version may be saved in the standard formats using File→Save As

Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm

Jalview will by default append the sequence start and end to each sequence name, in the format /start-end. If you do not want this behaviour for a particular file -output, open the "Output" tab on the Preferences window where you can +output, open the "Output" tab on the Preferences window where you can select which file formats you want to append the start and end sequence positions -for. +for. +

Quantitative and symbolic alignment annotation can be exported as a +comma separated value file by right clicking on an annotation row +under the alignment.

You can also save the current set of alignments and their colours, annotations and trees in a Jalview archive file using Desktop→Save project.

 

diff --git a/help/html/keys.html b/help/html/keys.html index 085c343..6db5df4 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -69,18 +69,22 @@ parameters (prefixing the command key and separated by commas).

- - - - - + + + + + - - -
Compound CommandModeAction (and parameter description)
0-9CursorBegin entering a -numeric parameter ([p]) or repetition number for a cursor movement or edit +numeric parameter (p) or repetition number for a cursor movement or edit command.
,CursorSeparates one or more numeric parameters ([p1],[p2]) for a command.
[p1],[p2]
Return		CursorMove cursor to a particular column (p1) and row (p2) in the alignment.
e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
[p1]SCursorJump to the p1'th sequence in the alignment.
[p1]PCursorJump to p1'th amino acid in current sequence.
[p1]CCursorJump to p1'th column in the alignment.
,CursorSeparates one or +more numeric parameters (e.g. p1,p2) for a command.
p1,p2
Return		CursorMove cursor to a particular column (p1) and row (p2) in the alignment.
e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
pSCursorJump to the p'th sequence in the alignment.
pPCursorJump to p'th amino acid in current sequence.
pCCursorJump to p'th column in the alignment.
QCursorMarks the top left corner of the selection area
MCursorMarks the bottom right corner of the selection area
[p1]
Space		CursorInserts p1 gaps at the current position.
p1 is optional. Hold down Control or Shift to insert gaps over a sequence group
[p1]
Delete		CursorRemove p1 gaps at the cursor position.
p1 is optional. Hold down Control or Shift to insert gaps over a sequence group
+[p]
SpaceCursorInserts +one (or optionally p) gaps at the current position.
Hold down Control or Shift to insert gaps over a sequence group +[p]
Delete
CursorRemoves +one (or optionally p) gaps at the cursor position.
Hold down Control or Shift to insert gaps over a sequence group +[p]
Backspace
CursorRemoves +one (or optionally p) gaps at the cursor position.
Hold down Control or Shift to insert gaps over a sequence group

 

 

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