Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) NAME _M_A_S_E intrinsic functions SYNOPSIS _M_A_S_E provides the user with many intrinsic functions. These functions may be selected via a menu by calling the function _C_O_M_M_A_N_D-_M_O_D_E that is bound to the colon key (``:'') by default. All these functions can be bound to a key code via the _B_I_N_D function. Some functions may read the current cursor position and use this in establishing defaults. Others may modify the current cursor position. _M_U_L_T is a numeric multiplying pre- fix that may modify some commands. To specify a _M_U_L_T fac- tor, just type in the digits before running the function. If _M_U_L_T is not specified, it defaults to ``1''. Functions employing these values are noted. _N_O_T_E: Due to the way _M_U_L_T is implemented, it is not possible to _B_I_N_D nor _M_A_P the digits (``0'' through ``9''). This list is in alphabetical order; functional groups of commands are noted in the other help files. Most commands may be terminated before they finish by hit- ting C-C. DESCRIPTION @ABORT-COMMAND Do nothing - use this to exit _C_O_M_M_A_N_D-_M_O_D_E with no effect. ALIAS Create an alias. You will be prompted for the name + of the alias to create, and what it should alias to. + ALIAS-LOAD Load aliases from an alias file. + ALIAS-SAVE Save current aliases to a file. + ALIGN-ON-PATTERN Given a pattern, insert gaps (either at the begin- + ning of the sequence, or after the most recent + period (anchor point)) to align all occurences of + that pattern. No allowance is made to do this for + just some subset of sequences (sigh!). If a given + locus doesn't have the specified pattern pattern, + user will be notified, and the sequence will be + untouched. Before the actual insertions are done, + the user will be informed of the position to which + MBCRR Last change: DFCI 1 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) the pattern will be aligned. Control-C out at this + point if this is not what you want done. + See also: Anchor functions, _S_Q_U_E_E_Z_E-_O_U_T-_G_A_P_S (might + be useful to clean up some messes!). + ALIGNMENT-MODE Set up keyboard bindings and mappings for editing the _A_L_I_G_N_M_E_N_T of sequences: All letters are unbound. Minus sign inserts a gap. Keys ``x'' and ``d'' delete under the cursor. _P_R_O_T_E_C_T is turned _O_N. Alias for _M_O_D_E-_A_L_I_G_N_M_E_N_T. ALPHABETIZE-LISTS Put function and variable lists into alphabetical order. This makes _I_N_C_R_E_M_E_N_T_A_L _C_O_M_P_L_E_T_E work better, as alphabetically close names appear adjacent to each other. Hierarchy of command nomenclature has been organized to simplify this. _N_O_T_E: this is now the default situation. ANCHOR-CHECK See if each sequence contains the same number of + anchors + ANCHOR-CREATE Create an anchor at the specified column (insert a + ``.'' in each sequence at specified position) + ANCHOR-DELETE Delete anchor at specified offset. ANCHOR-STRIP Strip all anchors from all sequences (perhaps to execute some other sort of analysis ...) ANCHOR-SYNCHRONIZE Insert gaps where needed to align all of the + anchors. + APPEND-TO-YANK Append the next _M_U_L_T sequence positions to the Yank + Buffer. + The sequence is not modified. + APROPOS Display short information about all commands, vari- ables ... that contain a key string. I.E. running _A_P_R_O_P_O_S for _C_O_N_S_E_N_S_U_S would display information about all commands and variables that talk about MBCRR Last change: DFCI 2 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) _C_O_N_S_E_N_S_U_S. AUTO-INSERT The key typed will have the high bit stripped, and | then be inserted | _M_U_L_T times at the current cursor position. This is useful only when bound to a key. If one binds ``A'' to _A_U_T_O-_I_N_S_E_R_T, then types ``A'', an ``A'' will be inserted at the current cursor position. AUTO-OVERTYPE The key typed will be replace the letter under the + cursor. This is only useful when bound to a key. + The old letter is deleted, so _P_R_O_T_E_C_T will be refer- + enced. + BELL Ring bell and do nothing. This is used as the default binding for otherwise unbound keys. BIND Bind a key to a specific function. First, one will be prompted to strike the key to be bound. Next, one will be prompted for the name of the command to bind it to via the _M_E_N_U interface. Callable from _T_A_K_E files as ``BIND key-code function-name''. BIND-ALL-ALPHA Bind all alpha keys starting at some modification of + "A" to some function. ( _A_U_T_O-_I_N_S_E_R_T, _A_U_T_O-_O_V_E_R_T_Y_P_E, + _I_N_S-_C_O_M_P_E_N_S_A_T_E_D-_B_A_C_K_W_A_R_D, and _I_N_S-_C_O_M_P_E_N_S_A_T_E_D- + _F_O_R_W_A_R_D would be the most logical functions.) Thus, + saying "Bind-All-Alpha a Auto-Insert" would bind "a" + though "z" to "Auto-Overtype", and saying "Bind- + All-Alpha M-A" woul bind "M-A" though "M-Z" to + "Auto-Overtype". + NOTE: specifying anything other than a modification + of the letter "A" is an error. + It is valid to specify prefix characters... + CHARACTER-SET Change the display character aliasing set. This allows one to view the sequences with an aliasing character set - i.e. display serines and threonines both as ``t''. This _D_O_E_S _N_O_T affect the actual sequence, nor the _S_E_A_R_C_H or _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T rou- tines. It DOES affect _C_O_N_S_E_N_S_U_S generation, and _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S. MBCRR Last change: DFCI 3 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) Callable from _T_A_K_E files as ``CHARACTER-SET filename''. If _D_I_S_P_L_A_Y-_A_L_T_E_R_N_A_T_E-_C_H_A_R_A_C_T_E_R-_M_A_P is disabled, the + actual letters will be displayed. + See _F_I_L_E _F_O_R_M_A_T_S for alias file format. Affects: _C_O_N_S_E_N_S_U_S, basic display, _H_I_G_H_L_I_G_H_T- + _D_I_F_F_E_R_E_N_C_E_S, and _O_U_T_P_U_T-_A_L_I_G_N_E_D + COLUMN-COMPOSITION Report the frequency of all characters found in a given column COLUMN-CORRELATION Look at coordinated changes down columns. References _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E_S ``_C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N- _F_I_X_E_D-_P'', ``_C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N-_T_H_R_E_S_H_O_L_D'', and ``_C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N-_M_O_D_E_L-_S_E_Q'' COMMAND-MODE Select a function to run. This works via the menu + interface. When you have typed enough of the com- + mand name to make it unique, it will be filled in + automatically. If the variable _I_N_C_R_E_M_E_N_T_A_L-_C_O_M_P_L_E_T_E + is set, the command will be filled in as far as pos- + sible. + COMMENTS-EDIT Edit the comment field of a locus. The editor to use will be read from your environmental variable ``EDITOR''. This may be set via ``EDITOR=your- editor-choice; export EDITOR'' for the Bourne shell (sh), or via ``setenv EDITOR=your-editor-choice'' for the C-shell (csh), and may be set up in your ``~/.profile'' or ``~/.login'' (respectively) ini- tialization files. If ``EDITOR'' is not set, _v_i will be used. You will be prompted for the number of the locus on which to operate (default to the current sequence). The file name will consist of the locus name with a number appended. Spaces in this file name will be converted to carets (``^''), since CCA-EMACS barfs for file names with spaces. + When you are finished, instruct the editor to save + your changes and exit. + When the comments are read back in, a ``;'' will be placed at the beginning of each line if it isn't already there. COMMENTS-VIEW Display comment lines from a set of sequences that MBCRR Last change: DFCI 4 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) contain a specified regular expression. The com- ments for the requested sequence will be passed to ``grep -i string''. The string you respond with may contain flags to ``grep'' (like ``-v''). Also note that if the pattern you want to search for has spaces, it must be surrounded by quotes. CONSENSUS - Generate a consensus sequence from a set of sequences. This consensus sequence will be displayed at the bottom of the window. The aliasing character set (see _C_H_A_R_A_C_T_E_R-_S_E_T) is referenced and used to generate the consensus. The base occurring most frequently down a column will be placed into the consensus sequence. In there is a tie, a ques- tion mark (``?'') will be placed in the consensus sequence. The variable _C_O_N_S_E_N_S_U_S-_U_S_E-_G_A_P affects the way the consensus routine looks at gaps (``-''). If this variable is _O_N, gaps will be treated as any other sequence element. If it is _O_F_F, gaps will be ignored unless there are no other bases down that column. The variable _C_O_N_S_E_N_S_U_S-_T_H_R_E_S_H_O_L_D is also referenced. The most frequently occurring base must occur in at least this fraction of active sequence before the base will be placed in the consensus sequence. This variable defaults to ``0.0''. Callable from _T_A_K_E files as ``CONSENSUS range''. If ``range'' is not specified, ``1-$'' will be used. CONSENSUS-ALTERNATE Generate and display a consensus sequence, as in + _C_O_N_S_E_N_S_U_S above, by a slightly different method. + You will be asked to define a ``model sequence'', + and an extra sequence set. The ``Consensus'' + sequence will be built as follows: for each posi- + tion, the consensus will be the character from the + master sequence if that character appears in at + least _C_O_N_S_E_N_S_U_S-_T_H_R_E_S_H_O_L_D fraction of the ``other'' + sequences specified. + CONSENSUS-OFF Disable display of the consensus line, giving one additional line of sequence information. COPY-TO-YANK First, clear out the Yank buffer. + Then, copy the next _M_U_L_T sequence positions into the + Yank Buffer. The sequence is not modified. + CREATE-LOCUS Create a new locus. The new locus can be ``All MBCRR Last change: DFCI 5 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) New'', copied from a ``Sequence in Memory'' (with the option to translate it (in either one or three letter code), or ``Imported'' from another sequence file. - You will be asked to assign a new name for the locus, what file you would like to place it in, and where you would like to place it on the screen. If you ask for a translation, you will be prompted + for the frame (1, 2, or 3). + If the variable _T_R_A_N_S_L_A_T_E-_I_G_N_O_R_E-_G_A_P_S is _O_N, gaps + and anchor points will be stripped before doing the + translation. The product peptide will be resyn- + chronized with the nucleotide sequence. + CURSOR-OTHER-WINDOW Position cursor to the equivalent position in the other window. DEL-BACK Delete _M_U_L_T positions _B_E_H_I_N_D cursor. Most useful when typing in new sequence information. References _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E ``_P_R_O_T_E_C_T''. _M_o_u_s_e _F_u_n_c_t_i_o_n_s. DEL-COLUMNS Delete multiple columns from multiple sequences (delete a column of positions). You will be prompted for: Delete columns in which sequences Which sequences to act on (default to the current sequence), Delete at which column At which position to do the deletions (default to the current cursor position Delete how many columns How many positions to delete (default to _M_U_L_T) NOTE that _D_E_L-_C_O_L_U_M_N_S observes the status of the vari- able _P_R_O_T_E_C_T. If one attempts to delete non-gaps when _P_R_O_T_E_C_T is set, you will be asked how to proceed. You may: PRESERVE this sequence and continue to act on subsequent sequences, MBCRR Last change: DFCI 6 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) OVERRIDE protection of this sequence - delete positions in this sequence regardless of the protection ABORT the delete operation. See Also: _M_o_u_s_e _F_u_n_c_t_i_o_n_s. DEL-COMPENSATED-BACKWARD Delete the character under the cursor, then compen- + sate backward. + DEL-COMPENSATED-FORWARD Delete the character under the cursor, then compen- + sate forward. + DEL-GAP Delete _M_U_L_T positions _U_N_D_E_R cursor. References _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E ``_P_R_O_T_E_C_T''. See Also: _M_O_U_S_E _F_U_N_C_T_I_O_N_S DNA-MODE Set up the keyboard bindings and mappings for edit- ing nucleic acid sequences: The letters ACT- GYRJKLMBDHVN, and X insert themselves. All other letters beep. Minus sign inserts a gap. _P_R_O_T_E_C_T is turned _O_F_F Alias for _M_O_D_E-_D_N_A. DYNAMIC-HIGHLIGHT This function should be considered to be in "alpha- + test". It will search for matches to a weight + matrix. This is a SCORING method rather than a + plus/minus method. (The regular expression handlers + are plus/minus). This method can allow different + weights for each letter to be associated with each + position of the oligo. + GRIPE Send a complaint, question, comment, or observation to the _M_A_S_E administrator. This is done via the system _m_a_i_l (_1) command. Terminate your message with C-D. HELP View the MASE online documentation. This is displayed via _B_R_O_W_S_E_R. HIGHLIGHT-DIFFERENCES Highlight positions where the display letter that | MBCRR Last change: DFCI 7 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) differ from a specific sequence. The test is made | between the ``display'' characters from _C_H_A_R_A_C_T_E_R- | _S_E_T, and is not affected by _D_I_S_P_L_A_Y-_A_L_T_E_R_N_A_T_E- | _C_H_A_R_A_C_T_E_R-_M_A_P. | The ``model'' sequence is specified in this command. If this variable is set to ``0'', letters differing from the _C_O_N_S_E_N_S_U_S sequence will be highlighted. These highlights can be printed via _O_U_T_P_U_T-_A_L_I_G_N_E_D. Alternate method of getting at _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S. HIGHLIGHT-LOAD Load the highlight flags from a file. Current + highlights will be discarded. NOTE - the highlights + file MUST be syncronus with the sequences file. + HIGHLIGHT-POSITION Highlight _M_U_L_T positions following cursor. Highlight type ``1'' will be used. HIGHLIGHT-SAVE Store the highlight flags to a file, for later use + by _H_I_G_H_L_I_G_H_T-_L_O_A_D. + INS-COLUMNS Insert multiple columns into multiple sequences (insert a column of gaps). You will be prompted for: Insert columns into which sequences Which sequences to act on (default to the current sequence), Insert at which column At which position to do the insertions (default to the current cursor position, and Insert how many columns How many gaps to insert (default to _M_U_L_T) See Also: _M_o_u_s_e _F_u_n_c_t_i_o_n_s. INS-COMPENSATED-BACKWARD Insert the TYPED key (one that has been bound to the + fuction) under the cursor, then compensate backward. + This is similar to _A_U_T_O-_I_N_S_E_R_T + INS-COMPENSATED-FORWARD Insert the TYPED key (one that has been bound to the + fuction) under the cursor, then compensate forward. + This is similar to _A_U_T_O-_I_N_S_E_R_T + MBCRR Last change: DFCI 8 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) INS-GAP Insert _M_U_L_T gaps at the current cursor position. See Also: _M_o_u_s_e _F_u_n_c_t_i_o_n_s. INS-NEXT-CHARACTER Read a key, then insert MULT characters of that key. + INTERPRET-LINE Type in a line in _T_A_K_E format that should be inter- preted. This may be an easier way to get to _B_I_N_D and _M_A_P because it will allow you to use the _S_T_R_I_N_G-_C_O_N_V_E_R_S_I_O_N conventions. JUMP-TO-END-OF-SEQUENCE Move cursor to _M_U_L_T positions before the end of the current sequence. JUMP-TO-LOCUS-NAME Jump to a specific locus name (you will be prompted for the name of the locus you want to jump to). The locus will be selected by the menu interface. JUMP-TO-LOCUS-NUMBER Go to sequence numbered _M_U_L_T. JUMP-TO-POSITION Move cursor to position _M_U_L_T in the current sequence. JUMP-TO-POSITION-ABSOLUTE Move cursor to position _M_U_L_T IGNORING GAPS in the + current sequence. + LITERAL-NEXT The next character will not be remapped. See _M_A_P in _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S for information on mapping. LOAD Read in another sequence file. Callable from _T_A_K_E files as ``LOAD filename''. References _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E ``_S_I_L_E_N_T''; If _S_I_L_E_N_T is not set, the name and length of each locus will be displayed at the bottom of the screen. LOAD-FUNCTION Load an object file. This lets you link functions + into _M_A_S_E with out having to relink the entire + source. The objects to be loaded are usually the + output of a compiler, like the ".o" file from "cc -c + MBCRR Last change: DFCI 9 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) file.c". If you are interested in this, please con- + tact Don Faulkner. + MAP Set key remapping. You will be prompted for which key stroke to map, then the strokes that key should send. Terminate the list of strokes to send with ``^@'' (may be sent by ``CTRL-SPACE'' on some key- boards). Callable from _T_A_K_E files as ``MAP key-code string''. MARK-JUMP Go to mark number _M_U_L_T. Change both the active sequence and active column. The marks jumped to are those that have been set by _M_A_R_K-_S_E_T. If the mark | number | _M_U_L_T was never set, the cursor will not be moved. | MARK-SET Set mark number _M_U_L_T to be the current sequence and column. You may return to this position later via _M_A_R_K-_J_U_M_P. META-NEXT The next character will be ``meta-sized'' - it will have the high bit set. Think of this as an extra ``shift'' function. NOTE you should investigate the _P_R_E_F_I_X-_C_H_A_R_A_C_T_E_R + function before making much use of _M_E_T_A-_N_E_X_T. + MODE-ALIGNMENT Set up keyboard bindings and mappings for editing the _A_L_I_G_N_M_E_N_T of sequences: All letters are unbound. Minus sign inserts a gap. Keys ``x'' and ``d'' delete under the cursor. _P_R_O_T_E_C_T is turned _O_N. Alias for _A_L_I_G_N_M_E_N_T-_M_O_D_E. MODE-DNA Set up the keyboard bindings and mappings for edit- ing nucleic acid sequences: The letters ACTGUYRJKLMBDHVN, and X insert themselves. All other letters beep. Minus sign inserts a gap. _P_R_O_- _T_E_C_T is turned _O_F_F Alias for _D_N_A-_M_O_D_E. MODE-PROTEIN Set up the keyboard bindings and mappings for edit- ing amino acid sequences: The letters JOU beep; all other letters insert themselves. Minus sign inserts MBCRR Last change: DFCI 10 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) a gap. _P_R_O_T_E_C_T is turned _O_F_F Alias for _P_R_O_T_E_I_N-_M_O_D_E. MOUSE-FUNCTIONS Full discussion of the mouse is contained in another document. MOVE-LOCUS-FILE Move a sequence into another file (no provision for copy). You will be prompted for a) which sequences to move (default to the current sequence) and b) the name of the file to move them to. NO OUTPUT will occur until _S_A_V_E is called. See Also: _C_R_E_A_T_E-_L_O_C_U_S + MOVE-LOCUS-POSITION Move a locus to another position within the current file. MOVE-TO-INSIDE-LEFT If _M_U_L_T is not specified, or set to ``1'', move the position under the cursor to the right margin of the left window. If _M_U_L_T is specified and not set to ``1'', put column number _M_U_L_T to the right margin of the left window. MOVE-TO-INSIDE-RIGHT If _M_U_L_T is not specified, or set to ``1'', move the position under the cursor to the left margin of the right window. If _M_U_L_T is specified and not set to ``1'', put column number _M_U_L_T to the left margin of the right window. Problem: it is not possible to put position ``1'' on the inside right margin via this mechanism. MV-DOWN Move cursor to same position _M_U_L_T sequences down. MV-LEFT Move cursor to _M_U_L_T base earlier in the current sequence. If the variable _S_T_O_P-_A_T-_B_O_R_D_E_R_S is set (not zero), then _M_V-_L_E_F_T will stop when it reaches a window border. See _S_T_O_P-_A_T-_B_O_R_D_E_R_S in the _V_A_R_I_A_B_L_E_S discussion. MV-RIGHT Move cursor to _M_U_L_T base later in the current sequence. If the variable _S_T_O_P-_A_T-_B_O_R_D_E_R_S is set MBCRR Last change: DFCI 11 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) (not zero), then _M_V-_L_E_F_T will stop when it reaches a window border. See _S_T_O_P-_A_T-_B_O_R_D_E_R_S in the _V_A_R_I_A_B_L_E_S discussion. MV-UP Move cursor to same position _M_U_L_T sequences up. OUTPUT-ALIGNED Generate an output of the aligned sequences. Provi- sion is made for mapping strings depending on either the composition (i.e. print A, L, V, and I in ``green'', and Y, F, and T in ``yellow''), on the highlighted patterns, or on highlighted differences compared to a reference sequence (see _V_A_R_I_A_B_L_E _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S). If you prefix the file name with an equals sign (``=''), the file will be searched for in the _M_A_S_E directory. _O_U_T_P_U_T-_A_L_I_G_N_E_D will display the number of the page being written. This is done to give the user some- thing to watch lest he thinks _M_A_S_E is idle. See ``MAPPING FOR OUTPUT'' in _F_I_L_E _F_O_R_M_A_T_S for informa- tion on the format of mapping files. This explains how to have different patterns show up differently in the output. The _T_U_T_O_R_I_A_L document contains a section on _O_U_T_P_U_T-_A_L_I_G_N_E_D. References the _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E_S ``_O_U_T_P_U_T- _C_H_A_R_A_C_T_E_R_S-_B_E_T_W_E_E_N-_V_E_R_T_I_C_A_L-_B_R_E_A_K_S'', ``_O_U_T_P_U_T- _C_H_A_R_A_C_T_E_R_S-_P_E_R-_L_I_N_E'', ``_O_U_T_P_U_T-_L_I_N_E_S-_B_E_T_W_E_E_N- _H_O_R_I_Z_O_N_T_A_L-_B_R_E_A_K_S'', ``_O_U_T_P_U_T-_L_A_B_E_L-_E_A_C_H-_P_A_G_E'', ``_O_U_T_P_U_T-_P_O_S_I_T_I_O_N'', ``_O_U_T_P_U_T-_L_I_N_E_S-_P_E_R-_P_A_G_E'', ``_D_I_S_P_L_A_Y-_A_L_T_E_R_N_A_T_E-_C_H_A_R_A_C_T_E_R-_M_A_P'', ``_O_U_T_P_U_T-_U_S_E- _F_O_R_M-_F_E_E_D'', ``_O_U_T_P_U_T-_S_U_P_P_R_E_S_S-_L_O_C_U_S-_N_U_M_B_E_R_S'', and ``_H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S''. to modify the output style. See the discussions in _I_N_T_E_R_N_A_L-_V_A_R_I_A_B_L_E_S for details. WARNING: _O_U_T_P_U_T and the CRT display are independent. Every attempt has been made to allow _O_U_T_P_U_T to mimic as closely as possible the behavior of the screen. There are bound to be failures in this attempt. OVERTYPE-NEXT-CHARACTER Read a key, then overtype MULT characters of that + key. + PATTERN-HIGHLIGHT Highlight all occurrences of a Regular Expression in all sequences. This is done via the GNU-EMACS regu- lar expression handler. Use ``man regex-gnu'' for MBCRR Last change: DFCI 12 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) detailed information (also available from _B_R_O_W_S_E_R in the _M_A_S_E node.) The _M_U_L_T is used to specify which ``color'' should be used to highlight this pattern for _C_O_L_O_R _C_U_R_S_E_S, | use under System V UNIX curses library, | and for _A_L_I_G_N_E_D _O_U_T_P_U_T. You will be asked if you want to clear the existing highlights. The default answer is determined by _P_A_T_T_E_R_N-_C_L_E_A_R-_D_E_F_A_U_L_T. If the variable _P_A_T_T_E_R_N-_A_S_K- _C_L_E_A_R is set to ``_N_O'', you WILL NOT be asked if the existing highlights should be cleared; if _P_A_T_T_E_R_N- _C_L_E_A_R-_D_E_F_A_U_L_T is ``_O_N'', then the existing highlights will be cleared; otherwise, they will be left. Sequences which had matches to the pattern + specified will be indicated with an asterisk at the + left margin of the display. See discussion in vari- + ables section about _H_I_G_H_L_I_G_H_T-_M_E_R_G_E-_M_E_T_H_O_D. + _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T will display the sequence numbers as the pattern is highlighted. This is done to give the user something to watch lest he thinks _M_A_S_E is idle. References _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E_S _P_A_T_T_E_R_N-_I_G_N_O_R_E-_C_A_S_E, _P_A_T_T_E_R_N-_I_G_N_O_R_E-_G_A_P_S, _P_A_T_T_E_R_N-_A_S_K-_C_L_E_A_R, and _P_A_T_T_E_R_N-_C_L_E_A_R-_D_E_F_A_U_L_T. Callable from _T_A_K_E files as ``PATTERN-HIGHLIGHT [pattern-number] pattern''. Optional ``pattern- number'' replaces _M_U_L_T from the interactive case. The history lists for _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T and _S_E_A_R_C_H + are shared. + PATTERN-HIGHLIGHT-CLEAR Clear existing highlights. Callable from _T_A_K_E files as ``PATTERN-HIGHLIGHT- CLEAR''. PREFIX-CHARACTER The character specified will have a uniq entry in a + "Prefix" table. Thus, if you bind "^X" to _P_R_E_F_I_X- + _C_H_A_R_A_C_T_E_R, you could then bind "^X" to some + other function than . This provides a more + flexible binding interface than "META-NEXT". You + can nest prefix characters as deeply as you want: + You could bind "^A" to _P_R_E_F_I_X-_C_H_A_R_A_C_T_E_R, then bind + "^A^R" to _P_R_E_F_I_X-_C_H_A_R_A_C_T_E_R, then bind "^A^Ra" to + _O_V_E_R_T_Y_P_E ... + MBCRR Last change: DFCI 13 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) PROTEIN-MODE Set up the keyboard bindings and mappings for edit- ing amino acid sequences: The letters JOU beep; all other letters insert themselves. Minus sign inserts a gap. _P_R_O_T_E_C_T is turned _O_F_F Alias for _M_O_D_E-_P_R_O_T_E_I_N. QUIT Exit _M_A_S_E. If you have made changes that have not been saved, you will be given the option to _S_A_V_E. Beware: _Q_U_I_T unmaps ``N'', ``n'', ``Y'', ``y'', , and . This is to guarantee that one will be able to respond correctly to the _Q_U_I_T queries. _Q_U_I_T will verify that you really want to exit _M_A_S_E. If you say ``NO'', you will resume editing. Remember that your mappings for ``NnYy'' will be lost. REFRESH Refresh (replot) the screen; useful if the display gets barfed on. RENAME-LOCI Rename loci with the same name, appending a semi- colon (``;'') and a number where needed to make all names unique. Callable from _T_A_K_E files. RENAME-LOCUS Assign a new name to a specified locus. + REPEAT Repeat the specified macro-character _M_U_L_T times. + The character should be something that maps into a + series of non-interactive functions. An example + might be: _B_I_N_D the key ``period'' (``.'') to + ``3ij3h3ik'' (insert three gaps, go down, back + three, insert three more gaps, then go back up). + Then do: ``3'', ``:REPEAT'', then ``.''. This + would execute the macro string 3 times. _R_E_P_E_A_T will + probably be most useful if you _B_I_N_D it to a key, + like ``r''; then, you would be able to do something + like ``3r.'' - lots of key-strokes saved! + SAVE Save all modified files (those with modified or rearranged sequences). The sequence will be written with _S_E_Q_U_E_N_C_E-_L_I_N_E-_L_E_N_G_T_H bases per line. The user MBCRR Last change: DFCI 14 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) name and time will be added as a note to the top of modified files and to the end of the comments of all modified sequences. SAVE-CONSENSUS Store the consensus sequence to a file in standard sequence format. Callable from _T_A_K_E files as ``SAVE-CONSENSUS filename''. See Also: _C_R_E_A_T_E-_L_O_C_U_S. + SEARCH Search for a GNU-EMACS Regular Expression, beginning at cursor position to the end of the current sequence. See ``man regex-gnu'' for detailed infor- mation on the syntax of the regular expression handler. References _I_N_T_E_R_N_A_L _V_A_R_I_A_B_L_E_S _S_E_A_R_C_H-_I_G_N_O_R_E-_C_A_S_E and _S_E_A_R_C_H-_I_G_N_O_R_E-_G_A_P_S. The history lists for _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T and _S_E_A_R_C_H + are shared. + SEARCH-AGAIN Search again for the pattern specified in the last _S_E_A_R_C_H AHEAD of the cursor. | SEARCH-BACKWARDS Like _S_E_A_R_C_H, but searches from the current cursor + position backwards. + SEARCH-BACKWARDS-AGAIN Look for last pattern specified occuring behind the + cursor. + SEQUENCE-SLAVE-SYNCHRONIZE Synchronize gap placement of one sequence to that of + another. This can be useful if one sequence is a + slave of another, (as three-letter amino acids, and + nucleic acid code), and they have somehow gotten out + of synch. + SET-VARIABLE Modify the environmental variables. The variable to set is specified via the menu interface. To see what a given variable in the menu is for, hit a question mark (``?'') for a short, online help mes- sage. MBCRR Last change: DFCI 15 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) SHIFT-LEFT Shift current window left by _M_U_L_T position. SHIFT-RIGHT Shift current window right by _M_U_L_T position. SHIFT-LEFT-BOTH Shift both windows left by _M_U_L_T positions. SHIFT-RIGHT-BOTH Shift both windows right by _M_U_L_T positions. SHIFT-LEFT-BOTH-WIDE Shift both windows left by _M_U_L_T screen widths. SHIFT-RIGHT-BOTH-WIDE Shift both windows right by _M_U_L_T screen width. SHIFT-LEFT-WIDE Shift current window left by _M_U_L_T screen width. SHIFT-RIGHT-WIDE Shift current window right by _M_U_L_T screen width. SHOW-BINDINGS Display current key-to-function bindings. SHOW-FUNCTIONS List the functions that are available. SHOW-MAPPING Display current key-stroke mappings. SHOW-VARIABLES Display current contents of variables. SHOW-YANK-BUFFER Display the current contents of the Yank Buffer: + Report the number of sequence positions currently in + the Yank Buffer, then as much of the sequence as + will fit on one line. If there is more than one + line of sequence, an ellipsis ("...") will appear at + the end of the string. + SIMILARITY Generate a set of similarity scores between sets of sequences. You will be prompted for: Query sequences The set of sequences to form the query (default to the current sequence), MBCRR Last change: DFCI 16 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) Run against which sequences The set of sequences to form the library (default to the current sequence), Start of region to compare End of region to compare The regions of the sequences that are to be used in the calculation Output to file Where should the output be stored. Specify ``SCREEN'' to display and discard out- put. Specify ``HPLOT'' to display the score histogram graphically Specify a file name to put the output in a file If the variable _S_I_M_I_L_A_R_I_T_Y-_I_G_N_O_R_E-_S_E_L_V_E_S is set, com- parisons of a sequence against itself will be ignored. SIMILARITY-MATRIX-LOAD Load in an alternate similarity matrix. The format is described in _F_I_L_E _F_O_R_M_A_T_S. Callable from _T_A_K_E files as ``SIMILARITY-MATRIX-LOAD filename''. SQUEEZE-OUT-GAPS Squeeze out gaps that occur in each of a set of sequences. You will be prompted for the set of sequences to squeeze. _S_Q_U_E_E_Z_E-_O_U_T-_G_A_P_S will find which positions are gaps for ALL the specified sequences, and delete them. SQUEEZE-OUT-GAPS-RESTRICTED Like _S_Q_U_E_E_Z_E-_O_U_T-_G_A_P_S, except user will be prompted + for the sub-range of the sequences to squeeze (like + between positions 100 and 150). + STORE-ALL Save mapping, binding, and variable status to a file, as other STORE functions. STORE-BINDING Store the current key bindings to a file (specify the file name) formatted so that it may be _T_A_K_Een. MBCRR Last change: DFCI 17 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) STORE-HISTORY Not activated. This will allow one to save the "history" lists. STORE-MAPPING Store the current key mappings to a file (specify the file name) formatted so that it may be _T_A_K_Een. STORE-VARIABLES Store the current variable values to a file (specify the file name) formatted so that it may be _T_A_K_Een. TAKE Read _M_A_S_E commands from a text file. You will be prompted for the name of the file to read. If you prefix the file name with an equals sign (``=''), the file will be searched for in the _M_A_S_E directory. Only a subset of the _M_A_S_E functions are available to this interface. They are: ALIAS + ALIAS-LOAD + ALIAS-SAVE + ALIGN-ON-PATTERN + ALIGNMENT-MODE + ALPHABETIZE-LISTS ANCHOR-CHECK + ANCHOR-SYNCHRONIZE + BIND key-code function-name CHARACTER-SET character-set-file CONSENSUS [range] CONSENSUS-OFF DNA-MODE + HIGHLIGHT-DIFFERENCES + HIGHLIGHT-LOAD + HIGHLIGHT-SAVE + LOAD sequence-file MAP key-code string MODE-ALIGNMENT | MODE-DNA + MODE-PROTEIN + PATTERN-HIGHLIGHT [pattern-number] pattern-to- highlight PATTERN-HIGHLIGHT-CLEAR PROTEIN-MODE + RENAME-LOCI SAVE-CONSENSUS filename SET-VARIABLE variable-name variable-value SIMILARITY-MATRIX-LOAD + TAKE mase-commands-file UNBIND UNBIND-ALPHA MBCRR Last change: DFCI 18 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) UNMAP UNMAP-ALPHA WRITE-TO-FILE filename + UNBIND Bind all key strokes to _B_E_L_L. This will probably inactivate the cursors. Callable from _T_A_K_E files. UNBIND-ALPHA Same as UNBIND, but only works on alphabetic charac- ters a-z and A-Z. UNDO-EDIT Undo the most recent CHANGE. Changes which can be + undone are: inserts, deletes, create new sequences, + zap sequences. (NOTE - functions like "INSERT- + COLUMNS" and such do their work by executing multi- + ple simple inserts). This is a new function, and + should be considered in "alpha-test". + UNMAP Remove all key mappings. This will probably inac- tivate the cursors. Callable from _T_A_K_E files. UNMAP-ALPHA Same as UNMAP, but only works on alphabetic charac- ters a-z and A-Z. UN-HIGHLIGHT-POSITION Remove highlight from _M_U_L_T positions following cur- + sor. + VERIFY If the key typed matches the letter under the cur- + sor, the cursor advances and nothing else happens. + If the key doesn't match the letter under the cur- + sor, _M_A_S_E will beep. If the variable _V_E_R_I_F_Y-_P_A_U_S_E + is set, the user would then have to hit to con- + tinue. This is useful only when bound to a key. + WINDOW-SYNCHRONIZE Align the ``other'' window to the ``active'' window (the one where the cursor is). - WRITE-TO-FILE Write a specified set of loci to a specified file. The loci will NOT have their modified flags reset. This may be useful if you are trying to retrieve a MBCRR Last change: DFCI 19 Mase(Intrinsic Functions)MISC. REFERENCE MANUAL PAGESMase(Intrinsic Functions) set of loci from some larger data base file. WRITE-REGION-TO-FILE Like _W_R_I_T_E-_T_O-_F_I_L_E, but only writes out a specified + region. + YANK-LAST-DELETE Insert contents of Yank Buffer at current cursor + position. The Yank Buffer is filled in by three + different mechanisms: + _C_O_P_Y-_T_O-_Y_A_N_K + Copys sequence into the Yank Buffer. + _A_P_P_E_N_D-_T_O-_Y_A_N_K + Appends sequence to the Yank Buffer. + All functions that delete positions. _M_A_S_E will + attempt to concatenate adjacent deletes into one + yank. + There is only ONE Yank Buffer; it is cleared by + _C_O_P_Y-_T_O-_Y_A_N_K and all non-adjacent deletions. + ZAP-SEQUENCES Delete an entire locus. FILES SEE ALSO FILE FORMATS BUGS Are you kidding? OF COURSE! MBCRR Last change: DFCI 20