                                    emnu



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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Simple menu of EMBOSS applications

Description

   emnu displays a simple character-based menu that allows you to display
   the names of emboss programs and select them.

   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

   This is the menu that is initially displayed.
     __________________________________________________________________

                                   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
     __________________________________________________________________
     __________________________________________________________________

                                  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...
     __________________________________________________________________

  Programs menus

   A typical EMBOSS PROGRAMS MENU is displayed below.

   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
     __________________________________________________________________
     __________________________________________________________________

                                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...
     __________________________________________________________________

  All files menu

   Get to this menu by selecting the 'ALL FILES' option from the main
   GROUPS menu, or type ^T in any menu.

   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
     __________________________________________________________________
     __________________________________________________________________

                                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...
     __________________________________________________________________

  New files menu

   The NEW FILES menu is exactly the same at the ALL FILES menu except
   that it only holds those files that have been created or modified since
   you started the menu program.

   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
     __________________________________________________________________
     __________________________________________________________________

                                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...
     __________________________________________________________________

   The name of this program, emnu, comes from the observation that the
   EMBOSS Menu is Not UNIX.

Usage

  General

   Key Name                 Description
   ?   Help Help on the current menu, or current program
   ^X  Exit Exit back to the prvious menu

  Menu navigation

   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

  Command-line editing

   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

  Files

   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

Command line arguments

Simple menu of EMBOSS applications
Version: EMBOSS:6.2.0

   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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   None.

Output file format

   None.

Data files

   None.

Notes

   The name of this program, emnu, comes from the observation that 'emnu'
   is a mangled 'menu'.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   It crashes if you resize the xterm window to make it smaller than when
   the menu system started.

   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.

Author(s)

   This application was written by Gary Williams

History

   Many concepts (but no code) for this application cames from the editor
   pico and the file browser 'Midnight Commander' (mc).

   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

Target users

   This program is intended to be used by naive users.

Comments
