\n"
+"We have extended the Newick format to allow spaces \n"
+"and other non-alphanumeric characters in node labels. \n"
+"If you need a backslash, comma, semi-colon, colon, or parenthesis, \n"
+"it must be escaped with a back-slash character. \n"
+"
\n"
+"5. PhastCons branch lengths are expected substitutions per site, allowing for\n"
+"multiple hits. So a branch length of 0.5 means an average of one\n"
+"substitution every two nucleotide sites, but the percent id will be\n"
+"less than 50% because some of those substitutions are obscured by\n"
+"subsequent substitutions. They are estimated from neutral sites,\n"
+"sometimes fourfold degenerate sites in coding regions, or sometimes\n"
+"\"nonconserved\" sites according to phastCons. The numbers are significant\n"
+"to two or three figures. \n"
+" \n"
+"6. Wrap-in-html is useful when the browser automatically shinks a large image.\n"
+"This option keeps the image view full in the browser automatically.\n"
+"However, do not use with IE6 when performing save-as.\n"
+" "
+ );
+ cartWebEnd();
+ return 0;
+ }
+ else
+ usage("-phyloPng_tree is a required 'option' or cgi variable.");
+ }
+
+if (htmlPageWrapper)
+ {
+ printf("Content-type: text/html\r\n");
+ printf("\r\n");
+ puts("Phylogenetic Tree");
+ printf("");
+ freez(&phyloData);
+ return 0;
+ }
+
+
+
+if (!onWeb && phyloData[0] != '(')
+ {
+ int fd = 0; /* default to stdin */
+ if (!sameString(phyloData,"stdin"))
+ fd = open(phyloData,O_RDONLY);
+ struct dyString *dy = netSlurpFile(fd);
+ if (fd)
+ close(fd);
+ freez(&phyloData);
+ phyloData = dyStringCannibalize(&dy);
+ }
+
+/* remove carriage returns which are a side-effect of html forms */
+if (strchr(phyloData,'\r'))
+ {
+ char *temp = phyloData;
+ phyloData = replaceChars(temp,"\r","");
+ freez(&temp);
+ }
+
+/* add trailing semi-colon if it got stripped off */
+if (!strchr(phyloData,';'))
+ {
+ temp = phyloData;
+ phyloData = addSuffix(phyloData,";");
+ freez(&temp);
+ }
+
+/* parse phyloTree, but catch errAborts if any */
+
+{
+struct errCatch *errCatch = errCatchNew();
+char *errMsg = NULL;
+if (errCatchStart(errCatch))
+ {
+ phyloTree = phyloParseString(phyloData);
+ }
+errCatchEnd(errCatch);
+if (errCatch->gotError)
+ {
+ errMsg = cloneString(errCatch->message->string);
+ }
+errCatchFree(&errCatch);
+if (errMsg)
+ {
+ if (onWeb)
+ {
+ printf("Content-type: text/html\r\n");
+ printf("\r\n");
+ puts("PhyloTree parse error
");
+ /* we dont think the specific error message coming back are correct or useful
+ * so supply a generic err msg */
+ htmlPrintf("Original input tree:\n[%s]\n\n",cgiString("phyloPng_tree"));
+ htmlPrintf("Input tree as passed to parser:\n[%s]\n\n",phyloData);
+ printf("Parser syntax error:\n%s",errMsg);
+ puts("