Merge bugfixes-4.2#556
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…n CIF output CIF categories are represented as a simple bean, typically extending AbstractBean. By default, all fields from the bean are taken as the CIF labels. Fields may be omitted by annotating them as @IgnoreField. The CIF label for a field may be changed by defining a function, `static Map<String,String> getCIFLabelMap();`, mapping from the field's name to the correct label. This commit also changes the MMCIFFileTools.toMMCIF method to be generic, so that we enforce at compile time that all loop rows must be of the same type.
This replaces the short-lived getCIFLabelMap static function. It lets you associate the label directly with the applicable field
biojava#505 biojava#522 switching to https for all NCBI traffic.
CathNames and CathDomainDescriptionFile
Add WrapLayout (fixes default FlowLayout wrapping behaviour) WrapLayout is public domain.
Conflicts: biojava-aa-prop/pom.xml biojava-alignment/pom.xml biojava-core/pom.xml biojava-genome/pom.xml biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java biojava-integrationtest/pom.xml biojava-modfinder/pom.xml biojava-ontology/pom.xml biojava-phylo/pom.xml biojava-protein-disorder/pom.xml biojava-sequencing/pom.xml biojava-structure-gui/pom.xml biojava-structure/pom.xml biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java biojava-survival/pom.xml biojava-ws/pom.xml pom.xml
Also fix a minor bug with ZipChemCompProvider & some warnings
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