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Merged
josemduarte merged 13 commits into from
Nov 12, 2015
Merged

SearchIO module #329

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51262c5
Deleted test files that can be delegated to superclass
paolopavan Sep 9, 2015
5ad3cc9
Massive refactoring: moved alignment data structures from biojava-ali…
paolopavan Sep 15, 2015
dd5b463
Merge branch 'API_variation' into SearchIO_branch
paolopavan Sep 17, 2015
967168d
Fixed reference to resource file.
paolopavan Sep 18, 2015
42f3337
Modified method with more appropriate access level.
paolopavan Sep 22, 2015
911ba72
Better exception handling.
paolopavan Sep 24, 2015
d9c17d7
Tests enhancement.
paolopavan Sep 28, 2015
b78d387
bugfix
paolopavan Oct 5, 2015
26eaebf
Change in the way equals() is evaluated for Results, Hits, Hsps.Modif…
paolopavan Oct 5, 2015
31f3729
Added setter method for parsing fine tuning configuration.
paolopavan Oct 6, 2015
f059f0e
Refactoring proposed by Jose Manuel Duarte to separate this module fr…
paolopavan Oct 9, 2015
9cbd9ee
Changed logger to slf4j
paolopavan Oct 31, 2015
248cc08
Increased type checking.
paolopavan Nov 1, 2015
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Massive refactoring: moved alignment data structures from biojava-ali… 
…gnment 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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@paolopavan
paolopavan committed Sep 16, 2015
commit 5ad3cc9e93ee928561a4423a0ac9a3835370b1b7
2 changes: 1 addition & 1 deletion biojava-alignment/src/main/java/demo/CookbookMSA.java
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package demo;

import org.biojava.nbio.alignment.Alignments;
import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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6 changes: 3 additions & 3 deletions biojava-alignment/src/main/java/demo/DemoAlignProteins.java
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import org.biojava.nbio.alignment.Alignments;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.SimpleGapPenalty;
import org.biojava.nbio.alignment.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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4 changes: 2 additions & 2 deletions biojava-alignment/src/main/java/demo/DemoLoadSubstMax.java
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*/
package demo;

import org.biojava.nbio.alignment.SubstitutionMatrixHelper;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;

public class DemoLoadSubstMax {
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4 changes: 2 additions & 2 deletions biojava-alignment/src/main/java/demo/TestDNANeedlemanWunsch.java
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import org.biojava.nbio.alignment.Alignments;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.SimpleGapPenalty;
import org.biojava.nbio.alignment.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
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5 changes: 5 additions & 0 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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5 changes: 3 additions & 2 deletions ...alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityInProfileScorer.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.SimpleSequencePair;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.alignment.template.PairInProfileScorer;
import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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1 change: 1 addition & 0 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
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5 changes: 3 additions & 2 deletions ...ignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityInProfileScorer.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.SimpleSequencePair;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.alignment.template.PairInProfileScorer;
import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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1 change: 1 addition & 0 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
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5 changes: 3 additions & 2 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.SimpleProfile;
import org.biojava.nbio.alignment.template.GuideTreeNode;
import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.sequence.AccessionID;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
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4 changes: 2 additions & 2 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/NeedlemanWunsch.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner;
import org.biojava.nbio.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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6 changes: 5 additions & 1 deletion biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.SimpleProfilePair;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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7 changes: 4 additions & 3 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/SmithWaterman.java
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package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.SimpleSequencePair;
import org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner;
import org.biojava.nbio.alignment.template.AlignedSequence;
import org.biojava.nbio.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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2 changes: 1 addition & 1 deletion biojava-alignment/src/main/java/org/biojava/nbio/alignment/StandardRescoreRefiner.java
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import org.biojava.nbio.alignment.Alignments.PairInProfileScorerType;
import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava.nbio.alignment.template.AbstractScorer;
import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.alignment.template.RescoreRefiner;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
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4 changes: 2 additions & 2 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/SubstitutionMatrixScorer.java
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import org.biojava.nbio.alignment.template.AbstractScorer;
import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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2 changes: 1 addition & 1 deletion biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
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package org.biojava.nbio.alignment.routines;

import org.biojava.nbio.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;

import java.util.ArrayList;
import java.util.Collections;
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8 changes: 4 additions & 4 deletions ...nt/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
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package org.biojava.nbio.alignment.routines;

import org.biojava.nbio.alignment.SimpleSequencePair;
import org.biojava.nbio.core.alignment.SimpleSequencePair;
import org.biojava.nbio.alignment.routines.AlignerHelper.Anchor;
import org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner;
import org.biojava.nbio.alignment.template.AlignedSequence;
import org.biojava.nbio.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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4 changes: 2 additions & 2 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
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package org.biojava.nbio.alignment.routines;

import org.biojava.nbio.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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4 changes: 3 additions & 1 deletion ...va-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.alignment.routines.AlignerHelper.Anchor;
import org.biojava.nbio.alignment.routines.AlignerHelper.Last;
import org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem;
import org.biojava.nbio.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.Sequence;
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2 changes: 2 additions & 0 deletions ...nt/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.Sequence;
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3 changes: 3 additions & 0 deletions ...ment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.alignment.template.GapPenalty.Type;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
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1 change: 1 addition & 0 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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1 change: 1 addition & 0 deletions ...nt/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
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package org.biojava.nbio.alignment.template;

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

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1 change: 1 addition & 0 deletions ...ment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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2 changes: 2 additions & 0 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/GuideTreeNode.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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1 change: 1 addition & 0 deletions biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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1 change: 1 addition & 0 deletions ...-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
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package org.biojava.nbio.alignment.template;

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

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1 change: 1 addition & 0 deletions ...va-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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1 change: 1 addition & 0 deletions ...ava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
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package org.biojava.nbio.alignment.template;

import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;

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5 changes: 3 additions & 2 deletions biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllGlobal.java
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*/
package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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5 changes: 3 additions & 2 deletions biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignAllLocal.java
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*/
package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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5 changes: 3 additions & 2 deletions biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairGlobal.java
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*/
package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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5 changes: 3 additions & 2 deletions biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookAlignPairLocal.java
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*/
package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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2 changes: 1 addition & 1 deletion biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSA.java
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*/
package org.biojava.nbio.alignment;

import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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5 changes: 3 additions & 2 deletions biojava-alignment/src/test/java/org/biojava/nbio/alignment/CookbookMSAProfiler.java
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*/
package org.biojava.nbio.alignment;

import org.biojava.nbio.core.alignment.matrices.SimpleSubstitutionMatrix;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceScorerType;
import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.PairwiseSequenceScorer;
import org.biojava.nbio.alignment.template.Profile;
import org.biojava.nbio.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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