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Jose Manuel Duarteandreasprlic
Jose Manuel Duarte
authored and
andreasprlic
committed
Updating to biojava 4
1 parent 17cdf49 commit f337325

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+60
-56
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2 files changed

+60
-56
lines changed

‎wiki/BioJava:CookBook3:PSA.md‎

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@@ -10,16 +10,17 @@ Global alignment
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<java>
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package org.biojava3.alignment;
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package org.biojava.nbio.alignment;
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import java.net.URL;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair; import
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org.biojava3.alignment.template.SubstitutionMatrix; import
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org.biojava3.core.sequence.ProteinSequence; import
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org.biojava3.core.sequence.compound.AminoAcidCompound; import
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org.biojava3.core.sequence.io.FastaReaderHelper;
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import
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org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava.nbio.alignment.template.SequencePair; import
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org.biojava.nbio.alignment.template.SubstitutionMatrix; import
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org.biojava.nbio.core.sequence.ProteinSequence; import
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org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
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org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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public class CookbookAlignPairGlobal {
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@@ -56,16 +57,17 @@ Local alignment
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<java>
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package org.biojava3.alignment;
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package org.biojava.nbio.alignment;
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import java.net.URL;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair; import
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org.biojava3.alignment.template.SubstitutionMatrix; import
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org.biojava3.core.sequence.ProteinSequence; import
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org.biojava3.core.sequence.compound.AminoAcidCompound; import
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org.biojava3.core.sequence.io.FastaReaderHelper;
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import
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org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava.nbio.alignment.template.SequencePair; import
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org.biojava.nbio.alignment.template.SubstitutionMatrix; import
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org.biojava.nbio.core.sequence.ProteinSequence; import
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org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
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org.biojava.nbio.core.sequence.io.FastaReaderHelper;
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public class CookbookAlignPairLocal {
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@@ -109,13 +111,14 @@ package org.biojava3.alignment;
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import java.net.URL; import java.util.ArrayList; import java.util.List;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair; import
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org.biojava3.alignment.template.SubstitutionMatrix; import
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org.biojava3.core.sequence.ProteinSequence; import
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org.biojava3.core.sequence.compound.AminoAcidCompound; import
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org.biojava3.core.sequence.io.FastaReaderHelper; import
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org.biojava3.core.util.ConcurrencyTools;
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import
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org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava.nbio.alignment.template.SequencePair; import
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org.biojava.nbio.alignment.template.SubstitutionMatrix; import
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org.biojava.nbio.core.sequence.ProteinSequence; import
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org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
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org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
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org.biojava.nbio.core.util.ConcurrencyTools;
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public class CookbookAlignAllGlobal {
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@@ -162,13 +165,14 @@ package org.biojava3.alignment;
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import java.net.URL; import java.util.ArrayList; import java.util.List;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair; import
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org.biojava3.alignment.template.SubstitutionMatrix; import
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org.biojava3.core.sequence.ProteinSequence; import
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org.biojava3.core.sequence.compound.AminoAcidCompound; import
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org.biojava3.core.sequence.io.FastaReaderHelper; import
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org.biojava3.core.util.ConcurrencyTools;
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import
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org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava.nbio.alignment.template.SequencePair; import
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org.biojava.nbio.alignment.template.SubstitutionMatrix; import
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org.biojava.nbio.core.sequence.ProteinSequence; import
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org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
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org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
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org.biojava.nbio.core.util.ConcurrencyTools;
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public class CookbookAlignAllLocal {
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‎wiki/BioJava:CookBook3:PSA.mediawiki‎

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<java>
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package org.biojava3.alignment;
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package org.biojava.nbio.alignment;
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import java.net.URL;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair;
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import org.biojava3.alignment.template.SubstitutionMatrix;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.io.FastaReaderHelper;
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import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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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.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;
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public class CookbookAlignPairGlobal {
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<java>
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package org.biojava3.alignment;
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package org.biojava.nbio.alignment;
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import java.net.URL;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair;
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import org.biojava3.alignment.template.SubstitutionMatrix;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.io.FastaReaderHelper;
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import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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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.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;
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public class CookbookAlignPairLocal {
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import java.util.ArrayList;
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import java.util.List;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair;
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import org.biojava3.alignment.template.SubstitutionMatrix;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.io.FastaReaderHelper;
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import org.biojava3.core.util.ConcurrencyTools;
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import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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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.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;
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import org.biojava.nbio.core.util.ConcurrencyTools;
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public class CookbookAlignAllGlobal {
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import java.util.ArrayList;
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import java.util.List;
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import org.biojava3.alignment.Alignments.PairwiseSequenceAlignerType;
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import org.biojava3.alignment.template.SequencePair;
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import org.biojava3.alignment.template.SubstitutionMatrix;
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import org.biojava3.core.sequence.ProteinSequence;
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import org.biojava3.core.sequence.compound.AminoAcidCompound;
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import org.biojava3.core.sequence.io.FastaReaderHelper;
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import org.biojava3.core.util.ConcurrencyTools;
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import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
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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.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;
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import org.biojava.nbio.core.util.ConcurrencyTools;
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public class CookbookAlignAllLocal {
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