Removing warnings
Improving logging & exceptions in JFatCatClient
Minor changes to xtal and contacts packages

- Converted all classes to use log4j
- Fixed warnings
Add default parameters for interface definitions
Added defaults to StructureInterfaceList asaCalc
Adding toXYZString method to prettify CrystalTransform output
Merging local changes to master

Minor additions and logging fixes
Adding CrystalCell methods & tests

getCellIndices()
transfToOriginCell()
Added a quadratic-space global alignment class. Made Alignments.getPairwiseAligner() return the expected global alignment algorithm. Made Alignments methods throw an UnsupportedOperationException instead of returning null.
Added comments to SubstitutionMatrixScorer.
Modifying CrystalTransform toString method
Removing Java version from modules

This allows easier modification in the top-level pom
Removing empty class
Reverting 8faf1889, which intoduced Java 1.7-specific code
Reverting vecmath to 1.3.1

The older version has several practical advantages:
- The Mac JRE includes an old version of vecmath, so trying to use 1.5.1
  results in subtle runtime errors
- 1.3.1 is available through maven central
Merge 'main/master' with 'sbliven/master'

This adds some pom cleanups:
- Use vecmath 1.3.1
- Take JDK version from the parent pom

Also some code changes:
- Improvements to CrystalTransform class & xtal package
- Warnings and logging improvements

Conflicts:
	biojava3-alignment/pom.xml
	biojava3-core/pom.xml
	biojava3-modfinder/pom.xml
	biojava3-phylo/pom.xml
	biojava3-protein-disorder/pom.xml
Adding array version of CrystalCell#transfToOriginCell
Partially reverted #685b81c by deleting NeedlemanWunschQuadratic and removing it from Alignments.
Fixed this issue:
        NucleotideCompound A = new DNASequence("A").getCompoundAt(1);
        NucleotideCompound a = new DNASequence("a").getCompoundAt(1);
        SubstitutionMatrix<NucleotideCompound> matrix = new SimpleSubstitutionMatrix<>(DNACompoundSet.getDNACompoundSet(), (short)1, (short)0);
        System.out.println(matrix.getValue(A, a)); // prints 1
        System.out.println(matrix.getValue(a, A)); // prints 1
        System.out.println(matrix.getValue(a, a)); // prints 0!!!
        System.out.println(matrix.getValue(A, A)); // prints 0!!!
 The simple solution: compoundsEquivalent should always return true if the two are equal.
 Added a test for this.

 Also deprecated the no-args constructor SimpleSubstitutionMatrix() in favor of a static factory method getBlosum62(). The former was dangerous, since the generic type couldn't be checked. Plus, we should be explicit about what it is, since it only applies to amino acid sequences.
Merge branch 'master' of github.com:biojava/biojava