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lafitalafita
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Organize MultipleAlignment code in a util package
1 parent ed95b34 commit 488d071

23 files changed

Lines changed: 292 additions & 232 deletions

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentDisplay.java‎

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import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
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import org.biojava.nbio.structure.align.multiple.Block;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleSuperimposer;
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import org.biojava.nbio.structure.align.multiple.ReferenceSuperimposer;
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import org.biojava.nbio.structure.align.multiple.util.MultipleSuperimposer;
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import org.biojava.nbio.structure.align.multiple.util.ReferenceSuperimposer;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java‎

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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.align.model.AFPChain;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.align.util.UserConfiguration;
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import org.biojava.nbio.structure.align.webstart.WebStartMain;

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java‎

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import org.biojava.nbio.structure.align.model.AFPChain;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentEnsembleImpl;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentTools;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
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import org.biojava.nbio.structure.gui.events.AlignmentPositionListener;
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import org.biojava.nbio.structure.gui.util.AlignedPosition;

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleStatusDisplay.java‎

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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.align.gui.jmol.JmolTools;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentTools;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
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import org.biojava.nbio.structure.gui.events.AlignmentPositionListener;
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import org.biojava.nbio.structure.gui.util.AlignedPosition;
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‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java‎

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import org.biojava.nbio.structure.align.multiple.Block;
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import org.biojava.nbio.structure.align.multiple.BlockSet;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.webstart.AligUIManager;
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import org.biojava.nbio.structure.jama.Matrix;
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import org.jcolorbrewer.ColorBrewer;

‎biojava-structure/src/main/java/demo/DemoMultipleMC.java‎

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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.align.ce.CeCPMain;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
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import org.biojava.nbio.structure.align.multiple.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain;
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import org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
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import org.biojava.nbio.structure.align.util.AtomCache;
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/**

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java‎

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import java.util.ArrayList;
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import java.util.List;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
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/**
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* General implementation of a {@link Block} that supports any type of
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* alignment with gaps.
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* sequential alignment with gaps.
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*
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* @author Aleix Lafita
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* @since 4.1.0
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}
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protected void updateCoreLength() {
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coreLength = 0;
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//Count how many positions do not have gaps in any structure
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for (int col=0; col<length(); col++){
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boolean core = true;
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for (int str=0; str<size(); str++){
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if (alignRes.get(str).get(col) == null){
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core = false;
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break;
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}
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}
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if (core) coreLength++;
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}
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coreLength = MultipleAlignmentTools.getCorePositions(this).size();
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java‎

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import org.biojava.nbio.structure.StructureTools;
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import org.biojava.nbio.structure.align.helper.AlignTools;
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import org.biojava.nbio.structure.align.model.AFPChain;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.biojava.nbio.structure.jama.Matrix;
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleSuperimposer.java‎

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/ScoresCache.java‎

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import java.util.Set;
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import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
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/**
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* Interface for classes which implement a temporary cache for various numeric
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* scores, e.g. RMSD, TM-Score, etc.

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