--- /dev/null
+/****************************************************************************
+
+ ALSCRIPT - Sequence alignment to PostScript
+
+ Copyright: Geoffrey J. Barton (1992,1993,1997)
+ email: geoff@ebi.ac.uk
+
+ Please see the file README for limitations on the use of this program.
+
+All use of this program must cite: Barton, G. J. (1993), ALSCRIPT: A Tool to
+Format Multiple Sequence Alignments, Protein Engineering, Volume 6, No. 1,
+pp. 37-40.
+
+ $Id: alscript.c,v 1.2 1998/09/17 16:54:59 geoff Exp $
+ $Log: alscript.c,v $
+ Revision 1.2 1998/09/17 16:54:59 geoff
+ Check consistency with archive
+
+
+****************************************************************************
+
+ALSCRIPT is a program for producing pretty versions of multiple sequence aligments.
+ALSCRIPT will also format single sequences.
+A full description of the program is given in the file "alscript.doc".
+
+Ways of running alscript:
+
+1. Interactive mode: just type alscript.
+ You will be prompted for a command file name. The command file will
+ define the AMPS blocfile, and name of the file to store the PostScript
+ output - see alscript.doc for details.
+
+2. alscript <command_file> has same effect as 1, But does not prompt for the command file
+ e.g. alscript example1.com
+
+3. alscript -q < <blocfile> > <PostScript>
+ Quick mode - uses default commands, reads alignment from stdin, writes PostScript
+ to stdout.
+ e.g. alscript -q < example1.blc > example1.ps
+
+4. alscript -f <command_file>
+ Similar effect to 2.
+
+5. alscript -f <command_file> -s
+ Silent operation: No messages are written to stderr, unless fatal.
+ Silent operation may be toggled by the silent_mode command in the command file.
+
+6. alscript -f <command_file> -p < <blocfile> > <PostScript>
+ Make alscript work like a pipe - blocfile is read from stdin, postscript is written
+ to stdout. Messages are written to stderr. To supress messages include
+ the -s flag too
+ e.g. alscript -f example1.com -p -s < example1.blc > example1.ps
+
+Using alscript as a pipe has the advantage of allowing the blocfile to
+be created on the fly by the programs msf2blc or clus2blc. For example
+if we have a GCG .msf file called "pileup.msf" we can run alscript with
+default shading/fonts and send the results straight to the PostScript
+printer "lpr" as follows:
+
+msf2blc -q < pileup.msf | alscript -q -s | lpr
+
+See alps.c for revision history;
+fprintf(std_err,"\n Version 2.0 - 23 May 1995\n");
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "array.h"
+#include "gjutil.h"
+#include "version.h"
+
+int MAXtlen = 500;
+int MAXnbloc = 500;
+int MAXilen = 50;
+int precis = 100;
+int MAXslen = 8000;
+int MAXnseq;
+
+void ALwritestddefs(FILE *);
+int alps(char *command_file,int silent, int pipe, int single);
+
+main(int argc,char *argv[])
+{
+ char *alps_file;
+ int silent;
+ int quick;
+ int i;
+ int pipe;
+ int singlepage; /* flag for EPS output */
+ FILE *fp;
+ char *Alscript_Version = ALSCRIPT_VERSION;
+
+ extern FILE *std_out,*std_err,*std_in;
+
+ silent = 0;
+ quick = 0;
+ pipe = 0;
+
+ alps_file = NULL;
+
+ /* initialize the file streams for GJ... routines */
+ GJinitfile();
+
+ singlepage = 0;
+
+ if(argc > 1){
+ /* check for -f option - if present, then define name for command file */
+ i = 1;
+ while(i<argc){
+ if(argv[i][0] == '-'){
+ if(strcmp(argv[i],"-f")==0){
+ /* command file name */
+ alps_file = GJstrdup(argv[++i]);
+ }else if(strcmp(argv[i],"-s")==0){
+ /* silent mode */
+ silent = 1;
+ }else if(strcmp(argv[i],"-q")==0){
+ /* quick mode - defines its own command file */
+ quick = 1;
+ pipe = 1;
+ }else if(strcmp(argv[i],"-p")==0){
+ /* send all output to std_out rather than the file defined in the command file */
+ pipe = 1;
+ silent = 1;
+ }else if(strcmp(argv[i],"-single")==0){
+ /* single page mode - will generate a BoundingBox */
+ singlepage = 1;
+ }
+ ++i;
+ }else if(i == 1){
+ /* we have just defined the alscript command file */
+ alps_file = GJstrdup(argv[1]);
+ break;
+ }
+ }
+ }
+
+ if(!silent){
+ fprintf(std_err,"\nALSCRIPT (ALignment to PostScript)\n");
+
+ fprintf(std_err,"%s\n",Alscript_Version);
+ fprintf(std_err,"\nSee ALSCRIPT.DOC for details\n");
+
+ fprintf(std_err,"\nPlease Reference: Barton, G. J. (1993), Protein Engineering, 6, 37-40.\n");
+
+ fprintf(std_err,"\nBy: G. J. Barton\n");
+ fprintf(std_err,"\nCopyright: Geoffrey J. Barton (1992,1997)\n");
+ fprintf(std_err,"email: geoff@ebi.ac.uk\n\n");
+
+ fprintf(std_err,"Initial Defaults:\n");
+ fprintf(std_err,"Maximum number of sequences:\t %d \t(Change using MAX_NSEQ command)\n",MAXnbloc);
+ fprintf(std_err,"Maximum sequence length:\t %d \t(Change using MAX_SEQ_LEN command)\n",MAXslen);
+ fprintf(std_err,"Maximum identifier length:\t %d \t(Change using MAX_ID_LEN command)\n",MAXilen);
+ }
+
+ if(alps_file == NULL && !quick){
+ fprintf(std_err,"Enter ALscript Command File name: ");
+ alps_file = (char *) GJmalloc(sizeof(char) * MAXtlen);
+ fscanf(std_in,"%s",alps_file);
+ }
+
+ if(quick){
+ /* create an alscript command file */
+ fp = GJfopen("ALPSQ.COM","w",1);
+ ALwritestddefs(fp);
+ GJfclose(fp,1);
+ alps_file = GJstrdup("ALPSQ.COM");
+ }
+
+ if(!silent)fprintf(std_err,"ALscript Command File: %s\n",alps_file);
+
+ if(alps(alps_file,silent,pipe,singlepage) == 1){
+ if(!silent)fprintf(std_err,"ALscript Finished\n");
+ exit(0);
+ }else{
+ error("Error in ALscript",1);
+ }
+}
+
+/* Write an alscript command file with some standard definitions */
+
+void ALwritestddefs(FILE *alps_file)
+{
+ fprintf(alps_file,"#ALSCRIPT - Default definitions\n");
+ fprintf(alps_file,"#For explanation of commands see file: alscript.doc\n");
+ fprintf(alps_file,"#Input from stdin and output to stdout by default\n");
+ fprintf(alps_file,"#block_file ?\n");
+ fprintf(alps_file,"#output_file ?\n");
+ fprintf(alps_file,"landscape\n");
+ fprintf(alps_file,"number_seqs\n");
+ fprintf(alps_file,"pointsize 8\n");
+ fprintf(alps_file,"define_font 0 Helvetica DEFAULT\n");
+ fprintf(alps_file,"define_font 1 Helvetica REL 0.5 \n");
+ fprintf(alps_file,"define_font 2 Helvetica-Bold DEFAULT\n");
+ fprintf(alps_file,"define_font 3 Times-Bold DEFAULT\n");
+ fprintf(alps_file,"define_font 4 Helvetica-BoldOblique DEFAULT\n");
+ fprintf(alps_file,"setup\n");
+ fprintf(alps_file,"mask SETUP\n");
+ fprintf(alps_file,"mask LEGAL \"ARNDCQEGHILKMFPSTWYVBZX\"\n");
+ fprintf(alps_file,"mask FRE ALL\n");
+ fprintf(alps_file,"mask SHADE ALL 0\n");
+ fprintf(alps_file,"mask INVERSE ALL\n");
+ fprintf(alps_file,"mask SHADE ALL 0\n");
+ fprintf(alps_file,"mask RESET\n");
+ fprintf(alps_file,"#shade_chars GP ALL 0\n");
+ fprintf(alps_file,"#inverse_chars GP ALL \n");
+ fprintf(alps_file,"#shade_chars LIVAWYFM ALL 0.8 \n");
+ fprintf(alps_file,"font_chars DEKRH ALL 4\n");
+}
+
+
+
+
+
+
+
+
+
+
+
+
git://source.jalview.org / jpred.git / blobdiff