String stockholmFile = sf.print(alWithSpaces.getSequencesArray(), true);
Pattern noSpacesInRnaSSAnnotation = Pattern
.compile("\\n#=GC SS_cons\\s+\\S{14}\\n");
- Matcher m = noSpacesInRnaSSAnnotation.matcher(stockholmFile);
+ Matcher m = noSpacesInRnaSSAnnotation
+ .matcher(stockholmFile.replace("\r\n", "\n"));
boolean matches = m.find();
Assert.assertTrue(matches,
"StockholmFile output does not contain expected output (may contain spaces):\n"