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emnu |
It also displays the names of files in your current directory and allows you to display their contents, copy them, delete them and do other things with them.
emnu allows to to move around the menus of programs or files using the arrow keys. Pressing RETURN when you have selected an item will run a program or display a file.
You can also navigate around the menu by typing the first few letters of the option that you desire. You will move to the item in the menu that first matches those letters.
You can also type in UNIX commands as if you were typing them in a UNIX session. (Of course, as you type, emnu will not know if you wish to run a UNIX command or go to a menu item starting with the letters you are typing, so you will see the menu selection changing as you type. If this irritates you and you are confident enough with UNIX commands to be typing them directly, maybe you do not need to use emnu?)
If you run a command or program that creates one or more files, then when you return to the menu, the command line will be set up to contain the command more followed by the names of the files. Pressing RETURN to run this command will display the contents of these files. If you do not wish to see these files, just press ^C to clear the command line.
You can also navigate around the menu and do many other things by typing control keys and Function keys. Control keys can be typed by pressing the Control key and another key. Control keys are written here and in the online help text as a ^ and then the key's letter, for example ^C means Control-C.
The control key commands that are most useful will be displayed in the bottom two lines of the screen. If in doubt, press the '?' key for further help.
If you are using emnu through a telnet session or in a 'xterm' window, you may be able to click on menu options and on the bottom two lines of help in the screen to select items. (Double click on the menu to run that item.)
The menus that are displayed are very simple. They consist of the title of the menu at the top of the screen, followed by several lines of things to select. The first two items are always 'EXIT' which takes you back to the previous menu, and 'HELP' which shows help for this menu.
The first menu you see (the GROUPS MENU) will consist of two columns of the groups of EMBOSS programs. You can move up and down, left and right using the arrow keys. The bottom two lines show useful control keys you can type to do things. You may be able to click on the help text or on the menu items to select them.
The line above the two help lines is the command line. This is where the currently selected menu item or any command you type is displayed. See the Usage section of this document below to see useful control codes for navigating and editing this command line. You may type in any UNIX command or any EMBOSS program name in this command line. It is common to add extra parameters or options to change the default behaviour of an EMBOSS program. You may edit the command line to do this. For example the program seqret can take many options. You may wish to type the command 'seqret -osf gcg' to make seqret write out sequences in GCG format.
Selecting any item in the GROUPS menu apart from 'EXIT' and 'HELP' will select a sub-menu. The 'ALL FILES' and 'NEW FILES' items will start a menu displaying files, all others will display a menu of EMBOSS programs.
GROUPS MENU
>EXIT HELP
ALL FILES NEW FILES
ALPHABETIC LISTING OF ALL PROGRAMS SEARCH FOR PROGRAMS
ALIGNMENT CONSENSUS
ALIGNMENT DIFFERENCES ALIGNMENT DOT PLOTS
ALIGNMENT GLOBAL ALIGNMENT LOCAL
ALIGNMENT MULTIPLE DISPLAY
EDIT ENZYME KINETICS
FEATURE TABLES INFORMATION
MENUS NUCLEIC 2D STRUCTURE
NUCLEIC CODON USAGE NUCLEIC COMPOSITION
NUCLEIC CPG ISLANDS NUCLEIC GENE FINDING
NUCLEIC MOTIFS NUCLEIC MUTATION
NUCLEIC PRIMERS NUCLEIC PROFILES
NUCLEIC REPEATS NUCLEIC RESTRICTION
NUCLEIC TRANSCRIPTION NUCLEIC TRANSLATION
PHYLOGENY PROTEIN 2D STRUCTURE
PROTEIN 3D STRUCTURE PROTEIN COMPOSITION
PROTEIN MOTIFS PROTEIN MUTATION
PROTEIN PROFILES TEST
UTILS DATABASE CREATION UTILS DATABASE INDEXING
> EXIT
? Help ^N New Files ^A StartLine ^B Back ^C Clear ^U Menu Up ^P Page Up
^X Exit ^T All Files ^E End Line ^F Forward ^K ClrEnd ^D Menu Dn ^Z Page Dn
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MAIN MENU HELP
This menu system aims to make it easy to run EMBOSS programs and manage files.
You now have a menu of EMBOSS program groups. You can select any program group
and select the programs. Move to an option and press RETURN to select it.
You can move to menu options by typing the first few letters of the option name
or by using the cursor (arrow) keys.
You can also type any normal UNIX command and run it.
Before the program group options, are the following special options:
EXIT - exit the program
HELP - this page of help
ALL FILES - display files in this directory, view them, change directory, etc.
NEW FILES - display the files that have been created since 'em' started running
ALPHABETIC - listing of all EMBOSS programs
SEARCH - search for EMBOSS programs by name or description
The following control keys edit the command line:
^F forward, ^B back, ^A start, ^E end, ^C delete line, ^K delete to end of line
The following keys get other things:
F1,F2,F3,F5 -view, view sequence, copy and delete the last file looked at
^X exit, ^N/^T file menus, ^R recall stored file, TAB complete name of option
Press any key to continue...
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It starts with the normal 'EXIT' and 'HELP' items. All the other items are EMBOSS programs. There is only one column of items. Each item is followed by a short description of the program. Use of the UP and DOWN arrow keys will move you up and down in the menu. Use of the LEFT and RIGHT arrow keys will also move you up and down in the menu.
To get back to the GROUPS MENU, select the 'EXIT' option or type ^X.
You may add any text you wish after the name of a selected EMBOSS program. For example, type ^E to go to the end of the command line and type -opt after the program name to make the program ask you for more than the minimal set of qualifiers when you run that program.
To see detailed help on a program, move to the appropriate item and press the ? key.
If you run a program that creates one or more files, then when you return to the menu, the command line will be set up to contain the command more followed by the names of the files. Pressing RETURN to run this command will display the contents of these files. If you do not wish to see these files, just press ^C to clear the command line.
To run the program, just press RETURN.
NOTE: Once you start running any program, you are no longer talking to the menu system, you are only talking to that program. Therefore all of the control codes for doing things like putting file names in the command line will have no effect.
PROGRAMS MENU
>EXIT
HELP
chaos Create a chaos game representation plot fro a sequence
cpgplot Plot CpG rich areas
cpgreport Reports all CpG rich regions
diffseq Find differences (SNPs) between nearly identical sequences
dotmatcher Displays a thresholded dotplot of two sequences
dotpath Displays a non-overlapping wordmatch dotplot of two sequences
dottup Displays a wordmatch dotplot of two sequences
einverted Finds DNA inverted repeats
equicktandem Finds tandem repeats
etandem Looks for tandem repeats in a nucleotide sequence
isochore Plots isochores in large DNA sequences
newcpgreport Report CpG rich areas
newcpgseek Reports CpG rich regions
palindrome Looks for inverted repeats in a nucleotide sequence
polydot Displays all-against-all dotplots of a set of sequences
redata Search REBASE for enzyme name, references, suppliers etc
restrict Finds restriction enzyme cleavage sites
showseq Display a sequence with features, translation etc
> EXIT
? Help ^N New Files ^G Get File ^J Complete ^C Clear ^U Menu Up ^P Page Up
^X Exit ^T All Files ^R RecalFile ^E End Line ^K ClrEnd ^D Menu Dn ^Z Page Dn
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PROGRAMS MENU HELP
This menu aims to make it easy to run the EMBOSS programs.
You now have a menu of EMBOSS programs. You can select any program.
Move to an option and press RETURN to select it.
You can move to menu options by typing the first few letters of the option name
or by using the cursor (arrow) keys.
You can also type any normal UNIX command and run it.
Before the program group options, are the following special options:
EXIT - exit the program
HELP - this page of help
The following control keys edit the command line:
^F forward, ^B back, ^A start, ^E end, ^C delete line, ^K delete to end of line
The following keys get other things:
F1,F2,F3,F5 -view, view sequence, copy and delete the last file looked at
^X exit, ^N/^T file menus, ^R recall stored file, ? see detailed help on program
Press any key to continue...
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This will show a list of the files in your current directory (folder).
The name of the current directory will be displayed as the title of the menu.
You can see the contents of a file by pressing RETURN when the file is the currently selected item in the menu. If the current item is a directory (marked by the word Dir by the name) then you will go into that directory and the FILES menu will change to display the files in that directory. All further programs will be run in that new directory until you exit the menu program or you change directory again. Exiting from the FILES menu will not change back to the previous menu.
There are many useful control keys for manipulating files:
The following change the way the files are sorted before displaying in the menu. Having pressed one of these function keys, all subsequent file menus will sort the files using the appropriate method.
F8 AlphaSort
Sort the files by name (Start a files menu if not already in one)
F9 TimeSort
Sort the files by time (Start a files menu if not already in one)
The following will use the current files menu item to display, copy of delete. If you are not currently in a FILES menu or if the current item is not a file, then the last valid file that you pressed RETURN on will be remembered and used.
The ^G key is useful for adding this default file name to a command you are typing into the command line.
Note: you can use the commands in any menu and they will work on the default file.
F1 ViewFile
Show the contents of the current menu item file, or last file viewed
F2 View Seq
Display the current file as a sequence
F4 CopyFile
Copy the current file to a new file
F5 DelFile
Delete the current file
^G GetFile
Add the name of the current file to the command line
Separate from the memory of the default file used by the above commands is a specific method of remembering the name of an item in the FILES menus and recalling it into the command line at a later date by using the following pair of key codes.
^S StoreFile
Remember the name of the current menu item file
^R RecalFile
Add the stored file name to the command line
And finally, it is often useful to be able to make a new directory (folder) and go directly into that new directory.
F3 New Dir
Create a new directory and go into it
FILES: /people/gwilliam/tmp
EXIT
HELP
TO HOME
PARENT DIRECTORY
five.needle 20 Nov 2000 16:51 29 Kb
five.rev 16 Nov 2000 14:48 178 b
five.seq 09 Nov 2000 17:08 178 b
five.seq.fasta 20 Nov 2000 15:42 210 b
five.seq.fasta.align 20 Nov 2000 15:42 1 Kb
five.seq.fasta.cat 20 Nov 2000 15:42 14 Kb
five.seq.fasta.masked 20 Nov 2000 15:42 210 b
five.seq.fasta.masked.log 20 Nov 2000 15:42 35 b
five.seq.fasta.out 20 Nov 2000 15:42 295 b
five.seq.fasta.stderr 20 Nov 2000 15:42 13 Kb
five.seq.fasta.tbl 20 Nov 2000 15:42 1 Kb
five.water 20 Nov 2000 09:34 1 Kb
four.seq 09 Nov 2000 17:08 159 b
>one.seq 09 Nov 2000 17:08 276 b
three.AC026020 20 Nov 2000 16:07 868 Kb
three.AC026051 20 Nov 2000 16:06 768 Kb
> one.seq
? Help F1 ViewFile F3 New Dir ^G GetFile ^S StoreFile F9 TimeSort ^N NewFile
^X Exit F2 View Seq F4 CopyFile F5 DelFile ^R RecalFile F8 AlphaSort
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ALL FILES MENU HELP
This menu aims to make it easy to view and manage the files output by programs.
You now have a menu of file names in the current directory.
You can select any file by moving to its menu option
You can move to menu options by typing the first few letters of the file name
or by using the cursor (arrow) keys.
Press RETURN to view the file (or if it is a directory, to go into it).
You can also type any normal UNIX command and run it.
Before the file name options, are the following special options:
EXIT - exit back to the previous menu screen
HELP - this page of help
TO HOME - go back to your 'Home' directory
PARENT DIRECTORY - go to the directory above this one
The current file becomes the default file for use by:
F1 view file, F2 display as sequence, F3 copy file, F5 delete file
The following keys do other things:
F4 makes a new directory, F8 sort files by name, F9 sort files by time
^X exit, ^N new files menu, ^S store current file name, ^R recall stored file
Press any key to continue...
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It therefore consists of a convenient way of quickly finding those files which you have worked on during this menu session.
NEW FILES: /people/gwilliam/tmp
>EXIT
HELP
TO HOME
PARENT DIRECTORY
five.needle 20 Nov 2000 16:51 29 Kb
> EXIT
? Help F1 ViewFile F3 New Dir ^G GetFile ^S StoreFile F9 TimeSort ^T AllFile
^X Exit F2 View Seq F4 CopyFile F5 DelFile ^R RecalFile F8 AlphaSort
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NEW FILES MENU HELP
This menu aims to make it easy to view and manage the files output by programs.
It shows the files that have been created since 'em' started.
You now have a menu of file names in the current directory.
You can select any file by moving to its menu option
You can move to menu options by typing the first few letters of the file name
or by using the cursor (arrow) keys.
Press RETURN to view the file (or if it is a directory, to go into it).
You can also type any normal UNIX command and run it.
Before the file name options, are the following special options:
EXIT - exit back to the previous menu screen
HELP - this page of help
TO HOME - go back to your 'Home' directory
PARENT DIRECTORY - go to the directory above this one
The current file becomes the default file for use by:
F1 view file, F2 display as sequence, F3 copy file, F5 delete file
The following keys do other things:
F4 makes a new directory, F8 sort files by name, F9 sort files by time
^X exit, ^T all files menu, ^S store current file name, ^R recall stored file
Press any key to continue...
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| Key | Name | Description |
|---|---|---|
| ? | Help | Help on the current menu, or current program |
| ^X | Exit | Exit back to the prvious menu |
| Key | Name | Description |
|---|---|---|
| ^U | Menu Up | Move up one menu item (same as UP ARROW) |
| ^D | Menu Dn | Move down one menu item (same as DOWN ARROW) |
| ^P | Page Up | Move down the menu by one screen |
| ^Z | Page Dn | Move up the menu by one screen |
| Key | Name | Description |
|---|---|---|
| ^A | StartLine | Move to the start of the command line |
| ^E | End Line | Move to the end of the command line |
| ^B | Back | Move back one character in the command line |
| ^F | Forward | Move forward one character in the command line |
| ^C | Clear | Clear all of the command line |
| ^K | ClrEnd | Clear from the cursor position to the end of the command line |
| ^J | Complete | Complete the command line to match the current menu item |
| Key | Name | Description |
|---|---|---|
| ^N | New Files | Display a menu showing only files created since the menu program started |
| ^T | All Files | Display a menu of all files in the current directory |
| F8 | AlphaSort | Sort the files by name (Start a files menu if not already in one) |
| F9 | TimeSort | Sort the files by time (Start a files menu if not already in one) |
| F1 | ViewFile | Show the contents of the current menu item file, or last file viewed |
| F2 | View Seq | Display the current file as a sequence |
| F3 | New Dir | Create a new directory and go into it |
| F4 | CopyFile | Copy the current file to a new file |
| F5 | DelFile | Delete the current file |
| ^G | GetFile | Add the name of the current file to the command line |
| ^S | StoreFile | Remember the name of the current menu item file |
| ^R | RecalFile | Add the stored file name to the command line |
Standard (Mandatory) qualifiers: (none)
Additional (Optional) qualifiers:
-[no]morefiles boolean [Y] After every command that you run in the
menu, either by selecting the name of an
EMBOSS program, or by typing the command in
the command line, a check is made to see if
any new files have been created by that
command. If so, the command 'more filenames'
will be put into the comamnd line ready for
you to quickly view those new files. If you
do not wish this to happen, set this to be
false.
-explode boolean [N] The groups that EMBOSS applications
belong to have two forms, exploded and not
exploded. The exploded group names are more
numerous and often vaguely phrased than the
non-exploded ones. The exploded names are
formed from definitions of the group names
that start like NAME1:NAME2 and which are
then expanded into many combinations of the
names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
NAME2 NAME1'. The non-expanded names are
simply like: 'NAME1 NAME2'.
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers: (none)
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| (none) | |||
| Additional (Optional) qualifiers | Allowed values | Default | |
| -[no]morefiles | After every command that you run in the menu, either by selecting the name of an EMBOSS program, or by typing the command in the command line, a check is made to see if any new files have been created by that command. If so, the command 'more filenames' will be put into the comamnd line ready for you to quickly view those new files. If you do not wish this to happen, set this to be false. | Boolean value Yes/No | Yes |
| -explode | The groups that EMBOSS applications belong to have two forms, exploded and not exploded. The exploded group names are more numerous and often vaguely phrased than the non-exploded ones. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: 'NAME1', 'NAME2', 'NAME1 NAME2', NAME2 NAME1'. The non-expanded names are simply like: 'NAME1 NAME2'. | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
When using the '-explode' option, one of the program groups is expanded to be 'HELP'. Selecting this option simply gives the help for the Groups Menu. I don't intend to alter this situation, it is a feature.
delete_file() doesn't delete directories - this is because we don't allow directories to be default files. Should we? It would complicate things like copy_file.
Code was taken liberally from the example programs in the ncurses package.
The name of this program, emnu, was a suggestion from Peter Rice after the author had run through many temporary names ('esme' - Extremely Simple Menu for EMBOSS, 'em' - EMBOSS Menu, 'm' - Menu).
April - Dec 2000 - written - Gary Williams