changed read stat function
Refactored connection and buffered service
Added Gene to Protein classes
Minor changes in Java Beans
Refactored TFBS prediction reader
Added FIMO input generator
Fixed null pointer exceptions
Code formating
Minimized logger
Added GTF reader
Minor changes
up
Added genome sequence extractor
refactored species look-up
Unit test update
Edited ignore list
Added GTF reader
Manual merge
Merge branch 'master' of https://github.com/croco-bio/croco-api

Conflicts:
	.gitignore
	src/de/lmu/ifi/bio/crco/data/genome/Gene.java
	src/de/lmu/ifi/bio/crco/data/genome/Transcript.java
	src/de/lmu/ifi/bio/crco/intervaltree/peaks/Promoter.java
	src/de/lmu/ifi/bio/crco/processor/TFBS/FIMOHandler.java
	src/de/lmu/ifi/bio/crco/util/CroCoLogger.java
	src/de/lmu/ifi/bio/crco/util/FileUtil.java