Merge pull request #3 from biojava/master

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Merge pull request #4 from biojava/master

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Merge pull request #5 from biojava/master

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Start of fix to issue #70. Updated BerkeleyScopInstallation to work with new version 2.0.x. Also advanced default version of BerkeleyScopInstallation to 2.0.3.
Continuation of fix to issue #70. Just added 2.0.x version names to ScopFactory.
Continued fix of issue #70. Corrected new version numbers: "2.03", not "2.0.3". Also, have VERSION1_75C point to "2.03", etc.
Merge pull request #6 from biojava/master

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Merge branch 'master' of https://github.com/biojava/biojava
Merge branch 'master' of https://github.com/biojava/biojava
Initialize list of bonds lazily. The bond list in an Atom is now
initialized with Collections.emptyList(), rather than an ArrayList. This
doubles the speed of allocating Atoms, since the bond list is not
created.
Merge branch 'master' of https://github.com/biojava/biojava
Merge branch 'master' of https://github.com/biojava/biojava
Merge pull request #7 from biojava/master

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Merge pull request #79 from pwrose/master

Initialize list of bonds lazily. The bond list in an Atom is now
Add a test case based on Daniel Cameron's example of failing FeatureList
code.  Modified FeatureList code to properly support adding indices both
before and after adding features.  Adding indicies between adds of
features are still not supported.  Ensure both adding index before
features and adding features before index are both tested.
Update method comment to indicate legal calling sequences for using
attribute features.
Merge pull request #8 from biojava/master

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Merge pull request #80 from emckee2006/master

Fix FeatureList bug (#77)
removing external dependency on log4j
cleanup