Tagging for eppic release 2.0.4:
no changes from last owl release.

Tagging for eppic release 2.0.3
- more PDB metadata parsing: biounit assembly and release date
- improved rmsd calculation: new OptimalSuperposition class introduced
- improvements in interface calculation: now going to 12th cell
- introduced chain clusters and interface clusters
- some more checks in cif file parsing: now won't crash on phenix files

Tagging for eppic release 2.0.2
- bug fix: null pointer in pdb file parsing when no TER records present or misplaced
- many improvements in SpaceGroup and its testing
- operators can now be classified into their types, including calculation of screw directions
- bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1
- bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.

Removing tag because another bug was found and we want to put it into the 2.0.2 release

Tagging for eppic release 2.0.2
- bug fix: null pointer in pdb file parsing when no TER records present or misplaced
- many improvements in SpaceGroup and its testing
- operators can now be classified into their types, including calculation of screw directions
- bug fix: the axis vectors were wrongly calculated for some operators of some space groups, e.g. in H 3 2 or P 32 2 1
- bug fix in jaligner: sequences longer than 32768 characters were not aligning correctly when the match was occurring after character 32768. We fixed it ourselves in the jaligner source and repackaged the jar into owl. The jaligner developer has fixed it in git.

Tagging for eppic release 2.0.1
- fixed bug: can't read 'I 1 2 1' space group. Now using both main and alternative names for looking up space groups

Tagging for eppic release 2.0.0
- many bug fixes, especially in cif and pdb parsers. Now hopefully a lot more robust. Cif parser was tested in whole PDB as of Feb 2013. File guesser will be more flexible with PDB files: it allows now a lot more possible first lines
- all elements added to AtomType
- better dealing with unknown elements when reading from PDB file
- fixed bug in ASA calculation: for finding neighbours we were taking default vdw radius instead of one set in setRadius
- BlastXML parser can now read both raw xml and gzipped xml blast output (autodetecting it)

Tagging for eppic release 1.9.6.
- totally redone interface calculation: huge improvements in runtime and memory usage, explores also 2nd neighbours, uses symmetry-redundancy elimination, bugs fixed
- introduced minimum ASA threshold for considering residue at surface
- cofactors can now be used for ASA calculation in interfaces
- blast runner now chooses matrix to use based on sequence length as it is standard use in blast servers
- introduced blast+ support
- introduced clustalo support in HomologsList
- improvements and important fixes in HomologsList alignments

Tagging for eppic release 1.9.5.
- better alignment in HomologsList
- better redundancy reduction in HomologList through clustering
- many bug fixes, a few of them in parsers

Tagging for crk release 1.9.4

Tagging for crk version 1.9.3

Tagging version for crk 1.9.2

Tagging version for crk 1.9.1

Tagging from bug fix branch for bug fixed version of CMView 1.9.4 (released as 1.1.1). Important bug fix of DaliRunner

Tagging version 1.9.5. Many bug fixes after introduction of hetatoms, especially with regards to read/write of PDB files. First tag with hetatoms-support.

Tagging version 1.9.4 before major change: support for HETATMs

Tagging owl-1.9.3 before major interface change.

tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5

Removing tag owl-1.9.2 because it doesn't include some minor fixes.

tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5

removing tag owl-1.9.2 which contained wrong contents (copy of all tags instead of trunk)

tagging version 1.9.2 to match CMView-1.9.2-released-as-1.1rc5

tagging version 1.9.1 to match CMView-1.9.1-released-as-1.1rc4

tagging version 1.9.0 matching CMView 1.9.0 released as 1.1rc3

tagging OWL 1.2.0 in sync with CMView 1.2.0 before major refactoring

Tagging version 1.1.2 before major refactoring.

Tagging 1.1.1 before major changes

Tagging ver 0.9.6 for CMView 0.9.6. Now using jung beta1 jars.

Tagging ver 1.1.0 for CMView 1.1.0. Now using jung beta1 jars.

tagging version 0.9.5 matching CMView 0.9.5

Tagging ver. 0.9.4 matching CMView 0.9.4

Tagging 0.9.3 for CMView release 0.9.3

Deleting tag 1.0-rc1. That was too premature for a RC

Tagging version 1.0-rc1 for CMView-1.0-rc1

Tagging ver 0.9.2 for CMView 0.9.2

tagging version 0.9.1 for CMView 0.9.1

Tagging version 0.9 to use with CMView 0.9 (same as aglappe-jung 0.1.2 but moved to trunk)

Tagging version 0.8.7 from trunk: last pre-JUNG before merging the JUNG branch to the trunk

version for CMView-jung-0.1.2

version for CMView-jung-0.1.1

to be used for CMView-jung-0.1

Tagging ver. 0.8.6. This will be the last pre-JUNG tag

tagging version 0.8.5 in sync with CMView-0.8.5

tagging version 0.8.3 corresponding to CMView 0.8.3

tagging version 0.8.2 to be used with CM2PyMol 0.8.2

tagging aglappe 0.8.1 to use with cmview 0.8.1

tagging version 0.7 matching CM2PyMol 0.7

Tagging version 0.6 for release of cmview 0.6

Tagging version 0.5 for release of CM2PyMol version 0.5

tagged version 0.3.4

Tagging version 0.3.3. at rev110 after adding some renaming getNodes method to getMySQLNodes in DataDistribution and adding some functionality

Tagging at rev104, slight modifications in DataDistributer. To be used with a slightly improved dumpnload.java

Tag 0.3.1 at rev 102. Introduced slight modifications in DataDistributer class to use with dumpnload.java

tools version 0.3 from rev98. To use with jed (includes new TableSorter)

Sorry that was wrong!!

tools version 0.3 from rev98. To use with jed (includes new TableSorter)

Creating of tools version 0.2:
Freeze of tools package at rev89.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)

This tag was wrongly created, should have contained a tools directory as a subdir. Deleting it

Creating of tools version 0.2:
Freeze of tools package at rev87.
New classes QueryThread and DataDistributer.
Reorganised DataDistribution (split into DataDistribution and DataDistributer)
Main functionality difference is that dump/loads of databases are now threaded thus being a lot faster (some parellelism in dumps/loads)

Creation of tools version 0.1:
Freezing tools rev81 to tag tools-0.1
I am planning to change completely some of the classes: DataDistribution and ClusterConnection. Will continue developing on trunk while we have this freeze so others can use programs as they are now.

Initial import of tools