Package: tree-puzzle / 5.2-11

spelling.patch Patch series | download
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Description: Fix some spelling issues
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 16 Oct 2018 10:51:06 +0200

--- a/src/ml2.c
+++ b/src/ml2.c
@@ -417,7 +417,7 @@ Node *internalnode(Tree *tr, char **chpp
 			
 			if (!strcmp(ident, idcomp)) {
 				if (usedtaxa[i]) {
-					fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence '");
+					fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurrence of sequence '");
 					fprintf(STDOUT, "%s' in tree)\n\n\n", ident);
 #					if PARALLEL
 						PP_Finalize();
--- a/src/puzzle1.c
+++ b/src/puzzle1.c
@@ -1967,7 +1967,7 @@ void initps(FILE *ofp)
 	/* PS definition of a centered print */
 	fprintf(ofp, "/centershow {\n");
 	fprintf(ofp, "   dup stringwidth pop %% get length of string\n");
-	fprintf(ofp, "   -2 div              %% devide length by -2\n");
+	fprintf(ofp, "   -2 div              %% divide length by -2\n");
 	fprintf(ofp, "   0 rmoveto           %% move half width to left\n");
 	fprintf(ofp, "   show\n");
 	fprintf(ofp, "} def\n");
@@ -3538,7 +3538,7 @@ void writeoutputfile(FILE *ofp, int part
 				i+1, Rates[i], (1.0-fracinv)/(double) numcats);	
 	}
 	if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) {
-		fprintf(ofp, "\nCategories 1-%d approximate a continous ", numcats);
+		fprintf(ofp, "\nCategories 1-%d approximate a continuous ", numcats);
 		fprintf(ofp, "Gamma-distribution with expectation 1\n"); 
 		fprintf(ofp, "and variance ");
 		if (Geta == 1.0) fprintf(ofp, "infinity");
@@ -5231,21 +5231,21 @@ void printusagehhh(char *fname)
 #ifdef HHH
                  /* |<---                      80 characters                                   --->| */
    fprintf(stderr, "  not yet implemented in this version:\n");
-   fprintf(stderr, "  -wslb            - write site lhs to PREFIX.sitelhb (binary)         [not yet]\n");
-   fprintf(stderr, "  -wsrb            - write site rates to PREFIX.siterateb (binary)     [not yet]\n");
-   fprintf(stderr, "  -wparam          - write params to PREFIX.param                      [not yet]\n");
-   fprintf(stderr, "  -qsupport        - prints quartet support for incorporated splits    [not yet]\n");
-   fprintf(stderr, "  -consth=<#>      - consensus threshold, e.g. 50=M_50 consensus       [not yet]\n");
-   fprintf(stderr, "  -wqnex           - write quartets in nexus format                    [not yet]\n");
-   fprintf(stderr, "  -wsnex           - write splits in nexus format                      [not yet]\n");
-   fprintf(stderr, "  -wsth=<#>        - split threshold, e.g. 50 - splits of the M_50     [not yet]\n");
-   fprintf(stderr, "  -wsnex=<#>       - write splits with > <#>%% occurence - nexus format[not yet]\n");
-   fprintf(stderr, "  -witnex          - write intermediate trees in nexus format          [not yet]\n");
-   fprintf(stderr, "  -quartml         - use ML values to evaluate quartets                [not yet]\n");
-   fprintf(stderr, "  -quartmlapprox   - use approximate ML values to evaluate quartets    [default]\n");
-   fprintf(stderr, "  -quartnj         - use NJ to evaluate quartets                       [not yet]\n");
-   fprintf(stderr, "  -quartme         - use ME to evaluate quartets                       [not yet]\n");
-   fprintf(stderr, "  -quartpars       - use parsimony to evaluate quartets                [not yet]\n");
+   fprintf(stderr, "  -wslb            - write site lhs to PREFIX.sitelhb (binary)          [not yet]\n");
+   fprintf(stderr, "  -wsrb            - write site rates to PREFIX.siterateb (binary)      [not yet]\n");
+   fprintf(stderr, "  -wparam          - write params to PREFIX.param                       [not yet]\n");
+   fprintf(stderr, "  -qsupport        - prints quartet support for incorporated splits     [not yet]\n");
+   fprintf(stderr, "  -consth=<#>      - consensus threshold, e.g. 50=M_50 consensus        [not yet]\n");
+   fprintf(stderr, "  -wqnex           - write quartets in nexus format                     [not yet]\n");
+   fprintf(stderr, "  -wsnex           - write splits in nexus format                       [not yet]\n");
+   fprintf(stderr, "  -wsth=<#>        - split threshold, e.g. 50 - splits of the M_50      [not yet]\n");
+   fprintf(stderr, "  -wsnex=<#>       - write splits with > <#>%% occurrence - nexus format[not yet]\n");
+   fprintf(stderr, "  -witnex          - write intermediate trees in nexus format           [not yet]\n");
+   fprintf(stderr, "  -quartml         - use ML values to evaluate quartets                 [not yet]\n");
+   fprintf(stderr, "  -quartmlapprox   - use approximate ML values to evaluate quartets     [default]\n");
+   fprintf(stderr, "  -quartnj         - use NJ to evaluate quartets                        [not yet]\n");
+   fprintf(stderr, "  -quartme         - use ME to evaluate quartets                        [not yet]\n");
+   fprintf(stderr, "  -quartpars       - use parsimony to evaluate quartets                 [not yet]\n");
    fprintf(stderr, "\n");
 #endif /* HHH */
 
--- a/src/puzzle2.c
+++ b/src/puzzle2.c
@@ -68,7 +68,7 @@ void readid(FILE *infp, int t)
 			if (Identif[t][j] != Identif[i][j])
 				flag = FALSE;
 		if (flag) {
-			fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence name '");
+			fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurrence of sequence name '");
 			fputid(STDOUT, t);
 			fprintf(STDOUT, "')\n\n\n");
 #			if PARALLEL
--- a/src/treesort.c
+++ b/src/treesort.c
@@ -601,7 +601,7 @@ treelistitemtype *addtree2list(char
 
 /**********/
 
-/* resort list of trees by number of occurences for output */
+/* resort list of trees by number of occurrences for output */
 void sortbynum(treelistitemtype *list, treelistitemtype **sortlist)
 {
 	treelistitemtype *tmpptr = NULL;
@@ -721,9 +721,9 @@ void fprintfsortedpstrees(FILE *output,
 				if (num == 1){
 					fprintf (output, "\n");
 					fprintf (output, "The following tree(s) occured in more than %.2f%% of the %d puzzling steps.\n", cutoff, itemsum);
-					fprintf (output, "The trees are orderd descending by the number of occurences.\n");
+					fprintf (output, "The trees are orderd descending by the number of occurrences.\n");
 					fprintf (output, "\n");
-					fprintf (output, "\n       occurences    ID  Phylip tree\n");
+					fprintf (output, "\n       occurrences    ID  Phylip tree\n");
 				}
 				fprintf (output, "%2d. %5d %6.2f%% %5d  ", num++, (*tmpptr).count, percent, (*tmpptr).id);
 			}