Menus

From c973cc268cbba93fa4ca9620c3910d30891a5abc Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 27 May 2005 14:28:34 +0000 Subject: [PATCH] menus --- help/html/menus/alignmentMenu.html | 176 ++++++++++++++++++++++++++++++++++++ help/html/menus/desktopMenu.html | 51 +++++++++++ help/html/menus/index.html | 17 ++++ help/html/menus/popupMenu.html | 22 +++++ 4 files changed, 266 insertions(+) create mode 100755 help/html/menus/alignmentMenu.html create mode 100755 help/html/menus/desktopMenu.html create mode 100755 help/html/menus/index.html create mode 100755 help/html/menus/popupMenu.html diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html new file mode 100755 index 0000000..00bca80 --- /dev/null +++ b/help/html/menus/alignmentMenu.html @@ -0,0 +1,176 @@ + +Menus + + +

Alignment Menu

File

Save As
+ Save the alignment to local file. A file selection window will + open, use the "Files of type:" selection box to determine which + alignment format to save as.
+
Export
+ Creates an alignment output maintaining the alignment background colours + and group colours. If the alignment is wrapped, the output will also be + wrapped and will have the same visible residue width as the open alignment. + +
- HTML
  + Create a web page + from your alignment.
- EPS
  + Create an Encapsulated + Postscript file from your alignment.
- PNG
  + Create a Portable Network + Graphics file from your alignment.
+
Output to Textbox
+ The alignment will be displayed in plain text in a new window + which you can "Copy and Paste" using the pull down menu, or your + standard operating system copy and paste keys.
+ Select the format of the text by selecting one of the following menu items. +
- FASTA
- MSF
- CLUSTAL
- BLC
- PIR
- PFAM
  +
+
Print
+ Jalview will print the alignment using the current fonts and + coloursof your alignment. If the alignment has annotations visible, these + will be printed below the alignment. If the alignment is wrapped the number + of residues per line of your alignment will depend on the paper width or + your alignment window width, whichever is the smaller.
Load Associated Tree
+ Jalview can load in trees which are in the Newick file format + and associate them with a particular alignment. Note: the ids of the tree + file and your alignment MUST be the same.
Close
+ Close the alignment window. Be aware that changes to your alignment + will not be save unless specifically actioned from the "Save As" + menu.
+

Edit

+
+
Undo
+ This will undo any edits you make to the alignment. This applies to insertion + or deletion of gaps, cutting residues or sequences from the alignment, pasting +
+
Redo
+
+
Cut
+
Copy
+
Paste +
+
To New Alignment
+
Add To This Alignment
+
+
+
Delete
+
Select All
+
Deselect All
+
Invert Selection
+
Undefine Groups
+
Remove Left
+
Remove Right
+
Remove Empty Columns
+
Remove All Gaps
+
Remove Redundancy
+
Pad Gaps
+
+

Search

+
+
Find
+
+

View

+
+
Font
+
Wrap
+
Show Full Sequence ID
+
Boxes
+
Text
+
Colour Text
+
Show Gaps
+
Show Annotations
+
Sequence Features
+
Overview Window
+
+

Colour

+
+
Apply Colour To All Groups
+
None
+
ClustalX
+
Blosum62 Score
+
Percentage Identity
+
Zappo
+
Taylor
+
Hydrophobicity
+
Helix Propensity
+
Strand Propensity
+
Turn Propensity
+
Buried Index
+
Nucleotide
+
User Defined
+
By Conservation
+
Modify Conservation Threshold
+
Above Identity Threshold
+
Modify Identity Threshold
+
+

Calculate

+
+
Sort +
+
by ID
+
by Group
+
by Pairwise Identity
+
+
+
Calculate Tree +
+
Average Distance Using % Identity
+
Neighbour Joining Using % Identity
+
Average Distance Using Blosum62
+
Neighbour Joining Using Blosum62
+
+
+
Paiwise Alignments
+
Principal Component Analysis
+
Web Service +
+
Clustal Alignment
+
JPred
+
Muscle Alignment
+
+
+
+

+

+ + diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html new file mode 100755 index 0000000..29857b9 --- /dev/null +++ b/help/html/menus/desktopMenu.html @@ -0,0 +1,51 @@ + +Desktop Menu + + +

Desktop Menu

File +
- Input Alignment from (See more on file + formats) +
  - File
    + open file(s) on your local file system
  - URL
    + open a file from a website. The URL MUST start with http://
  - Textbox
    + copy and paste an alignment into a text window
  +
- Save Project
  + Saves all currently open alignment windows with their current visible + settings as a Jalview File, with the .jar extension. Each alignment will + also save the currently active tree associated with the window, if one + exists.
- Load Project
  + Loads Jalview file formatted alignments only.
- Quit
  + Close Jalview. Warning - any annotations you have made on alignments + will be lost unless you Save your work before quitting.
  +
+
Tools +
- Preferences
  + Change the default visual settings for opening new alignment + windows.
  +
+
Help +
- About,
- Documentation
  +
+
Window

+ + diff --git a/help/html/menus/index.html b/help/html/menus/index.html new file mode 100755 index 0000000..4949e87 --- /dev/null +++ b/help/html/menus/index.html @@ -0,0 +1,17 @@ + +Menus + + +

Menus

Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment + Menu" and the "Popup Menu".

The Desktop Menu is always visible and is the + starting point for loading new alignments.

The Alignment Menu is visible once and alignment + has been opened.

The Popup Menu is made visible by clicking with + the right mouse button on a sequence or the name of a sequence in an alignment + window.

+ + + diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html new file mode 100755 index 0000000..10f8072 --- /dev/null +++ b/help/html/menus/popupMenu.html @@ -0,0 +1,22 @@ + +Popup Menu + + +

Popup Menu

Define

Group,
Remove Group
Group Colour
Boxes
Text
Colour Text
Border Colour

Sequence

Edit Name
View PDB Structure

+ + -- 1.7.10.2