diff options
Diffstat (limited to 'sci-biology/elph/files/elph-0.1.4-usage.patch')
| -rw-r--r-- | sci-biology/elph/files/elph-0.1.4-usage.patch | 133 |
1 files changed, 133 insertions, 0 deletions
diff --git a/sci-biology/elph/files/elph-0.1.4-usage.patch b/sci-biology/elph/files/elph-0.1.4-usage.patch new file mode 100644 index 000000000000..be49e2d1ebb8 --- /dev/null +++ b/sci-biology/elph/files/elph-0.1.4-usage.patch @@ -0,0 +1,133 @@ +--- elph.cc~ 2003-06-03 14:45:22.000000000 -0400 ++++ elph.cc 2004-10-30 10:14:49.220415168 -0400 +@@ -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:abglvdxt: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++) |