GNAT Code

Added a method to Context to return a list of identified genes instead of a list of strings. Renamed existing method to getIdentifiedGenes..._toBc3Tsv. The latter method was called in many pipeline clients and the tests.

Filename for go2go.obj now in isgnproperties.xml

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()