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Major mods in NCBIQBlastAlignmentProperties: it is now responsible for basic sanity checks of these properties instead of NCBIQBlastService. Also added get/set methods for blastp matrix selection and associated gap creation/extension costs.
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9476 7c6358e6-4a41-0410-a743-a5b2a554c398
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5 files changed

Lines changed: 449 additions & 155 deletions

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‎biojava3-ws/src/main/java/org/biojava3/ws/alignment/RemotePairwiseAlignmentProperties.java‎

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package org.biojava3.ws.alignment;
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import java.io.Serializable;
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import java.util.Properties;
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import java.util.Set;
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/**
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* wrapper methods that actually call either getAlignementOption or setAlignementOption
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* with specific values for parameter names and checking values for options.
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*
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* For an example, go see RemoteQBlastProperties
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* For an example, go see NCBIQBlastProperties
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*
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* @author Sylvain Foisy, Diploide BioIT
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* @since Biojava 3

‎biojava3-ws/src/main/java/org/biojava3/ws/alignment/RemotePairwiseAlignmentService.java‎

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import java.io.InputStream;
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//import org.biojavax.bio.seq.RichSequence;
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import org.biojava3.core.sequence.template.Sequence;
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import org.biojava3.core.sequence.template.Compound;
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/**
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* This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
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*
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*
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* @throws Exception
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*/
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public String sendAlignmentRequest(Sequence seq, RemotePairwiseAlignmentProperties rpa) throws Exception;
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public String sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) throws Exception;
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/**
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* Doing the actual analysis on the instantiated service using specified parameters on the string representation

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