X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fdisembl%2FTisean_3.0.1%2Fsource_c%2Fpca.c;fp=binaries%2Fsrc%2Fdisembl%2FTisean_3.0.1%2Fsource_c%2Fpca.c;h=cf3c42de3c0eeccff8f396497330b054d2e835f0;hb=a17c780665c109829426e062df4d75ff950725e0;hp=0000000000000000000000000000000000000000;hpb=f47da0247a9f9a8ac55571234064a0d3ded06b6c;p=jabaws.git diff --git a/binaries/src/disembl/Tisean_3.0.1/source_c/pca.c b/binaries/src/disembl/Tisean_3.0.1/source_c/pca.c new file mode 100644 index 0000000..cf3c42d --- /dev/null +++ b/binaries/src/disembl/Tisean_3.0.1/source_c/pca.c @@ -0,0 +1,329 @@ +/* + * This file is part of TISEAN + * + * Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber + * + * TISEAN is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * TISEAN is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with TISEAN; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +/*Author: Rainer Hegger Last modified: Jul 26, 2004 */ +#include +#include +#include +#include +#include +#include "routines/tsa.h" + +#define WID_STR "Performs a global PCA" + +unsigned long LENGTH=ULONG_MAX,exclude=0; +unsigned int DIM=2,EMB=1,dimemb,LDIM=2,DELAY=1; +unsigned int verbosity=0xff; +char *outfile=NULL,stout=1,dim_set=0; +unsigned int what_to_write=0,write_values=1,write_vectors=0; +unsigned int write_comp=0,write_proj=0; +unsigned int projection_set=0; +char *infile=NULL,dimset=0,*column=NULL; +double **series; + +void show_options(char *progname) +{ + what_i_do(progname,WID_STR); + fprintf(stderr," Usage: %s [options]\n",progname); + fprintf(stderr," Options:\n"); + fprintf(stderr,"Everything not being a valid option will be interpreted" + " as a possible" + " datafile.\nIf no datafile is given stdin is read. Just - also" + " means stdin\n"); + fprintf(stderr,"\t-l # of data to use [Default: whole file]\n"); + fprintf(stderr,"\t-x # of lines to be ignore [Default: 0]\n"); + fprintf(stderr,"\t-c columns to read [Default: 2]\n"); + fprintf(stderr,"\t-m columns,embedding dim. to use [Default: 2,1]\n"); + fprintf(stderr,"\t-d delay to use [Default: 1]\n"); + fprintf(stderr,"\t-q projection dimension [Default: no projection]\n"); + fprintf(stderr,"\t-W # what to write: [Default: 0]\n" + "\t\t0 write eigenvalues only\n" + "\t\t1 write eigenvectors\n" + "\t\t2 write (projected) pca components\n" + "\t\t3 write projected data\n"); + fprintf(stderr,"\t-o output file name \n\t\t[Default: stdout; -o without " + "value means 'datafile'.pca]\n"); + fprintf(stderr,"\t-V verbosity level [Default: 1]\n\t\t" + "0='only panic messages'\n\t\t" + "1='+ input/output messages'\n"); + fprintf(stderr,"\t-h show these options\n"); + exit(0); +} + +void scan_options(int n,char **in) +{ + char *out; + + if ((out=check_option(in,n,'l','u')) != NULL) + sscanf(out,"%lu",&LENGTH); + if ((out=check_option(in,n,'x','u')) != NULL) + sscanf(out,"%lu",&exclude); + if ((out=check_option(in,n,'c','s')) != NULL) + column=out; + if ((out=check_option(in,n,'m','2')) != NULL) { + sscanf(out,"%u,%u",&DIM,&EMB); + dimset=1; + } + if ((out=check_option(in,n,'d','u')) != NULL) + sscanf(out,"%u",&DELAY); + if ((out=check_option(in,n,'q','u')) != NULL) { + sscanf(out,"%u",&LDIM); + projection_set=1; + } + if ((out=check_option(in,n,'V','u')) != NULL) + sscanf(out,"%u",&verbosity); + if ((out=check_option(in,n,'W','u')) != NULL) { + sscanf(out,"%u",&what_to_write); + switch(what_to_write) { + case 0: write_values=1;break; + case 1: write_values=0;write_vectors=1;break; + case 2: write_values=0;write_comp=1;break; + case 3: write_values=0;write_proj=1;break; + default: { + fprintf(stderr,"Wrong value for the -W flag. Exiting!\n"); + exit(127); + } + } + } + if ((out=check_option(in,n,'o','o')) != NULL) { + stout=0; + if (strlen(out) > 0) + outfile=out; + } +} + +void ordne(double *lyap,int *ord) +{ + long i,j,maxi; + double max; + + for (i=0;i dimemb) LDIM=dimemb; + } + + check_alloc(av=(double*)malloc(sizeof(double)*DIM)); + for (j=0;j