diff options
Diffstat (limited to 'sci-biology/elph/files/elph-0.1.5-usage.patch')
| -rw-r--r-- | sci-biology/elph/files/elph-0.1.5-usage.patch | 133 |
1 files changed, 0 insertions, 133 deletions
diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch deleted file mode 100644 index 139b83c1c1c6..000000000000 --- a/sci-biology/elph/files/elph-0.1.5-usage.patch +++ /dev/null @@ -1,133 +0,0 @@ ---- elph.cc.old 2005-01-11 14:17:47.000000000 -0500 -+++ elph.cc 2005-01-27 19:42:30.218350552 -0500 -@@ -26,11 +26,11 @@ - period variable\n\ - -x : print maximum positions within sequences\n\ - -g : find significance of motif\n\ -- -t <matrix> : test if there is significant difference between the two -- input files for a given motif matrix; <matrix> is the file -+ -t <matrix> : test if there is significant difference between the two\n\ -+ input files for a given motif matrix; <matrix> is the file\n\ - containing the motif matrix\n\ -- -l : compute Least Likely Consensus (LLC) for given motif -- -c : in conjunction with -m option: motif is not necessarily in -+ -l : compute Least Likely Consensus (LLC) for given motif\n\ -+ -c : in conjunction with -m option: motif is not necessarily in\n\ - the closest edit distance from input motif\n\ - LEN=n : n = length of motif\n\ - ITERNO=n : n = no of iterations to compute the global maximum;\n\ -@@ -41,7 +41,7 @@ - default = 1000\n\ - " - --// global variables: -+// global variables: - int ITER_NO=10; - int MAX_LOOP=500; - int printmax=0; -@@ -66,7 +66,7 @@ - seqType t; - - GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO="); -- -+ - // == Process arguments. - - int e; -@@ -83,7 +83,7 @@ - - if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files - -- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); -+ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet); - M->twofilesignif(gdet,testfile,SignifNo,print,pattern); - - } -@@ -93,11 +93,11 @@ - // given motif - - M = new Motif(infile,outf,t,pattern); -- if(defLLC) { -+ if(defLLC) { - double llc=M->computeLLC(pattern,print); - fprintf(outf,"LLC = %f\n",llc); - } -- -+ - } - else { - -@@ -108,7 +108,7 @@ - } - - double globAlignProb; -- -+ - globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet); - - -@@ -116,13 +116,13 @@ - /*info=M->InfoPar(globAlignProb); - fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info); - M->printMotif();*/ -- -+ - // optimizing - fprintf(stderr,"Optimizing...\n"); - globAlignProb=M->optimize(globAlignProb,info,closest); - fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n"); - fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb)); -- -+ - if(runsignif) { - M->runforsignif(SignifNo,print,gdet,pattern); - } -@@ -134,17 +134,17 @@ - - seqType Process_Options(GArgs* args) - { -- -- if (args->startNonOpt()) { //parse the non-options arguments -+ -+ if (args->startNonOpt()) { //parse the non-options arguments - //(usually filenames) - infile=args->nextNonOpt(); - } - -- if (infile.is_empty() || args->getOpt('h')!=NULL) -+ if (infile.is_empty() || args->getOpt('h')!=NULL) - GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input - - testfile=args->nextNonOpt(); -- -+ - GString outfile=args->getOpt('o'); - if (!outfile.is_empty()) { - outf=fopen(outfile, "w"); -@@ -156,7 +156,7 @@ - matrixfile=args->getOpt('t'); - - GString param; -- -+ - pattern=args->getOpt('m'); - if(pattern.is_empty()) { - param=args->getOpt("LEN"); -@@ -200,7 +200,7 @@ - - seqType t; - if(args->getOpt('a')!=NULL) t=aac; else t=nucl; -- -+ - return(t); - - } -@@ -210,7 +210,7 @@ - Motif *M; - - double llcmax=-HUGE_VAL; -- GString seed; -+ GString seed; - for(int i1=0;i1<4;i1++) - for(int i2=0;i2<4;i2++) - for(int i3=0;i3<4;i3++) |