\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("-phyloGif_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("phyloGif_tree"));
- htmlPrintf("Input tree as passed to parser:\n[%s]\n\n",phyloData);
- printf("Parser syntax error:\n%s",errMsg);
- puts("