Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) NAME _M_A_S_E internal variables; ways to affect _M_A_S_E behavior SYNOPSIS _M_A_S_E provides a common interface to change several internal variables. These variables affect several of the _M_A_S_E intrinsic functions. All these variables are modified through two interfaces: _S_E_T-_V_A_R_I_A_B_L_E, which is described further in _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S for interac- tive use, and via _T_A_K_E files (including startup files) which is described in _S_T_A_R_T_U_P and in the discussion of _T_A_K_E in _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S. This list of variable names is alphabetical order; functional groups of variables are noted in other help files. Note also that current variable values may be stored in a _T_A_K_E-able format via _S_T_O_R_E-_V_A_R_I_A_B_L_E_S (see _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S _S_T_O_R_E-_V_A_R_I_A_B_L_E_S for more information). There are three types of variables. _I_N_T_E_G_E_R variables may contain any integer value. _F_L_O_A_T variables may contain any floating point value. _B_O_O_L_E_A_N variables may be set to either ``_Y_E_S'' or ``_N_O'' to reflect whether that property should be enabled. DESCRIPTION @NONE Null operation - to abort _S_E_T-_V_A_R_I_A_B_L_E. COLUMN-CORRELATION-FIXED-P Float For _C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N. The ``p'' value will be fixed (to the specified value) rather than calculated from per-case data. Set to ``-1.0'' to re-enable case-by- case calculation of ``p''. COLUMN-CORRELATION-MODEL-SEQ Integer For _C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N. Use the sequence specified by this variable rather than neighbors for counting changes. Set to ``0'' to count changes from the _C_O_N_S_E_N_S_U_S-_S_E_Q_U_E_N_C_E. Set to ``-1'' to change back to neighbors method. COLUMN-CORRELATION-THRESHOLD Float For _C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N. Correlation scores above this threshold will be Printed 10/27/88 DFCI 1 Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) discarded. COLUMN-HIGHLIGHT Integer For interactive editing mode. Provide highlighted columns to serve as rule marks; a rule will be placed every _C_O_L_U_M_N- _H_I_G_H_L_I_G_H_T'th column. Set to ``0'' for higher speed screen updating if rulers are not desired. CONSENSUS-THRESHOLD Float For _C_O_N_S_E_N_S_U_S. Minimum fraction of sequences that must contain a letter before that letter might be placed into the consensus. Defaults to 0.0 CONSENSUS-USE-GAP Boolean For _C_O_N_S_E_N_S_U_S. If set, gaps will be treated as any other sequence element. If unset, gaps will be ignored unless there are no other sequence ele- ments down that column. DISPLAY-ALTERNATE-CHARACTER-MAP Boolean + Affects the interactive display. + When _O_N, characters will be displayed according + to the status of the _C_H_A_R_A_C_T_E_R-_S_E_T. + When _O_F_F, characters will be displayed as them- + selves, regardless of the loaded _C_H_A_R_A_C_T_E_R-_S_E_T. + This variable does not affect the function of + _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S. Thus, it may be useful + to load an alternate _C_H_A_R_A_C_T_E_R-_S_E_T, generate a + _C_O_N_S_E_N_S_U_S, turn on _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S, then + turn off _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-_S_E_T. The + actual characters will be displayed, but ``con- + servative'' differences from a ``conservative'' + consensus would not be highlighted. + DISPLAY-POSITION Boolean For interactive editing mode. Display the current cursor position in real and effective positions (ignoring gaps) at the bot- tom of the screen. _N_O_T_E: the editor will be more ``responsive'' if this feature is disabled. Printed 10/27/88 DFCI 2 Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) HIGHLIGHT-DIFFERENCES Boolean For interactive editing mode. Highlight letters that differ from a specific sequence. The ``model'' sequence is defined by this variable. 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. IGNORE-CASE-FOR-SEARCHES OLD NAME - see _P_A_T_T_E_R_N-_I_G_N_O_R_E-_C_A_S_E and _S_E_A_R_C_H- - _I_G_N_O_R_E-_C_A_S_E IGNORE-SELVES-IN-SIMILARITY OLD NAME - use _S_I_M_I_L_A_R_I_T_Y-_I_G_N_O_R_E-_S_E_L_V_E_S. - INCREMENTAL-COMPLETE Boolean For interactive editing mode. Incremental completion of command names and variable names. When enabled, incremental com- pletion will partially fill in the response as far as no ambiguity results, i.e. typing in SHO will give SHOW- . LOCK-WINDOWS Boolean For interactive editing mode. Treat both windows as one continuous window. OUTPUT-CHARACTERS-BETWEEN-VERTICAL-BREAKS Integer For aligned _O_U_T_P_U_T. Number of sequence positions between vertical breaks. Set to ``0'' to disable vertical breaks. OUTPUT-CHARACTERS-PER-LINE Integer For aligned _O_U_T_P_U_T. Number of SEQUENCE POSITIONS horizontally fit- ting on a page. NOTE: this is _N_O_T the total number of COLUMNS per page, but of SEQUENCE POSITIONS per page. OUTPUT-LABEL-EACH-PAGE Boolean For aligned _O_U_T_P_U_T. Put the locus names in the left border of each page of the output. Printed 10/27/88 DFCI 3 Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) OUTPUT-LINES-BETWEEN-HORIZONTAL-BREAKS Integer For aligned _O_U_T_P_U_T. Number of sequences between horizontal breaks (makes it skip a line). If ``0'', no lines will be skipped. OUTPUT-LINES-PER-PAGE Integer For aligned _O_U_T_P_U_T. Number of SEQUENCE lines to occur on each page. The minimum page length is 5. NOTE: this is the number of SEQUENCE lines not including headers that will fit on each page. OUTPUT-POSITION Boolean For aligned _O_U_T_P_U_T. Print the effective position at the end of each output line (ignoring gaps). OUTPUT-SUPRESS-LOCUS-NAMES Boolean + For aligned _O_U_T_P_U_T. + Supress printing each locus's number at the + beginning of the line. + Allows more space on each line for sequence + data. + OUTPUT-USE-FORMFEED Boolean For aligned _O_U_T_P_U_T. Put a ``form feed'' between pages. Disabling will make the output more compact, but perhaps less readable. PATTERN-ASK-CLEAR Boolean For _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T. If ``_O_N'' - ask whether old patterns should be cleared at each call of _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T. If ``_O_F_F'' - use _P_A_T_T_E_R_N-_D_E_F_A_U_L_T-_C_L_E_A_R _t_o _d_e_t_e_r_m_i_n_e _w_h_e_t_h_e_r _o_r _n_o_t the old highlights. PATTERN-DEFAULT-CLEAR Boolean For _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T. When _P_A_T_T_E_R_N-_A_S_K-_C_L_E_A_R is ``_F_A_L_S_E'', this vari- able provides the default response when the user is asked if he wants to clear the old pat- terns. When _P_A_T_T_E_R_N-_A_S_K-_C_L_E_A_R is ``_O_F_F'', this variable DETERMINES whether old patterns will Printed 10/27/88 DFCI 4 Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) be cleared. PATTERN-IGNORE-CASE Boolean For _S_E_A_R_C_H, _S_E_A_R_C_H-_A_G_A_I_N, and _P_A_T_T_E_R_N- _H_I_G_H_L_I_G_H_T. Ignore case for regular expression searches and highlighting. SYNONYM for SEARCH-IGNORE-CASE PATTERN-IGNORE-GAPS Boolean For _S_E_A_R_C_H, _S_E_A_R_C_H-_A_G_A_I_N, and _P_A_T_T_E_R_N- _H_I_G_H_L_I_G_H_T. Ignore case for gaps for regular expression searches and highlighting. SYNONYM for SEARCH-IGNORE-GAPS PROTECT Boolean For interactive editing. When set, one will not be able to delete ``non-gap'' letters. Unset this variable if you want to delete actual sequence positions. This variable is treated specially within _D_E_L_E_T_E-_C_O_L_U_M_N_S. See _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S for more information. PROTECT-ASK- | OVERRIDE || When both _P_R_O_T_E_C_T-_A_S_K-_O_V_E_R_R_I_D_E and _P_R_O_T_E_C_T are | set, one will be prompted as to whether or not | ``non-gap'' letters should be actually deleted. | On a case by case basis, you can override or | observe the protection. | SEARCH-IGNORE-CASE Boolean For _S_E_A_R_C_H, _S_E_A_R_C_H-_A_G_A_I_N, and _P_A_T_T_E_R_N- _H_I_G_H_L_I_G_H_T. Ignore case for regular expression searches and highlighting. SYNONYM for PATTERN-IGNORE-CASE SEARCH-IGNORE-GAPS Boolean For _S_E_A_R_C_H, _S_E_A_R_C_H-_A_G_A_I_N, and _P_A_T_T_E_R_N- _H_I_G_H_L_I_G_H_T. Ignore case for gaps for regular expression Printed 10/27/88 DFCI 5 Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) searches and highlighting. SYNONYM for PATTERN-IGNORE-GAPS SEQUENCE-LINE-LENGTH Integer For _S_A_V_E. How many bases should be written per line. Defaults to 70. SILENT || Boolean For _L_O_A_D. Inhibits display of length and name information as each sequence is read. SIMILARITY-DISCARD-GAPS Boolean + For _S_I_M_I_L_A_R_I_T_Y. + When _O_N, positions containing gaps in both + sequences will be discared from the _S_I_M_I_L_A_R_I_T_Y + score computation. + SIMILARITY-IGNORE-SELVES Boolean For _S_I_M_I_L_A_R_I_T_Y. Ignore similarity comparisons of sequences against themselves. STOP-AT-BORDERS Boolean For _M_V-_L_E_F_T and _M_V-_R_I_G_H_T If set, horizontal cursor motion will pause at window borders. (the next _M_V- will go past the window border.) TRANSLATE-IGNORE-GAPS Boolean - For _C_R_E_A_T_E-_L_O_C_U_S. | INACTIVE. | Strip gaps and anchor points from sequences | before translating, then synchronize the pep- | tide sequence to the original nucleic acid | sequence. | USE-GAP-FOR- | CONSENSUS || OLD NAME - see _C_O_N_S_E_N_S_U_S-_U_S_E-_G_A_P. EXAMPLES FILES Printed 10/27/88 DFCI 6 Mase(Internal Variables)UNIX Programmer's ManualMase(Internal Variables) SEE ALSO _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S - _T_A_K_E _I_N_T_R_I_N_S_I_C _F_U_N_C_T_I_O_N_S - _S_E_T-_V_A_R_I_A_B_L_E _S_T_A_R_T_U_P BUGS Since most variables are interpreted by the intrinsic functions rather than _M_A_S_E proper, this document is likely to be out of date. Where there is a discrepancy, the information provided with the intrin- sic function should be considered more current. Printed 10/27/88 DFCI 7