From d6815a9bc0fc9b9c1fe8e1871a4b0e9d7bd7a11f Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 4 May 2018 15:49:22 +0100 Subject: [PATCH] JAL-1767 schema and Castor changes for Save PCA in project --- schemas/jalview.xsd | 93 +- src/jalview/gui/Jalview2XML.java | 296 ++++- src/jalview/schemabinding/version2/.castor.cdr | 19 +- src/jalview/schemabinding/version2/Axis.java | 276 ++++ .../schemabinding/version2/DoubleMatrix.java | 388 ++++++ .../schemabinding/version2/DoubleVector.java | 288 ++++ .../schemabinding/version2/EigenMatrix.java | 126 ++ .../schemabinding/version2/EigenMatrixD.java | 126 ++ .../schemabinding/version2/EigenMatrixE.java | 126 ++ .../version2/JalviewModelSequence.java | 213 ++- .../schemabinding/version2/PairwiseMatrix.java | 126 ++ src/jalview/schemabinding/version2/PcaData.java | 125 ++ .../schemabinding/version2/PcaDataType.java | 269 ++++ src/jalview/schemabinding/version2/PcaViewer.java | 1403 ++++++++++++++++++++ src/jalview/schemabinding/version2/Row.java | 124 ++ .../schemabinding/version2/SeqPointMax.java | 276 ++++ .../schemabinding/version2/SeqPointMin.java | 276 ++++ .../schemabinding/version2/SequencePoint.java | 302 +++++ .../version2/descriptors/AxisDescriptor.java | 319 +++++ .../descriptors/DoubleMatrixDescriptor.java | 322 +++++ .../descriptors/DoubleVectorDescriptor.java | 223 ++++ .../descriptors/EigenMatrixDDescriptor.java | 149 +++ .../descriptors/EigenMatrixDescriptor.java | 149 +++ .../descriptors/EigenMatrixEDescriptor.java | 149 +++ .../JalviewModelSequenceDescriptor.java | 90 +- .../descriptors/PairwiseMatrixDescriptor.java | 149 +++ .../version2/descriptors/PcaDataDescriptor.java | 149 +++ .../descriptors/PcaDataTypeDescriptor.java | 385 ++++++ .../version2/descriptors/PcaViewerDescriptor.java | 1320 ++++++++++++++++++ .../version2/descriptors/RowDescriptor.java | 149 +++ .../descriptors/SeqPointMaxDescriptor.java | 319 +++++ .../descriptors/SeqPointMinDescriptor.java | 319 +++++ .../descriptors/SequencePointDescriptor.java | 364 +++++ 33 files changed, 9365 insertions(+), 42 deletions(-) create mode 100644 src/jalview/schemabinding/version2/Axis.java create mode 100644 src/jalview/schemabinding/version2/DoubleMatrix.java create mode 100644 src/jalview/schemabinding/version2/DoubleVector.java create mode 100644 src/jalview/schemabinding/version2/EigenMatrix.java create mode 100644 src/jalview/schemabinding/version2/EigenMatrixD.java create mode 100644 src/jalview/schemabinding/version2/EigenMatrixE.java create mode 100644 src/jalview/schemabinding/version2/PairwiseMatrix.java create mode 100644 src/jalview/schemabinding/version2/PcaData.java create mode 100644 src/jalview/schemabinding/version2/PcaDataType.java create mode 100644 src/jalview/schemabinding/version2/PcaViewer.java create mode 100644 src/jalview/schemabinding/version2/Row.java create mode 100644 src/jalview/schemabinding/version2/SeqPointMax.java create mode 100644 src/jalview/schemabinding/version2/SeqPointMin.java create mode 100644 src/jalview/schemabinding/version2/SequencePoint.java create mode 100644 src/jalview/schemabinding/version2/descriptors/AxisDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/DoubleMatrixDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/DoubleVectorDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/EigenMatrixDDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/EigenMatrixDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/EigenMatrixEDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/PairwiseMatrixDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/PcaDataDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/PcaViewerDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/RowDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/SeqPointMaxDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/SeqPointMinDescriptor.java create mode 100644 src/jalview/schemabinding/version2/descriptors/SequencePointDescriptor.java diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index e5058c6..109b83b 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -496,6 +496,50 @@ + + + + + + + + + + + + + endpoints of X, Y and Z axes in that order + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -632,5 +676,52 @@ - + + + + parameters that condition a similarity score calculation + + + + + + + + + + + + + + + + The results of a PCA calculation + + + + + + + The text report of the calculation + + + + + + + + + + + + + + + + + + + + + diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index ffa8301..2b3e5ce 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,9 +20,18 @@ */ 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; @@ -31,6 +40,7 @@ import jalview.datamodel.AlignmentAnnotation; 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; @@ -45,15 +55,22 @@ import jalview.ext.varna.RnaModel; 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; @@ -68,12 +85,19 @@ import jalview.schemabinding.version2.MappingChoice; 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; @@ -100,6 +124,7 @@ import jalview.util.StringUtils; 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; @@ -1131,6 +1156,24 @@ public class Jalview2XML } } + /* + * 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 @@ -1508,6 +1551,122 @@ public class Jalview2XML } /** + * 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 *
    @@ -3621,6 +3780,7 @@ public class Jalview2XML if (loadTreesAndStructures) { loadTrees(jms, view, af, av, ap); + loadPCAViewers(jms, ap); loadPDBStructures(jprovider, jseqs, af, ap); loadRnaViewers(jprovider, jseqs, ap); } @@ -3763,9 +3923,7 @@ public class Jalview2XML 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; @@ -5714,6 +5872,138 @@ public class Jalview2XML } /** + * 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 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 diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index e1100a8..4248a04 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,5 @@ -#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 @@ -6,11 +7,15 @@ jalview.schemabinding.version2.CalcIdParam=jalview.schemabinding.version2.descri 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 @@ -19,19 +24,24 @@ jalview.schemabinding.version2.RnaViewer=jalview.schemabinding.version2.descript 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 @@ -46,8 +56,13 @@ jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors 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 diff --git a/src/jalview/schemabinding/version2/Axis.java b/src/jalview/schemabinding/version2/Axis.java new file mode 100644 index 0000000..9fe9660 --- /dev/null +++ b/src/jalview/schemabinding/version2/Axis.java @@ -0,0 +1,276 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/DoubleMatrix.java b/src/jalview/schemabinding/version2/DoubleMatrix.java new file mode 100644 index 0000000..ab21019 --- /dev/null +++ b/src/jalview/schemabinding/version2/DoubleMatrix.java @@ -0,0 +1,388 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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. + *

    + * 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 + * know 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); + } + +} diff --git a/src/jalview/schemabinding/version2/DoubleVector.java b/src/jalview/schemabinding/version2/DoubleVector.java new file mode 100644 index 0000000..75597ab --- /dev/null +++ b/src/jalview/schemabinding/version2/DoubleVector.java @@ -0,0 +1,288 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/EigenMatrix.java b/src/jalview/schemabinding/version2/EigenMatrix.java new file mode 100644 index 0000000..b04a50c --- /dev/null +++ b/src/jalview/schemabinding/version2/EigenMatrix.java @@ -0,0 +1,126 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/EigenMatrixD.java b/src/jalview/schemabinding/version2/EigenMatrixD.java new file mode 100644 index 0000000..16d8729 --- /dev/null +++ b/src/jalview/schemabinding/version2/EigenMatrixD.java @@ -0,0 +1,126 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/EigenMatrixE.java b/src/jalview/schemabinding/version2/EigenMatrixE.java new file mode 100644 index 0000000..1086d85 --- /dev/null +++ b/src/jalview/schemabinding/version2/EigenMatrixE.java @@ -0,0 +1,126 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index c7c02c5..932ba14 100644 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -52,6 +52,11 @@ public class JalviewModelSequence implements java.io.Serializable private java.util.Vector _treeList; /** + * Field _pcaViewerList. + */ + private java.util.Vector _pcaViewerList; + + /** * Field _featureSettings. */ private jalview.schemabinding.version2.FeatureSettings _featureSettings; @@ -68,6 +73,7 @@ public class JalviewModelSequence implements java.io.Serializable this._viewportList = new java.util.Vector(); this._userColoursList = new java.util.Vector(); this._treeList = new java.util.Vector(); + this._pcaViewerList = new java.util.Vector(); } // -----------/ @@ -133,6 +139,35 @@ public class JalviewModelSequence implements java.io.Serializable /** * * + * @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 @@ -239,6 +274,17 @@ public class JalviewModelSequence implements java.io.Serializable } /** + * 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 @@ -296,9 +342,9 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -379,6 +425,56 @@ public class JalviewModelSequence implements java.io.Serializable } /** + * 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. + *

    + * 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 + * know 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 @@ -485,15 +581,15 @@ public class JalviewModelSequence implements java.io.Serializable * @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 @@ -581,35 +677,42 @@ public class JalviewModelSequence implements java.io.Serializable } /** - */ + */ 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(); @@ -666,6 +769,32 @@ public class JalviewModelSequence implements java.io.Serializable } /** + * 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 @@ -768,9 +897,9 @@ public class JalviewModelSequence implements java.io.Serializable // 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); @@ -820,7 +949,8 @@ public class JalviewModelSequence implements java.io.Serializable * * @param vJSeqArray */ - public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray) + public void setJSeq( + final jalview.schemabinding.version2.JSeq[] vJSeqArray) { // -- copy array _JSeqList.clear(); @@ -835,6 +965,46 @@ public class JalviewModelSequence implements java.io.Serializable * * * @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 @@ -858,7 +1028,8 @@ public class JalviewModelSequence implements java.io.Serializable * * @param vTreeArray */ - public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray) + public void setTree( + final jalview.schemabinding.version2.Tree[] vTreeArray) { // -- copy array _treeList.clear(); @@ -924,9 +1095,9 @@ public class JalviewModelSequence implements java.io.Serializable // 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); diff --git a/src/jalview/schemabinding/version2/PairwiseMatrix.java b/src/jalview/schemabinding/version2/PairwiseMatrix.java new file mode 100644 index 0000000..3906111 --- /dev/null +++ b/src/jalview/schemabinding/version2/PairwiseMatrix.java @@ -0,0 +1,126 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/PcaData.java b/src/jalview/schemabinding/version2/PcaData.java new file mode 100644 index 0000000..dfce269 --- /dev/null +++ b/src/jalview/schemabinding/version2/PcaData.java @@ -0,0 +1,125 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/PcaDataType.java b/src/jalview/schemabinding/version2/PcaDataType.java new file mode 100644 index 0000000..0335b44 --- /dev/null +++ b/src/jalview/schemabinding/version2/PcaDataType.java @@ -0,0 +1,269 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/PcaViewer.java b/src/jalview/schemabinding/version2/PcaViewer.java new file mode 100644 index 0000000..3fce2d5 --- /dev/null +++ b/src/jalview/schemabinding/version2/PcaViewer.java @@ -0,0 +1,1403 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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. + *

    + * 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 + * know 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. + *

    + * 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 + * know 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); + } + +} diff --git a/src/jalview/schemabinding/version2/Row.java b/src/jalview/schemabinding/version2/Row.java new file mode 100644 index 0000000..d351d1d --- /dev/null +++ b/src/jalview/schemabinding/version2/Row.java @@ -0,0 +1,124 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/SeqPointMax.java b/src/jalview/schemabinding/version2/SeqPointMax.java new file mode 100644 index 0000000..3ca78a2 --- /dev/null +++ b/src/jalview/schemabinding/version2/SeqPointMax.java @@ -0,0 +1,276 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/SeqPointMin.java b/src/jalview/schemabinding/version2/SeqPointMin.java new file mode 100644 index 0000000..4ce9fab --- /dev/null +++ b/src/jalview/schemabinding/version2/SeqPointMin.java @@ -0,0 +1,276 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/SequencePoint.java b/src/jalview/schemabinding/version2/SequencePoint.java new file mode 100644 index 0000000..191c4dd --- /dev/null +++ b/src/jalview/schemabinding/version2/SequencePoint.java @@ -0,0 +1,302 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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); + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/AxisDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AxisDescriptor.java new file mode 100644 index 0000000..16444be --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/AxisDescriptor.java @@ -0,0 +1,319 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/DoubleMatrixDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DoubleMatrixDescriptor.java new file mode 100644 index 0000000..79245bc --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/DoubleMatrixDescriptor.java @@ -0,0 +1,322 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/DoubleVectorDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DoubleVectorDescriptor.java new file mode 100644 index 0000000..3d8c315 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/DoubleVectorDescriptor.java @@ -0,0 +1,223 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/EigenMatrixDDescriptor.java b/src/jalview/schemabinding/version2/descriptors/EigenMatrixDDescriptor.java new file mode 100644 index 0000000..b9ca070 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/EigenMatrixDDescriptor.java @@ -0,0 +1,149 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/EigenMatrixDescriptor.java b/src/jalview/schemabinding/version2/descriptors/EigenMatrixDescriptor.java new file mode 100644 index 0000000..92e2414 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/EigenMatrixDescriptor.java @@ -0,0 +1,149 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/EigenMatrixEDescriptor.java b/src/jalview/schemabinding/version2/descriptors/EigenMatrixEDescriptor.java new file mode 100644 index 0000000..25e7fea --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/EigenMatrixEDescriptor.java @@ -0,0 +1,149 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java index e8c4ef4..af40425 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java @@ -18,8 +18,8 @@ import jalview.schemabinding.version2.JalviewModelSequence; * * @version $Revision$ $Date$ */ -public class JalviewModelSequenceDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl +public class JalviewModelSequenceDescriptor + extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { // --------------------------/ @@ -91,8 +91,8 @@ public class JalviewModelSequenceDescriptor extends } } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException + public void resetValue(Object object) + throws IllegalStateException, IllegalArgumentException { try { @@ -146,8 +146,8 @@ public class JalviewModelSequenceDescriptor extends } } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException + public void resetValue(Object object) + throws IllegalStateException, IllegalArgumentException { try { @@ -194,15 +194,16 @@ public class JalviewModelSequenceDescriptor extends 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 { @@ -250,15 +251,16 @@ public class JalviewModelSequenceDescriptor extends 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 { @@ -312,8 +314,8 @@ public class JalviewModelSequenceDescriptor extends } } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException + public void resetValue(Object object) + throws IllegalStateException, IllegalArgumentException { try { @@ -341,6 +343,63 @@ public class JalviewModelSequenceDescriptor extends { // -- 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, @@ -361,7 +420,8 @@ public class JalviewModelSequenceDescriptor extends 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()); diff --git a/src/jalview/schemabinding/version2/descriptors/PairwiseMatrixDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PairwiseMatrixDescriptor.java new file mode 100644 index 0000000..9520f58 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/PairwiseMatrixDescriptor.java @@ -0,0 +1,149 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PcaDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PcaDataDescriptor.java new file mode 100644 index 0000000..29b551c --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/PcaDataDescriptor.java @@ -0,0 +1,149 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java new file mode 100644 index 0000000..6508ee2 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/PcaDataTypeDescriptor.java @@ -0,0 +1,385 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/PcaViewerDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PcaViewerDescriptor.java new file mode 100644 index 0000000..630ae9a --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/PcaViewerDescriptor.java @@ -0,0 +1,1320 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/RowDescriptor.java b/src/jalview/schemabinding/version2/descriptors/RowDescriptor.java new file mode 100644 index 0000000..f9ca1a6 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/RowDescriptor.java @@ -0,0 +1,149 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SeqPointMaxDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SeqPointMaxDescriptor.java new file mode 100644 index 0000000..18f0cb7 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/SeqPointMaxDescriptor.java @@ -0,0 +1,319 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SeqPointMinDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SeqPointMinDescriptor.java new file mode 100644 index 0000000..fbf978e --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/SeqPointMinDescriptor.java @@ -0,0 +1,319 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} diff --git a/src/jalview/schemabinding/version2/descriptors/SequencePointDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequencePointDescriptor.java new file mode 100644 index 0000000..0d48052 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/SequencePointDescriptor.java @@ -0,0 +1,364 @@ +/* + * This class was automatically generated with + * Castor 1.1, 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; + } + +} -- 1.7.10.2