Merge branch 'develop' into features/JAL-2349_matrixvis
[jalview.git] / src / jalview / datamodel /
drwxr-xr-x   ..
-rw-r--r-- 111 .cvsignore
-rwxr-xr-x 1075 ASequence.java
-rwxr-xr-x 1039 ASequenceI.java
-rw-r--r-- 3202 AlignedCodon.java
-rw-r--r-- 20652 AlignedCodonFrame.java
-rwxr-xr-x 45887 Alignment.java
-rwxr-xr-x 39516 AlignmentAnnotation.java
-rw-r--r-- 1986 AlignmentExportData.java
-rwxr-xr-x 16578 AlignmentI.java
-rwxr-xr-x 7250 AlignmentOrder.java
-rw-r--r-- 37145 AlignmentView.java
-rw-r--r-- 1416 AllColsCollection.java
-rw-r--r-- 1715 AllColsIterator.java
-rw-r--r-- 1585 AllRowsCollection.java
-rw-r--r-- 1758 AllRowsIterator.java
-rw-r--r-- 2067 AnnotatedCollectionI.java
-rwxr-xr-x 5340 Annotation.java
-rwxr-xr-x 5341 BinaryNode.java
-rwxr-xr-x 4283 BinarySequence.java
-rw-r--r-- 11089 CigarArray.java
-rw-r--r-- 19892 CigarBase.java
-rw-r--r-- 1697 CigarCigar.java
-rw-r--r-- 1172 CigarSimple.java
-rw-r--r-- 17919 ColumnSelection.java
-rw-r--r-- 281 ContactListI.java
-rw-r--r-- 1845 ContactListImpl.java
-rw-r--r-- 417 ContactListProviderI.java
-rw-r--r-- 2645 ContactMatrix.java
-rw-r--r-- 147 ContactMatrixI.java
-rw-r--r-- 2323 ContactRange.java
-rwxr-xr-x 8483 DBRefEntry.java
-rwxr-xr-x 3287 DBRefSource.java
-rw-r--r-- 2127 FeatureProperties.java
-rwxr-xr-x 2011 GraphLine.java
-rw-r--r-- 32528 HiddenColumns.java
-rwxr-xr-x 10280 HiddenSequences.java
-rw-r--r-- 1107 IncompleteCodonException.java
-rw-r--r-- 17706 Mapping.java
-rw-r--r-- 1911 MappingType.java
-rw-r--r-- 999 NodeTransformI.java
-rwxr-xr-x 10666 PDBEntry.java
-rw-r--r-- 3646 Profile.java
-rw-r--r-- 2781 Profile.java~
-rw-r--r-- 2370 ProfileI.java
-rw-r--r-- 1505 ProfileI.java~
-rw-r--r-- 1606 Profiles.java
-rw-r--r-- 741 Profiles.java~
-rw-r--r-- 997 ProfilesI.java
-rw-r--r-- 132 ProfilesI.java~
-rwxr-xr-x 1426 Provenance.java
-rwxr-xr-x 1331 ProvenanceEntry.java
-rw-r--r-- 14712 ResidueCount.java
-rw-r--r-- 13847 ResidueCount.java~
-rw-r--r-- 1677 RnaViewerModel.java
-rw-r--r-- 1394 SearchResultMatchI.java
-rw-r--r-- 529 SearchResultMatchI.java~
-rwxr-xr-x 9195 SearchResults.java
-rw-r--r-- 2815 SearchResultsI.java
-rw-r--r-- 1950 SearchResultsI.java~
-rw-r--r-- 1502 SecondaryStructureAnnotation.java
-rw-r--r-- 18781 SeqCigar.java
-rw-r--r-- 1352 SeqDistanceContactMatrix.java
-rwxr-xr-x 34221 Sequence.java
-rw-r--r-- 1950 SequenceCollectionI.java
-rw-r--r-- 1771 SequenceDummy.java
-rwxr-xr-x 11675 SequenceFeature.java
-rwxr-xr-x 32879 SequenceGroup.java
-rwxr-xr-x 13057 SequenceI.java
-rwxr-xr-x 4061 SequenceNode.java
-rwxr-xr-x 1477 SequencePoint.java
-rw-r--r-- 4401 StructureViewerModel.java
-rwxr-xr-x 2132 UniprotEntry.java
-rwxr-xr-x 1270 UniprotFile.java
-rwxr-xr-x 1336 UniprotProteinName.java
-rwxr-xr-x 1531 UniprotSequence.java
-rw-r--r-- 1412 VisibleColsCollection.java
-rw-r--r-- 3226 VisibleColsIterator.java
-rw-r--r-- 1517 VisibleRowsCollection.java
-rw-r--r-- 2326 VisibleRowsIterator.java
drwxr-xr-x - xdb