Hi Paolo,

At first sight it might seem like a good idea to change for example:
public Object clone() to public Atom clone() to avoid the casts,

however, there is a catch!

A class that implements the Cloneable interface must to overwrite public Object clone();

-Peter

From: Paolo Bizzarri <notifications@github.commailto:notifications@github.com>
Reply-To: biojava/biojava <reply@reply.github.commailto:reply@reply.github.com>
Date: Saturday, February 28, 2015 at 12:54 PM
To: biojava/biojava <biojava@noreply.github.commailto:biojava@noreply.github.com>
Subject: [biojava] Cleanup of unnecessary casts (#257)
Resent-From: Peter Rose <pwrose@ucsd.edumailto:pwrose@ucsd.edu>

I have tried to remove lots of unnecessary casts from the code.

You can view, comment on, or merge this pull request online at:

#257

Commit Summary

• Merge pull request added .gitignore #1 from biojava/master
• Code cleanup. Removed lots of unnecessary casts.

File Changes

• M biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-0 (19)
• M biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-1 (12)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-2 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-3 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-4 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-5 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-6 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-7 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/Group.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-8 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-9 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-10 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-11 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-12 (8)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-13 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-14 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-15 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-16 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-17 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-18 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-19 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-20 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-21 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/AlignTools.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-22 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-23 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-24 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-25 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentPair.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-26 (8)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/Gotoh.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-27 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPChainScorer.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-28 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-29 (4)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-30 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-31 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-32 (6)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-33 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-34 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStruc.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-35 (8)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-36 (2)
• M biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalBuilder.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-37 (2)
• M biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.javahttps://github.com/Cleanup of unnecessary casts #257/files#diff-38 (2)

Patch Links:

• https://github.com/biojava/biojava/pull/257.patch
• https://github.com/biojava/biojava/pull/257.diff

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/257.

Oh, I see. My mistake. You never stop learning something new. Thanks.

The other problem is you won't know you've broken anything until you try to
execute the statement.

Mark
On Feb 28, 2015 10:56 PM, "Paolo Bizzarri" notifications@github.com wrote:

Oh, I see. My mistake. You never stop learning something new. Thanks.

—
Reply to this email directly or view it on GitHub
#257 (comment).