GNAT Code

First version of an Annotator that reads single PubMed XML files. Moved recurring code to an abstract class 'XmlAnnotator'.

Getting rid of some Java Warnings.

'?' was missing from characters that need to be escaped so that an input string can be used as a pattern:

Exception in thread "main" java.util.regex.PatternSyntaxException: Dangling meta character '?' near index 44
.*(gene|protein|mRNA|cDNA)s?.*Transfection???Human embryonic kidney.*HEK.*
^
at java.util.regex.Pattern.error(Pattern.java:1924)
at java.util.regex.Pattern.sequence(Pattern.java:2090)
at java.util.regex.Pattern.expr(Pattern.java:1964)
at java.util.regex.Pattern.compile(Pattern.java:1665)
at java.util.regex.Pattern.<init>(Pattern.java:1337)
at java.util.regex.Pattern.compile(Pattern.java:1022)
at java.util.regex.Pattern.matches(Pattern.java:1128)
at java.lang.String.matches(String.java:2063)
at gnat.filter.nei.ImmediateContextFilter.filter(ImmediateContextFilter.java:201)
at gnat.client.Run.runFilters(Run.java:190)
at gnat.client.AnnotateMedline.main(AnnotateMedline.java:380)

This occured only now that we are converting PDF to text, producing unknown characters like the above sequence of '???'.

Error escaping the shortForm to form patterns that are matched against text.

Corrected type in name of function StringHelper.escapeString()