Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) NAME Changes made to _M_A_S_E November, 1987 Variables: Added Variable CONSENSUS-THRESHOLD for function CON- SENSUS Added Variable HIGHLIGHT-DIFFERENCES for main edit- ing mode Intrinsic Functions: CONSENSUS: references variable CONSENSUS-THRESHOLD Main editing mode (Introduction section) References variable HIGHLIGHT-DIFFERENCES; _M_A_S_E can now highlight all bases that differ from a reference sequence (the reference sequence may be the con- sensus sequence). December 1, 1987 Intrinsic Functions: OUTPUT: If consensus has been calculated, it will be printed in the output file. The output file will reflect _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S. December 3, 1987 Serious error fixed in _D_E_L_E_T_E-_C_O_L_U_M_N_S (within file ``ins- del.c'' February 4, 1988 DOCUMENTATION Added ``Tutorial'' document. General refinement of some phrases VIEW-COMMENTS You can now pass arguments to ``grep''. February 8, 1988 Fixed ``Output-Aligned'' handling of the Output-Use-Formfeed variable (it did not work before). February 9, 1988 Pattern-Highlight and Search share their history list February 10, 1988 Cleaned up documentation to work better with ``TROFF'' MBCRR Last change: DFCI 1 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) February 11, 1988 Added Function ``Create Locus'' to make a new locus or copy an existing one. Function ``Consensus'' looks at the aliasing characters (the current character set) rather than the real characters. This will make moderately ``degenerate'' consensus sequences to be formed. Modified the behavior of the ``Highlight Differences'' feature. It compares the aliased (displayed characters) rather than the real characters - to reduce the less signi- ficant highlighting. February 22, 1988 Fixed problem in the configuration file ``colors.la100.patterns'' the escape sequence lacked an ``m'' for the field ``2''. February 23, 1988 Oops in display.c (line 38) - numbers displayed for modified sequence names were invalid (reflect line number rather than sequence number. March 1, 1988 Added the ``CREATE-LOCUS'' function. Has provisions to copy or translate from an existing locus. March 16, 1988 Added mouse support for X-Windows and SunTools (and anything else, I guess). Mouse data should be in the following form: C-XC-@([124] x y) where left button is ``1'', middle button is ``2'', and the right button is ``4'', and x,y is the mouse position in CHARACTERS (NOT pixels). (C-X is control-x (octal \030), and C-@ is octal \000.) Currently, LEFT-MOUSE sets cursor posi- tion, MIDDLE-MOUSE sets cursor position, then inserts a gap, and MIDDLE-MOUSE sets cursor position, then deletes a gap. If you are on X-Windows, you need ``mouse_type'' running in your window. If you are on SunTools, MASE must be run under ``emacstool'' - the mouse trap used by GNU-EMACS (via ``emacstool -rc mase'', or ``emacstool -rc csh'', then run- ning ``mase'' in that shell. Happy Mousing!! March 18, 1988 Added two mouse functions: Shift-Middle-Mouse: Open Rectangle MBCRR Last change: DFCI 2 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) Shift-Right-Mouse: Close Rectangle Improved the X-Windows driver for the mouse. April 11, 1988 Many changes - trying to get _M_A_S_E in shape for a ``_r_e_a_l'' distribution!. Support for function _M_A_I_L-_N_O_T_E_S being removed. Added color curses support for _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T _C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N function enhanced. Can now use fixed ``p'' value via _C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N-_F_I_X_E_D-_P. Can use one sequence as the model via _C_O_L_U_M_N-_C_O_R_R_E_L_A_T_I_O_N-_M_O_D_E_L. Sug- gested by Jurek Jurka at Linus Pauling Institute. Improved the _S_A_V_E function: It displays file names as they are written, ``empty'' files (like when you have _M_O_V_E- _L_O_C_U_S-_F_I_L_E ed away all of the locus) are not written, and MULTIPLE backups are saved. _W_R_I_T_E-_T_O-_F_I_L_E function added - write specified loci to specified file. The generic ``_O_p_e_n _F_i_l_e'' interface allows you to ``_B_a_c_k_u_p''. All occurrences of ``_H_O_M_O_L_O_G_Y'' have been changed to ``_S_I_M_I_- _L_A_R_I_T_Y''. Added the ability to do one-letter translations to _C_R_E_A_T_E- _L_O_C_U_S Added some support for window size changes - seems to be O.K. for making windows BIGGER. On ``cold'' startup, _M_A_S_E asks if you want to read a file or create a new locus. Beep when there are _P_R_O_T_E_C_T violations. The string handed to _V_I_E_W-_C_O_M_M_E_N_T_S can actually be a pipe. April 14, 1988 Improved the refreshing mechanism; MASE should be better about not trying to refresh the screen if there are unused key strokes waiting to be read. April 15, 1988 _O_U_T_P_U_T-_A_L_I_G_N_E_D can now generate output like _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(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) April 21, 1988 Added function _H_I_G_H_L_I_G_H_T-_D_I_F_F_E_R_E_N_C_E_S with interactive and batch hooks. Fixed glitch with screen not being refreshed on startup. April 27, 1988 _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T, _S_E_A_R_C_H, and _S_E_A_R_C_H-_A_G_A_I_N reference the new variable _P_A_T_T_E_R_N-_I_G_N_O_R_E-_G_A_P_S and _S_E_A_R_C_H-_I_G_N_O_R_E-_G_A_P_S (they are synonyms). When this variable is set, gaps will be ignored for highlighting patterns and for executing searches for regular expressions. Searches and highlighting will be slightly slower when this mode is enabled. This was suggested repeatedly by MANY people (hence it's inclusion!). Many functions and variables were renamed. The old names will continue to be available for the near future. These changes are: Functions: Old Name New Name Delete-Columns Del-Columns Edit-Comments Comments-Edit Insert-Columns Ins-Columns Matrix Similarity-Matrix-Load Swap-Windows Cursor-Other-Window Synchronize-Windows Window-Synchronize View-Comments Comments-View Variables: Old Name New Name Ignore-Case-For-Searches Search-Ignore-Case and Pattern-Ignore-Case Ignore-Selves-In-Similarity Similarity-Ignore-Selves Use-Gap-For-Consensus Consensus-Use-Gaps These changes were made to increase consistency. May 4, 1988 Added functions _M_O_D_E-_A_L_I_G_N_M_E_N_T, _M_O_D_E-_D_N_A, _a_n_d _M_O_D_E-_P_R_O_T_E_I_N with aliases _A_L_I_G_N_M_E_N_T-_M_O_D_E, _D_N_A-_M_O_D_E, _a_n_d _P_R_O_T_E_I_N-_M_O_D_E to switch the environment. This is probably better than the ``TAKE =/keys.dna'' stuff. This opens the way to use some command tail switches to set up parts of the environment. Suggested by Jurek Jurka at Linus Pauling Institute. May 19, 1988 Improved automatic window shifting behavior: when _L_O_C_K- _W_I_N_D_O_W_S is _O_N, the cursor is in the second window, and you execute a jump into the beginning of the sequence, the win- dows are shifted in a manner that is more expected. MBCRR Last change: DFCI 4 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) August 5, 1988 Added several variables to better control display and some utilities, as _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, Added the function _C_O_N_S_E_N_S_U_S-_A_L_T_E_R_N_A_T_E. Added the variable _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. Enhanced _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T to work better in batch mode by adding variables _P_A_T_T_E_R_N-_A_S_K-_C_L_E_A_R and _P_A_T_T_E_R_N-_D_E_F_A_U_L_T- _C_L_E_A_R. Added variable _S_I_M_I_L_A_R_I_T_Y-_D_I_S_C_A_R_D-_G_A_P_S. Suggested by Ela Holsztynska and Jurek Jurka. Added function _S_E_Q_U_E_N_C_E-_S_L_A_V_E-_S_Y_N_C_H_R_O_N_I_Z_E. Suggested by Ela Holsztynska. Started to implement changes for UNIX System V compatibility August 8, 1988 Added function _R_E_N_A_M_E-_L_O_C_U_S to manually rename just one locus Suggested by Jurek Jurka at Linus Pauling Institute. Added function _U_N-_H_I_G_H_L_I_G_H_T-_P_O_S_I_T_I_O_N to complement _H_I_G_H_L_I_G_H_T-_P_O_S_I_T_I_O_N. Suggested by Terry Webster at MBCRR. Added function _J_U_M_P-_T_O-_P_O_S_I_T_I_O_N-_A_B_S_O_L_U_T_E Suggested by Jurek Jurka at Linus Pauling Institute. September 1, Added anchor functions: _A_N_C_H_O_R-_C_H_E_C_K, _A_N_C_H_O_R-_C_R_E_A_T_E, _A_N_C_H_O_R-_S_Y_N_C_H_R_O_N_I_Z_E, _D_E_L-_C_O_M_P_E_N_S_A_T_E_D-_B_A_C_K_W_A_R_D, _D_E_L- _C_O_M_P_E_N_S_A_T_E_D-_F_O_R_W_A_R_D, _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. The ``effective position'' or ``offset ignoring gaps'' rou- tine has been modified to treat periods as gaps The routine for _A_U_T_O-_I_N_S_E_R_T has been modified to strip the high bit before inserting the character. October 12, 1988 Added aliasing functions: _A_L_I_A_S, _A_L_I_A_S-_L_O_A_D, and _A_L_I_A_S-_S_A_V_E. The only way to access these is via ``M-A'' inside the string menu handler. Added _R_E_P_E_A_T function. This lets you repeat a macro- character multiple times. For menu-mode input - if you type ``*'', it looks for the string at any point in the menu items. Use M-n to go to the next match. Use M-p to go to the previous match. October 13, 1988 Added the function _A_L_I_G_N-_O_N-_P_A_T_T_E_R_N. Given a pattern, insert gaps (either at the beginning 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 MBCRR Last change: DFCI 5 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) have the specified pattern pattern, user will be notified, and the sequence will be untouched. Suggested by Temple Smith at MBCRR and others. October 25, 1988 Added variable _P_R_O_T_E_C_T-_A_S_K-_O_V_E_R_R_I_D_E to allow one-time over- ride of protection violations. Suggested by Kersti MacInnes at LANL/GenBank. Enbled the Import function inside _C_R_E_A_T_E-_L_O_C_U_S so one can import loci from external files. Added _W_R_I_T_E-_R_E_G_I_O_N-_T_O-_F_I_L_E function to dump some region from a set of loci to a file. Suggested by Kersti MacInnes at LANL/GenBank and others. October 26, 1988 The delete routine will treat anchors (``.'') as gaps with regards to _P_R_O_T_E_C_T. Added functions _A_N_C_H_O_R-_D_E_L_E_T_E and _A_N_C_H_O_R-_S_T_R_I_P. Suggested by Kersti MacInnes at LANL/GenBank. October 27, 1988 Batch interface to _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T puts pattern specified into the pattern / search history list. _S_E_Q_U_E_N_C_E-_S_L_A_V_E-_S_Y_N_C_H_R_O_N_I_Z_E will now synchronize anchor points (``.'') as well as gaps (``-''). November 1, 1988 Modified the display and pattern highlight routines. Now, sequences which had one or more matches to the _m_o_s_t _r_e_c_e_n_t _P_A_T_T_E_R_N-_H_I_G_H_L_I_G_H_T will be displayed with an asterisk (``*'') in the left hand margin. This provides a mechanism to rapidly see which sequences contain a given pattern. Sug- gested by Jurek Jurka at Linus Pauling Institute. Added wild-card mechanism for _M_E_N_U _I_N_T_E_R_F_A_C_E. If you type an asterisk (``*'') then some letters, the first menu item con- taining that string will be selected. Select the next match by M-n. Select the previous match by M-p. Suggested by Temple Smith at MBCRR and others. November 23, 1988 Fixed small glitch - - locus name displayed wrong when a locus was modified. SIGWINCH handled properly: you can change the size of the MASE window, and it will adjust accordingly. MBCRR Last change: DFCI 6 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) January 19, 1989 Release 1.6 March, 1989 Extended the mouse handler to allow the MIT-MOUSE sequences that _x_t_e_r_m can generate. Implemented an _U_N_D_O function that will undo the effects of inserting, deleting, creating, and zapping. Extended the key stroke model to allow _P_R_E_F_I_X keys. This is far more flexible than just _M_E_T_A. It allows to have prefixes of arbitrary length. Thus, ^I^Ia could be bound to _A_U_T_O- _I_N_S_E_R_T, while ^I^Ra could be bound to _O_V_E_R-_T_Y_P_E, and ^U^Ea could be bound to _I_N_S-_C_O_M_P_E_N_S_A_T_E_D-_F_O_R_W_A_R_D, ad nauseaum. Added function _D_Y_N_A_M_I_C-_H_I_G_H_L_I_G_H_T that will search for matches to a matrix (weighted search) Added _L_O_A_D-_F_U_N_C_T_I_O_N to dynamically load subroutines. This lets a _M_A_S_E user use his own functions within _M_A_S_E without having to modify the main _M_A_S_E source code. Attempted to increase System V UNIX compatibility - dif- ferent pattern numbers will be represented with different representations, and tried to take advantage of other System V curses inhancements. The signal handlers seem to be work- ing, but there may still be problems. Modified _C_R_E_A_T_E/_T_R_A_N_S_L_A_T_E to allow specifying any frame and to squeeze out gaps before translation. Also added ability to import sequences. Added functions to store and retreive highlights. _T_h_i_s _s_h_o_u_l_d _n_o_t _b_e _c_o_n_s_i_d_e_r_e_d _a Expanded the highlight model with variable _H_I_G_H_L_I_G_H_T-_M_E_R_G_E- _M_E_T_H_O_D to and, or, add, or replace. Fixed small problem when reading in files with FormFeeds (^L) for enhanced compatibility with files generated by IntelliGenetics suite. If environmental variable _M_A_S_E__D_I_R is set, this directory will be used for run-time lookups for help, extra files ... March 1989 Added function _S_Q_U_E_E_Z_E-_O_U_T-_G_A_P_S-_R_E_S_T_R_I_C_T_E_D to do the squeeze only in a sub region. Suggested by Jurek Jurka at Linus Pauling Institute. MBCRR Last change: DFCI 7 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) Added function _V_E_R_I_F_Y which works like _A_U_T_O-_I_N_S_E_R_T, except that it verifies the key rather than inserting it. If _V_E_R_I_F_Y-_P_A_U_S_E is set (default case), program will pause. Suggested by Jurek Jurka at Linus Pauling Instute. Added variable _C_O_N_S_E_N_S_U_S-_U_S_E-_S_T_A_R, which works like _C_O_N_S_E_N_S_U_S-_U_S_E-_G_A_P. Suggested by Jeff Lawrence at LANL/GenBank and others. Added _O_V_E_R-_T_Y_P_E function, analagous to _A_U_T_O-_I_N_S_E_R_T, but types over old sequence rather than inserting. When delet- ing under, obeys _P_R_O_T_E_C_T. Suggested by Jurek Jurka at Linus Pauling Institute and oth- ers. Added _S_E_A_R_C_H-_B_A_C_K_W_A_R_D_S and _S_E_A_R_C_H-_B_A_C_K_W_A_R_D_S-_A_G_A_I_N, like _S_E_A_R_C_H commands, but searches from the cursor backwards in the sequence. Suggested by Randy Linder at LANL. April 5, 1989 Cleaned up lots of little points in the code. Renamed all functions with lower case letters and spaces rather than dashes, to make it more readable. Deleted obsolete names: DELETE-COLUMNS EDIT-COMMENTS IGNORE-CASE-FOR-SEARCHES IGNORE-SELVES-IN-SIMILARITY INSERT-COLUMNS MATRIX SWAP-WINDOWS SYNCHRONIZE-WINDOWS USE-GAP-FOR-CONSENSUS VIEW-COMMENTS Added functions _I_N_S-_N_E_X_T-_C_H_A_R_A_C_T_E_R and _O_V_E_R_T_Y_P_E-_N_E_X_T- _C_H_A_R_A_C_T_E_R. Renamed _O_V_E_R-_T_Y_P_E to be _A_U_T_O-_O_V_E_R_T_Y_P_E. Fixed bug in _C_O_N_S_E_N_S_U_S: If some sequences were shorter than others, towards the end, the percent was calculated on the number of original sequences, not just the sequences which had data at this position. i.e. with _C_O_N_S_E_N_S_U_S-_T_H_R_E_S_H_O_L_D set at 0.5, and sequences: ONE actgactg TWO actgac THREE actccc MBCRR Last change: DFCI 8 Mase(Changes) MISC. REFERENCE MANUAL PAGES Mase(Changes) would have given consensus of "actgac??", but will now give "actgactg". Fixed bug in _C_O_N_S_E_N_S_U_S: threshold value was rounded incorrectly. April 19, 1989 Added a set of YANK functions: _Y_A_N_K-_L_A_S_T-_D_E_L_E_T_E, _C_O_P_Y-_T_O- _Y_A_N_K, _A_P_P_E_N_D-_T_O-_Y_A_N_K, and _S_H_O_W-_Y_A_N_K-_B_U_F_F_E_R. When you delete positiions, the deleted bases will be placed into a yank buffer. Adjacent deletions will concatenate into one contiguous yank. You can artificially place things into the yank buffer via _A_P_P_E_N_D-_T_O-_Y_A_N_K and _C_O_P_Y-_T_O-_Y_A_N_K. _A_P_P_E_N_D-_T_O-_Y_A_N_K will append _M_U_L_T positions to the yank buffer. _C_O_P_Y-_T_O-_Y_A_N_K will replace the current contents of the yank buffer with the next _M_U_L_T sequence positions. _S_H_O_W-_Y_A_N_K-_B_U_F_F_E_R will tell you how many characters are in the yank buffer, and will display as much of the yank buffer as will fit on one line. NOTE: All delete functions affect the yank buffer. The yank buffer will be cleared before each non-adjacent dele- tion. The YANK functions were suggested by Yurek Yurka. Added function _B_I_N_D-_A_L_L-_A_L_P_H_A to bind all alpha characters with some modification to a function. MBCRR Last change: DFCI 9