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josemduartejosemduarte
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Merge commit '248cc08c7fbbdc02249bcac0f10481127b7d3ac7'
2 parents 4dadf22 + 248cc08 commit 3abb93f

128 files changed

Lines changed: 849339 additions & 152 deletions

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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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