<xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
</xs:complexType>
</xs:element>
+ <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="sequenceRef" type="xs:string" />
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="axis" minOccurs="3" maxOccurs="3">
+ <xs:annotation>
+ <xs:documentation>
+ endpoints of X, Y and Z axes in that order
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMin">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMax">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="pcaData" type="jv:PcaDataType" />
+ </xs:sequence>
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="scoreModelName" type="xs:string" />
+ <xs:attribute name="xDim" type="xs:int" />
+ <xs:attribute name="yDim" type="xs:int" />
+ <xs:attribute name="zDim" type="xs:int" />
+ <xs:attribute name="bgColour" type="xs:int" />
+ <xs:attribute name="scaleFactor" type="xs:float" />
+ <xs:attribute name="showLabels" type="xs:boolean" />
+ <xs:attribute name="linkToAllViews" type="xs:boolean" />
+ <xs:attributeGroup ref="jv:SimilarityParams" />
+ <xs:attributeGroup ref="jv:swingwindow" />
+ </xs:complexType>
+ </xs:element>
<xs:element name="FeatureSettings" minOccurs="0">
<xs:complexType>
<xs:sequence>
<xs:attribute name="predefinedColours" type="xs:boolean"
use="optional" />
</xs:complexType>
-
+ <xs:attributeGroup name="SimilarityParams">
+ <xs:annotation>
+ <xs:documentation>
+ parameters that condition a similarity score calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="includeGaps" type="xs:boolean" />
+ <xs:attribute name="matchGaps" type="xs:boolean" />
+ <xs:attribute name="includeGappedColumns" type="xs:boolean" />
+ <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
+ </xs:attributeGroup>
+ <xs:attributeGroup name="position">
+ <xs:attribute name="xPos" type="xs:float" />
+ <xs:attribute name="yPos" type="xs:float" />
+ <xs:attribute name="zPos" type="xs:float" />
+ </xs:attributeGroup>
+ <xs:complexType name="PcaDataType">
+ <xs:annotation>
+ <xs:documentation>
+ The results of a PCA calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="details" type="xs:string">
+ <xs:annotation>
+ <xs:documentation>
+ The text report of the calculation
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="eigenMatrixD" type="jv:DoubleVector" />
+ <xs:element name="eigenMatrixE" type="jv:DoubleVector" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleVector">
+ <xs:sequence>
+ <xs:element name="d" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleMatrix">
+ <xs:sequence>
+ <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
+ </xs:sequence>
+ <xs:attribute name="rows" type="xs:int" />
+ <xs:attribute name="columns" type="xs:int" />
+ </xs:complexType>
</xs:schema>
*/
package jalview.gui;
+import static jalview.math.RotatableMatrix.Axis.X;
+import static jalview.math.RotatableMatrix.Axis.Y;
+import static jalview.math.RotatableMatrix.Axis.Z;
+
import jalview.analysis.Conservation;
+import jalview.analysis.PCA;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemabinding.version2.AnnotationColours;
import jalview.schemabinding.version2.AnnotationElement;
+import jalview.schemabinding.version2.Axis;
import jalview.schemabinding.version2.CalcIdParam;
import jalview.schemabinding.version2.CompoundMatcher;
import jalview.schemabinding.version2.DBRef;
+import jalview.schemabinding.version2.DoubleMatrix;
+import jalview.schemabinding.version2.EigenMatrix;
+import jalview.schemabinding.version2.EigenMatrixD;
+import jalview.schemabinding.version2.EigenMatrixE;
import jalview.schemabinding.version2.Features;
import jalview.schemabinding.version2.Group;
import jalview.schemabinding.version2.HiddenColumns;
import jalview.schemabinding.version2.MatchCondition;
import jalview.schemabinding.version2.MatcherSet;
import jalview.schemabinding.version2.OtherData;
+import jalview.schemabinding.version2.PairwiseMatrix;
+import jalview.schemabinding.version2.PcaData;
+import jalview.schemabinding.version2.PcaViewer;
import jalview.schemabinding.version2.PdbentryItem;
import jalview.schemabinding.version2.Pdbids;
import jalview.schemabinding.version2.Property;
import jalview.schemabinding.version2.RnaViewer;
+import jalview.schemabinding.version2.Row;
import jalview.schemabinding.version2.SecondaryStructure;
+import jalview.schemabinding.version2.SeqPointMax;
+import jalview.schemabinding.version2.SeqPointMin;
import jalview.schemabinding.version2.Sequence;
+import jalview.schemabinding.version2.SequencePoint;
import jalview.schemabinding.version2.SequenceSet;
import jalview.schemabinding.version2.SequenceSetProperties;
import jalview.schemabinding.version2.Setting;
import jalview.util.jarInputStreamProvider;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
}
}
+ /*
+ * save PCA viewers
+ */
+ if (!storeDS && Desktop.desktop != null)
+ {
+ for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+ {
+ if (frame instanceof PCAPanel)
+ {
+ PCAPanel panel = (PCAPanel) frame;
+ if (panel.av.getAlignment() == jal)
+ {
+ savePCA(panel, jms);
+ }
+ }
+ }
+ }
+
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
}
/**
+ * Writes PCA viewer attributes and computed values to an XML model object and adds it to the JalviewModel. Any exceptions are reported by logging.
+ */
+ protected void savePCA(PCAPanel panel, JalviewModelSequence jms)
+ {
+ try
+ {
+ PcaViewer viewer = new PcaViewer();
+ viewer.setHeight(panel.getHeight());
+ viewer.setWidth(panel.getWidth());
+ viewer.setXpos(panel.getX());
+ viewer.setYpos(panel.getY());
+ viewer.setTitle(panel.getTitle());
+ PCAModel pcaModel = panel.pcaModel;
+ viewer.setScoreModelName(pcaModel.getScoreModelName());
+ viewer.setXDim(panel.getSelectedDimensionIndex(X));
+ viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+ viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+ viewer.setBgColour(panel.rc.getBackgroundColour().getRGB());
+ viewer.setScaleFactor(panel.rc.scaleFactor);
+ float[] spMin = panel.rc.getSeqMin();
+ SeqPointMin spmin = new SeqPointMin();
+ spmin.setXPos(spMin[0]);
+ spmin.setYPos(spMin[1]);
+ spmin.setZPos(spMin[2]);
+ viewer.setSeqPointMin(spmin);
+ float[] spMax = panel.rc.getSeqMax();
+ SeqPointMax spmax = new SeqPointMax();
+ spmax.setXPos(spMax[0]);
+ spmax.setYPos(spMax[1]);
+ spmax.setZPos(spMax[2]);
+ viewer.setSeqPointMax(spmax);
+ viewer.setShowLabels(panel.rc.showLabels);
+ viewer.setLinkToAllViews(panel.rc.applyToAllViews);
+ SimilarityParamsI sp = pcaModel.getSimilarityParameters();
+ viewer.setIncludeGaps(sp.includeGaps());
+ viewer.setMatchGaps(sp.matchGaps());
+ viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+ viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+
+ /*
+ * sequence points on display
+ */
+ for (jalview.datamodel.SequencePoint spt : pcaModel
+ .getSequencePoints())
+ {
+ SequencePoint point = new SequencePoint();
+ point.setSequenceRef(seqHash(spt.getSequence()));
+ point.setXPos(spt.coord.x);
+ point.setYPos(spt.coord.y);
+ point.setZPos(spt.coord.z);
+ viewer.addSequencePoint(point);
+ }
+
+ /*
+ * (end points of) axes on display
+ */
+ for (Point p : panel.rc.axisEndPoints)
+ {
+ Axis axis = new Axis();
+ axis.setXPos(p.x);
+ axis.setYPos(p.y);
+ axis.setZPos(p.z);
+ viewer.addAxis(axis);
+ }
+
+ /*
+ * raw PCA data
+ */
+ PcaData data = new PcaData();
+ viewer.setPcaData(data);
+ PCA pca = pcaModel.getPcaData();
+ data.setDetails(pca.getDetails());
+ MatrixI m = pca.getEigenmatrix();
+ EigenMatrix eigenMatrix = new EigenMatrix();
+ eigenMatrix.setRows(m.height());
+ eigenMatrix.setColumns(m.width());
+ data.setEigenMatrix(eigenMatrix);
+ for (int i = 0; i < m.height(); i++)
+ {
+ Row row = new Row();
+ for (int j = 0; j < m.width(); j++)
+ {
+ row.addD(m.getValue(i, j));
+ }
+ eigenMatrix.addRow(row);
+ }
+ EigenMatrixD eigenMatrixD = new EigenMatrixD();
+ eigenMatrixD.setD(m.getD());
+ data.setEigenMatrixD(eigenMatrixD);
+ EigenMatrixE eigenMatrixE = new EigenMatrixE();
+ eigenMatrixE.setD(m.getE());
+ data.setEigenMatrixE(eigenMatrixE);
+
+ PairwiseMatrix pm = new PairwiseMatrix();
+ m = pca.getPairwiseScores();
+ pm.setRows(m.height());
+ pm.setColumns(m.width());
+ data.setPairwiseMatrix(pm);
+ for (int i = 0; i < m.height(); i++)
+ {
+ Row row = new Row();
+ for (int j = 0; j < m.width(); j++)
+ {
+ row.addD(m.getValue(i, j));
+ }
+ pm.addRow(row);
+ }
+
+ jms.addPcaViewer(viewer);
+ } catch (Throwable t)
+ {
+ Cache.log.error("Error saving PCA: " + t.getMessage());
+ }
+ }
+
+ /**
* Save any Varna viewers linked to this sequence. Writes an rnaViewer element
* for each viewer, with
* <ul>
if (loadTreesAndStructures)
{
loadTrees(jms, view, af, av, ap);
+ loadPCAViewers(jms, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
tp.setTitle(tree.getTitle());
tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
tree.getWidth(), tree.getHeight()));
- tp.av = av; // af.viewport; // TODO: verify 'associate with all
- // views'
- // works still
+ tp.av = av;
tp.treeCanvas.av = av; // af.viewport;
tp.treeCanvas.ap = ap; // af.alignPanel;
}
/**
+ * Loads any saved PCA viewers
+ *
+ * @param jms
+ * @param ap
+ */
+ protected void loadPCAViewers(JalviewModelSequence jms, AlignmentPanel ap)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getPcaViewerCount(); t++)
+ {
+ PcaViewer viewer = jms.getPcaViewer(t);
+ String modelName = viewer.getScoreModelName();
+ SimilarityParamsI params = new SimilarityParams(
+ viewer.isIncludeGappedColumns(),
+ viewer.isMatchGaps(), viewer.isIncludeGaps(),
+ viewer.isDenominateByShortestLength());
+
+ /*
+ * create the panel (without computing the PCA)
+ */
+ PCAPanel panel = new PCAPanel(ap, modelName, params);
+
+ panel.setTitle(viewer.getTitle());
+ panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(),
+ viewer.getWidth(), viewer.getHeight()));
+
+ boolean showLabels = viewer.isShowLabels();
+ panel.setShowLabels(showLabels);
+ panel.rc.showLabels = showLabels;
+ panel.rc.bgColour = new Color(viewer.getBgColour());
+ panel.rc.applyToAllViews = viewer.isLinkToAllViews();
+
+ /*
+ * load PCA output data
+ */
+ ScoreModelI scoreModel = ScoreModels.getInstance()
+ .getScoreModel(modelName, ap);
+ PCA pca = new PCA(null, scoreModel, params);
+ PcaData pcaData = viewer.getPcaData();
+ pca.setDetails(pcaData.getDetails());
+ MatrixI pairwise = loadMatrix(pcaData.getPairwiseMatrix());
+ pca.setPairwiseScores(pairwise);
+ MatrixI result = loadMatrix(pcaData.getEigenMatrix());
+ result.setD(pcaData.getEigenMatrixD().getD());
+ result.setE(pcaData.getEigenMatrixE().getD());
+ pca.setEigenmatrix(result);
+ panel.pcaModel.setPCA(pca);
+
+ /*
+ * add the sequence points for the PCA display
+ */
+ List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
+ for (SequencePoint sp : viewer.getSequencePoint())
+ {
+ String seqId = sp.getSequenceRef();
+ SequenceI seq = seqRefIds.get(seqId);
+ if (seq == null)
+ {
+ throw new IllegalStateException(
+ "Unmatched seqref for PCA: " + seqId);
+ }
+ Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
+ jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
+ seq, pt);
+ seqPoints.add(seqPoint);
+ }
+ panel.rc.setPoints(seqPoints, seqPoints.size());
+
+ /*
+ * set min-max ranges and scale after setPoints (which recomputes them)
+ */
+ panel.rc.scaleFactor = viewer.getScaleFactor();
+ SeqPointMin spMin = viewer.getSeqPointMin();
+ float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
+ spMin.getZPos() };
+ SeqPointMax spMax = viewer.getSeqPointMax();
+ float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
+ spMax.getZPos() };
+ panel.rc.setSeqMinMax(min, max);
+
+ // todo: hold points list in PCAModel only
+ panel.pcaModel.setSequencePoints(seqPoints);
+
+ panel.setSelectedDimensionIndex(viewer.getXDim(), X);
+ panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
+ panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
+
+ // is this duplication needed?
+ panel.top = seqPoints.size() - 1;
+ panel.pcaModel.setTop(seqPoints.size() - 1);
+
+ /*
+ * add the axes' end points for the display
+ */
+ for (int i = 0; i < 3; i++)
+ {
+ Axis axis = viewer.getAxis(i);
+ panel.rc.axisEndPoints[i] = new Point(axis.getXPos(),
+ axis.getYPos(), axis.getZPos());
+ }
+
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), 475, 450);
+ }
+ } catch (Exception ex)
+ {
+ Cache.log.error("Error loading PCA: " + ex.toString());
+ }
+ }
+
+ /**
+ * Loads XML matrix data into a new Matrix object
+ *
+ * @param mData
+ * @return
+ */
+ protected MatrixI loadMatrix(DoubleMatrix mData)
+ {
+ int rows = mData.getRows();
+ double[][] vals = new double[rows][];
+
+ for (int i = 0; i < rows; i++)
+ {
+ vals[i] = mData.getRow(i).getD();
+ }
+
+ MatrixI m = new Matrix(vals);
+ return m;
+ }
+
+ /**
* Populates an XML model of the feature colour scheme for one feature type
*
* @param featureType
-#Thu Dec 14 09:10:14 GMT 2017
+#Fri May 04 15:18:48 BST 2018
+jalview.schemabinding.version2.SeqPointMax=jalview.schemabinding.version2.descriptors.SeqPointMaxDescriptor
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor
jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor
jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
+jalview.schemabinding.version2.SequencePoint=jalview.schemabinding.version2.descriptors.SequencePointDescriptor
jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descriptors.OtherDataDescriptor
jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor
+jalview.schemabinding.version2.Axis=jalview.schemabinding.version2.descriptors.AxisDescriptor
jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor
jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor
+jalview.schemabinding.version2.Row=jalview.schemabinding.version2.descriptors.RowDescriptor
jalview.schemabinding.version2.FeatureMatcherSet=jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor
+jalview.schemabinding.version2.EigenMatrix=jalview.schemabinding.version2.descriptors.EigenMatrixDescriptor
jalview.schemabinding.version2.SecondaryStructure=jalview.schemabinding.version2.descriptors.SecondaryStructureDescriptor
jalview.schemabinding.version2.MatchCondition=jalview.schemabinding.version2.descriptors.MatchConditionDescriptor
jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor
jalview.schemabinding.version2.MapListType=jalview.schemabinding.version2.descriptors.MapListTypeDescriptor
jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor
jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor
+jalview.schemabinding.version2.DoubleMatrix=jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor
jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor
jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor
+jalview.schemabinding.version2.SymmMatrix=jalview.schemabinding.version2.descriptors.SymmMatrixDescriptor
jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor
+jalview.schemabinding.version2.SeqPointMin=jalview.schemabinding.version2.descriptors.SeqPointMinDescriptor
jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor
jalview.schemabinding.version2.MatcherSet=jalview.schemabinding.version2.descriptors.MatcherSetDescriptor
jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor
+jalview.schemabinding.version2.Filter=jalview.schemabinding.version2.descriptors.FilterDescriptor
jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.version2.descriptors.WebServiceParameterSetDescriptor
jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor
-jalview.schemabinding.version2.Filter=jalview.schemabinding.version2.descriptors.FilterDescriptor
jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor
jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor
jalview.schemabinding.version2.AnnotationColourScheme=jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor
jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor
+jalview.schemabinding.version2.PcaData=jalview.schemabinding.version2.descriptors.PcaDataDescriptor
+jalview.schemabinding.version2.PcaViewer=jalview.schemabinding.version2.descriptors.PcaViewerDescriptor
jalview.schemabinding.version2.CompoundMatcher=jalview.schemabinding.version2.descriptors.CompoundMatcherDescriptor
jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor
jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor
jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor
jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor
jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor
+jalview.schemabinding.version2.PcaDataType=jalview.schemabinding.version2.descriptors.PcaDataTypeDescriptor
jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor
jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor
+jalview.schemabinding.version2.EigenMatrixE=jalview.schemabinding.version2.descriptors.EigenMatrixEDescriptor
jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor
+jalview.schemabinding.version2.EigenMatrixD=jalview.schemabinding.version2.descriptors.EigenMatrixDDescriptor
+jalview.schemabinding.version2.PairwiseMatrix=jalview.schemabinding.version2.descriptors.PairwiseMatrixDescriptor
jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor
+jalview.schemabinding.version2.DoubleVector=jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor
jalview.schemabinding.version2.FeatureMatcher=jalview.schemabinding.version2.descriptors.FeatureMatcherDescriptor
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * endpoints of X, Y and Z axes in that order
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Axis implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Axis()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Axis
+ */
+ public static jalview.schemabinding.version2.Axis unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Axis) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Axis.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class DoubleMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleMatrix implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _rows.
+ */
+ private int _rows;
+
+ /**
+ * keeps track of state for field: _rows
+ */
+ private boolean _has_rows;
+
+ /**
+ * Field _columns.
+ */
+ private int _columns;
+
+ /**
+ * keeps track of state for field: _columns
+ */
+ private boolean _has_columns;
+
+ /**
+ * Field _rowList.
+ */
+ private java.util.Vector _rowList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleMatrix()
+ {
+ super();
+ this._rowList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vRow
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addRow(final jalview.schemabinding.version2.Row vRow)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._rowList.addElement(vRow);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRow
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addRow(final int index,
+ final jalview.schemabinding.version2.Row vRow)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._rowList.add(index, vRow);
+ }
+
+ /**
+ */
+ public void deleteColumns()
+ {
+ this._has_columns = false;
+ }
+
+ /**
+ */
+ public void deleteRows()
+ {
+ this._has_rows = false;
+ }
+
+ /**
+ * Method enumerateRow.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Row elements
+ */
+ public java.util.Enumeration enumerateRow()
+ {
+ return this._rowList.elements();
+ }
+
+ /**
+ * Returns the value of field 'columns'.
+ *
+ * @return the value of field 'Columns'.
+ */
+ public int getColumns()
+ {
+ return this._columns;
+ }
+
+ /**
+ * Method getRow.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Row at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Row getRow(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rowList.size())
+ {
+ throw new IndexOutOfBoundsException("getRow: Index value '" + index
+ + "' not in range [0.." + (this._rowList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Row) _rowList.get(index);
+ }
+
+ /**
+ * Method getRow.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Row[] getRow()
+ {
+ jalview.schemabinding.version2.Row[] array = new jalview.schemabinding.version2.Row[0];
+ return (jalview.schemabinding.version2.Row[]) this._rowList
+ .toArray(array);
+ }
+
+ /**
+ * Method getRowCount.
+ *
+ * @return the size of this collection
+ */
+ public int getRowCount()
+ {
+ return this._rowList.size();
+ }
+
+ /**
+ * Returns the value of field 'rows'.
+ *
+ * @return the value of field 'Rows'.
+ */
+ public int getRows()
+ {
+ return this._rows;
+ }
+
+ /**
+ * Method hasColumns.
+ *
+ * @return true if at least one Columns has been added
+ */
+ public boolean hasColumns()
+ {
+ return this._has_columns;
+ }
+
+ /**
+ * Method hasRows.
+ *
+ * @return true if at least one Rows has been added
+ */
+ public boolean hasRows()
+ {
+ return this._has_rows;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllRow()
+ {
+ this._rowList.clear();
+ }
+
+ /**
+ * Method removeRow.
+ *
+ * @param vRow
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeRow(final jalview.schemabinding.version2.Row vRow)
+ {
+ boolean removed = _rowList.remove(vRow);
+ return removed;
+ }
+
+ /**
+ * Method removeRowAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Row removeRowAt(final int index)
+ {
+ java.lang.Object obj = this._rowList.remove(index);
+ return (jalview.schemabinding.version2.Row) obj;
+ }
+
+ /**
+ * Sets the value of field 'columns'.
+ *
+ * @param columns
+ * the value of field 'columns'.
+ */
+ public void setColumns(final int columns)
+ {
+ this._columns = columns;
+ this._has_columns = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRow
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setRow(final int index,
+ final jalview.schemabinding.version2.Row vRow)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rowList.size())
+ {
+ throw new IndexOutOfBoundsException("setRow: Index value '" + index
+ + "' not in range [0.." + (this._rowList.size() - 1) + "]");
+ }
+
+ this._rowList.set(index, vRow);
+ }
+
+ /**
+ *
+ *
+ * @param vRowArray
+ */
+ public void setRow(final jalview.schemabinding.version2.Row[] vRowArray)
+ {
+ // -- copy array
+ _rowList.clear();
+
+ for (int i = 0; i < vRowArray.length; i++)
+ {
+ this._rowList.add(vRowArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'rows'.
+ *
+ * @param rows
+ * the value of field 'rows'.
+ */
+ public void setRows(final int rows)
+ {
+ this._rows = rows;
+ this._has_rows = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleMatrix
+ */
+ public static jalview.schemabinding.version2.DoubleMatrix unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleMatrix) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.DoubleMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class DoubleVector.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleVector implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _dList.
+ */
+ private java.util.Vector _dList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleVector()
+ {
+ super();
+ this._dList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vD
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addD(final double vD)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._dList.addElement(new java.lang.Double(vD));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vD
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addD(final int index, final double vD)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._dList.add(index, new java.lang.Double(vD));
+ }
+
+ /**
+ * Method enumerateD.
+ *
+ * @return an Enumeration over all double elements
+ */
+ public java.util.Enumeration enumerateD()
+ {
+ return this._dList.elements();
+ }
+
+ /**
+ * Method getD.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the double at the given index
+ */
+ public double getD(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._dList.size())
+ {
+ throw new IndexOutOfBoundsException("getD: Index value '" + index
+ + "' not in range [0.." + (this._dList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Double) _dList.get(index)).doubleValue();
+ }
+
+ /**
+ * Method getD.Returns the contents of the collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public double[] getD()
+ {
+ int size = this._dList.size();
+ double[] array = new double[size];
+ java.util.Iterator iter = _dList.iterator();
+ for (int index = 0; index < size; index++)
+ {
+ array[index] = ((java.lang.Double) iter.next()).doubleValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getDCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDCount()
+ {
+ return this._dList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllD()
+ {
+ this._dList.clear();
+ }
+
+ /**
+ * Method removeD.
+ *
+ * @param vD
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeD(final double vD)
+ {
+ boolean removed = _dList.remove(new java.lang.Double(vD));
+ return removed;
+ }
+
+ /**
+ * Method removeDAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public double removeDAt(final int index)
+ {
+ java.lang.Object obj = this._dList.remove(index);
+ return ((java.lang.Double) obj).doubleValue();
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vD
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setD(final int index, final double vD)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._dList.size())
+ {
+ throw new IndexOutOfBoundsException("setD: Index value '" + index
+ + "' not in range [0.." + (this._dList.size() - 1) + "]");
+ }
+
+ this._dList.set(index, new java.lang.Double(vD));
+ }
+
+ /**
+ *
+ *
+ * @param vDArray
+ */
+ public void setD(final double[] vDArray)
+ {
+ // -- copy array
+ _dList.clear();
+
+ for (int i = 0; i < vDArray.length; i++)
+ {
+ this._dList.add(new java.lang.Double(vDArray[i]));
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleVector
+ */
+ public static jalview.schemabinding.version2.DoubleVector unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleVector) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.DoubleVector.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class EigenMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrix extends DoubleMatrix
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrix()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleMatrix
+ */
+ public static jalview.schemabinding.version2.DoubleMatrix unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleMatrix) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.EigenMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class EigenMatrixD.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrixD extends DoubleVector
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrixD()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleVector
+ */
+ public static jalview.schemabinding.version2.DoubleVector unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleVector) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.EigenMatrixD.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class EigenMatrixE.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrixE extends DoubleVector
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrixE()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleVector
+ */
+ public static jalview.schemabinding.version2.DoubleVector unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleVector) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.EigenMatrixE.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
private java.util.Vector _treeList;
/**
+ * Field _pcaViewerList.
+ */
+ private java.util.Vector _pcaViewerList;
+
+ /**
* Field _featureSettings.
*/
private jalview.schemabinding.version2.FeatureSettings _featureSettings;
this._viewportList = new java.util.Vector();
this._userColoursList = new java.util.Vector();
this._treeList = new java.util.Vector();
+ this._pcaViewerList = new java.util.Vector();
}
// -----------/
/**
*
*
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPcaViewer(
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pcaViewerList.addElement(vPcaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPcaViewer(final int index,
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pcaViewerList.add(index, vPcaViewer);
+ }
+
+ /**
+ *
+ *
* @param vTree
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
}
/**
+ * Method enumeratePcaViewer.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.PcaViewer
+ * elements
+ */
+ public java.util.Enumeration enumeratePcaViewer()
+ {
+ return this._pcaViewerList.elements();
+ }
+
+ /**
* Method enumerateTree.
*
* @return an Enumeration over all jalview.schemabinding.version2.Tree
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
}
/**
+ * Method getPcaViewer.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.PcaViewer at the
+ * given index
+ */
+ public jalview.schemabinding.version2.PcaViewer getPcaViewer(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pcaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getPcaViewer: Index value '" + index + "' not in range [0.."
+ + (this._pcaViewerList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.PcaViewer) _pcaViewerList
+ .get(index);
+ }
+
+ /**
+ * Method getPcaViewer.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.PcaViewer[] getPcaViewer()
+ {
+ jalview.schemabinding.version2.PcaViewer[] array = new jalview.schemabinding.version2.PcaViewer[0];
+ return (jalview.schemabinding.version2.PcaViewer[]) this._pcaViewerList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPcaViewerCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPcaViewerCount()
+ {
+ return this._pcaViewerList.size();
+ }
+
+ /**
* Method getTree.
*
* @param index
* @return the value of the jalview.schemabinding.version2.Viewport at the
* given index
*/
- public jalview.schemabinding.version2.Viewport getViewport(final int index)
- throws java.lang.IndexOutOfBoundsException
+ public jalview.schemabinding.version2.Viewport getViewport(
+ final int index) throws java.lang.IndexOutOfBoundsException
{
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.Viewport) _viewportList
}
/**
- */
+ */
public void removeAllJGroup()
{
this._JGroupList.clear();
}
/**
- */
+ */
public void removeAllJSeq()
{
this._JSeqList.clear();
}
/**
- */
+ */
+ public void removeAllPcaViewer()
+ {
+ this._pcaViewerList.clear();
+ }
+
+ /**
+ */
public void removeAllTree()
{
this._treeList.clear();
}
/**
- */
+ */
public void removeAllUserColours()
{
this._userColoursList.clear();
}
/**
- */
+ */
public void removeAllViewport()
{
this._viewportList.clear();
}
/**
+ * Method removePcaViewer.
+ *
+ * @param vPcaViewer
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePcaViewer(
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ {
+ boolean removed = _pcaViewerList.remove(vPcaViewer);
+ return removed;
+ }
+
+ /**
+ * Method removePcaViewerAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.PcaViewer removePcaViewerAt(
+ final int index)
+ {
+ java.lang.Object obj = this._pcaViewerList.remove(index);
+ return (jalview.schemabinding.version2.PcaViewer) obj;
+ }
+
+ /**
* Method removeTree.
*
* @param vTree
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
this._JGroupList.set(index, vJGroup);
*
* @param vJSeqArray
*/
- public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+ public void setJSeq(
+ final jalview.schemabinding.version2.JSeq[] vJSeqArray)
{
// -- copy array
_JSeqList.clear();
*
*
* @param index
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPcaViewer(final int index,
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pcaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setPcaViewer: Index value '" + index + "' not in range [0.."
+ + (this._pcaViewerList.size() - 1) + "]");
+ }
+
+ this._pcaViewerList.set(index, vPcaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param vPcaViewerArray
+ */
+ public void setPcaViewer(
+ final jalview.schemabinding.version2.PcaViewer[] vPcaViewerArray)
+ {
+ // -- copy array
+ _pcaViewerList.clear();
+
+ for (int i = 0; i < vPcaViewerArray.length; i++)
+ {
+ this._pcaViewerList.add(vPcaViewerArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
* @param vTree
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*
* @param vTreeArray
*/
- public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+ public void setTree(
+ final jalview.schemabinding.version2.Tree[] vTreeArray)
{
// -- copy array
_treeList.clear();
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
this._viewportList.set(index, vViewport);
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PairwiseMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PairwiseMatrix extends DoubleMatrix
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PairwiseMatrix()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleMatrix
+ */
+ public static jalview.schemabinding.version2.DoubleMatrix unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleMatrix) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PairwiseMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PcaData.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaData extends PcaDataType implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaData()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.PcaDataType
+ */
+ public static jalview.schemabinding.version2.PcaDataType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.PcaDataType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PcaData.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * The results of a PCA calculation
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaDataType implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * The text report of the calculation
+ *
+ */
+ private java.lang.String _details;
+
+ /**
+ * Field _pairwiseMatrix.
+ */
+ private jalview.schemabinding.version2.PairwiseMatrix _pairwiseMatrix;
+
+ /**
+ * Field _eigenMatrix.
+ */
+ private jalview.schemabinding.version2.EigenMatrix _eigenMatrix;
+
+ /**
+ * Field _eigenMatrixD.
+ */
+ private jalview.schemabinding.version2.EigenMatrixD _eigenMatrixD;
+
+ /**
+ * Field _eigenMatrixE.
+ */
+ private jalview.schemabinding.version2.EigenMatrixE _eigenMatrixE;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaDataType()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Returns the value of field 'details'. The field 'details' has the following
+ * description: The text report of the calculation
+ *
+ *
+ * @return the value of field 'Details'.
+ */
+ public java.lang.String getDetails()
+ {
+ return this._details;
+ }
+
+ /**
+ * Returns the value of field 'eigenMatrix'.
+ *
+ * @return the value of field 'EigenMatrix'.
+ */
+ public jalview.schemabinding.version2.EigenMatrix getEigenMatrix()
+ {
+ return this._eigenMatrix;
+ }
+
+ /**
+ * Returns the value of field 'eigenMatrixD'.
+ *
+ * @return the value of field 'EigenMatrixD'.
+ */
+ public jalview.schemabinding.version2.EigenMatrixD getEigenMatrixD()
+ {
+ return this._eigenMatrixD;
+ }
+
+ /**
+ * Returns the value of field 'eigenMatrixE'.
+ *
+ * @return the value of field 'EigenMatrixE'.
+ */
+ public jalview.schemabinding.version2.EigenMatrixE getEigenMatrixE()
+ {
+ return this._eigenMatrixE;
+ }
+
+ /**
+ * Returns the value of field 'pairwiseMatrix'.
+ *
+ * @return the value of field 'PairwiseMatrix'.
+ */
+ public jalview.schemabinding.version2.PairwiseMatrix getPairwiseMatrix()
+ {
+ return this._pairwiseMatrix;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'details'. The field 'details' has the following
+ * description: The text report of the calculation
+ *
+ *
+ * @param details
+ * the value of field 'details'.
+ */
+ public void setDetails(final java.lang.String details)
+ {
+ this._details = details;
+ }
+
+ /**
+ * Sets the value of field 'eigenMatrix'.
+ *
+ * @param eigenMatrix
+ * the value of field 'eigenMatrix'.
+ */
+ public void setEigenMatrix(
+ final jalview.schemabinding.version2.EigenMatrix eigenMatrix)
+ {
+ this._eigenMatrix = eigenMatrix;
+ }
+
+ /**
+ * Sets the value of field 'eigenMatrixD'.
+ *
+ * @param eigenMatrixD
+ * the value of field 'eigenMatrixD'.
+ */
+ public void setEigenMatrixD(
+ final jalview.schemabinding.version2.EigenMatrixD eigenMatrixD)
+ {
+ this._eigenMatrixD = eigenMatrixD;
+ }
+
+ /**
+ * Sets the value of field 'eigenMatrixE'.
+ *
+ * @param eigenMatrixE
+ * the value of field 'eigenMatrixE'.
+ */
+ public void setEigenMatrixE(
+ final jalview.schemabinding.version2.EigenMatrixE eigenMatrixE)
+ {
+ this._eigenMatrixE = eigenMatrixE;
+ }
+
+ /**
+ * Sets the value of field 'pairwiseMatrix'.
+ *
+ * @param pairwiseMatrix
+ * the value of field 'pairwiseMatrix'.
+ */
+ public void setPairwiseMatrix(
+ final jalview.schemabinding.version2.PairwiseMatrix pairwiseMatrix)
+ {
+ this._pairwiseMatrix = pairwiseMatrix;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.PcaDataType
+ */
+ public static jalview.schemabinding.version2.PcaDataType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.PcaDataType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PcaDataType.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PcaViewer.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaViewer implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _scoreModelName.
+ */
+ private java.lang.String _scoreModelName;
+
+ /**
+ * Field _xDim.
+ */
+ private int _xDim;
+
+ /**
+ * keeps track of state for field: _xDim
+ */
+ private boolean _has_xDim;
+
+ /**
+ * Field _yDim.
+ */
+ private int _yDim;
+
+ /**
+ * keeps track of state for field: _yDim
+ */
+ private boolean _has_yDim;
+
+ /**
+ * Field _zDim.
+ */
+ private int _zDim;
+
+ /**
+ * keeps track of state for field: _zDim
+ */
+ private boolean _has_zDim;
+
+ /**
+ * Field _bgColour.
+ */
+ private int _bgColour;
+
+ /**
+ * keeps track of state for field: _bgColour
+ */
+ private boolean _has_bgColour;
+
+ /**
+ * Field _scaleFactor.
+ */
+ private float _scaleFactor;
+
+ /**
+ * keeps track of state for field: _scaleFactor
+ */
+ private boolean _has_scaleFactor;
+
+ /**
+ * Field _showLabels.
+ */
+ private boolean _showLabels;
+
+ /**
+ * keeps track of state for field: _showLabels
+ */
+ private boolean _has_showLabels;
+
+ /**
+ * Field _linkToAllViews.
+ */
+ private boolean _linkToAllViews;
+
+ /**
+ * keeps track of state for field: _linkToAllViews
+ */
+ private boolean _has_linkToAllViews;
+
+ /**
+ * Field _includeGaps.
+ */
+ private boolean _includeGaps;
+
+ /**
+ * keeps track of state for field: _includeGaps
+ */
+ private boolean _has_includeGaps;
+
+ /**
+ * Field _matchGaps.
+ */
+ private boolean _matchGaps;
+
+ /**
+ * keeps track of state for field: _matchGaps
+ */
+ private boolean _has_matchGaps;
+
+ /**
+ * Field _includeGappedColumns.
+ */
+ private boolean _includeGappedColumns;
+
+ /**
+ * keeps track of state for field: _includeGappedColumns
+ */
+ private boolean _has_includeGappedColumns;
+
+ /**
+ * Field _denominateByShortestLength.
+ */
+ private boolean _denominateByShortestLength;
+
+ /**
+ * keeps track of state for field: _denominateByShortestLength
+ */
+ private boolean _has_denominateByShortestLength;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _sequencePointList.
+ */
+ private java.util.Vector _sequencePointList;
+
+ /**
+ * endpoints of X, Y and Z axes in that order
+ *
+ */
+ private java.util.Vector _axisList;
+
+ /**
+ * Field _seqPointMin.
+ */
+ private jalview.schemabinding.version2.SeqPointMin _seqPointMin;
+
+ /**
+ * Field _seqPointMax.
+ */
+ private jalview.schemabinding.version2.SeqPointMax _seqPointMax;
+
+ /**
+ * Field _pcaData.
+ */
+ private jalview.schemabinding.version2.PcaData _pcaData;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaViewer()
+ {
+ super();
+ this._sequencePointList = new java.util.Vector();
+ this._axisList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAxis
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAxis(final jalview.schemabinding.version2.Axis vAxis)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._axisList.size() >= 3)
+ {
+ throw new IndexOutOfBoundsException("addAxis has a maximum of 3");
+ }
+
+ this._axisList.addElement(vAxis);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAxis
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAxis(final int index,
+ final jalview.schemabinding.version2.Axis vAxis)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._axisList.size() >= 3)
+ {
+ throw new IndexOutOfBoundsException("addAxis has a maximum of 3");
+ }
+
+ this._axisList.add(index, vAxis);
+ }
+
+ /**
+ *
+ *
+ * @param vSequencePoint
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequencePoint(
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequencePointList.addElement(vSequencePoint);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequencePoint
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequencePoint(final int index,
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequencePointList.add(index, vSequencePoint);
+ }
+
+ /**
+ */
+ public void deleteBgColour()
+ {
+ this._has_bgColour = false;
+ }
+
+ /**
+ */
+ public void deleteDenominateByShortestLength()
+ {
+ this._has_denominateByShortestLength = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteIncludeGappedColumns()
+ {
+ this._has_includeGappedColumns = false;
+ }
+
+ /**
+ */
+ public void deleteIncludeGaps()
+ {
+ this._has_includeGaps = false;
+ }
+
+ /**
+ */
+ public void deleteLinkToAllViews()
+ {
+ this._has_linkToAllViews = false;
+ }
+
+ /**
+ */
+ public void deleteMatchGaps()
+ {
+ this._has_matchGaps = false;
+ }
+
+ /**
+ */
+ public void deleteScaleFactor()
+ {
+ this._has_scaleFactor = false;
+ }
+
+ /**
+ */
+ public void deleteShowLabels()
+ {
+ this._has_showLabels = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXDim()
+ {
+ this._has_xDim = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYDim()
+ {
+ this._has_yDim = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ */
+ public void deleteZDim()
+ {
+ this._has_zDim = false;
+ }
+
+ /**
+ * Method enumerateAxis.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Axis
+ * elements
+ */
+ public java.util.Enumeration enumerateAxis()
+ {
+ return this._axisList.elements();
+ }
+
+ /**
+ * Method enumerateSequencePoint.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SequencePoint elements
+ */
+ public java.util.Enumeration enumerateSequencePoint()
+ {
+ return this._sequencePointList.elements();
+ }
+
+ /**
+ * Method getAxis.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Axis at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Axis getAxis(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._axisList.size())
+ {
+ throw new IndexOutOfBoundsException("getAxis: Index value '" + index
+ + "' not in range [0.." + (this._axisList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Axis) _axisList.get(index);
+ }
+
+ /**
+ * Method getAxis.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Axis[] getAxis()
+ {
+ jalview.schemabinding.version2.Axis[] array = new jalview.schemabinding.version2.Axis[0];
+ return (jalview.schemabinding.version2.Axis[]) this._axisList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAxisCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAxisCount()
+ {
+ return this._axisList.size();
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public int getBgColour()
+ {
+ return this._bgColour;
+ }
+
+ /**
+ * Returns the value of field 'denominateByShortestLength'.
+ *
+ * @return the value of field 'DenominateByShortestLength'.
+ */
+ public boolean getDenominateByShortestLength()
+ {
+ return this._denominateByShortestLength;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'includeGappedColumns'.
+ *
+ * @return the value of field 'IncludeGappedColumns'.
+ */
+ public boolean getIncludeGappedColumns()
+ {
+ return this._includeGappedColumns;
+ }
+
+ /**
+ * Returns the value of field 'includeGaps'.
+ *
+ * @return the value of field 'IncludeGaps'.
+ */
+ public boolean getIncludeGaps()
+ {
+ return this._includeGaps;
+ }
+
+ /**
+ * Returns the value of field 'linkToAllViews'.
+ *
+ * @return the value of field 'LinkToAllViews'.
+ */
+ public boolean getLinkToAllViews()
+ {
+ return this._linkToAllViews;
+ }
+
+ /**
+ * Returns the value of field 'matchGaps'.
+ *
+ * @return the value of field 'MatchGaps'.
+ */
+ public boolean getMatchGaps()
+ {
+ return this._matchGaps;
+ }
+
+ /**
+ * Returns the value of field 'pcaData'.
+ *
+ * @return the value of field 'PcaData'.
+ */
+ public jalview.schemabinding.version2.PcaData getPcaData()
+ {
+ return this._pcaData;
+ }
+
+ /**
+ * Returns the value of field 'scaleFactor'.
+ *
+ * @return the value of field 'ScaleFactor'.
+ */
+ public float getScaleFactor()
+ {
+ return this._scaleFactor;
+ }
+
+ /**
+ * Returns the value of field 'scoreModelName'.
+ *
+ * @return the value of field 'ScoreModelName'.
+ */
+ public java.lang.String getScoreModelName()
+ {
+ return this._scoreModelName;
+ }
+
+ /**
+ * Returns the value of field 'seqPointMax'.
+ *
+ * @return the value of field 'SeqPointMax'.
+ */
+ public jalview.schemabinding.version2.SeqPointMax getSeqPointMax()
+ {
+ return this._seqPointMax;
+ }
+
+ /**
+ * Returns the value of field 'seqPointMin'.
+ *
+ * @return the value of field 'SeqPointMin'.
+ */
+ public jalview.schemabinding.version2.SeqPointMin getSeqPointMin()
+ {
+ return this._seqPointMin;
+ }
+
+ /**
+ * Method getSequencePoint.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.SequencePoint at
+ * the given index
+ */
+ public jalview.schemabinding.version2.SequencePoint getSequencePoint(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequencePointList.size())
+ {
+ throw new IndexOutOfBoundsException("getSequencePoint: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequencePointList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SequencePoint) _sequencePointList
+ .get(index);
+ }
+
+ /**
+ * Method getSequencePoint.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SequencePoint[] getSequencePoint()
+ {
+ jalview.schemabinding.version2.SequencePoint[] array = new jalview.schemabinding.version2.SequencePoint[0];
+ return (jalview.schemabinding.version2.SequencePoint[]) this._sequencePointList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequencePointCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequencePointCount()
+ {
+ return this._sequencePointList.size();
+ }
+
+ /**
+ * Returns the value of field 'showLabels'.
+ *
+ * @return the value of field 'ShowLabels'.
+ */
+ public boolean getShowLabels()
+ {
+ return this._showLabels;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xDim'.
+ *
+ * @return the value of field 'XDim'.
+ */
+ public int getXDim()
+ {
+ return this._xDim;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'yDim'.
+ *
+ * @return the value of field 'YDim'.
+ */
+ public int getYDim()
+ {
+ return this._yDim;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Returns the value of field 'zDim'.
+ *
+ * @return the value of field 'ZDim'.
+ */
+ public int getZDim()
+ {
+ return this._zDim;
+ }
+
+ /**
+ * Method hasBgColour.
+ *
+ * @return true if at least one BgColour has been added
+ */
+ public boolean hasBgColour()
+ {
+ return this._has_bgColour;
+ }
+
+ /**
+ * Method hasDenominateByShortestLength.
+ *
+ * @return true if at least one DenominateByShortestLength has been added
+ */
+ public boolean hasDenominateByShortestLength()
+ {
+ return this._has_denominateByShortestLength;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIncludeGappedColumns.
+ *
+ * @return true if at least one IncludeGappedColumns has been added
+ */
+ public boolean hasIncludeGappedColumns()
+ {
+ return this._has_includeGappedColumns;
+ }
+
+ /**
+ * Method hasIncludeGaps.
+ *
+ * @return true if at least one IncludeGaps has been added
+ */
+ public boolean hasIncludeGaps()
+ {
+ return this._has_includeGaps;
+ }
+
+ /**
+ * Method hasLinkToAllViews.
+ *
+ * @return true if at least one LinkToAllViews has been added
+ */
+ public boolean hasLinkToAllViews()
+ {
+ return this._has_linkToAllViews;
+ }
+
+ /**
+ * Method hasMatchGaps.
+ *
+ * @return true if at least one MatchGaps has been added
+ */
+ public boolean hasMatchGaps()
+ {
+ return this._has_matchGaps;
+ }
+
+ /**
+ * Method hasScaleFactor.
+ *
+ * @return true if at least one ScaleFactor has been added
+ */
+ public boolean hasScaleFactor()
+ {
+ return this._has_scaleFactor;
+ }
+
+ /**
+ * Method hasShowLabels.
+ *
+ * @return true if at least one ShowLabels has been added
+ */
+ public boolean hasShowLabels()
+ {
+ return this._has_showLabels;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXDim.
+ *
+ * @return true if at least one XDim has been added
+ */
+ public boolean hasXDim()
+ {
+ return this._has_xDim;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYDim.
+ *
+ * @return true if at least one YDim has been added
+ */
+ public boolean hasYDim()
+ {
+ return this._has_yDim;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Method hasZDim.
+ *
+ * @return true if at least one ZDim has been added
+ */
+ public boolean hasZDim()
+ {
+ return this._has_zDim;
+ }
+
+ /**
+ * Returns the value of field 'denominateByShortestLength'.
+ *
+ * @return the value of field 'DenominateByShortestLength'.
+ */
+ public boolean isDenominateByShortestLength()
+ {
+ return this._denominateByShortestLength;
+ }
+
+ /**
+ * Returns the value of field 'includeGappedColumns'.
+ *
+ * @return the value of field 'IncludeGappedColumns'.
+ */
+ public boolean isIncludeGappedColumns()
+ {
+ return this._includeGappedColumns;
+ }
+
+ /**
+ * Returns the value of field 'includeGaps'.
+ *
+ * @return the value of field 'IncludeGaps'.
+ */
+ public boolean isIncludeGaps()
+ {
+ return this._includeGaps;
+ }
+
+ /**
+ * Returns the value of field 'linkToAllViews'.
+ *
+ * @return the value of field 'LinkToAllViews'.
+ */
+ public boolean isLinkToAllViews()
+ {
+ return this._linkToAllViews;
+ }
+
+ /**
+ * Returns the value of field 'matchGaps'.
+ *
+ * @return the value of field 'MatchGaps'.
+ */
+ public boolean isMatchGaps()
+ {
+ return this._matchGaps;
+ }
+
+ /**
+ * Returns the value of field 'showLabels'.
+ *
+ * @return the value of field 'ShowLabels'.
+ */
+ public boolean isShowLabels()
+ {
+ return this._showLabels;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAxis()
+ {
+ this._axisList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequencePoint()
+ {
+ this._sequencePointList.clear();
+ }
+
+ /**
+ * Method removeAxis.
+ *
+ * @param vAxis
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAxis(final jalview.schemabinding.version2.Axis vAxis)
+ {
+ boolean removed = _axisList.remove(vAxis);
+ return removed;
+ }
+
+ /**
+ * Method removeAxisAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Axis removeAxisAt(final int index)
+ {
+ java.lang.Object obj = this._axisList.remove(index);
+ return (jalview.schemabinding.version2.Axis) obj;
+ }
+
+ /**
+ * Method removeSequencePoint.
+ *
+ * @param vSequencePoint
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequencePoint(
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ {
+ boolean removed = _sequencePointList.remove(vSequencePoint);
+ return removed;
+ }
+
+ /**
+ * Method removeSequencePointAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequencePoint removeSequencePointAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequencePointList.remove(index);
+ return (jalview.schemabinding.version2.SequencePoint) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAxis
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAxis(final int index,
+ final jalview.schemabinding.version2.Axis vAxis)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._axisList.size())
+ {
+ throw new IndexOutOfBoundsException("setAxis: Index value '" + index
+ + "' not in range [0.." + (this._axisList.size() - 1) + "]");
+ }
+
+ this._axisList.set(index, vAxis);
+ }
+
+ /**
+ *
+ *
+ * @param vAxisArray
+ */
+ public void setAxis(
+ final jalview.schemabinding.version2.Axis[] vAxisArray)
+ {
+ // -- copy array
+ _axisList.clear();
+
+ for (int i = 0; i < vAxisArray.length; i++)
+ {
+ this._axisList.add(vAxisArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour
+ * the value of field 'bgColour'.
+ */
+ public void setBgColour(final int bgColour)
+ {
+ this._bgColour = bgColour;
+ this._has_bgColour = true;
+ }
+
+ /**
+ * Sets the value of field 'denominateByShortestLength'.
+ *
+ * @param denominateByShortestLength
+ * the value of field 'denominateByShortestLength'.
+ */
+ public void setDenominateByShortestLength(
+ final boolean denominateByShortestLength)
+ {
+ this._denominateByShortestLength = denominateByShortestLength;
+ this._has_denominateByShortestLength = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'includeGappedColumns'.
+ *
+ * @param includeGappedColumns
+ * the value of field 'includeGappedColumns'.
+ */
+ public void setIncludeGappedColumns(final boolean includeGappedColumns)
+ {
+ this._includeGappedColumns = includeGappedColumns;
+ this._has_includeGappedColumns = true;
+ }
+
+ /**
+ * Sets the value of field 'includeGaps'.
+ *
+ * @param includeGaps
+ * the value of field 'includeGaps'.
+ */
+ public void setIncludeGaps(final boolean includeGaps)
+ {
+ this._includeGaps = includeGaps;
+ this._has_includeGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'linkToAllViews'.
+ *
+ * @param linkToAllViews
+ * the value of field 'linkToAllViews'.
+ */
+ public void setLinkToAllViews(final boolean linkToAllViews)
+ {
+ this._linkToAllViews = linkToAllViews;
+ this._has_linkToAllViews = true;
+ }
+
+ /**
+ * Sets the value of field 'matchGaps'.
+ *
+ * @param matchGaps
+ * the value of field 'matchGaps'.
+ */
+ public void setMatchGaps(final boolean matchGaps)
+ {
+ this._matchGaps = matchGaps;
+ this._has_matchGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'pcaData'.
+ *
+ * @param pcaData
+ * the value of field 'pcaData'.
+ */
+ public void setPcaData(
+ final jalview.schemabinding.version2.PcaData pcaData)
+ {
+ this._pcaData = pcaData;
+ }
+
+ /**
+ * Sets the value of field 'scaleFactor'.
+ *
+ * @param scaleFactor
+ * the value of field 'scaleFactor'.
+ */
+ public void setScaleFactor(final float scaleFactor)
+ {
+ this._scaleFactor = scaleFactor;
+ this._has_scaleFactor = true;
+ }
+
+ /**
+ * Sets the value of field 'scoreModelName'.
+ *
+ * @param scoreModelName
+ * the value of field 'scoreModelName'.
+ */
+ public void setScoreModelName(final java.lang.String scoreModelName)
+ {
+ this._scoreModelName = scoreModelName;
+ }
+
+ /**
+ * Sets the value of field 'seqPointMax'.
+ *
+ * @param seqPointMax
+ * the value of field 'seqPointMax'.
+ */
+ public void setSeqPointMax(
+ final jalview.schemabinding.version2.SeqPointMax seqPointMax)
+ {
+ this._seqPointMax = seqPointMax;
+ }
+
+ /**
+ * Sets the value of field 'seqPointMin'.
+ *
+ * @param seqPointMin
+ * the value of field 'seqPointMin'.
+ */
+ public void setSeqPointMin(
+ final jalview.schemabinding.version2.SeqPointMin seqPointMin)
+ {
+ this._seqPointMin = seqPointMin;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequencePoint
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequencePoint(final int index,
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequencePointList.size())
+ {
+ throw new IndexOutOfBoundsException("setSequencePoint: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequencePointList.size() - 1) + "]");
+ }
+
+ this._sequencePointList.set(index, vSequencePoint);
+ }
+
+ /**
+ *
+ *
+ * @param vSequencePointArray
+ */
+ public void setSequencePoint(
+ final jalview.schemabinding.version2.SequencePoint[] vSequencePointArray)
+ {
+ // -- copy array
+ _sequencePointList.clear();
+
+ for (int i = 0; i < vSequencePointArray.length; i++)
+ {
+ this._sequencePointList.add(vSequencePointArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'showLabels'.
+ *
+ * @param showLabels
+ * the value of field 'showLabels'.
+ */
+ public void setShowLabels(final boolean showLabels)
+ {
+ this._showLabels = showLabels;
+ this._has_showLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xDim'.
+ *
+ * @param xDim
+ * the value of field 'xDim'.
+ */
+ public void setXDim(final int xDim)
+ {
+ this._xDim = xDim;
+ this._has_xDim = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'yDim'.
+ *
+ * @param yDim
+ * the value of field 'yDim'.
+ */
+ public void setYDim(final int yDim)
+ {
+ this._yDim = yDim;
+ this._has_yDim = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Sets the value of field 'zDim'.
+ *
+ * @param zDim
+ * the value of field 'zDim'.
+ */
+ public void setZDim(final int zDim)
+ {
+ this._zDim = zDim;
+ this._has_zDim = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.PcaViewer
+ */
+ public static jalview.schemabinding.version2.PcaViewer unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.PcaViewer) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PcaViewer.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Row.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Row extends DoubleVector implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Row()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleVector
+ */
+ public static jalview.schemabinding.version2.DoubleVector unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleVector) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Row.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SeqPointMax.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMax implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMax()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SeqPointMax
+ */
+ public static jalview.schemabinding.version2.SeqPointMax unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SeqPointMax) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SeqPointMax.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SeqPointMin.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMin implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMin()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SeqPointMin
+ */
+ public static jalview.schemabinding.version2.SeqPointMin unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SeqPointMin) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SeqPointMin.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SequencePoint.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequencePoint implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _sequenceRef.
+ */
+ private java.lang.String _sequenceRef;
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequencePoint()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'sequenceRef'.
+ *
+ * @return the value of field 'SequenceRef'.
+ */
+ public java.lang.String getSequenceRef()
+ {
+ return this._sequenceRef;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'sequenceRef'.
+ *
+ * @param sequenceRef
+ * the value of field 'sequenceRef'.
+ */
+ public void setSequenceRef(final java.lang.String sequenceRef)
+ {
+ this._sequenceRef = sequenceRef;
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SequencePoint
+ */
+ public static jalview.schemabinding.version2.SequencePoint unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequencePoint) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SequencePoint.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.Axis;
+
+/**
+ * Class AxisDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AxisDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AxisDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "axis";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Axis target = (Axis) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Axis target = (Axis) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Axis target = (Axis) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Axis target = (Axis) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Axis target = (Axis) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Axis target = (Axis) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Axis.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.DoubleMatrix;
+
+/**
+ * Class DoubleMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleMatrixDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleMatrixDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "DoubleMatrix";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _rows
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_rows", "rows",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ if (!target.hasRows())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getRows());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteRows();
+ return;
+ }
+ target.setRows(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _rows
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _columns
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_columns", "columns",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ if (!target.hasColumns())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getColumns());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColumns();
+ return;
+ }
+ target.setColumns(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _columns
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _rowList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Row.class, "_rowList", "row",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ return target.getRow();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ target.addRow((jalview.schemabinding.version2.Row) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ target.removeAllRow();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Row();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _rowList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.DoubleMatrix.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.DoubleVector;
+
+/**
+ * Class DoubleVectorDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleVectorDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleVectorDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "DoubleVector";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _dList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Double.TYPE, "_dList", "d",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleVector target = (DoubleVector) object;
+ return target.getD();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleVector target = (DoubleVector) object;
+ // ignore null values for non optional primitives
+ if (value == null)
+ {
+ return;
+ }
+
+ target.addD(((java.lang.Double) value).doubleValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleVector target = (DoubleVector) object;
+ target.removeAllD();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _dList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ org.exolab.castor.xml.validators.DoubleValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-1.7976931348623157E308);
+ typeValidator.setMaxInclusive(1.7976931348623157E308);
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.DoubleVector.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.EigenMatrixD;
+
+/**
+ * Class EigenMatrixDDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrixDDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrixDDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "eigenMatrixD";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.EigenMatrixD.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.EigenMatrix;
+
+/**
+ * Class EigenMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrixDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrixDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "eigenMatrix";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.EigenMatrix.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.EigenMatrixE;
+
+/**
+ * Class EigenMatrixEDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrixEDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrixEDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "eigenMatrixE";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.EigenMatrixE.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequenceDescriptor extends
- org.exolab.castor.xml.util.XMLClassDescriptorImpl
+public class JalviewModelSequenceDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
{
// --------------------------/
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
try
{
JalviewModelSequence target = (JalviewModelSequence) object;
- target.addViewport((jalview.schemabinding.version2.Viewport) value);
+ target.addViewport(
+ (jalview.schemabinding.version2.Viewport) value);
} catch (java.lang.Exception ex)
{
throw new IllegalStateException(ex.toString());
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
try
{
JalviewModelSequence target = (JalviewModelSequence) object;
- target.addUserColours((jalview.schemabinding.version2.UserColours) value);
+ target.addUserColours(
+ (jalview.schemabinding.version2.UserColours) value);
} catch (java.lang.Exception ex)
{
throw new IllegalStateException(ex.toString());
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
{ // -- local scope
}
desc.setValidator(fieldValidator);
+ // -- _pcaViewerList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.PcaViewer.class,
+ "_pcaViewerList", "PcaViewer",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getPcaViewer();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addPcaViewer(
+ (jalview.schemabinding.version2.PcaViewer) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllPcaViewer();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.PcaViewer();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pcaViewerList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
// -- _featureSettings
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
jalview.schemabinding.version2.FeatureSettings.class,
try
{
JalviewModelSequence target = (JalviewModelSequence) object;
- target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value);
+ target.setFeatureSettings(
+ (jalview.schemabinding.version2.FeatureSettings) value);
} catch (java.lang.Exception ex)
{
throw new IllegalStateException(ex.toString());
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PairwiseMatrix;
+
+/**
+ * Class PairwiseMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PairwiseMatrixDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PairwiseMatrixDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "pairwiseMatrix";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PairwiseMatrix.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PcaData;
+
+/**
+ * Class PcaDataDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaDataDescriptor extends
+ jalview.schemabinding.version2.descriptors.PcaDataTypeDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaDataDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.PcaDataTypeDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "pcaData";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PcaData.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PcaDataType;
+
+/**
+ * Class PcaDataTypeDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaDataTypeDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaDataTypeDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "PcaDataType";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _details
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_details", "details",
+ org.exolab.castor.xml.NodeType.Element);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaDataType target = (PcaDataType) object;
+ return target.getDetails();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaDataType target = (PcaDataType) object;
+ target.setDetails((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _details
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pairwiseMatrix
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.PairwiseMatrix.class,
+ "_pairwiseMatrix", "pairwiseMatrix",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaDataType target = (PcaDataType) object;
+ return target.getPairwiseMatrix();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaDataType target = (PcaDataType) object;
+ target.setPairwiseMatrix(
+ (jalview.schemabinding.version2.PairwiseMatrix) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.PairwiseMatrix();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pairwiseMatrix
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _eigenMatrix
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.EigenMatrix.class,
+ "_eigenMatrix", "eigenMatrix",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaDataType target = (PcaDataType) object;
+ return target.getEigenMatrix();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaDataType target = (PcaDataType) object;
+ target.setEigenMatrix(
+ (jalview.schemabinding.version2.EigenMatrix) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.EigenMatrix();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _eigenMatrix
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _eigenMatrixD
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.EigenMatrixD.class,
+ "_eigenMatrixD", "eigenMatrixD",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaDataType target = (PcaDataType) object;
+ return target.getEigenMatrixD();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaDataType target = (PcaDataType) object;
+ target.setEigenMatrixD(
+ (jalview.schemabinding.version2.EigenMatrixD) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.EigenMatrixD();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _eigenMatrixD
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _eigenMatrixE
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.EigenMatrixE.class,
+ "_eigenMatrixE", "eigenMatrixE",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaDataType target = (PcaDataType) object;
+ return target.getEigenMatrixE();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaDataType target = (PcaDataType) object;
+ target.setEigenMatrixE(
+ (jalview.schemabinding.version2.EigenMatrixE) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.EigenMatrixE();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _eigenMatrixE
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PcaDataType.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PcaViewer;
+
+/**
+ * Class PcaViewerDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaViewerDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaViewerDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "PcaViewer";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_title", "title",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getTitle();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setTitle((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _scoreModelName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_scoreModelName", "scoreModelName",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getScoreModelName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setScoreModelName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scoreModelName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xDim
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xDim", "xDim",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasXDim())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXDim());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXDim();
+ return;
+ }
+ target.setXDim(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xDim
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yDim
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_yDim", "yDim",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasYDim())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYDim());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYDim();
+ return;
+ }
+ target.setYDim(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yDim
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zDim
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_zDim", "zDim",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasZDim())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getZDim());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZDim();
+ return;
+ }
+ target.setZDim(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zDim
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _bgColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_bgColour", "bgColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasBgColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getBgColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteBgColour();
+ return;
+ }
+ target.setBgColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _bgColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _scaleFactor
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_scaleFactor", "scaleFactor",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasScaleFactor())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getScaleFactor());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScaleFactor();
+ return;
+ }
+ target.setScaleFactor(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scaleFactor
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showLabels", "showLabels",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasShowLabels())
+ {
+ return null;
+ }
+ return (target.getShowLabels() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowLabels();
+ return;
+ }
+ target.setShowLabels(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _linkToAllViews
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_linkToAllViews", "linkToAllViews",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasLinkToAllViews())
+ {
+ return null;
+ }
+ return (target.getLinkToAllViews() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteLinkToAllViews();
+ return;
+ }
+ target.setLinkToAllViews(
+ ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _linkToAllViews
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _includeGaps
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_includeGaps", "includeGaps",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasIncludeGaps())
+ {
+ return null;
+ }
+ return (target.getIncludeGaps() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteIncludeGaps();
+ return;
+ }
+ target.setIncludeGaps(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _includeGaps
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _matchGaps
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_matchGaps", "matchGaps",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasMatchGaps())
+ {
+ return null;
+ }
+ return (target.getMatchGaps() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMatchGaps();
+ return;
+ }
+ target.setMatchGaps(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _matchGaps
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _includeGappedColumns
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_includeGappedColumns",
+ "includeGappedColumns",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasIncludeGappedColumns())
+ {
+ return null;
+ }
+ return (target.getIncludeGappedColumns() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteIncludeGappedColumns();
+ return;
+ }
+ target.setIncludeGappedColumns(
+ ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _includeGappedColumns
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _denominateByShortestLength
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_denominateByShortestLength",
+ "denominateByShortestLength",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasDenominateByShortestLength())
+ {
+ return null;
+ }
+ return (target.getDenominateByShortestLength()
+ ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteDenominateByShortestLength();
+ return;
+ }
+ target.setDenominateByShortestLength(
+ ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _denominateByShortestLength
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_width", "width",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasWidth())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getWidth());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_height", "height",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasHeight())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getHeight());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xpos", "xpos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasXpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_ypos", "ypos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasYpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _sequencePointList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SequencePoint.class,
+ "_sequencePointList", "sequencePoint",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getSequencePoint();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.addSequencePoint(
+ (jalview.schemabinding.version2.SequencePoint) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.removeAllSequencePoint();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SequencePoint();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequencePointList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _axisList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Axis.class, "_axisList", "axis",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getAxis();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.addAxis((jalview.schemabinding.version2.Axis) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.removeAllAxis();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Axis();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _axisList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(3);
+ fieldValidator.setMaxOccurs(3);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _seqPointMin
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SeqPointMin.class,
+ "_seqPointMin", "seqPointMin",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getSeqPointMin();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setSeqPointMin(
+ (jalview.schemabinding.version2.SeqPointMin) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SeqPointMin();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _seqPointMin
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _seqPointMax
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SeqPointMax.class,
+ "_seqPointMax", "seqPointMax",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getSeqPointMax();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setSeqPointMax(
+ (jalview.schemabinding.version2.SeqPointMax) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SeqPointMax();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _seqPointMax
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pcaData
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.PcaData.class, "_pcaData",
+ "pcaData", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getPcaData();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setPcaData((jalview.schemabinding.version2.PcaData) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.PcaData();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pcaData
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PcaViewer.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.Row;
+
+/**
+ * Class RowDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class RowDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public RowDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "row";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Row.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.SeqPointMax;
+
+/**
+ * Class SeqPointMaxDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMaxDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMaxDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "seqPointMax";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SeqPointMax.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.SeqPointMin;
+
+/**
+ * Class SeqPointMinDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMinDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMinDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "seqPointMin";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SeqPointMin.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.SequencePoint;
+
+/**
+ * Class SequencePointDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequencePointDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequencePointDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "sequencePoint";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _sequenceRef
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_sequenceRef", "sequenceRef",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ return target.getSequenceRef();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ target.setSequenceRef((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequenceRef
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SequencePoint.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff