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paolopavanpaolopavan
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Massive refactoring: moved alignment data structures from biojava-alignment to biojava-core.
Mantaining main biological data structures in core will help to avoid problems of unwanted dependency. Unfortunately the substitution matrices related classes are tight coupled with SimpleSequencePair class and were moved too from alignment. Updated pom file to remove dependency of core from alignment module temporary added by first implementation of SearchIO.
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106 files changed

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‎biojava-alignment/src/main/java/demo/CookbookMSA.java‎

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package demo;
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import org.biojava.nbio.alignment.Alignments;
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import org.biojava.nbio.alignment.template.Profile;
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import org.biojava.nbio.core.alignment.template.Profile;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.io.FastaReaderHelper;

‎biojava-alignment/src/main/java/demo/DemoAlignProteins.java‎

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import org.biojava.nbio.alignment.Alignments;
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import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava.nbio.alignment.SimpleGapPenalty;
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import org.biojava.nbio.alignment.SubstitutionMatrixHelper;
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import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
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import org.biojava.nbio.alignment.template.GapPenalty;
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import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
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import org.biojava.nbio.alignment.template.SequencePair;
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import org.biojava.nbio.alignment.template.SubstitutionMatrix;
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import org.biojava.nbio.core.alignment.template.SequencePair;
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import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.io.FastaReaderHelper;

‎biojava-alignment/src/main/java/demo/DemoLoadSubstMax.java‎

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*/
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package demo;
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import org.biojava.nbio.alignment.SubstitutionMatrixHelper;
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import org.biojava.nbio.alignment.template.SubstitutionMatrix;
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import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
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import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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public class DemoLoadSubstMax {

‎biojava-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java‎

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import org.biojava.nbio.alignment.Alignments;
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import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava.nbio.alignment.SimpleGapPenalty;
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import org.biojava.nbio.alignment.SubstitutionMatrixHelper;
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import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
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import org.biojava.nbio.alignment.template.GapPenalty;
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import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
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import org.biojava.nbio.alignment.template.SequencePair;
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import org.biojava.nbio.core.alignment.template.SequencePair;
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import org.biojava.nbio.core.sequence.DNASequence;
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import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java‎

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package org.biojava.nbio.alignment;
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import org.biojava.nbio.core.alignment.template.ProfilePair;
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import org.biojava.nbio.core.alignment.template.SequencePair;
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import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
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import org.biojava.nbio.core.alignment.template.Profile;
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import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
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import org.biojava.nbio.alignment.template.*;
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import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java‎

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package org.biojava.nbio.alignment;
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import org.biojava.nbio.alignment.template.AlignedSequence;
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import org.biojava.nbio.core.alignment.SimpleSequencePair;
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import org.biojava.nbio.core.alignment.template.AlignedSequence;
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import org.biojava.nbio.alignment.template.PairInProfileScorer;
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import org.biojava.nbio.alignment.template.Profile;
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import org.biojava.nbio.core.alignment.template.Profile;
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import org.biojava.nbio.core.sequence.template.Compound;
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import org.biojava.nbio.core.sequence.template.Sequence;
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‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java‎

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package org.biojava.nbio.alignment;
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import org.biojava.nbio.core.alignment.template.SequencePair;
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import org.biojava.nbio.alignment.template.*;
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import org.biojava.nbio.core.sequence.template.Compound;
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import org.biojava.nbio.core.sequence.template.Sequence;

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java‎

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package org.biojava.nbio.alignment;
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import org.biojava.nbio.alignment.template.AlignedSequence;
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import org.biojava.nbio.core.alignment.SimpleSequencePair;
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import org.biojava.nbio.core.alignment.template.AlignedSequence;
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import org.biojava.nbio.alignment.template.PairInProfileScorer;
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import org.biojava.nbio.alignment.template.Profile;
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import org.biojava.nbio.core.alignment.template.Profile;
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import org.biojava.nbio.core.sequence.template.Compound;
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import org.biojava.nbio.core.sequence.template.Sequence;
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‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java‎

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package org.biojava.nbio.alignment;
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import org.biojava.nbio.core.alignment.template.SequencePair;
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import org.biojava.nbio.alignment.template.*;
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import org.biojava.nbio.core.sequence.template.Compound;
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import org.biojava.nbio.core.sequence.template.Sequence;

‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java‎

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package org.biojava.nbio.alignment;
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import org.biojava.nbio.core.alignment.SimpleProfile;
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import org.biojava.nbio.alignment.template.GuideTreeNode;
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import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
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import org.biojava.nbio.alignment.template.Profile;
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import org.biojava.nbio.alignment.template.ProfilePair;
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import org.biojava.nbio.core.alignment.template.Profile;
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import org.biojava.nbio.core.alignment.template.ProfilePair;
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import org.biojava.nbio.core.sequence.AccessionID;
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import org.biojava.nbio.core.sequence.template.Compound;
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import org.biojava.nbio.core.sequence.template.Sequence;

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