<em>Calculating PCAs for aligned sequences</em><br />Jalview can
perform PCA analysis on both proteins and nucleotide sequence
alignments. In both cases, components are generated by an
- eigenvector decomposition of the matrix formed from the sum of
- substitution matrix scores at each aligned position between each
- pair of sequences - computed with one of the available score
- matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the <a href="calculations.html">calculations dialog</a>, and
+ may use one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>,
<a href="scorematrices.html#pam250">PAM250</a>, or the <a
href="scorematrices.html#simplenucleotide">simple single
- nucleotide substitution matrix</a>. The options available for
- calculation are given in the <strong><em>Change
- Parameters</em></strong> menu.
+ nucleotide substitution matrix</a>, or by sequence percentage identity,
+ or sequence feature similarity.
</p>
<img src="pcaviewer.gif">
<p>
label.average_distance_identity = Average Distance Using % Identity
label.neighbour_joining_identity = Neighbour Joining Using % Identity
label.choose_calculation = Choose Calculation
-label.treecalc_title = {0} Using {1}
+label.calc_title = {0} Using {1}
label.tree_calc_av = Average Distance
label.tree_calc_nj = Neighbour Joining
-label.select_score_model = Select score model
label.score_model_pid = % Identity
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
label.save_alignment_to_file = Save Alignment to file
label.save_features_to_file = Save Features to File
label.save_annotation_to_file = Save Annotation to File
-label.no_features_on_alignment = No features found on alignment
label.save_pdb_file = Save PDB File
label.save_text_to_file = Save Text to File
label.save_state = Save State
label.average_distance_identity = Distancia Media Usando % de Identidad
label.neighbour_joining_identity = Unir vecinos utilizando % de Identidad
label.choose_calculation = Elegir el cálculo
-label.treecalc_title = {0} utilizando {1}
+label.calc_title = {0} utilizando {1}
label.tree_calc_av = Distancia media
label.tree_calc_nj = Unir vecinos
-label.select_score_model = Selecciones modelo de puntuación
label.score_model_pid = % Identidad
label.score_model_blosum62 = BLOSUM62
label.score_model_pam250 = PAM 250
label.save_alignment_to_file = Guardar Alineamiento en fichero
label.save_features_to_file = Guardar Características en un fichero
label.save_annotation_to_file = Guardar Anotación en un fichero
-label.no_features_on_alignment = No se han encontrado características en el alineamiento
label.save_pdb_file = Guardar fichero PDB
label.save_text_to_file = Guardar Texto en un fichero
label.save_state = Guardar estado
</xs:annotation>
</xs:attribute>
<xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="linkToAllViews" use="optional" default="false" type="xs:boolean" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="PcaViewer" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element name="sequencePoint" minOccurs="1" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:attribute name="sequenceRef" type="xs:string" />
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="axis" minOccurs="3" maxOccurs="3">
+ <xs:annotation>
+ <xs:documentation>
+ endpoints of X, Y and Z axes in that order
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMin">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="seqPointMax">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:position" />
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="pcaData" type="jv:PcaDataType" />
+ </xs:sequence>
+ <xs:attribute name="title" type="xs:string" />
+ <xs:attribute name="scoreModelName" type="xs:string" />
+ <xs:attribute name="xDim" type="xs:int" />
+ <xs:attribute name="yDim" type="xs:int" />
+ <xs:attribute name="zDim" type="xs:int" />
+ <xs:attribute name="bgColour" type="xs:int" />
+ <xs:attribute name="scaleFactor" type="xs:float" />
+ <xs:attribute name="showLabels" type="xs:boolean" />
+ <xs:attribute name="linkToAllViews" type="xs:boolean" />
+ <xs:attributeGroup ref="jv:SimilarityParams" />
+ <xs:attributeGroup ref="jv:swingwindow" />
</xs:complexType>
</xs:element>
<xs:element name="FeatureSettings" minOccurs="0">
<xs:attribute name="predefinedColours" type="xs:boolean"
use="optional" />
</xs:complexType>
-
+ <xs:attributeGroup name="SimilarityParams">
+ <xs:annotation>
+ <xs:documentation>
+ parameters that condition a similarity score calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:attribute name="includeGaps" type="xs:boolean" />
+ <xs:attribute name="matchGaps" type="xs:boolean" />
+ <xs:attribute name="includeGappedColumns" type="xs:boolean" />
+ <xs:attribute name="denominateByShortestLength" type="xs:boolean" />
+ </xs:attributeGroup>
+ <xs:attributeGroup name="position">
+ <xs:attribute name="xPos" type="xs:float" />
+ <xs:attribute name="yPos" type="xs:float" />
+ <xs:attribute name="zPos" type="xs:float" />
+ </xs:attributeGroup>
+ <xs:complexType name="PcaDataType">
+ <xs:annotation>
+ <xs:documentation>
+ The results of a PCA calculation
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="pairwiseMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="tridiagonalMatrix" type="jv:DoubleMatrix" />
+ <xs:element name="eigenMatrix" type="jv:DoubleMatrix" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleVector">
+ <xs:sequence>
+ <xs:element name="v" type="xs:double" minOccurs="0" maxOccurs="unbounded" />
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="DoubleMatrix">
+ <xs:sequence>
+ <xs:element name="row" type="jv:DoubleVector" minOccurs="0" maxOccurs="unbounded" />
+ <xs:element name="D" minOccurs="0" type="jv:DoubleVector" />
+ <xs:element name="E" minOccurs="0" type="jv:DoubleVector" />
+ </xs:sequence>
+ <xs:attribute name="rows" type="xs:int" />
+ <xs:attribute name="columns" type="xs:int" />
+ </xs:complexType>
</xs:schema>
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Point;
import jalview.math.MatrixI;
import java.io.PrintStream;
*/
public class PCA implements Runnable
{
- MatrixI symm;
-
- double[] eigenvalue;
+ /*
+ * inputs
+ */
+ final private AlignmentView seqs;
- MatrixI eigenvector;
+ final private ScoreModelI scoreModel;
- StringBuilder details = new StringBuilder(1024);
+ final private SimilarityParamsI similarityParams;
- final private AlignmentView seqs;
+ /*
+ * outputs
+ */
+ private MatrixI pairwiseScores;
- private ScoreModelI scoreModel;
+ private MatrixI tridiagonal;
- private SimilarityParamsI similarityParams;
+ private MatrixI eigenMatrix;
- public PCA(AlignmentView s, ScoreModelI sm, SimilarityParamsI options)
+ /**
+ * Constructor given the sequences to compute for, the similarity model to
+ * use, and a set of parameters for sequence comparison
+ *
+ * @param sequences
+ * @param sm
+ * @param options
+ */
+ public PCA(AlignmentView sequences, ScoreModelI sm, SimilarityParamsI options)
{
- this.seqs = s;
- this.similarityParams = options;
+ this.seqs = sequences;
this.scoreModel = sm;
-
- details.append("PCA calculation using " + sm.getName()
- + " sequence similarity matrix\n========\n\n");
+ this.similarityParams = options;
}
/**
*/
public double getEigenvalue(int i)
{
- return eigenvector.getD()[i];
+ return eigenMatrix.getD()[i];
}
/**
*
* @return DOCUMENT ME!
*/
- public float[][] getComponents(int l, int n, int mm, float factor)
+ public Point[] getComponents(int l, int n, int mm, float factor)
{
- float[][] out = new float[getHeight()][3];
+ Point[] out = new Point[getHeight()];
for (int i = 0; i < getHeight(); i++)
{
- out[i][0] = (float) component(i, l) * factor;
- out[i][1] = (float) component(i, n) * factor;
- out[i][2] = (float) component(i, mm) * factor;
+ float x = (float) component(i, l) * factor;
+ float y = (float) component(i, n) * factor;
+ float z = (float) component(i, mm) * factor;
+ out[i] = new Point(x, y, z);
}
return out;
{
double out = 0.0;
- for (int i = 0; i < symm.width(); i++)
+ for (int i = 0; i < pairwiseScores.width(); i++)
{
- out += (symm.getValue(row, i) * eigenvector.getValue(i, n));
+ out += (pairwiseScores.getValue(row, i) * eigenMatrix.getValue(i, n));
}
- return out / eigenvector.getD()[n];
+ return out / eigenMatrix.getD()[n];
}
+ /**
+ * Answers a formatted text report of the PCA calculation results (matrices
+ * and eigenvalues) suitable for display
+ *
+ * @return
+ */
public String getDetails()
{
- return details.toString();
+ StringBuilder sb = new StringBuilder(1024);
+ sb.append("PCA calculation using ").append(scoreModel.getName())
+ .append(" sequence similarity matrix\n========\n\n");
+ PrintStream ps = wrapOutputBuffer(sb);
+
+ /*
+ * pairwise similarity scores
+ */
+ sb.append(" --- OrigT * Orig ---- \n");
+ pairwiseScores.print(ps, "%8.2f");
+
+ /*
+ * tridiagonal matrix, with D and E vectors
+ */
+ sb.append(" ---Tridiag transform matrix ---\n");
+ sb.append(" --- D vector ---\n");
+ tridiagonal.printD(ps, "%15.4e");
+ ps.println();
+ sb.append("--- E vector ---\n");
+ tridiagonal.printE(ps, "%15.4e");
+ ps.println();
+
+ /*
+ * eigenvalues matrix, with D vector
+ */
+ sb.append(" --- New diagonalization matrix ---\n");
+ eigenMatrix.print(ps, "%8.2f");
+ sb.append(" --- Eigenvalues ---\n");
+ eigenMatrix.printD(ps, "%15.4e");
+ ps.println();
+
+ return sb.toString();
}
/**
- * DOCUMENT ME!
+ * Performs the PCA calculation
*/
@Override
public void run()
{
+ try
+ {
+ /*
+ * sequence pairwise similarity scores
+ */
+ pairwiseScores = scoreModel.findSimilarities(seqs, similarityParams);
+
+ /*
+ * tridiagonal matrix
+ */
+ tridiagonal = pairwiseScores.copy();
+ tridiagonal.tred();
+
+ /*
+ * the diagonalization matrix
+ */
+ eigenMatrix = tridiagonal.copy();
+ eigenMatrix.tqli();
+ } catch (Exception q)
+ {
+ Cache.log.error("Error computing PCA: " + q.getMessage());
+ q.printStackTrace();
+ }
+ }
+
+ /**
+ * Returns a PrintStream that wraps (appends its output to) the given
+ * StringBuilder
+ *
+ * @param sb
+ * @return
+ */
+ protected PrintStream wrapOutputBuffer(StringBuilder sb)
+ {
PrintStream ps = new PrintStream(System.out)
{
@Override
public void print(String x)
{
- details.append(x);
+ sb.append(x);
}
@Override
public void println()
{
- details.append("\n");
+ sb.append("\n");
}
};
-
- // long now = System.currentTimeMillis();
- try
- {
- eigenvector = scoreModel.findSimilarities(seqs, similarityParams);
-
- details.append(" --- OrigT * Orig ---- \n");
- eigenvector.print(ps, "%8.2f");
-
- symm = eigenvector.copy();
-
- eigenvector.tred();
-
- details.append(" ---Tridiag transform matrix ---\n");
- details.append(" --- D vector ---\n");
- eigenvector.printD(ps, "%15.4e");
- ps.println();
- details.append("--- E vector ---\n");
- eigenvector.printE(ps, "%15.4e");
- ps.println();
-
- // Now produce the diagonalization matrix
- eigenvector.tqli();
- } catch (Exception q)
- {
- q.printStackTrace();
- details.append("\n*** Unexpected exception when performing PCA ***\n"
- + q.getLocalizedMessage());
- details.append(
- "*** Matrices below may not be fully diagonalised. ***\n");
- }
-
- details.append(" --- New diagonalization matrix ---\n");
- eigenvector.print(ps, "%8.2f");
- details.append(" --- Eigenvalues ---\n");
- eigenvector.printD(ps, "%15.4e");
- ps.println();
- /*
- * for (int seq=0;seq<symm.rows;seq++) { ps.print("\"Seq"+seq+"\""); for
- * (int ev=0;ev<symm.rows; ev++) {
- *
- * ps.print(","+component(seq, ev)); } ps.println(); }
- */
- // System.out.println(("PCA.run() took "
- // + (System.currentTimeMillis() - now) + "ms"));
+ return ps;
}
/**
public int getHeight()
{
// TODO can any of seqs[] be null?
- return seqs.getSequences().length;
+ return pairwiseScores.height();// seqs.getSequences().length;
+ }
+
+ /**
+ * Answers the sequence pairwise similarity scores which were the first step
+ * of the PCA calculation
+ *
+ * @return
+ */
+ public MatrixI getPairwiseScores()
+ {
+ return pairwiseScores;
+ }
+
+ public void setPairwiseScores(MatrixI m)
+ {
+ pairwiseScores = m;
+ }
+
+ public MatrixI getEigenmatrix()
+ {
+ return eigenMatrix;
+ }
+
+ public void setEigenmatrix(MatrixI m)
+ {
+ eigenMatrix = m;
+ }
+
+ public MatrixI getTridiagonal()
+ {
+ return tridiagonal;
+ }
+
+ public void setTridiagonal(MatrixI tridiagonal)
+ {
+ this.tridiagonal = tridiagonal;
}
}
/*
* using LinkedHashMap keeps models ordered as added
*/
- models = new LinkedHashMap<String, ScoreModelI>();
+ models = new LinkedHashMap<>();
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
- registerScoreModel(new PIDModel());
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
}
{
return matchGaps;
}
+
+ /**
+ * IDE-generated hashCode method
+ */
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + (denominateByShortestLength ? 1231 : 1237);
+ result = prime * result + (includeGappedColumns ? 1231 : 1237);
+ result = prime * result + (includeGaps ? 1231 : 1237);
+ result = prime * result + (matchGaps ? 1231 : 1237);
+ return result;
+ }
+
+ /**
+ * IDE-generated equals method
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ SimilarityParams other = (SimilarityParams) obj;
+ if (denominateByShortestLength != other.denominateByShortestLength)
+ {
+ return false;
+ }
+ if (includeGappedColumns != other.includeGappedColumns)
+ {
+ return false;
+ }
+ if (includeGaps != other.includeGaps)
+ {
+ return false;
+ }
+ if (matchGaps != other.matchGaps)
+ {
+ return false;
+ }
+ return true;
+ }
}
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequencePoint;
-import java.util.Vector;
+import java.util.List;
/**
* interface implemented by RotatatableCanvas GUI elements (such as point clouds
*/
public interface RotatableCanvasI
{
+ void setPoints(List<SequencePoint> points, int rows);
- void setPoints(Vector<SequencePoint> points, int rows);
+ /**
+ * Zoom the view in (or out) by the given factor, which should be >= 0. A
+ * factor greater than 1 zooms in (expands the display), a factor less than 1
+ * zooms out (shrinks the display).
+ *
+ * @param factor
+ */
+ void zoom(float factor);
+ /**
+ * Rotates the view by the specified number of degrees about the x and/or y
+ * axis
+ *
+ * @param x
+ * @param y
+ */
+ void rotate(float x, float y);
}
{
nuclSetting.setState(pcaModel.isNucleotide());
protSetting.setState(!pcaModel.isNucleotide());
- pcaModel.run();
+ pcaModel.calculate();
// ////////////////
xCombobox.select(0);
yCombobox.select(1);
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
+ rc.resetView();
rc.paint(rc.getGraphics());
}
{
}
;
- Object[] alAndColsel = pcaModel.getSeqtrings()
+ Object[] alAndColsel = pcaModel.getInputData()
.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
package jalview.appletgui;
import jalview.api.RotatableCanvasI;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
import jalview.math.RotatableMatrix;
-import jalview.util.Format;
+import jalview.math.RotatableMatrix.Axis;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
-import java.util.Vector;
+import java.util.List;
public class RotatableCanvas extends Panel implements MouseListener,
MouseMotionListener, KeyListener, RotatableCanvasI
{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+ private static final int DIMS = 3;
String tooltip;
- int toolx, tooly;
+ int toolx;
+
+ int tooly;
// RubberbandRectangle rubberband;
boolean drawAxes = true;
- int omx = 0;
-
- int mx = 0;
-
- int omy = 0;
+ int mouseX = 0;
- int my = 0;
+ int mouseY = 0;
Image img;
Dimension prefsize;
- float centre[] = new float[3];
+ Point centre;
- float width[] = new float[3];
+ float[] width = new float[DIMS];
- float max[] = new float[3];
+ float[] max = new float[DIMS];
- float min[] = new float[3];
+ float[] min = new float[DIMS];
float maxwidth;
int npoint;
- Vector points;
+ List<SequencePoint> points;
- float[][] orig;
+ Point[] orig;
- float[][] axes;
+ Point[] axisEndPoints;
int startx;
boolean showLabels = false;
- public RotatableCanvas(AlignmentViewport av)
+ public RotatableCanvas(AlignmentViewport viewport)
{
- this.av = av;
+ this.av = viewport;
+ axisEndPoints = new Point[DIMS];
}
public void showLabels(boolean b)
repaint();
}
- public void setPoints(Vector points, int npoint)
+ @Override
+ public void setPoints(List<SequencePoint> points, int npoint)
{
this.points = points;
this.npoint = npoint;
PaintRefresher.Register(this, av.getSequenceSetId());
prefsize = getPreferredSize();
- orig = new float[npoint][3];
+ orig = new Point[npoint];
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- for (int j = 0; j < 3; j++)
- {
- orig[i][j] = sp.coord[j];
- }
- }
- // Initialize the matrices to identity
-
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- }
+ SequencePoint sp = points.get(i);
+ orig[i] = sp.coord;
}
- axes = new float[3][3];
- initAxes();
+ resetAxes();
findCentre();
findWidth();
* super.removeNotify(); }
*/
- public void initAxes()
+ /**
+ * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+ * back (so obscured in a 2-D display)
+ */
+ public void resetAxes()
{
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- axes[i][j] = 0;
- }
- else
- {
- axes[i][j] = 1;
- }
- }
- }
+ axisEndPoints[0] = new Point(1f, 0f, 0f);
+ axisEndPoints[1] = new Point(0f, 1f, 0f);
+ axisEndPoints[2] = new Point(0f, 0f, 1f);
}
+ /**
+ * Computes and saves the maximum and minimum (x, y, z) positions of any
+ * sequence point, and also the min-max range (width) for each dimension, and
+ * the maximum width for all dimensions
+ */
public void findWidth()
{
max = new float[3];
min = new float[3];
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
+ max[0] = Float.MIN_VALUE;
+ max[1] = Float.MIN_VALUE;
+ max[2] = Float.MIN_VALUE;
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
- for (int i = 0; i < 3; i++)
+ for (SequencePoint sp : points)
{
- for (int j = 0; j < npoint; j++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(j);
- if (sp.coord[i] >= max[i])
- {
- max[i] = sp.coord[i];
- }
- if (sp.coord[i] <= min[i])
- {
- min[i] = sp.coord[i];
- }
- }
+ max[0] = Math.max(max[0], sp.coord.x);
+ max[1] = Math.max(max[1], sp.coord.y);
+ max[2] = Math.max(max[2], sp.coord.z);
+ min[0] = Math.min(min[0], sp.coord.x);
+ min[1] = Math.min(min[1], sp.coord.y);
+ min[2] = Math.min(min[2], sp.coord.z);
}
- // System.out.println("xmax " + max[0] + " min " + min[0]);
- // System.out.println("ymax " + max[1] + " min " + min[1]);
- // System.out.println("zmax " + max[2] + " min " + min[2]);
-
width[0] = Math.abs(max[0] - min[0]);
width[1] = Math.abs(max[1] - min[1]);
width[2] = Math.abs(max[2] - min[2]);
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
+ maxwidth = Math.max(width[0], Math.max(width[1], width[2]));
}
public float findScale()
{
- int dim, width, height;
+ int dim, w, height;
if (getSize().width != 0)
{
- width = getSize().width;
+ w = getSize().width;
height = getSize().height;
}
else
{
- width = prefsize.width;
+ w = prefsize.width;
height = prefsize.height;
}
- if (width < height)
+ if (w < height)
{
- dim = width;
+ dim = w;
}
else
{
dim = height;
}
- return (float) (dim * scalefactor / (2 * maxwidth));
+ return dim * scalefactor / (2 * maxwidth);
}
+ /**
+ * Computes and saves the position of the centre of the view
+ */
public void findCentre()
{
- // Find centre coordinate
findWidth();
- centre[0] = (max[0] + min[0]) / 2;
- centre[1] = (max[1] + min[1]) / 2;
- centre[2] = (max[2] + min[2]) / 2;
+ float x = (max[0] + min[0]) / 2;
+ float y = (max[1] + min[1]) / 2;
+ float z = (max[2] + min[2]) / 2;
- // System.out.println("Centre x " + centre[0]);
- // System.out.println("Centre y " + centre[1]);
- // System.out.println("Centre z " + centre[2]);
+ centre = new Point(x, y, z);
}
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
}
}
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (points == null)
drawBackground(ig, Color.black);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
for (int i = 0; i < 3; i++)
{
g.drawLine(getSize().width / 2, getSize().height / 2,
- (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
- (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
+ (int) (axisEndPoints[i].x * scale * max[0] + getSize().width / 2),
+ (int) (axisEndPoints[i].y * scale * max[1] + getSize().height / 2));
}
}
public void drawScene(Graphics g)
{
- // boolean darker = false;
-
- int halfwidth = getSize().width / 2;
- int halfheight = getSize().height / 2;
-
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
- + halfheight;
- float z = sp.coord[1] - centre[2];
-
- if (av.getSequenceColour(sp.sequence) == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(av.getSequenceColour(sp.sequence));
- }
-
+ SequencePoint sp = points.get(i);
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ g.setColor(
+ sequenceColour == Color.black ? Color.white : sequenceColour);
if (av.getSelectionGroup() != null)
{
if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
+ .contains(sequence))
{
g.setColor(Color.gray);
}
}
- if (z < 0)
+
+ if (sp.coord.z < centre.z)
{
g.setColor(g.getColor().darker());
}
+ int halfwidth = getSize().width / 2;
+ int halfheight = getSize().height / 2;
+ int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+ int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
g.fillRect(x - 3, y - 3, 6, 6);
+
if (showLabels)
{
g.setColor(Color.red);
- g.drawString(
- ((SequencePoint) points.elementAt(i)).sequence.getName(),
- x - 3, y - 4);
+ g.drawString(sequence.getName(), x - 3, y - 4);
}
}
}
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyPressed(KeyEvent evt)
{
- if (evt.getKeyCode() == KeyEvent.VK_UP)
+ boolean shiftDown = evt.isShiftDown();
+ int keyCode = evt.getKeyCode();
+ if (keyCode == KeyEvent.VK_UP)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(1.1f);
+ }
+ }
+ else if (keyCode == KeyEvent.VK_DOWN)
{
- scalefactor = (float) (scalefactor * 1.1);
- scale = findScale();
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(0.9f);
+ }
}
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
{
- scalefactor = (float) (scalefactor * 0.9);
- scale = findScale();
+ rotate(1f, 0f);
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
+ {
+ rotate(-1f, 0f);
}
else if (evt.getKeyChar() == 's')
{
repaint();
}
- public void printPoints()
- {
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- Format.print(System.out, "%5d ", i);
- for (int j = 0; j < 3; j++)
- {
- Format.print(System.out, "%13.3f ", sp.coord[j]);
- }
- System.out.println();
- }
- }
-
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
int y = evt.getY();
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
+ mouseX = x;
+ mouseY = y;
startx = x;
starty = y;
rectx2 = -1;
recty2 = -1;
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
repaint();
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
- SequenceI found = findPoint(evt.getX(), evt.getY());
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
if (found == null)
{
tooltip = null;
repaint();
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
- mx = evt.getX();
- my = evt.getY();
-
- rotmat.setIdentity();
+ int xPos = evt.getX();
+ int yPos = evt.getY();
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
-
- for (int i = 0; i < npoint; i++)
+ if (xPos == mouseX && yPos == mouseY)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- sp.coord[0] -= centre[0];
- sp.coord[1] -= centre[1];
- sp.coord[2] -= centre[2];
-
- // Now apply the rotation matrix
- sp.coord = rotmat.vectorMultiply(sp.coord);
-
- // Now translate back again
- sp.coord[0] += centre[0];
- sp.coord[1] += centre[1];
- sp.coord[2] += centre[2];
+ return;
}
- for (int i = 0; i < 3; i++)
- {
- axes[i] = rotmat.vectorMultiply(axes[i]);
- }
- omx = mx;
- omy = my;
+ int xDelta = xPos - mouseX;
+ int yDelta = yPos - mouseY;
- paint(this.getGraphics());
+ rotate(xDelta, yDelta);
+ repaint();
}
public void rectSelect(int x1, int y1, int x2, int y2)
// boolean changedSel = false;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
- + (float) getSize().width / 2.0);
- int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
- + (float) getSize().height / 2.0);
+ SequencePoint sp = points.get(i);
+ int tmp1 = (int) ((sp.coord.x - centre.x) * scale
+ + getSize().width / 2.0);
+ int tmp2 = (int) ((sp.coord.y - centre.y) * scale
+ + getSize().height / 2.0);
+ SequenceI sequence = sp.getSequence();
if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
{
if (av != null)
{
if (!av.getSelectionGroup().getSequences(null)
- .contains(sp.sequence))
+ .contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
}
}
- public SequenceI findPoint(int x, int y)
+ /**
+ * Answers the first sequence found whose point on the display is within 2
+ * pixels of the given coordinates, or null if none is found
+ *
+ * @param x
+ * @param y
+ *
+ * @return
+ */
+ public SequenceI findSequenceAtPoint(int x, int y)
{
-
int halfwidth = getSize().width / 2;
int halfheight = getSize().height / 2;
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = points.get(i);
+ int px = (int) ((sp.coord.x - centre.x) * scale)
+ halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord.y - centre.y) * scale)
+ halfheight;
if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
{
found = i;
+ break;
}
}
+
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.get(found).getSequence();
}
else
{
}
}
+ /**
+ * Resets the view to initial state (no rotation)
+ */
+ public void resetView()
+ {
+ img = null;
+ resetAxes();
+ }
+
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ scalefactor *= factor;
+ }
+ scale = findScale();
+ }
+
+ @Override
+ public void rotate(float x, float y)
+ {
+ if (x == 0f && y == 0f)
+ {
+ return;
+ }
+
+ /*
+ * get the identity transformation...
+ */
+ RotatableMatrix rotmat = new RotatableMatrix();
+
+ /*
+ * rotate around the X axis for change in Y
+ * (mouse movement up/down); note we are equating a
+ * number of pixels with degrees of rotation here!
+ */
+ if (y != 0)
+ {
+ rotmat.rotate(y, Axis.X);
+ }
+
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (x != 0)
+ {
+ rotmat.rotate(x, Axis.Y);
+ }
+
+ /*
+ * apply the composite transformation to sequence points
+ */
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ sp.translate(-centre.x, -centre.y, -centre.z);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre.x, centre.y, centre.z);
+ }
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
+ }
+ }
+
}
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * A bean that models an (x, y, z) position in 3-D space
+ */
+public final class Point
+{
+ public final float x;
+
+ public final float y;
+
+ public final float z;
+
+ public Point(float xVal, float yVal, float zVal)
+ {
+ x = xVal;
+ y = yVal;
+ z = zVal;
+ }
+
+ /**
+ * toString for convenience of inspection in debugging or logging
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("[%f, %f, %f]", x, y, z);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + Float.floatToIntBits(x);
+ result = prime * result + Float.floatToIntBits(y);
+ result = prime * result + Float.floatToIntBits(z);
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ Point other = (Point) obj;
+ if (Float.floatToIntBits(x) != Float.floatToIntBits(other.x))
+ {
+ return false;
+ }
+ if (Float.floatToIntBits(y) != Float.floatToIntBits(other.y))
+ {
+ return false;
+ }
+ if (Float.floatToIntBits(z) != Float.floatToIntBits(other.z))
+ {
+ return false;
+ }
+ return true;
+ }
+}
package jalview.datamodel;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * A bean that models a set of (x, y, z) values and a reference to a sequence.
+ * As used in Principal Component Analysis, the (x, y, z) values are the
+ * sequence's score for the currently selected first, second and third
+ * dimensions of the PCA.
*/
public class SequencePoint
{
- // SMJS PUBLIC
+ /*
+ * Associated alignment sequence, or dummy sequence object
+ */
+ private final SequenceI sequence;
+
+ /*
+ * x, y, z values
+ */
+ public Point coord;
+
/**
- * for points with no real physical association with an alignment sequence
+ * Constructor
+ *
+ * @param sequence
+ * @param coord
*/
- public boolean isPlaceholder = false;
+ public SequencePoint(SequenceI sequence, Point pt)
+ {
+ this.sequence = sequence;
+ this.coord = pt;
+ }
/**
- * Associated alignment sequence, or dummy sequence object.
+ * Constructor given a sequence and an array of x, y, z coordinate positions
+ *
+ * @param sequence
+ * @param coords
+ * @throws ArrayIndexOutOfBoundsException
+ * if array length is less than 3
*/
- public SequenceI sequence;
+ public SequencePoint(SequenceI sequence, float[] coords)
+ {
+ this(sequence, new Point(coords[0], coords[1], coords[2]));
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
/**
- * array of coordinates in embedded sequence space.
+ * Applies a translation to the (x, y, z) coordinates
+ *
+ * @param centre
*/
- public float[] coord;
+ public void translate(float x, float y, float z)
+ {
+ coord = new Point(coord.x + x, coord.y + y, coord.z + z);
+ }
- // SMJS ENDPUBLIC
- public SequencePoint(SequenceI sequence, float[] coord)
+ /**
+ * string representation for ease of inspection in debugging or logging only
+ */
+ @Override
+ public String toString()
{
- this.sequence = sequence;
- this.coord = coord;
+ return sequence.getName() + " " + coord.toString();
}
}
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
/*
* the most recently opened PCA results panel
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ final JComboBox<String> scoreModelsCombo = new JComboBox<>();
scoreModelsCombo.setRenderer(renderer);
/*
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+
+ /*
+ * select the score models applicable to the alignment type
+ */
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+ pca.isSelected());
/*
* now we can actually add entries to the combobox,
* remembering their descriptions for tooltips
*/
- ScoreModels scoreModels = ScoreModels.getInstance();
boolean selectedIsPresent = false;
- for (ScoreModelI sm : scoreModels.getModels())
+ for (ScoreModelI sm : models)
{
- boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+ if (curSel != null && sm.getName().equals(curSel))
+ {
+ selectedIsPresent = true;
+ curSel = sm.getName();
+ }
+ model.addElement(sm.getName());
+
+ /*
+ * tooltip is description if provided, else text lookup with
+ * fallback on the model name
+ */
+ String tooltip = sm.getDescription();
+ if (tooltip == null)
{
- if (curSel != null && sm.getName().equals(curSel))
- {
- selectedIsPresent = true;
- curSel = sm.getName();
- }
- model.addElement(sm.getName());
-
- /*
- * tooltip is description if provided, else text lookup with
- * fallback on the model name
- */
- String tooltip = sm.getDescription();
- if (tooltip == null)
- {
- tooltip = MessageManager.getStringOrReturn("label.score_model_",
- sm.getName());
- }
- toolTips.add(tooltip);
+ tooltip = MessageManager.getStringOrReturn("label.score_model_",
+ sm.getName());
}
+ toolTips.add(tooltip);
}
+
if (selectedIsPresent)
{
model.setSelectedItem(curSel);
}
/**
+ * Builds a list of score models which are applicable for the alignment and
+ * calculation type (peptide or generic models for protein, nucleotide or
+ * generic models for nucleotide).
+ * <p>
+ * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA.
+ * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62
+ * was the only score matrix supported. This is included if property
+ * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file.
+ *
+ * @param nucleotide
+ * @param forPca
+ * @return
+ */
+ protected static List<ScoreModelI> getApplicableScoreModels(
+ boolean nucleotide, boolean forPca)
+ {
+ List<ScoreModelI> filtered = new ArrayList<>();
+
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+ {
+ filtered.add(sm);
+ }
+ }
+
+ /*
+ * special case: add BLOSUM62 as last option for nucleotide PCA,
+ * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+ */
+ if (nucleotide && forPca
+ && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+ {
+ filtered.add(scoreModels.getBlosum62());
+ }
+
+ return filtered;
+ }
+
+ /**
* Open and calculate the selected tree or PCA on 'OK'
*/
protected void calculate_actionPerformed()
JvOptionPane.WARNING_MESSAGE);
return;
}
+
+ /*
+ * construct the panel and kick off its calculation thread
+ */
pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
+ new Thread(pcaPanel).start();
+
}
/**
*/
package jalview.gui;
+import static jalview.math.RotatableMatrix.Axis.X;
+import static jalview.math.RotatableMatrix.Axis.Y;
+import static jalview.math.RotatableMatrix.Axis.Z;
+
import jalview.analysis.Conservation;
+import jalview.analysis.PCA;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
import jalview.schemabinding.version2.Annotation;
import jalview.schemabinding.version2.AnnotationColours;
import jalview.schemabinding.version2.AnnotationElement;
+import jalview.schemabinding.version2.Axis;
import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
import jalview.schemabinding.version2.CompoundMatcher;
+import jalview.schemabinding.version2.D;
import jalview.schemabinding.version2.DBRef;
+import jalview.schemabinding.version2.DoubleMatrix;
+import jalview.schemabinding.version2.E;
+import jalview.schemabinding.version2.EigenMatrix;
import jalview.schemabinding.version2.Features;
import jalview.schemabinding.version2.Group;
import jalview.schemabinding.version2.HiddenColumns;
import jalview.schemabinding.version2.MatchCondition;
import jalview.schemabinding.version2.MatcherSet;
import jalview.schemabinding.version2.OtherData;
+import jalview.schemabinding.version2.PairwiseMatrix;
+import jalview.schemabinding.version2.PcaData;
+import jalview.schemabinding.version2.PcaViewer;
import jalview.schemabinding.version2.PdbentryItem;
import jalview.schemabinding.version2.Pdbids;
import jalview.schemabinding.version2.Property;
import jalview.schemabinding.version2.RnaViewer;
+import jalview.schemabinding.version2.Row;
import jalview.schemabinding.version2.SecondaryStructure;
+import jalview.schemabinding.version2.SeqPointMax;
+import jalview.schemabinding.version2.SeqPointMin;
import jalview.schemabinding.version2.Sequence;
+import jalview.schemabinding.version2.SequencePoint;
import jalview.schemabinding.version2.SequenceSet;
import jalview.schemabinding.version2.SequenceSetProperties;
import jalview.schemabinding.version2.Setting;
import jalview.schemabinding.version2.StructureState;
import jalview.schemabinding.version2.ThresholdLine;
import jalview.schemabinding.version2.Tree;
+import jalview.schemabinding.version2.TridiagonalMatrix;
import jalview.schemabinding.version2.UserColours;
import jalview.schemabinding.version2.Viewport;
import jalview.schemabinding.version2.types.ColourThreshTypeType;
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;
tree.setXpos(tp.getX());
tree.setYpos(tp.getY());
tree.setId(makeHashCode(tp, null));
+ tree.setLinkToAllViews(tp.treeCanvas.applyToAllViews);
jms.addTree(tree);
}
}
}
}
+ /*
+ * save PCA viewers
+ */
+ if (!storeDS && Desktop.desktop != null)
+ {
+ for (JInternalFrame frame : Desktop.desktop.getAllFrames())
+ {
+ if (frame instanceof PCAPanel)
+ {
+ PCAPanel panel = (PCAPanel) frame;
+ if (panel.av.getAlignment() == jal)
+ {
+ savePCA(panel, jms);
+ }
+ }
+ }
+ }
+
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
}
/**
+ * Writes PCA viewer attributes and computed values to an XML model object and adds it to the JalviewModel. Any exceptions are reported by logging.
+ */
+ protected void savePCA(PCAPanel panel, JalviewModelSequence jms)
+ {
+ try
+ {
+ PcaViewer viewer = new PcaViewer();
+ viewer.setHeight(panel.getHeight());
+ viewer.setWidth(panel.getWidth());
+ viewer.setXpos(panel.getX());
+ viewer.setYpos(panel.getY());
+ viewer.setTitle(panel.getTitle());
+ PCAModel pcaModel = panel.pcaModel;
+ viewer.setScoreModelName(pcaModel.getScoreModelName());
+ viewer.setXDim(panel.getSelectedDimensionIndex(X));
+ viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+ viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+ viewer.setBgColour(panel.rc.getBackgroundColour().getRGB());
+ viewer.setScaleFactor(panel.rc.scaleFactor);
+ float[] spMin = panel.rc.getSeqMin();
+ SeqPointMin spmin = new SeqPointMin();
+ spmin.setXPos(spMin[0]);
+ spmin.setYPos(spMin[1]);
+ spmin.setZPos(spMin[2]);
+ viewer.setSeqPointMin(spmin);
+ float[] spMax = panel.rc.getSeqMax();
+ SeqPointMax spmax = new SeqPointMax();
+ spmax.setXPos(spMax[0]);
+ spmax.setYPos(spMax[1]);
+ spmax.setZPos(spMax[2]);
+ viewer.setSeqPointMax(spmax);
+ viewer.setShowLabels(panel.rc.showLabels);
+ viewer.setLinkToAllViews(panel.rc.applyToAllViews);
+ SimilarityParamsI sp = pcaModel.getSimilarityParameters();
+ viewer.setIncludeGaps(sp.includeGaps());
+ viewer.setMatchGaps(sp.matchGaps());
+ viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+ viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+
+ /*
+ * sequence points on display
+ */
+ for (jalview.datamodel.SequencePoint spt : pcaModel
+ .getSequencePoints())
+ {
+ SequencePoint point = new SequencePoint();
+ point.setSequenceRef(seqHash(spt.getSequence()));
+ point.setXPos(spt.coord.x);
+ point.setYPos(spt.coord.y);
+ point.setZPos(spt.coord.z);
+ viewer.addSequencePoint(point);
+ }
+
+ /*
+ * (end points of) axes on display
+ */
+ for (Point p : panel.rc.axisEndPoints)
+ {
+ Axis axis = new Axis();
+ axis.setXPos(p.x);
+ axis.setYPos(p.y);
+ axis.setZPos(p.z);
+ viewer.addAxis(axis);
+ }
+
+ /*
+ * raw PCA data (note we are not restoring PCA inputs here -
+ * alignment view, score model, similarity parameters)
+ */
+ PcaData data = new PcaData();
+ viewer.setPcaData(data);
+ PCA pca = pcaModel.getPcaData();
+
+ PairwiseMatrix pm = new PairwiseMatrix();
+ saveDoubleMatrix(pca.getPairwiseScores(), pm);
+ data.setPairwiseMatrix(pm);
+
+ TridiagonalMatrix tm = new TridiagonalMatrix();
+ saveDoubleMatrix(pca.getTridiagonal(), tm);
+ data.setTridiagonalMatrix(tm);
+
+ EigenMatrix eigenMatrix = new EigenMatrix();
+ data.setEigenMatrix(eigenMatrix);
+ saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
+
+ jms.addPcaViewer(viewer);
+ } catch (Throwable t)
+ {
+ Cache.log.error("Error saving PCA: " + t.getMessage());
+ }
+ }
+
+ /**
+ * Stores values from a matrix into an XML element, including (if present) the
+ * D or E vectors
+ *
+ * @param m
+ * @param xmlMatrix
+ * @see #loadDoubleMatrix(DoubleMatrix)
+ */
+ protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
+ {
+ xmlMatrix.setRows(m.height());
+ xmlMatrix.setColumns(m.width());
+ for (int i = 0; i < m.height(); i++)
+ {
+ Row row = new Row();
+ for (int j = 0; j < m.width(); j++)
+ {
+ row.addV(m.getValue(i, j));
+ }
+ xmlMatrix.addRow(row);
+ }
+ if (m.getD() != null)
+ {
+ D dVector = new D();
+ dVector.setV(m.getD());
+ xmlMatrix.setD(dVector);
+ }
+ if (m.getE() != null)
+ {
+ E eVector = new E();
+ eVector.setV(m.getE());
+ xmlMatrix.setE(eVector);
+ }
+ }
+
+ /**
+ * Loads XML matrix data into a new Matrix object, including the D and/or E
+ * vectors (if present)
+ *
+ * @param mData
+ * @return
+ * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
+ */
+ protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
+ {
+ int rows = mData.getRows();
+ double[][] vals = new double[rows][];
+
+ for (int i = 0; i < rows; i++)
+ {
+ vals[i] = mData.getRow(i).getV();
+ }
+
+ MatrixI m = new Matrix(vals);
+
+ if (mData.getD() != null) {
+ m.setD(mData.getD().getV());
+ }
+ if (mData.getE() != null)
+ {
+ m.setE(mData.getE().getV());
+ }
+
+ return m;
+ }
+
+ /**
* Save any Varna viewers linked to this sequence. Writes an rnaViewer element
* for each viewer, with
* <ul>
if (loadTreesAndStructures)
{
loadTrees(jms, view, af, av, ap);
+ loadPCAViewers(jms, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
// works still
tp.getTreeCanvas().setViewport(av); // af.viewport;
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-
}
if (tp == null)
{
tp.showDistances(tree.getShowDistances());
tp.getTreeCanvas().setThreshold(tree.getThreshold());
+ tp.treeCanvas.applyToAllViews = tree.isLinkToAllViews();
if (tree.getCurrentTree())
{
}
/**
+ * 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();
+
+ MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix());
+ pca.setPairwiseScores(pairwise);
+
+ MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix());
+ pca.setTridiagonal(triDiag);
+
+ MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
+ pca.setEigenmatrix(result);
+
+ panel.pcaModel.setPCA(pca);
+
+ /*
+ * we haven't saved the input data! (JAL-2647 to do)
+ */
+ panel.setInputData(null);
+
+ /*
+ * add the sequence points for the PCA display
+ */
+ List<jalview.datamodel.SequencePoint> seqPoints = new ArrayList<>();
+ for (SequencePoint sp : viewer.getSequencePoint())
+ {
+ String seqId = sp.getSequenceRef();
+ SequenceI seq = seqRefIds.get(seqId);
+ if (seq == null)
+ {
+ throw new IllegalStateException(
+ "Unmatched seqref for PCA: " + seqId);
+ }
+ Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos());
+ jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint(
+ seq, pt);
+ seqPoints.add(seqPoint);
+ }
+ panel.rc.setPoints(seqPoints, seqPoints.size());
+
+ /*
+ * set min-max ranges and scale after setPoints (which recomputes them)
+ */
+ panel.rc.scaleFactor = viewer.getScaleFactor();
+ SeqPointMin spMin = viewer.getSeqPointMin();
+ float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
+ spMin.getZPos() };
+ SeqPointMax spMax = viewer.getSeqPointMax();
+ float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
+ spMax.getZPos() };
+ panel.rc.setSeqMinMax(min, max);
+
+ // todo: hold points list in PCAModel only
+ panel.pcaModel.setSequencePoints(seqPoints);
+
+ panel.setSelectedDimensionIndex(viewer.getXDim(), X);
+ panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
+ panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
+
+ // is this duplication needed?
+ panel.top = seqPoints.size() - 1;
+ panel.pcaModel.setTop(seqPoints.size() - 1);
+
+ /*
+ * add the axes' end points for the display
+ */
+ for (int i = 0; i < 3; i++)
+ {
+ Axis axis = viewer.getAxis(i);
+ panel.rc.axisEndPoints[i] = new Point(axis.getXPos(),
+ axis.getYPos(), axis.getZPos());
+ }
+
+ Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+ "label.calc_title", "PCA", modelName), 475, 450);
+ }
+ } catch (Exception ex)
+ {
+ Cache.log.error("Error loading PCA: " + ex.toString());
+ }
+ }
+
+ /**
* Populates an XML model of the feature colour scheme for one feature type
*
* @param featureType
package jalview.gui;
import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GPCAPanel;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import java.awt.print.PrinterJob;
import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.event.InternalFrameEvent;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * The panel holding the Principal Component Analysis 3-D visualisation
*/
public class PCAPanel extends GPCAPanel
implements Runnable, IProgressIndicator
{
+ private static final int MIN_WIDTH = 470;
- private IProgressIndicator progressBar;
+ private static final int MIN_HEIGHT = 250;
RotatableCanvas rc;
PCAModel pcaModel;
- private static final int MIN_WIDTH = 470;
-
- private static final int MIN_HEIGHT = 250;
-
int top = 0;
- private boolean working;
+ private IProgressIndicator progressBar;
- /**
- * Creates a new PCAPanel object using default score model and parameters
- *
- * @param alignPanel
- */
- public PCAPanel(AlignmentPanel alignPanel)
- {
- this(alignPanel,
- ScoreModels.getInstance()
- .getDefaultModel(
- !alignPanel.av.getAlignment().isNucleotide())
- .getName(),
- SimilarityParams.SeqSpace);
- }
+ private boolean working;
/**
* Constructor given sequence data, a similarity (or distance) score model
rc = new RotatableCanvas(alignPanel);
this.getContentPane().add(rc, BorderLayout.CENTER);
- Thread worker = new Thread(this);
- worker.start();
+
+ addKeyListener(rc);
+ validate();
+
+ this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
/**
pcaModel = null;
}
- /**
- * Repopulate the options and actions under the score model menu when it is
- * selected. Options will depend on whether 'nucleotide' or 'peptide'
- * modelling is selected (and also possibly on whether any additional score
- * models have been added).
- */
- @Override
- protected void scoreModel_menuSelected()
- {
- scoreModelMenu.removeAll();
- for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
- {
- final String name = sm.getName();
- JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
-
- /*
- * if the score model doesn't provide a description, try to look one
- * up in the text bundle, falling back on its name
- */
- String tooltip = sm.getDescription();
- if (tooltip == null)
- {
- tooltip = MessageManager.getStringOrReturn("label.score_model_",
- name);
- }
- jm.setToolTipText(tooltip);
- jm.setSelected(pcaModel.getScoreModelName().equals(name));
- if ((pcaModel.isNucleotide() && sm.isDNA())
- || (!pcaModel.isNucleotide() && sm.isProtein()))
- {
- jm.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (!pcaModel.getScoreModelName().equals(name))
- {
- ScoreModelI sm2 = ScoreModels.getInstance()
- .getScoreModel(name, ap);
- pcaModel.setScoreModel(sm2);
- Thread worker = new Thread(PCAPanel.this);
- worker.start();
- }
- }
- });
- scoreModelMenu.add(jm);
- }
- }
- }
-
@Override
- public void bgcolour_actionPerformed(ActionEvent e)
+ protected void bgcolour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_background_colour"),
}
/**
- * DOCUMENT ME!
+ * Calculates the PCA and displays the results
*/
@Override
public void run()
{
+ working = true;
long progId = System.currentTimeMillis();
IProgressIndicator progress = this;
String message = MessageManager.getString("label.pca_recalculating");
message = MessageManager.getString("label.pca_calculating");
}
progress.setProgressBar(message, progId);
- working = true;
try
{
- calcSettings.setEnabled(false);
- pcaModel.run();
- // ////////////////
+ pcaModel.calculate();
+
xCombobox.setSelectedIndex(0);
yCombobox.setSelectedIndex(1);
zCombobox.setSelectedIndex(2);
pcaModel.updateRc(rc);
// rc.invalidate();
- nuclSetting.setSelected(pcaModel.isNucleotide());
- protSetting.setSelected(!pcaModel.isNucleotide());
top = pcaModel.getTop();
} catch (OutOfMemoryError er)
{
progress.setProgressBar("", progId);
}
- calcSettings.setEnabled(true);
+
repaint();
if (getParent() == null)
{
- addKeyListener(rc);
- Desktop.addInternalFrame(this, MessageManager
- .getString("label.principal_component_analysis"), 475, 450);
- this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.calc_title", "PCA",
+ pcaModel.getScoreModelName()),
+ 475, 450);
}
working = false;
}
- @Override
- protected void nuclSetting_actionPerfomed(ActionEvent arg0)
- {
- if (!pcaModel.isNucleotide())
- {
- pcaModel.setNucleotide(true);
- pcaModel.setScoreModel(
- ScoreModels.getInstance().getDefaultModel(false));
- Thread worker = new Thread(this);
- worker.start();
- }
-
- }
-
- @Override
- protected void protSetting_actionPerfomed(ActionEvent arg0)
- {
-
- if (pcaModel.isNucleotide())
- {
- pcaModel.setNucleotide(false);
- pcaModel.setScoreModel(
- ScoreModels.getInstance().getDefaultModel(true));
- Thread worker = new Thread(this);
- worker.start();
- }
- }
-
/**
- * DOCUMENT ME!
+ * Updates the PCA display after a change of component to use for x, y or z
+ * axis
*/
- void doDimensionChange()
+ @Override
+ protected void doDimensionChange()
{
if (top == 0)
{
int dim2 = top - yCombobox.getSelectedIndex();
int dim3 = top - zCombobox.getSelectedIndex();
pcaModel.updateRcView(dim1, dim2, dim3);
- rc.img = null;
- rc.rotmat.setIdentity();
- rc.initAxes();
- rc.paint(rc.getGraphics());
+ rc.resetView();
}
/**
- * DOCUMENT ME!
+ * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
+ * the given axis (X/Y/Z)
*
- * @param e
- * DOCUMENT ME!
+ * @param index
+ * @param axis
*/
- @Override
- protected void xCombobox_actionPerformed(ActionEvent e)
+ public void setSelectedDimensionIndex(int index, Axis axis)
{
- doDimensionChange();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void yCombobox_actionPerformed(ActionEvent e)
- {
- doDimensionChange();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void zCombobox_actionPerformed(ActionEvent e)
- {
- doDimensionChange();
+ switch (axis)
+ {
+ case X:
+ xCombobox.setSelectedIndex(index);
+ break;
+ case Y:
+ yCombobox.setSelectedIndex(index);
+ break;
+ case Z:
+ zCombobox.setSelectedIndex(index);
+ break;
+ default:
+ }
}
@Override
- public void outputValues_actionPerformed(ActionEvent e)
+ protected void outputValues_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
}
@Override
- public void showLabels_actionPerformed(ActionEvent e)
+ protected void showLabels_actionPerformed()
{
rc.showLabels(showLabels.getState());
}
@Override
- public void print_actionPerformed(ActionEvent e)
+ protected void print_actionPerformed()
{
PCAPrinter printer = new PCAPrinter();
printer.start();
}
+ /**
+ * If available, shows the data which formed the inputs for the PCA as a new
+ * alignment
+ */
@Override
- public void originalSeqData_actionPerformed(ActionEvent e)
+ public void originalSeqData_actionPerformed()
{
- // this was cut'n'pasted from the equivalent TreePanel method - we should
- // make this an abstract function of all jalview analysis windows
- if (pcaModel.getSeqtrings() == null)
+ // JAL-2647 disabled after load from project (until save to project done)
+ if (pcaModel.getInputData() == null)
{
- jalview.bin.Cache.log.info(
+ Cache.log.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
// decide if av alignment is sufficiently different to original data to
// warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions
+ // create new alignment window with hidden regions (unhiding hidden regions
// yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = pcaModel.getSeqtrings()
+
+ Object[] alAndColsel = pcaModel.getInputData()
.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
- rc.drawBackground(pg, rc.bgColour);
+ rc.drawBackground(pg);
rc.drawScene(pg);
- if (rc.drawAxes == true)
+ if (rc.drawAxes)
{
rc.drawAxes(pg);
}
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Handler for 'Save as EPS' option
*/
@Override
- public void eps_actionPerformed(ActionEvent e)
+ protected void eps_actionPerformed()
{
- makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
+ makePCAImage(ImageMaker.TYPE.EPS);
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Handler for 'Save as PNG' option
*/
@Override
- public void png_actionPerformed(ActionEvent e)
+ protected void png_actionPerformed()
{
- makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
+ makePCAImage(ImageMaker.TYPE.PNG);
}
- void makePCAImage(jalview.util.ImageMaker.TYPE type)
+ void makePCAImage(ImageMaker.TYPE type)
{
int width = rc.getWidth();
int height = rc.getHeight();
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.TYPE.PNG)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
- width, height, null, null, null, 0, false);
- }
- else if (type == jalview.util.ImageMaker.TYPE.EPS)
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
- }
- else
- {
- im = new jalview.util.ImageMaker(this,
- jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
- width, height, null, this.getTitle(), null, 0, false);
-
+ ImageMaker im;
+
+ switch (type)
+ {
+ case PNG:
+ im = new ImageMaker(this, ImageMaker.TYPE.PNG,
+ "Make PNG image from PCA", width, height, null, null, null, 0,
+ false);
+ break;
+ case EPS:
+ im = new ImageMaker(this, ImageMaker.TYPE.EPS,
+ "Make EPS file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
+ break;
+ default:
+ im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+ "Make SVG file from PCA", width, height, null,
+ this.getTitle(), null, 0, false);
}
if (im.getGraphics() != null)
{
- rc.drawBackground(im.getGraphics(), Color.black);
+ rc.drawBackground(im.getGraphics());
rc.drawScene(im.getGraphics());
- if (rc.drawAxes == true)
+ if (rc.drawAxes)
{
rc.drawAxes(im.getGraphics());
}
}
@Override
- public void viewMenu_menuSelected()
+ protected void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
}
+ /**
+ * Builds the menu showing the choice of possible views (for the associated
+ * sequence data) to which the PCA may be linked
+ */
void buildAssociatedViewMenu()
{
AlignmentPanel[] aps = PaintRefresher
JRadioButtonMenuItem item;
ButtonGroup buttonGroup = new ButtonGroup();
- int i, iSize = aps.length;
- final PCAPanel thisPCAPanel = this;
- for (i = 0; i < iSize; i++)
+ int iSize = aps.length;
+
+ for (int i = 0; i < iSize; i++)
{
final AlignmentPanel ap = aps[i];
item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
public void actionPerformed(ActionEvent evt)
{
rc.applyToAllViews = false;
- rc.av = ap.av;
- rc.ap = ap;
- PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
+ rc.av = panel.av;
+ rc.ap = panel;
+ PaintRefresher.Register(PCAPanel.this,
+ panel.av.getSequenceSetId());
}
});
* )
*/
@Override
- protected void outputPoints_actionPerformed(ActionEvent e)
+ protected void outputPoints_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
* .ActionEvent)
*/
@Override
- protected void outputProjPoints_actionPerformed(ActionEvent e)
+ protected void outputProjPoints_actionPerformed()
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
try
}
@Override
- protected void resetButton_actionPerformed(ActionEvent e)
+ protected void resetButton_actionPerformed()
{
int t = top;
top = 0; // ugly - prevents dimensionChanged events from being processed
{
return working;
}
+
+ /**
+ * Answers the selected checkbox item index for PCA dimension for the X, Y or
+ * Z axis of the display
+ *
+ * @param axis
+ * @return
+ */
+ public int getSelectedDimensionIndex(Axis axis)
+ {
+ switch (axis)
+ {
+ case X:
+ return xCombobox.getSelectedIndex();
+ case Y:
+ return yCombobox.getSelectedIndex();
+ default:
+ return zCombobox.getSelectedIndex();
+ }
+ }
+
+ public void setShowLabels(boolean show)
+ {
+ showLabels.setSelected(show);
+ }
+
+ /**
+ * Sets the input data used to calculate the PCA. This is provided for
+ * 'restore from project', which does not currently support this (AL-2647), so
+ * sets the value to null, and hides the menu option for "Input Data...". J
+ *
+ * @param data
+ */
+ public void setInputData(AlignmentView data)
+ {
+ pcaModel.setInputData(data);
+ originalSeqData.setVisible(data != null);
+ }
}
package jalview.gui;
import jalview.api.RotatableCanvasI;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
import jalview.math.RotatableMatrix;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
-import java.util.Vector;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
import javax.swing.JPanel;
import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Models a Panel on which a set of points, and optionally x/y/z axes, can be
+ * drawn, and rotated or zoomed with the mouse
*/
public class RotatableCanvas extends JPanel implements MouseListener,
- MouseMotionListener, KeyListener, RotatableCanvasI
+ MouseMotionListener, KeyListener, RotatableCanvasI,
+ MouseWheelListener
{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
+ private static final float ZOOM_OUT = 0.9f;
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
+ private static final float ZOOM_IN = 1.1f;
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+ /*
+ * pixels distance within which tooltip shows sequence name
+ */
+ private static final int NEARBY = 3;
- // RubberbandRectangle rubberband;
- boolean drawAxes = true;
+ private static final List<String> AXES = Arrays.asList("x", "y", "z");
- int omx = 0;
+ private static final Color AXIS_COLOUR = Color.yellow;
- int mx = 0;
+ private static final int DIMS = 3;
+
+ boolean drawAxes = true;
- int omy = 0;
+ int mouseX;
- int my = 0;
+ int mouseY;
Image img;
Graphics ig;
- Dimension prefsize;
+ Dimension prefSize;
- float[] centre = new float[3];
-
- float[] width = new float[3];
-
- float[] max = new float[3];
-
- float[] min = new float[3];
+ /*
+ * the min-max [x, y, z] values of sequence points when the points
+ * were set on the object, or when the view is reset;
+ * x and y ranges are not recomputed as points are rotated, as this
+ * would make scaling (zoom) unstable, but z ranges are (for correct
+ * graduated colour brightness based on z-coordinate)
+ */
+ float[] seqMin;
- float maxwidth;
+ float[] seqMax;
- float scale;
+ /*
+ * a scale factor used in drawing; when equal to 1, the points span
+ * half the available width or height (whichever is less); increase this
+ * factor to zoom in, decrease it to zoom out
+ */
+ float scaleFactor;
int npoint;
- Vector points;
-
- float[][] orig;
-
- float[][] axes;
-
- int startx;
-
- int starty;
-
- int lastx;
-
- int lasty;
-
- int rectx1;
-
- int recty1;
-
- int rectx2;
+ /*
+ * sequences and their (x, y, z) PCA dimension values
+ */
+ List<SequencePoint> sequencePoints;
- int recty2;
+ /*
+ * x, y, z axis end points (PCA dimension values)
+ */
+ Point[] axisEndPoints;
- float scalefactor = 1;
+ // fields for 'select rectangle' (JAL-1124)
+ // int rectx1;
+ // int recty1;
+ // int rectx2;
+ // int recty2;
AlignmentViewport av;
AlignmentPanel ap;
- boolean showLabels = false;
+ boolean showLabels;
- Color bgColour = Color.black;
+ Color bgColour;
- boolean applyToAllViews = false;
+ boolean applyToAllViews;
- public RotatableCanvas(AlignmentPanel ap)
+ /**
+ * Constructor
+ *
+ * @param panel
+ */
+ public RotatableCanvas(AlignmentPanel panel)
{
- this.av = ap.av;
- this.ap = ap;
-
- addMouseWheelListener(new MouseWheelListener()
- {
- @Override
- public void mouseWheelMoved(MouseWheelEvent e)
- {
- double wheelRotation = e.getPreciseWheelRotation();
- if (wheelRotation > 0)
- {
- /*
- * zoom in
- */
- scale = (float) (scale * 1.1);
- repaint();
- }
- else if (wheelRotation < 0)
- {
- /*
- * zoom out
- */
- scale = (float) (scale * 0.9);
- repaint();
- }
- }
- });
-
+ this.av = panel.av;
+ this.ap = panel;
+ axisEndPoints = new Point[DIMS];
+ showLabels = false;
+ applyToAllViews = false;
+ bgColour = Color.BLACK;
+ resetAxes();
+
+ ToolTipManager.sharedInstance().registerComponent(this);
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(this);
}
- public void showLabels(boolean b)
+ /**
+ * Refreshes the display with labels shown (or not)
+ *
+ * @param show
+ */
+ public void showLabels(boolean show)
{
- showLabels = b;
+ showLabels = show;
repaint();
}
- boolean first = true;
-
@Override
- public void setPoints(Vector points, int npoint)
+ public void setPoints(List<SequencePoint> points, int np)
{
- this.points = points;
- this.npoint = npoint;
- if (first)
- {
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- }
- prefsize = getPreferredSize();
- orig = new float[npoint][3];
-
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
-
- for (int j = 0; j < 3; j++)
- {
- orig[i][j] = sp.coord[j];
- }
- }
-
- // Initialize the matrices to identity
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- }
- }
+ this.sequencePoints = points;
+ this.npoint = np;
+ prefSize = getPreferredSize();
- axes = new float[3][3];
- initAxes();
+ findWidths();
- findCentre();
- findWidth();
-
- scale = findScale();
- if (first)
- {
-
- addMouseListener(this);
-
- addMouseMotionListener(this);
- }
- first = false;
- }
-
- public void initAxes()
- {
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- axes[i][j] = 0;
- }
- else
- {
- axes[i][j] = 1;
- }
- }
- }
+ scaleFactor = 1f;
}
/**
- * DOCUMENT ME!
+ * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+ * back (so obscured in a 2-D display)
*/
- public void findWidth()
+ protected void resetAxes()
{
- max = new float[3];
- min = new float[3];
-
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
-
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
-
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < npoint; j++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(j);
-
- if (sp.coord[i] >= max[i])
- {
- max[i] = sp.coord[i];
- }
-
- if (sp.coord[i] <= min[i])
- {
- min[i] = sp.coord[i];
- }
- }
- }
-
- // System.out.println("xmax " + max[0] + " min " + min[0]);
- // System.out.println("ymax " + max[1] + " min " + min[1]);
- // System.out.println("zmax " + max[2] + " min " + min[2]);
- width[0] = Math.abs(max[0] - min[0]);
- width[1] = Math.abs(max[1] - min[1]);
- width[2] = Math.abs(max[2] - min[2]);
-
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
-
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
+ axisEndPoints[0] = new Point(1f, 0f, 0f);
+ axisEndPoints[1] = new Point(0f, 1f, 0f);
+ axisEndPoints[2] = new Point(0f, 0f, 1f);
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Computes and saves the min-max ranges of x/y/z positions of the sequence
+ * points
*/
- public float findScale()
+ protected void findWidths()
{
- int dim;
- int width;
- int height;
-
- if (getWidth() != 0)
- {
- width = getWidth();
- height = getHeight();
- }
- else
- {
- width = prefsize.width;
- height = prefsize.height;
- }
-
- if (width < height)
- {
- dim = width;
- }
- else
- {
- dim = height;
- }
-
- return (dim * scalefactor) / (2 * maxwidth);
+ float[] max = new float[DIMS];
+ float[] min = new float[DIMS];
+
+ max[0] = -Float.MAX_VALUE;
+ max[1] = -Float.MAX_VALUE;
+ max[2] = -Float.MAX_VALUE;
+
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
+
+ for (SequencePoint sp : sequencePoints)
+ {
+ max[0] = Math.max(max[0], sp.coord.x);
+ max[1] = Math.max(max[1], sp.coord.y);
+ max[2] = Math.max(max[2], sp.coord.z);
+ min[0] = Math.min(min[0], sp.coord.x);
+ min[1] = Math.min(min[1], sp.coord.y);
+ min[2] = Math.min(min[2], sp.coord.z);
+ }
+
+ seqMin = min;
+ seqMax = max;
}
/**
- * DOCUMENT ME!
- */
- public void findCentre()
- {
- // Find centre coordinate
- findWidth();
-
- centre[0] = (max[0] + min[0]) / 2;
- centre[1] = (max[1] + min[1]) / 2;
- centre[2] = (max[2] + min[2]) / 2;
-
- // System.out.println("Centre x " + centre[0]);
- // System.out.println("Centre y " + centre[1]);
- // System.out.println("Centre z " + centre[2]);
- }
-
- /**
- * DOCUMENT ME!
+ * Answers the preferred size if it has been set, else 400 x 400
*
- * @return DOCUMENT ME!
+ * @return
*/
@Override
public Dimension getPreferredSize()
{
- if (prefsize != null)
+ if (prefSize != null)
{
- return prefsize;
+ return prefSize;
}
else
{
}
/**
- * DOCUMENT ME!
+ * Answers the preferred size
*
- * @return DOCUMENT ME!
+ * @return
+ * @see RotatableCanvas#getPreferredSize()
*/
@Override
public Dimension getMinimumSize()
}
/**
- * DOCUMENT ME!
+ * Repaints the panel
*
* @param g
- * DOCUMENT ME!
*/
@Override
public void paintComponent(Graphics g1)
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
- if (points == null)
+ if (sequencePoints == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
g.drawString(
}
else
{
- // Only create the image at the beginning -
- if ((img == null) || (prefsize.width != getWidth())
- || (prefsize.height != getHeight()))
+ /*
+ * create the image at the beginning or after a resize
+ */
+ boolean resized = prefSize.width != getWidth()
+ || prefSize.height != getHeight();
+ if (img == null || resized)
{
- prefsize.width = getWidth();
- prefsize.height = getHeight();
+ prefSize.width = getWidth();
+ prefSize.height = getHeight();
- scale = findScale();
-
- // System.out.println("New scale = " + scale);
img = createImage(getWidth(), getHeight());
ig = img.getGraphics();
}
- drawBackground(ig, bgColour);
+ drawBackground(ig);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
}
/**
- * DOCUMENT ME!
+ * Resets the rotation and choice of axes to the initial state (without change
+ * of scale factor)
+ */
+ public void resetView()
+ {
+ img = null;
+ findWidths();
+ resetAxes();
+ repaint();
+ }
+
+ /**
+ * Draws lines for the x, y, z axes
*
* @param g
- * DOCUMENT ME!
*/
public void drawAxes(Graphics g)
{
+ g.setColor(AXIS_COLOUR);
- g.setColor(Color.yellow);
+ int midX = getWidth() / 2;
+ int midY = getHeight() / 2;
+ float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
+ Math.abs(seqMax[1] - seqMin[1]));
+ int pix = Math.min(getWidth(), getHeight());
+ float scaleBy = pix * scaleFactor / (2f * maxWidth);
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- g.drawLine(getWidth() / 2, getHeight() / 2,
- (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),
- (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));
+ g.drawLine(midX, midY,
+ midX + (int) (axisEndPoints[i].x * scaleBy * seqMax[0]),
+ midY + (int) (axisEndPoints[i].y * scaleBy * seqMax[1]));
}
}
/**
- * DOCUMENT ME!
+ * Fills the background with the currently configured background colour
*
* @param g
- * DOCUMENT ME!
- * @param col
- * DOCUMENT ME!
*/
- public void drawBackground(Graphics g, Color col)
+ public void drawBackground(Graphics g)
{
- g.setColor(col);
- g.fillRect(0, 0, prefsize.width, prefsize.height);
+ g.setColor(bgColour);
+ g.fillRect(0, 0, prefSize.width, prefSize.height);
}
/**
- * DOCUMENT ME!
+ * Draws points (6x6 squares) for the sequences of the PCA, and labels
+ * (sequence names) if configured to do so. The sequence points colours are
+ * taken from the sequence ids in the alignment (converting black to white).
+ * Sequences 'at the back' (z-coordinate is negative) are shaded slightly
+ * darker to help give a 3-D sensation.
*
* @param g
- * DOCUMENT ME!
*/
public void drawScene(Graphics g1)
{
-
Graphics2D g = (Graphics2D) g1;
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
+ int pix = Math.min(getWidth(), getHeight());
+ float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+ float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+ float maxWidth = Math.max(xWidth, yWidth);
+ float scaleBy = pix * scaleFactor / (2f * maxWidth);
- int halfwidth = getWidth() / 2;
- int halfheight = getHeight() / 2;
+ float[] centre = getCentre();
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((sp.coord[1] - centre[1]) * scale)
- + halfheight;
- float z = sp.coord[1] - centre[2];
-
- if (av.getSequenceColour(sp.sequence) == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(av.getSequenceColour(sp.sequence));
- }
-
- if (av.getSelectionGroup() != null)
- {
- if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
- {
- g.setColor(Color.gray);
- }
- }
-
- if (z < 0)
- {
- g.setColor(g.getColor().darker());
- }
-
+ /*
+ * sequence point colour as sequence id, but
+ * gray if sequence is currently selected
+ */
+ SequencePoint sp = sequencePoints.get(i);
+ Color sequenceColour = getSequencePointColour(sp);
+ g.setColor(sequenceColour);
+
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+ int x = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
+ int y = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
g.fillRect(x - 3, y - 3, 6, 6);
+
if (showLabels)
{
g.setColor(Color.red);
- g.drawString(
- ((SequencePoint) points.elementAt(i)).sequence.getName(),
- x - 3, y - 4);
+ g.drawString(sp.getSequence().getName(), x - 3, y - 4);
+ }
+ }
+ if (showLabels)
+ {
+ g.setColor(AXIS_COLOUR);
+ int midX = getWidth() / 2;
+ int midY = getHeight() / 2;
+ Iterator<String> axes = AXES.iterator();
+ for (Point p : axisEndPoints)
+ {
+ int x = midX + (int) (p.x * scaleBy * seqMax[0]);
+ int y = midY + (int) (p.y * scaleBy * seqMax[1]);
+ g.drawString(axes.next(), x - 3, y - 4);
}
}
-
// //Now the rectangle
// if (rectx2 != -1 && recty2 != -1) {
// g.setColor(Color.white);
}
/**
- * DOCUMENT ME!
+ * Determines the colour to use when drawing a sequence point. The colour is
+ * taken from the sequence id, with black converted to white, and then
+ * graduated from darker (at the back) to brighter (at the front) based on the
+ * z-axis coordinate of the point.
*
- * @return DOCUMENT ME!
+ * @param sp
+ * @return
*/
- public Dimension minimumsize()
+ protected Color getSequencePointColour(SequencePoint sp)
{
- return prefsize;
- }
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ if (sequenceColour == Color.black)
+ {
+ sequenceColour = Color.white;
+ }
+ if (av.getSelectionGroup() != null)
+ {
+ if (av.getSelectionGroup().getSequences(null).contains(sequence))
+ {
+ sequenceColour = Color.gray;
+ }
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension preferredsize()
- {
- return prefsize;
+ /*
+ * graduate brighter for point in front of centre, darker if behind centre
+ */
+ float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+ if (sp.coord.z > zCentre)
+ {
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, 0,
+ sequenceColour, seqMax[2], sequenceColour.brighter());
+ }
+ else if (sp.coord.z < zCentre)
+ {
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, seqMin[2],
+ sequenceColour.darker(), 0, sequenceColour);
+ }
+
+ return sequenceColour;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void keyTyped(KeyEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void keyReleased(KeyEvent evt)
{
}
/**
- * DOCUMENT ME!
+ * Responds to up or down arrow key by zooming in or out, respectively
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void keyPressed(KeyEvent evt)
{
- if (evt.getKeyCode() == KeyEvent.VK_UP)
+ int keyCode = evt.getKeyCode();
+ boolean shiftDown = evt.isShiftDown();
+
+ if (keyCode == KeyEvent.VK_UP)
{
- scalefactor = (float) (scalefactor * 1.1);
- scale = findScale();
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(ZOOM_IN);
+ }
}
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ else if (keyCode == KeyEvent.VK_DOWN)
{
- scalefactor = (float) (scalefactor * 0.9);
- scale = findScale();
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(ZOOM_OUT);
+ }
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
+ {
+ rotate(1f, 0f);
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
+ {
+ rotate(-1f, 0f);
}
else if (evt.getKeyChar() == 's')
{
- System.err.println("DEBUG: Rectangle selection"); // log.debug
-
- if ((rectx2 != -1) && (recty2 != -1))
- {
- rectSelect(rectx1, recty1, rectx2, recty2);
- }
+ // Cache.log.warn("DEBUG: Rectangle selection");
+ // todo not yet enabled as rectx2, recty2 are always -1
+ // need to set them in mouseDragged; JAL-1124
+ // if ((rectx2 != -1) && (recty2 != -1))
+ // {
+ // rectSelect(rectx1, recty1, rectx2, recty2);
+ // }
}
repaint();
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ scaleFactor *= factor;
+ }
+ }
+
@Override
public void mouseClicked(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseEntered(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseExited(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseReleased(MouseEvent evt)
{
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * If the mouse press is at (within 2 pixels of) a sequence point, toggles
+ * (adds or removes) the corresponding sequence as a member of the viewport
+ * selection group. This supports configuring a group in the alignment by
+ * clicking on points in the PCA display.
*/
@Override
public void mousePressed(MouseEvent evt)
int x = evt.getX();
int y = evt.getY();
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
-
- startx = x;
- starty = y;
+ mouseX = x;
+ mouseY = y;
- rectx1 = x;
- recty1 = y;
+ // rectx1 = x;
+ // recty1 = y;
+ // rectx2 = -1;
+ // recty2 = -1;
- rectx2 = -1;
- recty2 = -1;
-
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
repaint();
}
- // private void fireSequenceSelectionEvent(Selection sel) {
- // controller.handleSequenceSelectionEvent(new
- // SequenceSelectionEvent(this,sel));
- // }
+ /**
+ * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
+ * position, or clears the tooltip if none found
+ */
@Override
public void mouseMoved(MouseEvent evt)
{
- SequenceI found = findPoint(evt.getX(), evt.getY());
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
- if (found != null)
- {
- this.setToolTipText(found.getName());
- }
- else
- {
- this.setToolTipText(null);
- }
+ this.setToolTipText(found == null ? null : found.getName());
}
/**
- * DOCUMENT ME!
+ * Action handler for a mouse drag. Rotates the display around the X axis (for
+ * up/down mouse movement) and/or the Y axis (for left/right mouse movement).
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void mouseDragged(MouseEvent evt)
{
- mx = evt.getX();
- my = evt.getY();
+ int xPos = evt.getX();
+ int yPos = evt.getY();
+
+ if (xPos == mouseX && yPos == mouseY)
+ {
+ return;
+ }
+
+ int xDelta = xPos - mouseX;
+ int yDelta = yPos - mouseY;
// Check if this is a rectangle drawing drag
if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
}
else
{
- rotmat.setIdentity();
+ rotate(xDelta, yDelta);
- rotmat.rotate(my - omy, 'x');
- rotmat.rotate(mx - omx, 'y');
+ mouseX = xPos;
+ mouseY = yPos;
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- sp.coord[0] -= centre[0];
- sp.coord[1] -= centre[1];
- sp.coord[2] -= centre[2];
-
- // Now apply the rotation matrix
- sp.coord = rotmat.vectorMultiply(sp.coord);
-
- // Now translate back again
- sp.coord[0] += centre[0];
- sp.coord[1] += centre[1];
- sp.coord[2] += centre[2];
- }
+ // findWidths();
- for (int i = 0; i < 3; i++)
- {
- axes[i] = rotmat.vectorMultiply(axes[i]);
- }
+ repaint();
+ }
+ }
- omx = mx;
- omy = my;
+ @Override
+ public void rotate(float x, float y)
+ {
+ if (x == 0f && y == 0f)
+ {
+ return;
+ }
- paint(this.getGraphics());
+ /*
+ * get the identity transformation...
+ */
+ RotatableMatrix rotmat = new RotatableMatrix();
+
+ /*
+ * rotate around the X axis for change in Y
+ * (mouse movement up/down); note we are equating a
+ * number of pixels with degrees of rotation here!
+ */
+ if (y != 0)
+ {
+ rotmat.rotate(y, Axis.X);
+ }
+
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (x != 0)
+ {
+ rotmat.rotate(x, Axis.Y);
+ }
+
+ /*
+ * apply the composite transformation to sequence points;
+ * update z min-max range (affects colour graduation), but not
+ * x or y min-max (as this would affect axis scaling)
+ */
+ float[] centre = getCentre();
+ float zMin = Float.MAX_VALUE;
+ float zMax = -Float.MAX_VALUE;
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = sequencePoints.get(i);
+ sp.translate(-centre[0], -centre[1], -centre[2]);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre[0], centre[1], centre[2]);
+
+ zMin = Math.min(zMin, sp.coord.z);
+ zMax = Math.max(zMax, sp.coord.z);
+ }
+
+ seqMin[2] = zMin;
+ seqMax[2] = zMax;
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
}
}
/**
- * DOCUMENT ME!
+ * Answers the x/y/z coordinates that are midway between the maximum and
+ * minimum sequence point values
+ *
+ * @return
+ */
+ private float[] getCentre()
+ {
+ float xCentre = (seqMin[0] + seqMax[0]) / 2f;
+ float yCentre = (seqMin[1] + seqMax[1]) / 2f;
+ float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+
+ return new float[] { xCentre, yCentre, zCentre };
+ }
+
+ /**
+ * Adds any sequences whose displayed points are within the given rectangle to
+ * the viewport's current selection. Intended for key 's' after dragging to
+ * select a region of the PCA.
*
* @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
* @param x2
- * DOCUMENT ME!
* @param y2
- * DOCUMENT ME!
*/
- public void rectSelect(int x1, int y1, int x2, int y2)
+ protected void rectSelect(int x1, int y1, int x2, int y2)
{
+ float[] centre = getCentre();
+
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = sequencePoints.get(i);
+ int tmp1 = (int) (((sp.coord.x - centre[0]) * scaleFactor)
+ (getWidth() / 2.0));
- int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
+ int tmp2 = (int) (((sp.coord.y - centre[1]) * scaleFactor)
+ (getHeight() / 2.0));
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
{
if (av != null)
{
+ SequenceI sequence = sp.getSequence();
if (!av.getSelectionGroup().getSequences(null)
- .contains(sp.sequence))
+ .contains(sequence))
{
- av.getSelectionGroup().addSequence(sp.sequence, true);
+ av.getSelectionGroup().addSequence(sequence, true);
}
}
}
}
-
- // if (changedSel) {
- // fireSequenceSelectionEvent(av.getSelection());
- // }
}
/**
- * DOCUMENT ME!
+ * Answers the first sequence found whose point on the display is within 2
+ * pixels of the given coordinates, or null if none is found
*
* @param x
- * DOCUMENT ME!
* @param y
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
- public SequenceI findPoint(int x, int y)
+ protected SequenceI findSequenceAtPoint(int x, int y)
{
int halfwidth = getWidth() / 2;
int halfheight = getHeight() / 2;
int found = -1;
+ int pix = Math.min(getWidth(), getHeight());
+ float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+ float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+ float maxWidth = Math.max(xWidth, yWidth);
+ float scaleBy = pix * scaleFactor / (2f * maxWidth);
+
+ float[] centre = getCentre();
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((sp.coord[0] - centre[0]) * scale)
+ SequencePoint sp = sequencePoints.get(i);
+ int px = (int) ((sp.coord.x - centre[0]) * scaleBy)
+ halfwidth;
- int py = (int) ((sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord.y - centre[1]) * scaleBy)
+ halfheight;
- if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+ if ((Math.abs(px - x) < NEARBY) && (Math.abs(py - y) < NEARBY))
{
found = i;
+ break;
}
}
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return sequencePoints.get(found).getSequence();
}
else
{
}
}
+ /**
+ * Answers the panel the PCA is associated with (all panels for this alignment
+ * if 'associate with all panels' is selected).
+ *
+ * @return
+ */
AlignmentPanel[] getAssociatedPanels()
{
if (applyToAllViews)
}
}
+ public Color getBackgroundColour()
+ {
+ return bgColour;
+ }
+
+ /**
+ * Zooms in or out in response to mouse wheel movement
+ */
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ zoom(ZOOM_IN);
+ repaint();
+ }
+ else if (wheelRotation < 0)
+ {
+ zoom(ZOOM_OUT);
+ repaint();
+ }
+ }
+
+ /**
+ * Answers the sequence point minimum [x, y, z] values. Note these are derived
+ * when sequence points are set, but x and y values are not updated on
+ * rotation (because this would result in changes to scaling).
+ *
+ * @return
+ */
+ public float[] getSeqMin()
+ {
+ return seqMin;
+ }
+
/**
+ * Answers the sequence point maximum [x, y, z] values. Note these are derived
+ * when sequence points are set, but x and y values are not updated on
+ * rotation (because this would result in changes to scaling).
*
- * @return x,y,z positions of point s (index into points) under current
- * transform.
+ * @return
*/
- public double[] getPointPosition(int s)
+ public float[] getSeqMax()
{
- double pts[] = new double[3];
- float[] p = ((SequencePoint) points.elementAt(s)).coord;
- pts[0] = p[0];
- pts[1] = p[1];
- pts[2] = p[2];
- return pts;
+ return seqMax;
}
+ /**
+ * Sets the minimum and maximum [x, y, z] positions for sequence points. For
+ * use when restoring a saved PCA from state data.
+ *
+ * @param min
+ * @param max
+ */
+ public void setSeqMinMax(float[] min, float[] max)
+ {
+ seqMin = min;
+ seqMax = max;
+ }
}
/*
* put them together as <method> Using <model>
*/
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ final String ttl = MessageManager.formatMessage("label.calc_title",
treecalcnm, smn);
return ttl;
}
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
- protected JComboBox<String> xCombobox = new JComboBox<String>();
+ protected JComboBox<String> xCombobox = new JComboBox<>();
- protected JComboBox<String> yCombobox = new JComboBox<String>();
+ protected JComboBox<String> yCombobox = new JComboBox<>();
- protected JComboBox<String> zCombobox = new JComboBox<String>();
-
- protected JMenu scoreModelMenu = new JMenu();
+ protected JComboBox<String> zCombobox = new JComboBox<>();
protected JMenu viewMenu = new JMenu();
protected JMenu associateViewsMenu = new JMenu();
- protected JMenu calcSettings = new JMenu();
-
- protected JCheckBoxMenuItem nuclSetting = new JCheckBoxMenuItem();
-
- protected JCheckBoxMenuItem protSetting = new JCheckBoxMenuItem();
-
protected JLabel statusBar = new JLabel();
protected JPanel statusPanel = new JPanel();
+ protected JMenuItem originalSeqData;
+
+ /**
+ * Constructor
+ */
public GPCAPanel()
{
try
@Override
public void actionPerformed(ActionEvent e)
{
- zCombobox_actionPerformed(e);
+ doDimensionChange();
}
});
yCombobox.setFont(VERDANA_12);
@Override
public void actionPerformed(ActionEvent e)
{
- yCombobox_actionPerformed(e);
+ doDimensionChange();
}
});
xCombobox.setFont(VERDANA_12);
@Override
public void actionPerformed(ActionEvent e)
{
- xCombobox_actionPerformed(e);
+ doDimensionChange();
}
});
JButton resetButton = new JButton();
@Override
public void actionPerformed(ActionEvent e)
{
- resetButton_actionPerformed(e);
+ resetButton_actionPerformed();
}
});
JMenu fileMenu = new JMenu();
@Override
public void actionPerformed(ActionEvent e)
{
- eps_actionPerformed(e);
+ eps_actionPerformed();
}
});
JMenuItem png = new JMenuItem("PNG");
@Override
public void actionPerformed(ActionEvent e)
{
- png_actionPerformed(e);
+ png_actionPerformed();
}
});
JMenuItem outputValues = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- outputValues_actionPerformed(e);
+ outputValues_actionPerformed();
}
});
JMenuItem outputPoints = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- outputPoints_actionPerformed(e);
+ outputPoints_actionPerformed();
}
});
JMenuItem outputProjPoints = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- outputProjPoints_actionPerformed(e);
+ outputProjPoints_actionPerformed();
}
});
JMenuItem print = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- print_actionPerformed(e);
+ print_actionPerformed();
}
});
viewMenu.setText(MessageManager.getString("action.view"));
{
}
});
- scoreModelMenu
- .setText(MessageManager.getString("label.select_score_model"));
- scoreModelMenu.addMenuListener(new MenuListener()
- {
- @Override
- public void menuSelected(MenuEvent e)
- {
- scoreModel_menuSelected();
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- }
- });
showLabels.setText(MessageManager.getString("label.show_labels"));
showLabels.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- showLabels_actionPerformed(e);
+ showLabels_actionPerformed();
}
});
JMenuItem bgcolour = new JMenuItem();
@Override
public void actionPerformed(ActionEvent e)
{
- bgcolour_actionPerformed(e);
+ bgcolour_actionPerformed();
}
});
- JMenuItem originalSeqData = new JMenuItem();
+ originalSeqData = new JMenuItem();
originalSeqData.setText(MessageManager.getString("label.input_data"));
originalSeqData.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- originalSeqData_actionPerformed(e);
+ originalSeqData_actionPerformed();
}
});
associateViewsMenu.setText(
MessageManager.getString("label.associate_nodes_with"));
- calcSettings.setText(MessageManager.getString("action.change_params"));
- nuclSetting
- .setText(MessageManager.getString("label.nucleotide_matrix"));
- protSetting.setText(MessageManager.getString("label.protein_matrix"));
- nuclSetting.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- nuclSetting_actionPerfomed(arg0);
- }
- });
- protSetting.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- protSetting_actionPerfomed(arg0);
- }
- });
- calcSettings.add(nuclSetting);
- calcSettings.add(protSetting);
- calcSettings.add(scoreModelMenu);
statusPanel.setLayout(new GridLayout());
statusBar.setFont(VERDANA_12);
// statusPanel.setBackground(Color.lightGray);
JMenuBar jMenuBar1 = new JMenuBar();
jMenuBar1.add(fileMenu);
jMenuBar1.add(viewMenu);
- jMenuBar1.add(calcSettings);
setJMenuBar(jMenuBar1);
fileMenu.add(saveMenu);
fileMenu.add(outputValues);
viewMenu.add(associateViewsMenu);
}
- protected void scoreModel_menuSelected()
- {
- // TODO Auto-generated method stub
-
- }
-
- protected void resetButton_actionPerformed(ActionEvent e)
+ protected void resetButton_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void protSetting_actionPerfomed(ActionEvent arg0)
+ protected void outputPoints_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void nuclSetting_actionPerfomed(ActionEvent arg0)
+ protected void outputProjPoints_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void outputPoints_actionPerformed(ActionEvent e)
+ protected void eps_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void outputProjPoints_actionPerformed(ActionEvent e)
+ protected void png_actionPerformed()
{
- // TODO Auto-generated method stub
-
}
- protected void xCombobox_actionPerformed(ActionEvent e)
+ protected void outputValues_actionPerformed()
{
}
- protected void yCombobox_actionPerformed(ActionEvent e)
+ protected void print_actionPerformed()
{
}
- protected void zCombobox_actionPerformed(ActionEvent e)
+ protected void showLabels_actionPerformed()
{
}
- public void eps_actionPerformed(ActionEvent e)
+ protected void bgcolour_actionPerformed()
{
-
}
- public void png_actionPerformed(ActionEvent e)
+ protected void originalSeqData_actionPerformed()
{
-
}
- public void outputValues_actionPerformed(ActionEvent e)
+ protected void viewMenu_menuSelected()
{
-
}
- public void print_actionPerformed(ActionEvent e)
+ protected void doDimensionChange()
{
-
- }
-
- public void showLabels_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void bgcolour_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void originalSeqData_actionPerformed(ActionEvent e)
- {
-
- }
-
- public void viewMenu_menuSelected()
- {
-
}
}
import jalview.util.MessageManager;
import java.io.PrintStream;
+import java.util.Arrays;
/**
* A class to model rectangular matrices of double values and operations on them
public class Matrix implements MatrixI
{
/*
- * the cell values in row-major order
+ * maximum number of iterations for tqli
*/
- private double[][] value;
+ private static final int MAX_ITER = 45;
+ // fudge - add 15 iterations, just in case
/*
* the number of rows
*/
- protected int rows;
+ final protected int rows;
/*
* the number of columns
*/
- protected int cols;
+ final protected int cols;
+
+ /*
+ * the cell values in row-major order
+ */
+ private double[][] value;
protected double[] d; // Diagonal
protected double[] e; // off diagonal
/**
- * maximum number of iterations for tqli
+ * Constructor given number of rows and columns
*
+ * @param colCount
+ * @param rowCount
*/
- private static final int maxIter = 45; // fudge - add 15 iterations, just in
- // case
-
- /**
- * Default constructor
- */
- public Matrix()
+ protected Matrix(int rowCount, int colCount)
{
-
+ rows = rowCount;
+ cols = colCount;
}
/**
}
}
- /**
- * Returns a new matrix which is the transpose of this one
- *
- * @return
- */
@Override
public MatrixI transpose()
{
}
}
- /**
- * Returns a new matrix which is the result of premultiplying this matrix by
- * the supplied argument. If this of size AxB (A rows and B columns), and the
- * argument is CxA (C rows and A columns), the result is of size CxB.
- *
- * @param in
- *
- * @return
- * @throws IllegalArgumentException
- * if the number of columns in the pre-multiplier is not equal to
- * the number of rows in the multiplicand (this)
- */
@Override
public MatrixI preMultiply(MatrixI in)
{
return out;
}
- /**
- * Returns a new matrix which is the result of postmultiplying this matrix by
- * the supplied argument. If this of size AxB (A rows and B columns), and the
- * argument is BxC (B rows and C columns), the result is of size AxC.
- * <p>
- * This method simply returns the result of in.preMultiply(this)
- *
- * @param in
- *
- * @return
- * @throws IllegalArgumentException
- * if the number of rows in the post-multiplier is not equal to the
- * number of columns in the multiplicand (this)
- * @see #preMultiply(Matrix)
- */
@Override
public MatrixI postMultiply(MatrixI in)
{
return in.preMultiply(this);
}
- /**
- * Answers a new matrix with a copy of the values in this one
- *
- * @return
- */
@Override
public MatrixI copy()
{
System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
}
- return new Matrix(newmat);
+ Matrix m = new Matrix(newmat);
+ if (this.d != null)
+ {
+ m.d = Arrays.copyOf(this.d, this.d.length);
+ }
+ if (this.e != null)
+ {
+ m.e = Arrays.copyOf(this.e, this.e.length);
+ }
+
+ return m;
}
/**
{
iter++;
- if (iter == maxIter)
+ if (iter == MAX_ITER)
{
throw new Exception(MessageManager.formatMessage(
"exception.matrix_too_many_iteration", new String[]
- { "tqli", Integer.valueOf(maxIter).toString() }));
+ { "tqli", Integer.valueOf(MAX_ITER).toString() }));
}
else
{
{
iter++;
- if (iter == maxIter)
+ if (iter == MAX_ITER)
{
throw new Exception(MessageManager.formatMessage(
"exception.matrix_too_many_iteration", new String[]
- { "tqli2", Integer.valueOf(maxIter).toString() }));
+ { "tqli2", Integer.valueOf(MAX_ITER).toString() }));
}
else
{
}
}
}
+
+ @Override
+ public void setD(double[] v)
+ {
+ d = v;
+ }
+
+ @Override
+ public void setE(double[] v)
+ {
+ e = v;
+ }
}
import java.io.PrintStream;
+/**
+ * An interface that describes a rectangular matrix of double values and
+ * operations on it
+ */
public interface MatrixI
{
/**
*/
double[] getRow(int i);
+ /**
+ * Answers a new matrix with a copy of the values in this one
+ *
+ * @return
+ */
MatrixI copy();
+ /**
+ * Returns a new matrix which is the transpose of this one
+ *
+ * @return
+ */
MatrixI transpose();
+ /**
+ * Returns a new matrix which is the result of premultiplying this matrix by
+ * the supplied argument. If this of size AxB (A rows and B columns), and the
+ * argument is CxA (C rows and A columns), the result is of size CxB.
+ *
+ * @param in
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if the number of columns in the pre-multiplier is not equal to
+ * the number of rows in the multiplicand (this)
+ */
MatrixI preMultiply(MatrixI m);
+ /**
+ * Returns a new matrix which is the result of postmultiplying this matrix by
+ * the supplied argument. If this of size AxB (A rows and B columns), and the
+ * argument is BxC (B rows and C columns), the result is of size AxC.
+ * <p>
+ * This method simply returns the result of in.preMultiply(this)
+ *
+ * @param in
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if the number of rows in the post-multiplier is not equal to the
+ * number of columns in the multiplicand (this)
+ * @see #preMultiply(Matrix)
+ */
MatrixI postMultiply(MatrixI m);
double[] getD();
double[] getE();
+ void setD(double[] v);
+
+ void setE(double[] v);
+
void print(PrintStream ps, String format);
void printD(PrintStream ps, String format);
*/
package jalview.math;
+import jalview.datamodel.Point;
+
+import java.util.HashMap;
+import java.util.Map;
+
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Model for a 3x3 matrix which provides methods for rotation in 3-D space
*/
public class RotatableMatrix
{
- float[][] matrix;
+ private static final int DIMS = 3;
- float[] temp;
+ /*
+ * cache the most used rotations: +/- 1, 2, 3, 4 degrees around x or y axis
+ */
+ private static Map<Axis, Map<Float, float[][]>> cachedRotations;
- float[][] rot;
+ static
+ {
+ cachedRotations = new HashMap<>();
+ for (Axis axis : Axis.values())
+ {
+ HashMap<Float, float[][]> map = new HashMap<>();
+ cachedRotations.put(axis, map);
+ for (int deg = 1; deg < 5; deg++)
+ {
+ float[][] rotation = getRotation(deg, axis);
+ map.put(Float.valueOf(deg), rotation);
+ rotation = getRotation(-deg, axis);
+ map.put(Float.valueOf(-deg), rotation);
+ }
+ }
+ }
- /**
- * Creates a new RotatableMatrix object.
- *
- * @param rows
- * DOCUMENT ME!
- * @param cols
- * DOCUMENT ME!
- */
- public RotatableMatrix(int rows, int cols)
+ public enum Axis
{
- matrix = new float[rows][cols];
+ X, Y, Z
+ };
- temp = new float[3];
+ float[][] matrix;
- rot = new float[3][3];
+ /**
+ * Constructor creates a new identity matrix (all values zero except for 1 on
+ * the diagonal)
+ */
+ public RotatableMatrix()
+ {
+ matrix = new float[DIMS][DIMS];
+ for (int j = 0; j < DIMS; j++)
+ {
+ matrix[j][j] = 1f;
+ }
}
/**
- * DOCUMENT ME!
+ * Sets the value at position (i, j) of the matrix
*
* @param i
- * DOCUMENT ME!
* @param j
- * DOCUMENT ME!
* @param value
- * DOCUMENT ME!
*/
- public void addElement(int i, int j, float value)
+ public void setValue(int i, int j, float value)
{
matrix[i][j] = value;
}
/**
- * DOCUMENT ME!
+ * Answers the value at position (i, j) of the matrix
+ *
+ * @param i
+ * @param j
+ * @return
+ */
+ public float getValue(int i, int j)
+ {
+ return matrix[i][j];
+ }
+
+ /**
+ * Prints the matrix in rows of space-delimited values
*/
public void print()
{
}
/**
- * DOCUMENT ME!
+ * Rotates the matrix through the specified number of degrees around the
+ * specified axis
*
* @param degrees
- * DOCUMENT ME!
* @param axis
- * DOCUMENT ME!
*/
- public void rotate(float degrees, char axis)
+ public void rotate(float degrees, Axis axis)
{
- float costheta = (float) Math.cos((degrees * Math.PI) / (float) 180.0);
+ float[][] rot = getRotation(degrees, axis);
- float sintheta = (float) Math.sin((degrees * Math.PI) / (float) 180.0);
+ preMultiply(rot);
+ }
- if (axis == 'z')
+ /**
+ * Answers a matrix which, when it pre-multiplies another matrix, applies a
+ * rotation of the specified number of degrees around the specified axis
+ *
+ * @param degrees
+ * @param axis
+ * @return
+ * @see https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+ */
+ protected static float[][] getRotation(float degrees, Axis axis)
+ {
+ Float floatValue = Float.valueOf(degrees);
+ if (cachedRotations.get(axis).containsKey(floatValue))
{
- rot[0][0] = (float) costheta;
-
- rot[0][1] = (float) -sintheta;
-
- rot[0][2] = (float) 0.0;
-
- rot[1][0] = (float) sintheta;
-
- rot[1][1] = (float) costheta;
-
- rot[1][2] = (float) 0.0;
-
- rot[2][0] = (float) 0.0;
-
- rot[2][1] = (float) 0.0;
-
- rot[2][2] = (float) 1.0;
-
- preMultiply(rot);
+ // System.out.println("getRotation from cache: " + (int) degrees);
+ return cachedRotations.get(axis).get(floatValue);
}
- if (axis == 'x')
- {
- rot[0][0] = (float) 1.0;
-
- rot[0][1] = (float) 0.0;
-
- rot[0][2] = (float) 0.0;
-
- rot[1][0] = (float) 0.0;
+ float costheta = (float) Math.cos(degrees * Math.PI / 180f);
- rot[1][1] = (float) costheta;
+ float sintheta = (float) Math.sin(degrees * Math.PI / 180f);
- rot[1][2] = (float) sintheta;
+ float[][] rot = new float[DIMS][DIMS];
- rot[2][0] = (float) 0.0;
-
- rot[2][1] = (float) -sintheta;
-
- rot[2][2] = (float) costheta;
-
- preMultiply(rot);
- }
-
- if (axis == 'y')
+ switch (axis)
{
- rot[0][0] = (float) costheta;
-
- rot[0][1] = (float) 0.0;
-
- rot[0][2] = (float) -sintheta;
-
- rot[1][0] = (float) 0.0;
-
- rot[1][1] = (float) 1.0;
-
- rot[1][2] = (float) 0.0;
-
- rot[2][0] = (float) sintheta;
-
- rot[2][1] = (float) 0.0;
-
- rot[2][2] = (float) costheta;
-
- preMultiply(rot);
+ case X:
+ rot[0][0] = 1f;
+ rot[1][1] = costheta;
+ rot[1][2] = sintheta;
+ rot[2][1] = -sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Y:
+ rot[0][0] = costheta;
+ rot[0][2] = -sintheta;
+ rot[1][1] = 1f;
+ rot[2][0] = sintheta;
+ rot[2][2] = costheta;
+ break;
+ case Z:
+ rot[0][0] = costheta;
+ rot[0][1] = -sintheta;
+ rot[1][0] = sintheta;
+ rot[1][1] = costheta;
+ rot[2][2] = 1f;
+ break;
}
+ return rot;
}
/**
- * DOCUMENT ME!
+ * Answers a new array of float values which is the result of pre-multiplying
+ * this matrix by the given vector. Each value of the result is the dot
+ * product of the vector with one column of this matrix. The matrix and input
+ * vector are not modified.
*
* @param vect
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
public float[] vectorMultiply(float[] vect)
{
- temp[0] = vect[0];
-
- temp[1] = vect[1];
-
- temp[2] = vect[2];
+ float[] result = new float[DIMS];
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- temp[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+ result[i] = (matrix[i][0] * vect[0]) + (matrix[i][1] * vect[1])
+ (matrix[i][2] * vect[2]);
}
- vect[0] = temp[0];
-
- vect[1] = temp[1];
-
- vect[2] = temp[2];
-
- return vect;
+ return result;
}
/**
- * DOCUMENT ME!
+ * Performs pre-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of <code>mat</code> with
+ * the j'th column of this matrix.
*
* @param mat
- * DOCUMENT ME!
*/
public void preMultiply(float[][] mat)
{
- float[][] tmp = new float[3][3];
+ float[][] tmp = new float[DIMS][DIMS];
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- for (int j = 0; j < 3; j++)
+ for (int j = 0; j < DIMS; j++)
{
tmp[i][j] = (mat[i][0] * matrix[0][j]) + (mat[i][1] * matrix[1][j])
+ (mat[i][2] * matrix[2][j]);
}
}
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- matrix[i][j] = tmp[i][j];
- }
- }
+ matrix = tmp;
}
/**
- * DOCUMENT ME!
+ * Performs post-multiplication of this matrix by the given one. Value (i, j)
+ * of the result is the dot product of the i'th row of this matrix with the
+ * j'th column of <code>mat</code>.
*
* @param mat
- * DOCUMENT ME!
*/
public void postMultiply(float[][] mat)
{
- float[][] tmp = new float[3][3];
+ float[][] tmp = new float[DIMS][DIMS];
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- for (int j = 0; j < 3; j++)
+ for (int j = 0; j < DIMS; j++)
{
tmp[i][j] = (matrix[i][0] * mat[0][j]) + (matrix[i][1] * mat[1][j])
+ (matrix[i][2] * mat[2][j]);
}
}
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- matrix[i][j] = tmp[i][j];
- }
- }
+ matrix = tmp;
}
/**
*/
public static void main(String[] args)
{
- RotatableMatrix m = new RotatableMatrix(3, 3);
+ RotatableMatrix m = new RotatableMatrix();
- m.addElement(0, 0, 1);
+ m.setValue(0, 0, 1);
- m.addElement(0, 1, 0);
+ m.setValue(0, 1, 0);
- m.addElement(0, 2, 0);
+ m.setValue(0, 2, 0);
- m.addElement(1, 0, 0);
+ m.setValue(1, 0, 0);
- m.addElement(1, 1, 2);
+ m.setValue(1, 1, 2);
- m.addElement(1, 2, 0);
+ m.setValue(1, 2, 0);
- m.addElement(2, 0, 0);
+ m.setValue(2, 0, 0);
- m.addElement(2, 1, 0);
+ m.setValue(2, 1, 0);
- m.addElement(2, 2, 1);
+ m.setValue(2, 2, 1);
m.print();
- RotatableMatrix n = new RotatableMatrix(3, 3);
+ RotatableMatrix n = new RotatableMatrix();
- n.addElement(0, 0, 2);
+ n.setValue(0, 0, 2);
- n.addElement(0, 1, 1);
+ n.setValue(0, 1, 1);
- n.addElement(0, 2, 1);
+ n.setValue(0, 2, 1);
- n.addElement(1, 0, 2);
+ n.setValue(1, 0, 2);
- n.addElement(1, 1, 1);
+ n.setValue(1, 1, 1);
- n.addElement(1, 2, 1);
+ n.setValue(1, 2, 1);
- n.addElement(2, 0, 2);
+ n.setValue(2, 0, 2);
- n.addElement(2, 1, 1);
+ n.setValue(2, 1, 1);
- n.addElement(2, 2, 1);
+ n.setValue(2, 2, 1);
n.print();
}
/**
- * DOCUMENT ME!
+ * Performs a vector multiplication whose result is the Point representing the
+ * input point's value vector post-multiplied by this matrix.
+ *
+ * @param coord
+ * @return
*/
- public void setIdentity()
+ public Point vectorMultiply(Point coord)
{
- matrix[0][0] = (float) 1.0;
-
- matrix[1][1] = (float) 1.0;
-
- matrix[2][2] = (float) 1.0;
-
- matrix[0][1] = (float) 0.0;
-
- matrix[0][2] = (float) 0.0;
-
- matrix[1][0] = (float) 0.0;
-
- matrix[1][2] = (float) 0.0;
-
- matrix[2][0] = (float) 0.0;
-
- matrix[2][1] = (float) 0.0;
+ float[] v = vectorMultiply(new float[] { coord.x, coord.y, coord.z });
+ return new Point(v[0], v[1], v[2]);
}
}
*/
public SparseMatrix(double[][] v)
{
- rows = v.length;
- if (rows > 0)
- {
- cols = v[0].length;
- }
+ super(v.length, v.length > 0 ? v[0].length : 0);
+
sparseColumns = new SparseDoubleArray[cols];
/*
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-jalview.schemabinding.version2.FeatureMatcherSet=jalview.schemabinding.version2.descriptors.FeatureMatcherSetDescriptor
+#Mon May 07 14:44:01 BST 2018
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--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * endpoints of X, Y and Z axes in that order
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class Axis implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Axis()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.Axis
+ */
+ public static jalview.schemabinding.version2.Axis unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.Axis) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Axis.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class D.
+ *
+ * @version $Revision$ $Date$
+ */
+public class D extends DoubleVector implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public D()
+ {
+ 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.D.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class DoubleMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleMatrix implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _rows.
+ */
+ private int _rows;
+
+ /**
+ * keeps track of state for field: _rows
+ */
+ private boolean _has_rows;
+
+ /**
+ * Field _columns.
+ */
+ private int _columns;
+
+ /**
+ * keeps track of state for field: _columns
+ */
+ private boolean _has_columns;
+
+ /**
+ * Field _rowList.
+ */
+ private java.util.Vector _rowList;
+
+ /**
+ * Field _d.
+ */
+ private jalview.schemabinding.version2.D _d;
+
+ /**
+ * Field _e.
+ */
+ private jalview.schemabinding.version2.E _e;
+
+ // ----------------/
+ // - 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;
+ }
+
+ /**
+ * Returns the value of field 'd'.
+ *
+ * @return the value of field 'D'.
+ */
+ public jalview.schemabinding.version2.D getD()
+ {
+ return this._d;
+ }
+
+ /**
+ * Returns the value of field 'e'.
+ *
+ * @return the value of field 'E'.
+ */
+ public jalview.schemabinding.version2.E getE()
+ {
+ return this._e;
+ }
+
+ /**
+ * Method getRow.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Row at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Row getRow(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rowList.size())
+ {
+ throw new IndexOutOfBoundsException("getRow: Index value '" + index
+ + "' not in range [0.." + (this._rowList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Row) _rowList.get(index);
+ }
+
+ /**
+ * Method getRow.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Row[] getRow()
+ {
+ jalview.schemabinding.version2.Row[] array = new jalview.schemabinding.version2.Row[0];
+ return (jalview.schemabinding.version2.Row[]) this._rowList
+ .toArray(array);
+ }
+
+ /**
+ * Method getRowCount.
+ *
+ * @return the size of this collection
+ */
+ public int getRowCount()
+ {
+ return this._rowList.size();
+ }
+
+ /**
+ * Returns the value of field 'rows'.
+ *
+ * @return the value of field 'Rows'.
+ */
+ public int getRows()
+ {
+ return this._rows;
+ }
+
+ /**
+ * Method hasColumns.
+ *
+ * @return true if at least one Columns has been added
+ */
+ public boolean hasColumns()
+ {
+ return this._has_columns;
+ }
+
+ /**
+ * Method hasRows.
+ *
+ * @return true if at least one Rows has been added
+ */
+ public boolean hasRows()
+ {
+ return this._has_rows;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllRow()
+ {
+ this._rowList.clear();
+ }
+
+ /**
+ * Method removeRow.
+ *
+ * @param vRow
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeRow(final jalview.schemabinding.version2.Row vRow)
+ {
+ boolean removed = _rowList.remove(vRow);
+ return removed;
+ }
+
+ /**
+ * Method removeRowAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Row removeRowAt(final int index)
+ {
+ java.lang.Object obj = this._rowList.remove(index);
+ return (jalview.schemabinding.version2.Row) obj;
+ }
+
+ /**
+ * Sets the value of field 'columns'.
+ *
+ * @param columns
+ * the value of field 'columns'.
+ */
+ public void setColumns(final int columns)
+ {
+ this._columns = columns;
+ this._has_columns = true;
+ }
+
+ /**
+ * Sets the value of field 'd'.
+ *
+ * @param d
+ * the value of field 'd'.
+ */
+ public void setD(final jalview.schemabinding.version2.D d)
+ {
+ this._d = d;
+ }
+
+ /**
+ * Sets the value of field 'e'.
+ *
+ * @param e
+ * the value of field 'e'.
+ */
+ public void setE(final jalview.schemabinding.version2.E e)
+ {
+ this._e = e;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vRow
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setRow(final int index,
+ final jalview.schemabinding.version2.Row vRow)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._rowList.size())
+ {
+ throw new IndexOutOfBoundsException("setRow: Index value '" + index
+ + "' not in range [0.." + (this._rowList.size() - 1) + "]");
+ }
+
+ this._rowList.set(index, vRow);
+ }
+
+ /**
+ *
+ *
+ * @param vRowArray
+ */
+ public void setRow(final jalview.schemabinding.version2.Row[] vRowArray)
+ {
+ // -- copy array
+ _rowList.clear();
+
+ for (int i = 0; i < vRowArray.length; i++)
+ {
+ this._rowList.add(vRowArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'rows'.
+ *
+ * @param rows
+ * the value of field 'rows'.
+ */
+ public void setRows(final int rows)
+ {
+ this._rows = rows;
+ this._has_rows = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleMatrix
+ */
+ public static jalview.schemabinding.version2.DoubleMatrix unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleMatrix) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.DoubleMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class DoubleVector.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleVector implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _vList.
+ */
+ private java.util.Vector _vList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleVector()
+ {
+ super();
+ this._vList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vV
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addV(final double vV)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._vList.addElement(new java.lang.Double(vV));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vV
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addV(final int index, final double vV)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._vList.add(index, new java.lang.Double(vV));
+ }
+
+ /**
+ * Method enumerateV.
+ *
+ * @return an Enumeration over all double elements
+ */
+ public java.util.Enumeration enumerateV()
+ {
+ return this._vList.elements();
+ }
+
+ /**
+ * Method getV.
+ *
+ * @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 getV(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._vList.size())
+ {
+ throw new IndexOutOfBoundsException("getV: Index value '" + index
+ + "' not in range [0.." + (this._vList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Double) _vList.get(index)).doubleValue();
+ }
+
+ /**
+ * Method getV.Returns the contents of the collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public double[] getV()
+ {
+ int size = this._vList.size();
+ double[] array = new double[size];
+ java.util.Iterator iter = _vList.iterator();
+ for (int index = 0; index < size; index++)
+ {
+ array[index] = ((java.lang.Double) iter.next()).doubleValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getVCount.
+ *
+ * @return the size of this collection
+ */
+ public int getVCount()
+ {
+ return this._vList.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 removeAllV()
+ {
+ this._vList.clear();
+ }
+
+ /**
+ * Method removeV.
+ *
+ * @param vV
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeV(final double vV)
+ {
+ boolean removed = _vList.remove(new java.lang.Double(vV));
+ return removed;
+ }
+
+ /**
+ * Method removeVAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public double removeVAt(final int index)
+ {
+ java.lang.Object obj = this._vList.remove(index);
+ return ((java.lang.Double) obj).doubleValue();
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vV
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setV(final int index, final double vV)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._vList.size())
+ {
+ throw new IndexOutOfBoundsException("setV: Index value '" + index
+ + "' not in range [0.." + (this._vList.size() - 1) + "]");
+ }
+
+ this._vList.set(index, new java.lang.Double(vV));
+ }
+
+ /**
+ *
+ *
+ * @param vVArray
+ */
+ public void setV(final double[] vVArray)
+ {
+ // -- copy array
+ _vList.clear();
+
+ for (int i = 0; i < vVArray.length; i++)
+ {
+ this._vList.add(new java.lang.Double(vVArray[i]));
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleVector
+ */
+ public static jalview.schemabinding.version2.DoubleVector unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleVector) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.DoubleVector.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class E.
+ *
+ * @version $Revision$ $Date$
+ */
+public class E extends DoubleVector implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public E()
+ {
+ 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.E.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class EigenMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrix extends DoubleMatrix
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrix()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleMatrix
+ */
+ public static jalview.schemabinding.version2.DoubleMatrix unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleMatrix) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.EigenMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
private java.util.Vector _treeList;
/**
+ * Field _pcaViewerList.
+ */
+ private java.util.Vector _pcaViewerList;
+
+ /**
* Field _featureSettings.
*/
private jalview.schemabinding.version2.FeatureSettings _featureSettings;
this._viewportList = new java.util.Vector();
this._userColoursList = new java.util.Vector();
this._treeList = new java.util.Vector();
+ this._pcaViewerList = new java.util.Vector();
}
// -----------/
/**
*
*
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPcaViewer(
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pcaViewerList.addElement(vPcaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPcaViewer(final int index,
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pcaViewerList.add(index, vPcaViewer);
+ }
+
+ /**
+ *
+ *
* @param vTree
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
}
/**
+ * Method enumeratePcaViewer.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.PcaViewer
+ * elements
+ */
+ public java.util.Enumeration enumeratePcaViewer()
+ {
+ return this._pcaViewerList.elements();
+ }
+
+ /**
* Method enumerateTree.
*
* @return an Enumeration over all jalview.schemabinding.version2.Tree
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("getJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
}
/**
+ * Method getPcaViewer.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.PcaViewer at the
+ * given index
+ */
+ public jalview.schemabinding.version2.PcaViewer getPcaViewer(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pcaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getPcaViewer: Index value '" + index + "' not in range [0.."
+ + (this._pcaViewerList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.PcaViewer) _pcaViewerList
+ .get(index);
+ }
+
+ /**
+ * Method getPcaViewer.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.PcaViewer[] getPcaViewer()
+ {
+ jalview.schemabinding.version2.PcaViewer[] array = new jalview.schemabinding.version2.PcaViewer[0];
+ return (jalview.schemabinding.version2.PcaViewer[]) this._pcaViewerList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPcaViewerCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPcaViewerCount()
+ {
+ return this._pcaViewerList.size();
+ }
+
+ /**
* Method getTree.
*
* @param index
* @return the value of the jalview.schemabinding.version2.Viewport at the
* given index
*/
- public jalview.schemabinding.version2.Viewport getViewport(final int index)
- throws java.lang.IndexOutOfBoundsException
+ public jalview.schemabinding.version2.Viewport getViewport(
+ final int index) throws java.lang.IndexOutOfBoundsException
{
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("getViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
return (jalview.schemabinding.version2.Viewport) _viewportList
}
/**
- */
+ */
public void removeAllJGroup()
{
this._JGroupList.clear();
}
/**
- */
+ */
public void removeAllJSeq()
{
this._JSeqList.clear();
}
/**
- */
+ */
+ public void removeAllPcaViewer()
+ {
+ this._pcaViewerList.clear();
+ }
+
+ /**
+ */
public void removeAllTree()
{
this._treeList.clear();
}
/**
- */
+ */
public void removeAllUserColours()
{
this._userColoursList.clear();
}
/**
- */
+ */
public void removeAllViewport()
{
this._viewportList.clear();
}
/**
+ * Method removePcaViewer.
+ *
+ * @param vPcaViewer
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePcaViewer(
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ {
+ boolean removed = _pcaViewerList.remove(vPcaViewer);
+ return removed;
+ }
+
+ /**
+ * Method removePcaViewerAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.PcaViewer removePcaViewerAt(
+ final int index)
+ {
+ java.lang.Object obj = this._pcaViewerList.remove(index);
+ return (jalview.schemabinding.version2.PcaViewer) obj;
+ }
+
+ /**
* Method removeTree.
*
* @param vTree
// check bounds for index
if (index < 0 || index >= this._JGroupList.size())
{
- throw new IndexOutOfBoundsException("setJGroup: Index value '"
- + index + "' not in range [0.."
- + (this._JGroupList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setJGroup: Index value '" + index + "' not in range [0.."
+ + (this._JGroupList.size() - 1) + "]");
}
this._JGroupList.set(index, vJGroup);
*
* @param vJSeqArray
*/
- public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
+ public void setJSeq(
+ final jalview.schemabinding.version2.JSeq[] vJSeqArray)
{
// -- copy array
_JSeqList.clear();
*
*
* @param index
+ * @param vPcaViewer
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setPcaViewer(final int index,
+ final jalview.schemabinding.version2.PcaViewer vPcaViewer)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._pcaViewerList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setPcaViewer: Index value '" + index + "' not in range [0.."
+ + (this._pcaViewerList.size() - 1) + "]");
+ }
+
+ this._pcaViewerList.set(index, vPcaViewer);
+ }
+
+ /**
+ *
+ *
+ * @param vPcaViewerArray
+ */
+ public void setPcaViewer(
+ final jalview.schemabinding.version2.PcaViewer[] vPcaViewerArray)
+ {
+ // -- copy array
+ _pcaViewerList.clear();
+
+ for (int i = 0; i < vPcaViewerArray.length; i++)
+ {
+ this._pcaViewerList.add(vPcaViewerArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
* @param vTree
* @throws java.lang.IndexOutOfBoundsException
* if the index given is outside the bounds of the collection
*
* @param vTreeArray
*/
- public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
+ public void setTree(
+ final jalview.schemabinding.version2.Tree[] vTreeArray)
{
// -- copy array
_treeList.clear();
// check bounds for index
if (index < 0 || index >= this._viewportList.size())
{
- throw new IndexOutOfBoundsException("setViewport: Index value '"
- + index + "' not in range [0.."
- + (this._viewportList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setViewport: Index value '" + index + "' not in range [0.."
+ + (this._viewportList.size() - 1) + "]");
}
this._viewportList.set(index, vViewport);
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PairwiseMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PairwiseMatrix extends DoubleMatrix
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PairwiseMatrix()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleMatrix
+ */
+ public static jalview.schemabinding.version2.DoubleMatrix unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleMatrix) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PairwiseMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PcaData.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaData extends PcaDataType implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaData()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.PcaDataType
+ */
+ public static jalview.schemabinding.version2.PcaDataType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.PcaDataType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PcaData.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * The results of a PCA calculation
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaDataType implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _pairwiseMatrix.
+ */
+ private jalview.schemabinding.version2.PairwiseMatrix _pairwiseMatrix;
+
+ /**
+ * Field _tridiagonalMatrix.
+ */
+ private jalview.schemabinding.version2.TridiagonalMatrix _tridiagonalMatrix;
+
+ /**
+ * Field _eigenMatrix.
+ */
+ private jalview.schemabinding.version2.EigenMatrix _eigenMatrix;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaDataType()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * 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 'pairwiseMatrix'.
+ *
+ * @return the value of field 'PairwiseMatrix'.
+ */
+ public jalview.schemabinding.version2.PairwiseMatrix getPairwiseMatrix()
+ {
+ return this._pairwiseMatrix;
+ }
+
+ /**
+ * Returns the value of field 'tridiagonalMatrix'.
+ *
+ * @return the value of field 'TridiagonalMatrix'.
+ */
+ public jalview.schemabinding.version2.TridiagonalMatrix getTridiagonalMatrix()
+ {
+ return this._tridiagonalMatrix;
+ }
+
+ /**
+ * 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 '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 'pairwiseMatrix'.
+ *
+ * @param pairwiseMatrix
+ * the value of field 'pairwiseMatrix'.
+ */
+ public void setPairwiseMatrix(
+ final jalview.schemabinding.version2.PairwiseMatrix pairwiseMatrix)
+ {
+ this._pairwiseMatrix = pairwiseMatrix;
+ }
+
+ /**
+ * Sets the value of field 'tridiagonalMatrix'.
+ *
+ * @param tridiagonalMatrix
+ * the value of field 'tridiagonalMatrix'.
+ */
+ public void setTridiagonalMatrix(
+ final jalview.schemabinding.version2.TridiagonalMatrix tridiagonalMatrix)
+ {
+ this._tridiagonalMatrix = tridiagonalMatrix;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.PcaDataType
+ */
+ public static jalview.schemabinding.version2.PcaDataType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.PcaDataType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PcaDataType.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class PcaViewer.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaViewer implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _scoreModelName.
+ */
+ private java.lang.String _scoreModelName;
+
+ /**
+ * Field _xDim.
+ */
+ private int _xDim;
+
+ /**
+ * keeps track of state for field: _xDim
+ */
+ private boolean _has_xDim;
+
+ /**
+ * Field _yDim.
+ */
+ private int _yDim;
+
+ /**
+ * keeps track of state for field: _yDim
+ */
+ private boolean _has_yDim;
+
+ /**
+ * Field _zDim.
+ */
+ private int _zDim;
+
+ /**
+ * keeps track of state for field: _zDim
+ */
+ private boolean _has_zDim;
+
+ /**
+ * Field _bgColour.
+ */
+ private int _bgColour;
+
+ /**
+ * keeps track of state for field: _bgColour
+ */
+ private boolean _has_bgColour;
+
+ /**
+ * Field _scaleFactor.
+ */
+ private float _scaleFactor;
+
+ /**
+ * keeps track of state for field: _scaleFactor
+ */
+ private boolean _has_scaleFactor;
+
+ /**
+ * Field _showLabels.
+ */
+ private boolean _showLabels;
+
+ /**
+ * keeps track of state for field: _showLabels
+ */
+ private boolean _has_showLabels;
+
+ /**
+ * Field _linkToAllViews.
+ */
+ private boolean _linkToAllViews;
+
+ /**
+ * keeps track of state for field: _linkToAllViews
+ */
+ private boolean _has_linkToAllViews;
+
+ /**
+ * Field _includeGaps.
+ */
+ private boolean _includeGaps;
+
+ /**
+ * keeps track of state for field: _includeGaps
+ */
+ private boolean _has_includeGaps;
+
+ /**
+ * Field _matchGaps.
+ */
+ private boolean _matchGaps;
+
+ /**
+ * keeps track of state for field: _matchGaps
+ */
+ private boolean _has_matchGaps;
+
+ /**
+ * Field _includeGappedColumns.
+ */
+ private boolean _includeGappedColumns;
+
+ /**
+ * keeps track of state for field: _includeGappedColumns
+ */
+ private boolean _has_includeGappedColumns;
+
+ /**
+ * Field _denominateByShortestLength.
+ */
+ private boolean _denominateByShortestLength;
+
+ /**
+ * keeps track of state for field: _denominateByShortestLength
+ */
+ private boolean _has_denominateByShortestLength;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _sequencePointList.
+ */
+ private java.util.Vector _sequencePointList;
+
+ /**
+ * endpoints of X, Y and Z axes in that order
+ *
+ */
+ private java.util.Vector _axisList;
+
+ /**
+ * Field _seqPointMin.
+ */
+ private jalview.schemabinding.version2.SeqPointMin _seqPointMin;
+
+ /**
+ * Field _seqPointMax.
+ */
+ private jalview.schemabinding.version2.SeqPointMax _seqPointMax;
+
+ /**
+ * Field _pcaData.
+ */
+ private jalview.schemabinding.version2.PcaData _pcaData;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaViewer()
+ {
+ super();
+ this._sequencePointList = new java.util.Vector();
+ this._axisList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAxis
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAxis(final jalview.schemabinding.version2.Axis vAxis)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._axisList.size() >= 3)
+ {
+ throw new IndexOutOfBoundsException("addAxis has a maximum of 3");
+ }
+
+ this._axisList.addElement(vAxis);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAxis
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAxis(final int index,
+ final jalview.schemabinding.version2.Axis vAxis)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._axisList.size() >= 3)
+ {
+ throw new IndexOutOfBoundsException("addAxis has a maximum of 3");
+ }
+
+ this._axisList.add(index, vAxis);
+ }
+
+ /**
+ *
+ *
+ * @param vSequencePoint
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequencePoint(
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequencePointList.addElement(vSequencePoint);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequencePoint
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequencePoint(final int index,
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequencePointList.add(index, vSequencePoint);
+ }
+
+ /**
+ */
+ public void deleteBgColour()
+ {
+ this._has_bgColour = false;
+ }
+
+ /**
+ */
+ public void deleteDenominateByShortestLength()
+ {
+ this._has_denominateByShortestLength = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteIncludeGappedColumns()
+ {
+ this._has_includeGappedColumns = false;
+ }
+
+ /**
+ */
+ public void deleteIncludeGaps()
+ {
+ this._has_includeGaps = false;
+ }
+
+ /**
+ */
+ public void deleteLinkToAllViews()
+ {
+ this._has_linkToAllViews = false;
+ }
+
+ /**
+ */
+ public void deleteMatchGaps()
+ {
+ this._has_matchGaps = false;
+ }
+
+ /**
+ */
+ public void deleteScaleFactor()
+ {
+ this._has_scaleFactor = false;
+ }
+
+ /**
+ */
+ public void deleteShowLabels()
+ {
+ this._has_showLabels = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXDim()
+ {
+ this._has_xDim = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYDim()
+ {
+ this._has_yDim = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ */
+ public void deleteZDim()
+ {
+ this._has_zDim = false;
+ }
+
+ /**
+ * Method enumerateAxis.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Axis
+ * elements
+ */
+ public java.util.Enumeration enumerateAxis()
+ {
+ return this._axisList.elements();
+ }
+
+ /**
+ * Method enumerateSequencePoint.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SequencePoint elements
+ */
+ public java.util.Enumeration enumerateSequencePoint()
+ {
+ return this._sequencePointList.elements();
+ }
+
+ /**
+ * Method getAxis.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Axis at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Axis getAxis(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._axisList.size())
+ {
+ throw new IndexOutOfBoundsException("getAxis: Index value '" + index
+ + "' not in range [0.." + (this._axisList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Axis) _axisList.get(index);
+ }
+
+ /**
+ * Method getAxis.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Axis[] getAxis()
+ {
+ jalview.schemabinding.version2.Axis[] array = new jalview.schemabinding.version2.Axis[0];
+ return (jalview.schemabinding.version2.Axis[]) this._axisList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAxisCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAxisCount()
+ {
+ return this._axisList.size();
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public int getBgColour()
+ {
+ return this._bgColour;
+ }
+
+ /**
+ * Returns the value of field 'denominateByShortestLength'.
+ *
+ * @return the value of field 'DenominateByShortestLength'.
+ */
+ public boolean getDenominateByShortestLength()
+ {
+ return this._denominateByShortestLength;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'includeGappedColumns'.
+ *
+ * @return the value of field 'IncludeGappedColumns'.
+ */
+ public boolean getIncludeGappedColumns()
+ {
+ return this._includeGappedColumns;
+ }
+
+ /**
+ * Returns the value of field 'includeGaps'.
+ *
+ * @return the value of field 'IncludeGaps'.
+ */
+ public boolean getIncludeGaps()
+ {
+ return this._includeGaps;
+ }
+
+ /**
+ * Returns the value of field 'linkToAllViews'.
+ *
+ * @return the value of field 'LinkToAllViews'.
+ */
+ public boolean getLinkToAllViews()
+ {
+ return this._linkToAllViews;
+ }
+
+ /**
+ * Returns the value of field 'matchGaps'.
+ *
+ * @return the value of field 'MatchGaps'.
+ */
+ public boolean getMatchGaps()
+ {
+ return this._matchGaps;
+ }
+
+ /**
+ * Returns the value of field 'pcaData'.
+ *
+ * @return the value of field 'PcaData'.
+ */
+ public jalview.schemabinding.version2.PcaData getPcaData()
+ {
+ return this._pcaData;
+ }
+
+ /**
+ * Returns the value of field 'scaleFactor'.
+ *
+ * @return the value of field 'ScaleFactor'.
+ */
+ public float getScaleFactor()
+ {
+ return this._scaleFactor;
+ }
+
+ /**
+ * Returns the value of field 'scoreModelName'.
+ *
+ * @return the value of field 'ScoreModelName'.
+ */
+ public java.lang.String getScoreModelName()
+ {
+ return this._scoreModelName;
+ }
+
+ /**
+ * Returns the value of field 'seqPointMax'.
+ *
+ * @return the value of field 'SeqPointMax'.
+ */
+ public jalview.schemabinding.version2.SeqPointMax getSeqPointMax()
+ {
+ return this._seqPointMax;
+ }
+
+ /**
+ * Returns the value of field 'seqPointMin'.
+ *
+ * @return the value of field 'SeqPointMin'.
+ */
+ public jalview.schemabinding.version2.SeqPointMin getSeqPointMin()
+ {
+ return this._seqPointMin;
+ }
+
+ /**
+ * Method getSequencePoint.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.SequencePoint at
+ * the given index
+ */
+ public jalview.schemabinding.version2.SequencePoint getSequencePoint(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequencePointList.size())
+ {
+ throw new IndexOutOfBoundsException("getSequencePoint: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequencePointList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SequencePoint) _sequencePointList
+ .get(index);
+ }
+
+ /**
+ * Method getSequencePoint.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SequencePoint[] getSequencePoint()
+ {
+ jalview.schemabinding.version2.SequencePoint[] array = new jalview.schemabinding.version2.SequencePoint[0];
+ return (jalview.schemabinding.version2.SequencePoint[]) this._sequencePointList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequencePointCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequencePointCount()
+ {
+ return this._sequencePointList.size();
+ }
+
+ /**
+ * Returns the value of field 'showLabels'.
+ *
+ * @return the value of field 'ShowLabels'.
+ */
+ public boolean getShowLabels()
+ {
+ return this._showLabels;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle()
+ {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xDim'.
+ *
+ * @return the value of field 'XDim'.
+ */
+ public int getXDim()
+ {
+ return this._xDim;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'yDim'.
+ *
+ * @return the value of field 'YDim'.
+ */
+ public int getYDim()
+ {
+ return this._yDim;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Returns the value of field 'zDim'.
+ *
+ * @return the value of field 'ZDim'.
+ */
+ public int getZDim()
+ {
+ return this._zDim;
+ }
+
+ /**
+ * Method hasBgColour.
+ *
+ * @return true if at least one BgColour has been added
+ */
+ public boolean hasBgColour()
+ {
+ return this._has_bgColour;
+ }
+
+ /**
+ * Method hasDenominateByShortestLength.
+ *
+ * @return true if at least one DenominateByShortestLength has been added
+ */
+ public boolean hasDenominateByShortestLength()
+ {
+ return this._has_denominateByShortestLength;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasIncludeGappedColumns.
+ *
+ * @return true if at least one IncludeGappedColumns has been added
+ */
+ public boolean hasIncludeGappedColumns()
+ {
+ return this._has_includeGappedColumns;
+ }
+
+ /**
+ * Method hasIncludeGaps.
+ *
+ * @return true if at least one IncludeGaps has been added
+ */
+ public boolean hasIncludeGaps()
+ {
+ return this._has_includeGaps;
+ }
+
+ /**
+ * Method hasLinkToAllViews.
+ *
+ * @return true if at least one LinkToAllViews has been added
+ */
+ public boolean hasLinkToAllViews()
+ {
+ return this._has_linkToAllViews;
+ }
+
+ /**
+ * Method hasMatchGaps.
+ *
+ * @return true if at least one MatchGaps has been added
+ */
+ public boolean hasMatchGaps()
+ {
+ return this._has_matchGaps;
+ }
+
+ /**
+ * Method hasScaleFactor.
+ *
+ * @return true if at least one ScaleFactor has been added
+ */
+ public boolean hasScaleFactor()
+ {
+ return this._has_scaleFactor;
+ }
+
+ /**
+ * Method hasShowLabels.
+ *
+ * @return true if at least one ShowLabels has been added
+ */
+ public boolean hasShowLabels()
+ {
+ return this._has_showLabels;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXDim.
+ *
+ * @return true if at least one XDim has been added
+ */
+ public boolean hasXDim()
+ {
+ return this._has_xDim;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYDim.
+ *
+ * @return true if at least one YDim has been added
+ */
+ public boolean hasYDim()
+ {
+ return this._has_yDim;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Method hasZDim.
+ *
+ * @return true if at least one ZDim has been added
+ */
+ public boolean hasZDim()
+ {
+ return this._has_zDim;
+ }
+
+ /**
+ * Returns the value of field 'denominateByShortestLength'.
+ *
+ * @return the value of field 'DenominateByShortestLength'.
+ */
+ public boolean isDenominateByShortestLength()
+ {
+ return this._denominateByShortestLength;
+ }
+
+ /**
+ * Returns the value of field 'includeGappedColumns'.
+ *
+ * @return the value of field 'IncludeGappedColumns'.
+ */
+ public boolean isIncludeGappedColumns()
+ {
+ return this._includeGappedColumns;
+ }
+
+ /**
+ * Returns the value of field 'includeGaps'.
+ *
+ * @return the value of field 'IncludeGaps'.
+ */
+ public boolean isIncludeGaps()
+ {
+ return this._includeGaps;
+ }
+
+ /**
+ * Returns the value of field 'linkToAllViews'.
+ *
+ * @return the value of field 'LinkToAllViews'.
+ */
+ public boolean isLinkToAllViews()
+ {
+ return this._linkToAllViews;
+ }
+
+ /**
+ * Returns the value of field 'matchGaps'.
+ *
+ * @return the value of field 'MatchGaps'.
+ */
+ public boolean isMatchGaps()
+ {
+ return this._matchGaps;
+ }
+
+ /**
+ * Returns the value of field 'showLabels'.
+ *
+ * @return the value of field 'ShowLabels'.
+ */
+ public boolean isShowLabels()
+ {
+ return this._showLabels;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAxis()
+ {
+ this._axisList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequencePoint()
+ {
+ this._sequencePointList.clear();
+ }
+
+ /**
+ * Method removeAxis.
+ *
+ * @param vAxis
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAxis(final jalview.schemabinding.version2.Axis vAxis)
+ {
+ boolean removed = _axisList.remove(vAxis);
+ return removed;
+ }
+
+ /**
+ * Method removeAxisAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Axis removeAxisAt(final int index)
+ {
+ java.lang.Object obj = this._axisList.remove(index);
+ return (jalview.schemabinding.version2.Axis) obj;
+ }
+
+ /**
+ * Method removeSequencePoint.
+ *
+ * @param vSequencePoint
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequencePoint(
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ {
+ boolean removed = _sequencePointList.remove(vSequencePoint);
+ return removed;
+ }
+
+ /**
+ * Method removeSequencePointAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequencePoint removeSequencePointAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequencePointList.remove(index);
+ return (jalview.schemabinding.version2.SequencePoint) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAxis
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAxis(final int index,
+ final jalview.schemabinding.version2.Axis vAxis)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._axisList.size())
+ {
+ throw new IndexOutOfBoundsException("setAxis: Index value '" + index
+ + "' not in range [0.." + (this._axisList.size() - 1) + "]");
+ }
+
+ this._axisList.set(index, vAxis);
+ }
+
+ /**
+ *
+ *
+ * @param vAxisArray
+ */
+ public void setAxis(
+ final jalview.schemabinding.version2.Axis[] vAxisArray)
+ {
+ // -- copy array
+ _axisList.clear();
+
+ for (int i = 0; i < vAxisArray.length; i++)
+ {
+ this._axisList.add(vAxisArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour
+ * the value of field 'bgColour'.
+ */
+ public void setBgColour(final int bgColour)
+ {
+ this._bgColour = bgColour;
+ this._has_bgColour = true;
+ }
+
+ /**
+ * Sets the value of field 'denominateByShortestLength'.
+ *
+ * @param denominateByShortestLength
+ * the value of field 'denominateByShortestLength'.
+ */
+ public void setDenominateByShortestLength(
+ final boolean denominateByShortestLength)
+ {
+ this._denominateByShortestLength = denominateByShortestLength;
+ this._has_denominateByShortestLength = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'includeGappedColumns'.
+ *
+ * @param includeGappedColumns
+ * the value of field 'includeGappedColumns'.
+ */
+ public void setIncludeGappedColumns(final boolean includeGappedColumns)
+ {
+ this._includeGappedColumns = includeGappedColumns;
+ this._has_includeGappedColumns = true;
+ }
+
+ /**
+ * Sets the value of field 'includeGaps'.
+ *
+ * @param includeGaps
+ * the value of field 'includeGaps'.
+ */
+ public void setIncludeGaps(final boolean includeGaps)
+ {
+ this._includeGaps = includeGaps;
+ this._has_includeGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'linkToAllViews'.
+ *
+ * @param linkToAllViews
+ * the value of field 'linkToAllViews'.
+ */
+ public void setLinkToAllViews(final boolean linkToAllViews)
+ {
+ this._linkToAllViews = linkToAllViews;
+ this._has_linkToAllViews = true;
+ }
+
+ /**
+ * Sets the value of field 'matchGaps'.
+ *
+ * @param matchGaps
+ * the value of field 'matchGaps'.
+ */
+ public void setMatchGaps(final boolean matchGaps)
+ {
+ this._matchGaps = matchGaps;
+ this._has_matchGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'pcaData'.
+ *
+ * @param pcaData
+ * the value of field 'pcaData'.
+ */
+ public void setPcaData(
+ final jalview.schemabinding.version2.PcaData pcaData)
+ {
+ this._pcaData = pcaData;
+ }
+
+ /**
+ * Sets the value of field 'scaleFactor'.
+ *
+ * @param scaleFactor
+ * the value of field 'scaleFactor'.
+ */
+ public void setScaleFactor(final float scaleFactor)
+ {
+ this._scaleFactor = scaleFactor;
+ this._has_scaleFactor = true;
+ }
+
+ /**
+ * Sets the value of field 'scoreModelName'.
+ *
+ * @param scoreModelName
+ * the value of field 'scoreModelName'.
+ */
+ public void setScoreModelName(final java.lang.String scoreModelName)
+ {
+ this._scoreModelName = scoreModelName;
+ }
+
+ /**
+ * Sets the value of field 'seqPointMax'.
+ *
+ * @param seqPointMax
+ * the value of field 'seqPointMax'.
+ */
+ public void setSeqPointMax(
+ final jalview.schemabinding.version2.SeqPointMax seqPointMax)
+ {
+ this._seqPointMax = seqPointMax;
+ }
+
+ /**
+ * Sets the value of field 'seqPointMin'.
+ *
+ * @param seqPointMin
+ * the value of field 'seqPointMin'.
+ */
+ public void setSeqPointMin(
+ final jalview.schemabinding.version2.SeqPointMin seqPointMin)
+ {
+ this._seqPointMin = seqPointMin;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequencePoint
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequencePoint(final int index,
+ final jalview.schemabinding.version2.SequencePoint vSequencePoint)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequencePointList.size())
+ {
+ throw new IndexOutOfBoundsException("setSequencePoint: Index value '"
+ + index + "' not in range [0.."
+ + (this._sequencePointList.size() - 1) + "]");
+ }
+
+ this._sequencePointList.set(index, vSequencePoint);
+ }
+
+ /**
+ *
+ *
+ * @param vSequencePointArray
+ */
+ public void setSequencePoint(
+ final jalview.schemabinding.version2.SequencePoint[] vSequencePointArray)
+ {
+ // -- copy array
+ _sequencePointList.clear();
+
+ for (int i = 0; i < vSequencePointArray.length; i++)
+ {
+ this._sequencePointList.add(vSequencePointArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'showLabels'.
+ *
+ * @param showLabels
+ * the value of field 'showLabels'.
+ */
+ public void setShowLabels(final boolean showLabels)
+ {
+ this._showLabels = showLabels;
+ this._has_showLabels = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title
+ * the value of field 'title'.
+ */
+ public void setTitle(final java.lang.String title)
+ {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xDim'.
+ *
+ * @param xDim
+ * the value of field 'xDim'.
+ */
+ public void setXDim(final int xDim)
+ {
+ this._xDim = xDim;
+ this._has_xDim = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'yDim'.
+ *
+ * @param yDim
+ * the value of field 'yDim'.
+ */
+ public void setYDim(final int yDim)
+ {
+ this._yDim = yDim;
+ this._has_yDim = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Sets the value of field 'zDim'.
+ *
+ * @param zDim
+ * the value of field 'zDim'.
+ */
+ public void setZDim(final int zDim)
+ {
+ this._zDim = zDim;
+ this._has_zDim = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.PcaViewer
+ */
+ public static jalview.schemabinding.version2.PcaViewer unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.PcaViewer) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.PcaViewer.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Row.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Row extends DoubleVector implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Row()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.DoubleVector
+ */
+ public static jalview.schemabinding.version2.DoubleVector unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.DoubleVector) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Row.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SeqPointMax.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMax implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMax()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SeqPointMax
+ */
+ public static jalview.schemabinding.version2.SeqPointMax unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SeqPointMax) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SeqPointMax.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SeqPointMin.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMin implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMin()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SeqPointMin
+ */
+ public static jalview.schemabinding.version2.SeqPointMin unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SeqPointMin) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SeqPointMin.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SequencePoint.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequencePoint implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _sequenceRef.
+ */
+ private java.lang.String _sequenceRef;
+
+ /**
+ * Field _xPos.
+ */
+ private float _xPos;
+
+ /**
+ * keeps track of state for field: _xPos
+ */
+ private boolean _has_xPos;
+
+ /**
+ * Field _yPos.
+ */
+ private float _yPos;
+
+ /**
+ * keeps track of state for field: _yPos
+ */
+ private boolean _has_yPos;
+
+ /**
+ * Field _zPos.
+ */
+ private float _zPos;
+
+ /**
+ * keeps track of state for field: _zPos
+ */
+ private boolean _has_zPos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequencePoint()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteXPos()
+ {
+ this._has_xPos = false;
+ }
+
+ /**
+ */
+ public void deleteYPos()
+ {
+ this._has_yPos = false;
+ }
+
+ /**
+ */
+ public void deleteZPos()
+ {
+ this._has_zPos = false;
+ }
+
+ /**
+ * Returns the value of field 'sequenceRef'.
+ *
+ * @return the value of field 'SequenceRef'.
+ */
+ public java.lang.String getSequenceRef()
+ {
+ return this._sequenceRef;
+ }
+
+ /**
+ * Returns the value of field 'xPos'.
+ *
+ * @return the value of field 'XPos'.
+ */
+ public float getXPos()
+ {
+ return this._xPos;
+ }
+
+ /**
+ * Returns the value of field 'yPos'.
+ *
+ * @return the value of field 'YPos'.
+ */
+ public float getYPos()
+ {
+ return this._yPos;
+ }
+
+ /**
+ * Returns the value of field 'zPos'.
+ *
+ * @return the value of field 'ZPos'.
+ */
+ public float getZPos()
+ {
+ return this._zPos;
+ }
+
+ /**
+ * Method hasXPos.
+ *
+ * @return true if at least one XPos has been added
+ */
+ public boolean hasXPos()
+ {
+ return this._has_xPos;
+ }
+
+ /**
+ * Method hasYPos.
+ *
+ * @return true if at least one YPos has been added
+ */
+ public boolean hasYPos()
+ {
+ return this._has_yPos;
+ }
+
+ /**
+ * Method hasZPos.
+ *
+ * @return true if at least one ZPos has been added
+ */
+ public boolean hasZPos()
+ {
+ return this._has_zPos;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'sequenceRef'.
+ *
+ * @param sequenceRef
+ * the value of field 'sequenceRef'.
+ */
+ public void setSequenceRef(final java.lang.String sequenceRef)
+ {
+ this._sequenceRef = sequenceRef;
+ }
+
+ /**
+ * Sets the value of field 'xPos'.
+ *
+ * @param xPos
+ * the value of field 'xPos'.
+ */
+ public void setXPos(final float xPos)
+ {
+ this._xPos = xPos;
+ this._has_xPos = true;
+ }
+
+ /**
+ * Sets the value of field 'yPos'.
+ *
+ * @param yPos
+ * the value of field 'yPos'.
+ */
+ public void setYPos(final float yPos)
+ {
+ this._yPos = yPos;
+ this._has_yPos = true;
+ }
+
+ /**
+ * Sets the value of field 'zPos'.
+ *
+ * @param zPos
+ * the value of field 'zPos'.
+ */
+ public void setZPos(final float zPos)
+ {
+ this._zPos = zPos;
+ this._has_zPos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.SequencePoint
+ */
+ public static jalview.schemabinding.version2.SequencePoint unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequencePoint) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.SequencePoint.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
package jalview.schemabinding.version2;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Tree implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * Field _fontName.
- */
- private java.lang.String _fontName;
-
- /**
- * Field _fontSize.
- */
- private int _fontSize;
-
- /**
- * keeps track of state for field: _fontSize
- */
- private boolean _has_fontSize;
-
- /**
- * Field _fontStyle.
- */
- private int _fontStyle;
-
- /**
- * keeps track of state for field: _fontStyle
- */
- private boolean _has_fontStyle;
-
- /**
- * Field _threshold.
- */
- private float _threshold;
-
- /**
- * keeps track of state for field: _threshold
- */
- private boolean _has_threshold;
-
- /**
- * Field _showBootstrap.
- */
- private boolean _showBootstrap;
-
- /**
- * keeps track of state for field: _showBootstrap
- */
- private boolean _has_showBootstrap;
-
- /**
- * Field _showDistances.
- */
- private boolean _showDistances;
-
- /**
- * keeps track of state for field: _showDistances
- */
- private boolean _has_showDistances;
-
- /**
- * Field _markUnlinked.
- */
- private boolean _markUnlinked;
-
- /**
- * keeps track of state for field: _markUnlinked
- */
- private boolean _has_markUnlinked;
-
- /**
- * Field _fitToWindow.
- */
- private boolean _fitToWindow;
-
- /**
- * keeps track of state for field: _fitToWindow
- */
- private boolean _has_fitToWindow;
-
- /**
- * Field _currentTree.
- */
- private boolean _currentTree;
-
- /**
- * keeps track of state for field: _currentTree
- */
- private boolean _has_currentTree;
-
- /**
- * Tree ID added for binding tree visualization settings to vamsas document
- * trees in jalview 2.4.1
- *
- */
- private java.lang.String _id;
-
- /**
- * 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 _title.
- */
- private java.lang.String _title;
-
- /**
- * Field _newick.
- */
- private java.lang.String _newick;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public Tree()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteCurrentTree()
- {
- this._has_currentTree = false;
- }
-
- /**
- */
- public void deleteFitToWindow()
- {
- this._has_fitToWindow = false;
- }
-
- /**
- */
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
-
- /**
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
-
- /**
- */
- public void deleteHeight()
- {
- this._has_height = false;
- }
-
- /**
- */
- public void deleteMarkUnlinked()
- {
- this._has_markUnlinked = false;
- }
-
- /**
- */
- public void deleteShowBootstrap()
- {
- this._has_showBootstrap = false;
- }
-
- /**
- */
- public void deleteShowDistances()
- {
- this._has_showDistances = false;
- }
-
- /**
- */
- public void deleteThreshold()
- {
- this._has_threshold = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean getCurrentTree()
- {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean getFitToWindow()
- {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the following
- * description: Tree ID added for binding tree visualization settings to
- * vamsas document trees in jalview 2.4.1
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean getMarkUnlinked()
- {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'newick'.
- *
- * @return the value of field 'Newick'.
- */
- public java.lang.String getNewick()
- {
- return this._newick;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean getShowBootstrap()
- {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean getShowDistances()
- {
- return this._showDistances;
- }
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return the value of field 'Threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- }
-
- /**
- * 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 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasCurrentTree.
- *
- * @return true if at least one CurrentTree has been added
- */
- public boolean hasCurrentTree()
- {
- return this._has_currentTree;
- }
-
- /**
- * Method hasFitToWindow.
- *
- * @return true if at least one FitToWindow has been added
- */
- public boolean hasFitToWindow()
- {
- return this._has_fitToWindow;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasMarkUnlinked.
- *
- * @return true if at least one MarkUnlinked has been added
- */
- public boolean hasMarkUnlinked()
- {
- return this._has_markUnlinked;
- }
-
- /**
- * Method hasShowBootstrap.
- *
- * @return true if at least one ShowBootstrap has been added
- */
- public boolean hasShowBootstrap()
- {
- return this._has_showBootstrap;
- }
-
- /**
- * Method hasShowDistances.
- *
- * @return true if at least one ShowDistances has been added
- */
- public boolean hasShowDistances()
- {
- return this._has_showDistances;
- }
-
- /**
- * Method hasThreshold.
- *
- * @return true if at least one Threshold has been added
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * 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;
- }
-
- /**
- * Returns the value of field 'currentTree'.
- *
- * @return the value of field 'CurrentTree'.
- */
- public boolean isCurrentTree()
- {
- return this._currentTree;
- }
-
- /**
- * Returns the value of field 'fitToWindow'.
- *
- * @return the value of field 'FitToWindow'.
- */
- public boolean isFitToWindow()
- {
- return this._fitToWindow;
- }
-
- /**
- * Returns the value of field 'markUnlinked'.
- *
- * @return the value of field 'MarkUnlinked'.
- */
- public boolean isMarkUnlinked()
- {
- return this._markUnlinked;
- }
-
- /**
- * Returns the value of field 'showBootstrap'.
- *
- * @return the value of field 'ShowBootstrap'.
- */
- public boolean isShowBootstrap()
- {
- return this._showBootstrap;
- }
-
- /**
- * Returns the value of field 'showDistances'.
- *
- * @return the value of field 'ShowDistances'.
- */
- public boolean isShowDistances()
- {
- return this._showDistances;
- }
-
- /**
- * 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 'currentTree'.
- *
- * @param currentTree
- * the value of field 'currentTree'.
- */
- public void setCurrentTree(final boolean currentTree)
- {
- this._currentTree = currentTree;
- this._has_currentTree = true;
- }
-
- /**
- * Sets the value of field 'fitToWindow'.
- *
- * @param fitToWindow
- * the value of field 'fitToWindow'.
- */
- public void setFitToWindow(final boolean fitToWindow)
- {
- this._fitToWindow = fitToWindow;
- this._has_fitToWindow = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = 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 'id'. The field 'id' has the following description:
- * Tree ID added for binding tree visualization settings to vamsas document
- * trees in jalview 2.4.1
- *
- *
- * @param id
- * the value of field 'id'.
- */
- public void setId(final java.lang.String id)
- {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'markUnlinked'.
- *
- * @param markUnlinked
- * the value of field 'markUnlinked'.
- */
- public void setMarkUnlinked(final boolean markUnlinked)
- {
- this._markUnlinked = markUnlinked;
- this._has_markUnlinked = true;
- }
-
- /**
- * Sets the value of field 'newick'.
- *
- * @param newick
- * the value of field 'newick'.
- */
- public void setNewick(final java.lang.String newick)
- {
- this._newick = newick;
- }
-
- /**
- * Sets the value of field 'showBootstrap'.
- *
- * @param showBootstrap
- * the value of field 'showBootstrap'.
- */
- public void setShowBootstrap(final boolean showBootstrap)
- {
- this._showBootstrap = showBootstrap;
- this._has_showBootstrap = true;
- }
-
- /**
- * Sets the value of field 'showDistances'.
- *
- * @param showDistances
- * the value of field 'showDistances'.
- */
- public void setShowDistances(final boolean showDistances)
- {
- this._showDistances = showDistances;
- this._has_showDistances = true;
- }
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold
- * the value of field 'threshold'.
- */
- public void setThreshold(final float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = 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 '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 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = 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.Tree
- */
- public static jalview.schemabinding.version2.Tree unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(
- jalview.schemabinding.version2.Tree.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);
- }
+public class Tree implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Tree ID added for binding tree
+ * visualization
+ * settings to vamsas
+ * document trees in jalview 2.4.1
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _linkToAllViews.
+ */
+ private boolean _linkToAllViews = false;
+
+ /**
+ * keeps track of state for field: _linkToAllViews
+ */
+ private boolean _has_linkToAllViews;
+
+ /**
+ * 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 _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteCurrentTree(
+ ) {
+ this._has_currentTree= false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow(
+ ) {
+ this._has_fitToWindow= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteLinkToAllViews(
+ ) {
+ this._has_linkToAllViews= false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked(
+ ) {
+ this._has_markUnlinked= false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap(
+ ) {
+ this._has_showBootstrap= false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances(
+ ) {
+ this._has_showDistances= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the
+ * following description: Tree ID added for binding tree
+ * visualization
+ * settings to vamsas
+ * document trees in jalview 2.4.1
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'linkToAllViews'.
+ *
+ * @return the value of field 'LinkToAllViews'.
+ */
+ public boolean getLinkToAllViews(
+ ) {
+ return this._linkToAllViews;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick(
+ ) {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * 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 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree(
+ ) {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow(
+ ) {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasLinkToAllViews.
+ *
+ * @return true if at least one LinkToAllViews has been added
+ */
+ public boolean hasLinkToAllViews(
+ ) {
+ return this._has_linkToAllViews;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked(
+ ) {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap(
+ ) {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances(
+ ) {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'linkToAllViews'.
+ *
+ * @return the value of field 'LinkToAllViews'.
+ */
+ public boolean isLinkToAllViews(
+ ) {
+ return this._linkToAllViews;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * 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 'currentTree'.
+ *
+ * @param currentTree the value of field 'currentTree'.
+ */
+ public void setCurrentTree(
+ final boolean currentTree) {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(
+ final boolean fitToWindow) {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = 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 'id'. The field 'id' has the
+ * following description: Tree ID added for binding tree
+ * visualization
+ * settings to vamsas
+ * document trees in jalview 2.4.1
+ *
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * 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 'markUnlinked'.
+ *
+ * @param markUnlinked the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(
+ final boolean markUnlinked) {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick the value of field 'newick'.
+ */
+ public void setNewick(
+ final java.lang.String newick) {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(
+ final boolean showBootstrap) {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances the value of field 'showDistances'.
+ */
+ public void setShowDistances(
+ final boolean showDistances) {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = 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 '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 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = 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.Tree
+ */
+ public static jalview.schemabinding.version2.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.Tree.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class TridiagonalMatrix.
+ *
+ * @version $Revision$ $Date$
+ */
+public class TridiagonalMatrix extends DoubleMatrix
+ implements java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public TridiagonalMatrix()
+ {
+ 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.TridiagonalMatrix.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.Axis;
+
+/**
+ * Class AxisDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AxisDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AxisDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "axis";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Axis target = (Axis) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Axis target = (Axis) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Axis target = (Axis) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Axis target = (Axis) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ Axis target = (Axis) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ Axis target = (Axis) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Axis.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.D;
+
+/**
+ * Class DDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DDescriptor 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 DDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "D";
+ _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.D.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.DoubleMatrix;
+
+/**
+ * Class DoubleMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleMatrixDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleMatrixDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "DoubleMatrix";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _rows
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_rows", "rows",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ if (!target.hasRows())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getRows());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteRows();
+ return;
+ }
+ target.setRows(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _rows
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _columns
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_columns", "columns",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ if (!target.hasColumns())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getColumns());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteColumns();
+ return;
+ }
+ target.setColumns(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _columns
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _rowList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Row.class, "_rowList", "row",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ return target.getRow();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ target.addRow((jalview.schemabinding.version2.Row) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ target.removeAllRow();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Row();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _rowList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _d
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.D.class, "_d", "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
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ return target.getD();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ target.setD((jalview.schemabinding.version2.D) 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.D();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _d
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _e
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.E.class, "_e", "E",
+ 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.getE();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ DoubleMatrix target = (DoubleMatrix) object;
+ target.setE((jalview.schemabinding.version2.E) 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.E();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _e
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.DoubleMatrix.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.DoubleVector;
+
+/**
+ * Class DoubleVectorDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DoubleVectorDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public DoubleVectorDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "DoubleVector";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _vList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Double.TYPE, "_vList", "v",
+ 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.getV();
+ }
+
+ 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.addV(((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.removeAllV();
+ } 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: _vList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ org.exolab.castor.xml.validators.DoubleValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.DoubleValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-1.7976931348623157E308);
+ typeValidator.setMaxInclusive(1.7976931348623157E308);
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.DoubleVector.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.E;
+
+/**
+ * Class EDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EDescriptor 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 EDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "E";
+ _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.E.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.EigenMatrix;
+
+/**
+ * Class EigenMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class EigenMatrixDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public EigenMatrixDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "eigenMatrix";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.EigenMatrix.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
*
* @version $Revision$ $Date$
*/
-public class JalviewModelSequenceDescriptor extends
- org.exolab.castor.xml.util.XMLClassDescriptorImpl
+public class JalviewModelSequenceDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
{
// --------------------------/
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
try
{
JalviewModelSequence target = (JalviewModelSequence) object;
- target.addViewport((jalview.schemabinding.version2.Viewport) value);
+ target.addViewport(
+ (jalview.schemabinding.version2.Viewport) value);
} catch (java.lang.Exception ex)
{
throw new IllegalStateException(ex.toString());
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
try
{
JalviewModelSequence target = (JalviewModelSequence) object;
- target.addUserColours((jalview.schemabinding.version2.UserColours) value);
+ target.addUserColours(
+ (jalview.schemabinding.version2.UserColours) value);
} catch (java.lang.Exception ex)
{
throw new IllegalStateException(ex.toString());
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
}
}
- public void resetValue(Object object) throws IllegalStateException,
- IllegalArgumentException
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
{
try
{
{ // -- local scope
}
desc.setValidator(fieldValidator);
+ // -- _pcaViewerList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.PcaViewer.class,
+ "_pcaViewerList", "PcaViewer",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ return target.getPcaViewer();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.addPcaViewer(
+ (jalview.schemabinding.version2.PcaViewer) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ JalviewModelSequence target = (JalviewModelSequence) object;
+ target.removeAllPcaViewer();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.PcaViewer();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pcaViewerList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
// -- _featureSettings
desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
jalview.schemabinding.version2.FeatureSettings.class,
try
{
JalviewModelSequence target = (JalviewModelSequence) object;
- target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value);
+ target.setFeatureSettings(
+ (jalview.schemabinding.version2.FeatureSettings) value);
} catch (java.lang.Exception ex)
{
throw new IllegalStateException(ex.toString());
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PairwiseMatrix;
+
+/**
+ * Class PairwiseMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PairwiseMatrixDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PairwiseMatrixDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "pairwiseMatrix";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PairwiseMatrix.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PcaData;
+
+/**
+ * Class PcaDataDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaDataDescriptor extends
+ jalview.schemabinding.version2.descriptors.PcaDataTypeDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaDataDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.PcaDataTypeDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "pcaData";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PcaData.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PcaDataType;
+
+/**
+ * Class PcaDataTypeDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaDataTypeDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaDataTypeDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "PcaDataType";
+ _elementDefinition = false;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- initialize element descriptors
+
+ // -- _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);
+ // -- _tridiagonalMatrix
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.TridiagonalMatrix.class,
+ "_tridiagonalMatrix", "tridiagonalMatrix",
+ 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.getTridiagonalMatrix();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaDataType target = (PcaDataType) object;
+ target.setTridiagonalMatrix(
+ (jalview.schemabinding.version2.TridiagonalMatrix) 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.TridiagonalMatrix();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _tridiagonalMatrix
+ 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);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PcaDataType.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.PcaViewer;
+
+/**
+ * Class PcaViewerDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PcaViewerDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public PcaViewerDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "PcaViewer";
+ _elementDefinition = true;
+
+ // -- set grouping compositor
+ setCompositorAsSequence();
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_title", "title",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getTitle();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setTitle((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _title
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _scoreModelName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_scoreModelName", "scoreModelName",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getScoreModelName();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setScoreModelName((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scoreModelName
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xDim
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xDim", "xDim",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasXDim())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXDim());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXDim();
+ return;
+ }
+ target.setXDim(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xDim
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yDim
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_yDim", "yDim",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasYDim())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYDim());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYDim();
+ return;
+ }
+ target.setYDim(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yDim
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zDim
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_zDim", "zDim",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasZDim())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getZDim());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZDim();
+ return;
+ }
+ target.setZDim(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zDim
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _bgColour
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_bgColour", "bgColour",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasBgColour())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getBgColour());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteBgColour();
+ return;
+ }
+ target.setBgColour(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _bgColour
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _scaleFactor
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_scaleFactor", "scaleFactor",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasScaleFactor())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getScaleFactor());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteScaleFactor();
+ return;
+ }
+ target.setScaleFactor(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _scaleFactor
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _showLabels
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_showLabels", "showLabels",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasShowLabels())
+ {
+ return null;
+ }
+ return (target.getShowLabels() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteShowLabels();
+ return;
+ }
+ target.setShowLabels(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _showLabels
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _linkToAllViews
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_linkToAllViews", "linkToAllViews",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasLinkToAllViews())
+ {
+ return null;
+ }
+ return (target.getLinkToAllViews() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteLinkToAllViews();
+ return;
+ }
+ target.setLinkToAllViews(
+ ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _linkToAllViews
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _includeGaps
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_includeGaps", "includeGaps",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasIncludeGaps())
+ {
+ return null;
+ }
+ return (target.getIncludeGaps() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteIncludeGaps();
+ return;
+ }
+ target.setIncludeGaps(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _includeGaps
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _matchGaps
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_matchGaps", "matchGaps",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasMatchGaps())
+ {
+ return null;
+ }
+ return (target.getMatchGaps() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteMatchGaps();
+ return;
+ }
+ target.setMatchGaps(((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _matchGaps
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _includeGappedColumns
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_includeGappedColumns",
+ "includeGappedColumns",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasIncludeGappedColumns())
+ {
+ return null;
+ }
+ return (target.getIncludeGappedColumns() ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteIncludeGappedColumns();
+ return;
+ }
+ target.setIncludeGappedColumns(
+ ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _includeGappedColumns
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _denominateByShortestLength
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Boolean.TYPE, "_denominateByShortestLength",
+ "denominateByShortestLength",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasDenominateByShortestLength())
+ {
+ return null;
+ }
+ return (target.getDenominateByShortestLength()
+ ? java.lang.Boolean.TRUE
+ : java.lang.Boolean.FALSE);
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteDenominateByShortestLength();
+ return;
+ }
+ target.setDenominateByShortestLength(
+ ((java.lang.Boolean) value).booleanValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _denominateByShortestLength
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _width
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_width", "width",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasWidth())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getWidth());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteWidth();
+ return;
+ }
+ target.setWidth(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _width
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _height
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_height", "height",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasHeight())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getHeight());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteHeight();
+ return;
+ }
+ target.setHeight(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _height
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xpos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_xpos", "xpos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasXpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getXpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXpos();
+ return;
+ }
+ target.setXpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xpos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _ypos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Integer.TYPE, "_ypos", "ypos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ if (!target.hasYpos())
+ {
+ return null;
+ }
+ return new java.lang.Integer(target.getYpos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYpos();
+ return;
+ }
+ target.setYpos(((java.lang.Integer) value).intValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _ypos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IntValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive(-2147483648);
+ typeValidator.setMaxInclusive(2147483647);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ // -- _sequencePointList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SequencePoint.class,
+ "_sequencePointList", "sequencePoint",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getSequencePoint();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.addSequencePoint(
+ (jalview.schemabinding.version2.SequencePoint) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.removeAllSequencePoint();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SequencePoint();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequencePointList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _axisList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.Axis.class, "_axisList", "axis",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getAxis();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.addAxis((jalview.schemabinding.version2.Axis) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public void resetValue(Object object)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.removeAllAxis();
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.Axis();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _axisList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(3);
+ fieldValidator.setMaxOccurs(3);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _seqPointMin
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SeqPointMin.class,
+ "_seqPointMin", "seqPointMin",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getSeqPointMin();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setSeqPointMin(
+ (jalview.schemabinding.version2.SeqPointMin) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SeqPointMin();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _seqPointMin
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _seqPointMax
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.SeqPointMax.class,
+ "_seqPointMax", "seqPointMax",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getSeqPointMax();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setSeqPointMax(
+ (jalview.schemabinding.version2.SeqPointMax) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.SeqPointMax();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _seqPointMax
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ // -- _pcaData
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ jalview.schemabinding.version2.PcaData.class, "_pcaData",
+ "pcaData", org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ PcaViewer target = (PcaViewer) object;
+ return target.getPcaData();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ PcaViewer target = (PcaViewer) object;
+ target.setPcaData((jalview.schemabinding.version2.PcaData) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return new jalview.schemabinding.version2.PcaData();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("www.jalview.org");
+ desc.setRequired(true);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _pcaData
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(1);
+ { // -- local scope
+ }
+ desc.setValidator(fieldValidator);
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.PcaViewer.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.Row;
+
+/**
+ * Class RowDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class RowDescriptor extends
+ jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public RowDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleVectorDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "row";
+ _elementDefinition = true;
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.Row.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.SeqPointMax;
+
+/**
+ * Class SeqPointMaxDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMaxDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMaxDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "seqPointMax";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMax target = (SeqPointMax) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SeqPointMax.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.SeqPointMin;
+
+/**
+ * Class SeqPointMinDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SeqPointMinDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SeqPointMinDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "seqPointMin";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SeqPointMin target = (SeqPointMin) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SeqPointMin.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.SequencePoint;
+
+/**
+ * Class SequencePointDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequencePointDescriptor
+ extends org.exolab.castor.xml.util.XMLClassDescriptorImpl
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _elementDefinition.
+ */
+ private boolean _elementDefinition;
+
+ /**
+ * Field _nsPrefix.
+ */
+ private java.lang.String _nsPrefix;
+
+ /**
+ * Field _nsURI.
+ */
+ private java.lang.String _nsURI;
+
+ /**
+ * Field _xmlName.
+ */
+ private java.lang.String _xmlName;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequencePointDescriptor()
+ {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "sequencePoint";
+ _elementDefinition = true;
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
+ org.exolab.castor.mapping.FieldHandler handler = null;
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;
+ // -- initialize attribute descriptors
+
+ // -- _sequenceRef
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_sequenceRef", "sequenceRef",
+ org.exolab.castor.xml.NodeType.Attribute);
+ desc.setImmutable(true);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ return target.getSequenceRef();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ target.setSequenceRef((java.lang.String) value);
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _sequenceRef
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.StringValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setWhiteSpace("preserve");
+ }
+ desc.setValidator(fieldValidator);
+ // -- _xPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_xPos", "xPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ if (!target.hasXPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getXPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteXPos();
+ return;
+ }
+ target.setXPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _xPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _yPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_yPos", "yPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ if (!target.hasYPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getYPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteYPos();
+ return;
+ }
+ target.setYPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _yPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _zPos
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.Float.TYPE, "_zPos", "zPos",
+ org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler()
+ {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException
+ {
+ SequencePoint target = (SequencePoint) object;
+ if (!target.hasZPos())
+ {
+ return null;
+ }
+ return new java.lang.Float(target.getZPos());
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try
+ {
+ SequencePoint target = (SequencePoint) object;
+ // if null, use delete method for optional primitives
+ if (value == null)
+ {
+ target.deleteZPos();
+ return;
+ }
+ target.setZPos(((java.lang.Float) value).floatValue());
+ } catch (java.lang.Exception ex)
+ {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent)
+ {
+ return null;
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _zPos
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
+ fieldValidator.setValidator(typeValidator);
+ typeValidator.setMinInclusive((float) -3.4028235E38);
+ typeValidator.setMaxInclusive((float) 3.4028235E38);
+ }
+ desc.setValidator(fieldValidator);
+ // -- initialize element descriptors
+
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode()
+ {
+ return null;
+ }
+
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+ {
+ return super.getIdentity();
+ }
+
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass()
+ {
+ return jalview.schemabinding.version2.SequencePoint.class;
+ }
+
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix()
+ {
+ return _nsPrefix;
+ }
+
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI()
+ {
+ return _nsURI;
+ }
+
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator()
+ {
+ return this;
+ }
+
+ /**
+ * Method getXMLName.
+ *
+ * @return the XML Name for the Class being described.
+ */
+ public java.lang.String getXMLName()
+ {
+ return _xmlName;
+ }
+
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition()
+ {
+ return _elementDefinition;
+ }
+
+}
package jalview.schemabinding.version2.descriptors;
-//---------------------------------/
-//- Imported classes and packages -/
+ //---------------------------------/
+ //- Imported classes and packages -/
//---------------------------------/
import jalview.schemabinding.version2.Tree;
*
* @version $Revision$ $Date$
*/
-public class TreeDescriptor 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 TreeDescriptor()
- {
- super();
- _nsURI = "www.jalview.org";
- _xmlName = "tree";
- _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
-
- // -- _fontName
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_fontName", "fontName",
- 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
- {
- Tree target = (Tree) object;
- return target.getFontName();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- target.setFontName((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+public class TreeDescriptor 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 TreeDescriptor() {
+ super();
+ _nsURI = "www.jalview.org";
+ _xmlName = "tree";
+ _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
+
+ //-- _fontName
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", 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
+ {
+ Tree target = (Tree) object;
+ return target.getFontName();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ target.setFontName( (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: _fontName
+ 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");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fontName
- 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);
- // -- _fontSize
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_fontSize", "fontSize",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasFontSize())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _fontSize
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasFontSize()) { return null; }
+ return new java.lang.Integer(target.getFontSize());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFontSize();
+ return;
+ }
+ target.setFontSize( ((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: _fontSize
+ 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);
}
- return new java.lang.Integer(target.getFontSize());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFontSize();
- return;
- }
- target.setFontSize(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _fontStyle
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasFontStyle()) { return null; }
+ return new java.lang.Integer(target.getFontStyle());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFontStyle();
+ return;
+ }
+ target.setFontStyle( ((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: _fontStyle
+ 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fontSize
- 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);
- // -- _fontStyle
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Integer.TYPE, "_fontStyle", "fontStyle",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasFontStyle())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _threshold
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasThreshold()) { return null; }
+ return new java.lang.Float(target.getThreshold());
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteThreshold();
+ return;
+ }
+ target.setThreshold( ((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: _threshold
+ 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);
}
- return new java.lang.Integer(target.getFontStyle());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFontStyle();
- return;
- }
- target.setFontStyle(((java.lang.Integer) value).intValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _showBootstrap
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasShowBootstrap()) { return null; }
+ return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowBootstrap();
+ return;
+ }
+ target.setShowBootstrap( ((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: _showBootstrap
+ 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fontStyle
- 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);
- // -- _threshold
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Float.TYPE, "_threshold", "threshold",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasThreshold())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _showDistances
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasShowDistances()) { return null; }
+ return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteShowDistances();
+ return;
+ }
+ target.setShowDistances( ((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: _showDistances
+ 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);
}
- return new java.lang.Float(target.getThreshold());
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteThreshold();
- return;
- }
- target.setThreshold(((java.lang.Float) value).floatValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _markUnlinked
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasMarkUnlinked()) { return null; }
+ return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteMarkUnlinked();
+ return;
+ }
+ target.setMarkUnlinked( ((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: _markUnlinked
+ 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _threshold
- 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);
- // -- _showBootstrap
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasShowBootstrap())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _fitToWindow
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasFitToWindow()) { return null; }
+ return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteFitToWindow();
+ return;
+ }
+ target.setFitToWindow( ((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: _fitToWindow
+ 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);
}
- return (target.getShowBootstrap() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowBootstrap();
- return;
- }
- target.setShowBootstrap(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _currentTree
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ if (!target.hasCurrentTree()) { return null; }
+ return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ // if null, use delete method for optional primitives
+ if (value == null) {
+ target.deleteCurrentTree();
+ return;
+ }
+ target.setCurrentTree( ((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: _currentTree
+ 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showBootstrap
- 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);
- // -- _showDistances
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_showDistances", "showDistances",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasShowDistances())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+ super.setIdentity(desc);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue( java.lang.Object object )
+ throws IllegalStateException
+ {
+ Tree target = (Tree) object;
+ return target.getId();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ target.setId( (java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { //-- local scope
+ org.exolab.castor.xml.validators.IdValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+ fieldValidator.setValidator(typeValidator);
}
- return (target.getShowDistances() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteShowDistances();
- return;
- }
- target.setShowDistances(((java.lang.Boolean) value)
- .booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ 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
+ {
+ Tree target = (Tree) 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 {
+ Tree target = (Tree) 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _showDistances
- 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);
- // -- _markUnlinked
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasMarkUnlinked())
- {
- return null;
+ 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
+ {
+ Tree target = (Tree) 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 {
+ Tree target = (Tree) 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);
}
- return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteMarkUnlinked();
- return;
- }
- target.setMarkUnlinked(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ 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
+ {
+ Tree target = (Tree) 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 {
+ Tree target = (Tree) 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _markUnlinked
- 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);
- // -- _fitToWindow
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasFitToWindow())
- {
- return null;
+ 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
+ {
+ Tree target = (Tree) 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 {
+ Tree target = (Tree) 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);
}
- return (target.getFitToWindow() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteFitToWindow();
- return;
- }
- target.setFitToWindow(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ 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
+ {
+ Tree target = (Tree) 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 {
+ Tree target = (Tree) 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);
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _fitToWindow
- 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);
- // -- _currentTree
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.Boolean.TYPE, "_currentTree", "currentTree",
- org.exolab.castor.xml.NodeType.Attribute);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- if (!target.hasCurrentTree())
- {
- return null;
+ desc.setValidator(fieldValidator);
+ //-- initialize element descriptors
+
+ //-- _title
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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
+ {
+ Tree target = (Tree) object;
+ return target.getTitle();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) 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.setNameSpaceURI("www.jalview.org");
+ 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");
}
- return (target.getCurrentTree() ? java.lang.Boolean.TRUE
- : java.lang.Boolean.FALSE);
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- // if null, use delete method for optional primitives
- if (value == null)
- {
- target.deleteCurrentTree();
- return;
- }
- target.setCurrentTree(((java.lang.Boolean) value).booleanValue());
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
+ desc.setValidator(fieldValidator);
+ //-- _newick
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", 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
+ {
+ Tree target = (Tree) object;
+ return target.getNewick();
+ }
+ public void setValue( java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException
+ {
+ try {
+ Tree target = (Tree) object;
+ target.setNewick( (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.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ //-- validation code for: _newick
+ 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");
}
- }
-
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return null;
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _currentTree
- 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);
}
- desc.setValidator(fieldValidator);
- // -- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_id", "id",
- org.exolab.castor.xml.NodeType.Attribute);
- super.setIdentity(desc);
- handler = new org.exolab.castor.xml.XMLFieldHandler()
- {
- public java.lang.Object getValue(java.lang.Object object)
- throws IllegalStateException
- {
- Tree target = (Tree) object;
- return target.getId();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- target.setId((java.lang.String) value);
- } catch (java.lang.Exception ex)
- {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent)
- {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { // -- local scope
- org.exolab.castor.xml.validators.IdValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();
- 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
- {
- Tree target = (Tree) 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
- {
- Tree target = (Tree) 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());
- }
- }
+ //-----------/
+ //- Methods -/
+ //-----------/
- public java.lang.Object newInstance(java.lang.Object parent)
- {
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode(
+ ) {
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
- {
- Tree target = (Tree) 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
- {
- Tree target = (Tree) 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);
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no
+ * identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+ ) {
+ return super.getIdentity();
}
- 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
- {
- Tree target = (Tree) 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
- {
- Tree target = (Tree) 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);
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass(
+ ) {
+ return jalview.schemabinding.version2.Tree.class;
}
- 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
- {
- Tree target = (Tree) 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
- {
- Tree target = (Tree) 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);
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix(
+ ) {
+ return _nsPrefix;
}
- desc.setValidator(fieldValidator);
- // -- initialize element descriptors
-
- // -- _title
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_title", "title",
- 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
- {
- Tree target = (Tree) object;
- return target.getTitle();
- }
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) 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.setNameSpaceURI("www.jalview.org");
- 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");
+ /**
+ * Method getNameSpaceURI.
+ *
+ * @return the namespace URI used when marshaling and
+ * unmarshaling as XML.
+ */
+ public java.lang.String getNameSpaceURI(
+ ) {
+ return _nsURI;
}
- desc.setValidator(fieldValidator);
- // -- _newick
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
- java.lang.String.class, "_newick", "newick",
- 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
- {
- Tree target = (Tree) object;
- return target.getNewick();
- }
-
- public void setValue(java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try
- {
- Tree target = (Tree) object;
- target.setNewick((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.setMultivalued(false);
- addFieldDescriptor(desc);
-
- // -- validation code for: _newick
- 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");
+ /**
+ * Method getValidator.
+ *
+ * @return a specific validator for the class described by this
+ * ClassDescriptor.
+ */
+ public org.exolab.castor.xml.TypeValidator getValidator(
+ ) {
+ return this;
}
- 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.Tree.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 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;
- }
+ /**
+ * Method isElementDefinition.
+ *
+ * @return true if XML schema definition of this Class is that
+ * of a global
+ * element or element with anonymous type definition.
+ */
+ public boolean isElementDefinition(
+ ) {
+ return _elementDefinition;
+ }
}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.TridiagonalMatrix;
+
+/**
+ * Class TridiagonalMatrixDescriptor.
+ *
+ * @version $Revision$ $Date$
+ */
+public class TridiagonalMatrixDescriptor 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 TridiagonalMatrixDescriptor()
+ {
+ super();
+ setExtendsWithoutFlatten(
+ new jalview.schemabinding.version2.descriptors.DoubleMatrixDescriptor());
+ _nsURI = "www.jalview.org";
+ _xmlName = "tridiagonalMatrix";
+ _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.TridiagonalMatrix.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;
+ }
+
+}
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
+import java.util.List;
import java.util.Vector;
public class PCAModel
{
- private volatile PCA pca;
-
- int top;
+ /*
+ * inputs
+ */
+ private AlignmentView inputData;
- AlignmentView seqstrings;
+ private final SequenceI[] seqs;
- SequenceI[] seqs;
+ private final SimilarityParamsI similarityParams;
/*
- * Name of score model used to calculate PCA
+ * options - score model, nucleotide / protein
*/
- ScoreModelI scoreModel;
+ private ScoreModelI scoreModel;
private boolean nucleotide = false;
- private Vector<SequencePoint> points;
+ /*
+ * outputs
+ */
+ private PCA pca;
- private SimilarityParamsI similarityParams;
+ int top;
+
+ private List<SequencePoint> points;
/**
* Constructor given sequence data, score model and score calculation
public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
- seqstrings = seqData;
+ inputData = seqData;
seqs = sqs;
nucleotide = nuc;
scoreModel = modelName;
similarityParams = params;
}
- public void run()
+ /**
+ * Performs the PCA calculation (in the same thread) and extracts result data
+ * needed for visualisation by PCAPanel
+ */
+ public void calculate()
{
- pca = new PCA(seqstrings, scoreModel, similarityParams);
- pca.run();
+ pca = new PCA(inputData, scoreModel, similarityParams);
+ pca.run(); // executes in same thread, wait for completion
// Now find the component coordinates
int ii = 0;
// top = pca.getM().height() - 1;
top = height - 1;
- points = new Vector<SequencePoint>();
- float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+ points = new Vector<>();
+ Point[] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
for (int i = 0; i < height; i++)
{
SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
- points.addElement(sp);
+ points.add(sp);
}
}
}
/**
+ * Answers the index of the principal dimension of the PCA
*
- *
- * @return index of principle dimension of PCA
+ * @return
*/
public int getTop()
{
return top;
}
+ public void setTop(int t)
+ {
+ top = t;
+ }
+
/**
- * update the 2d coordinates for the list of points to the given dimensions
+ * Updates the 3D coordinates for the list of points to the given dimensions.
* Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
* Note - pca.getComponents starts counting the spectrum from rank-2 to zero,
* rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
public void updateRcView(int dim1, int dim2, int dim3)
{
// note: actual indices for components are dim1-1, etc (patch for JAL-1123)
- float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
+ Point[] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
for (int i = 0; i < pca.getHeight(); i++)
{
- points.elementAt(i).coord = scores[i];
+ points.get(i).coord = scores[i];
}
}
return pca.getDetails();
}
- public AlignmentView getSeqtrings()
+ public AlignmentView getInputData()
+ {
+ return inputData;
+ }
+
+ public void setInputData(AlignmentView data)
{
- return seqstrings;
+ inputData = data;
}
public String getPointsasCsv(boolean transformed, int xdim, int ydim,
}
else
{
- // output current x,y,z coords for points
- fl = getPointPosition(s);
- for (int d = 0; d < fl.length; d++)
- {
- csv.append(",");
- csv.append(fl[d]);
- }
+ Point p = points.get(s).coord;
+ csv.append(",").append(p.x);
+ csv.append(",").append(p.y);
+ csv.append(",").append(p.z);
}
csv.append("\n");
}
return csv.toString();
}
+ public String getScoreModelName()
+ {
+ return scoreModel == null ? "" : scoreModel.getName();
+ }
+
+ public void setScoreModel(ScoreModelI sm)
+ {
+ this.scoreModel = sm;
+ }
+
/**
+ * Answers the parameters configured for pairwise similarity calculations
*
- * @return x,y,z positions of point s (index into points) under current
- * transform.
+ * @return
*/
- public double[] getPointPosition(int s)
+ public SimilarityParamsI getSimilarityParameters()
{
- double pts[] = new double[3];
- float[] p = points.elementAt(s).coord;
- pts[0] = p[0];
- pts[1] = p[1];
- pts[2] = p[2];
- return pts;
+ return similarityParams;
}
- public String getScoreModelName()
+ public List<SequencePoint> getSequencePoints()
{
- return scoreModel == null ? "" : scoreModel.getName();
+ return points;
}
- public void setScoreModel(ScoreModelI sm)
+ public void setSequencePoints(List<SequencePoint> sp)
{
- this.scoreModel = sm;
+ points = sp;
+ }
+
+ /**
+ * Answers the object holding the values of the computed PCA
+ *
+ * @return
+ */
+ public PCA getPcaData()
+ {
+ return pca;
}
+ public void setPCA(PCA data)
+ {
+ pca = data;
+ }
}
assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
assertFalse(sm instanceof DistanceScoreModel);
- assertEquals(sm.getName(), "PID");
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
+ assertEquals(sm.getName(), "DNA");
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
sm = models.next();
assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
assertFalse(sm instanceof DistanceScoreModel);
- assertEquals(sm.getName(), "DNA");
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('c', 'x'), 1f);
+ assertEquals(sm.getName(), "PID");
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), 0f);
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'r'), 1f);
sm = models.next();
assertFalse(sm instanceof SimilarityScoreModel);
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertSame;
+
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
+import jalview.bin.Cache;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CalculationChooserTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ // read-only Jalview properties
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+ Boolean.FALSE.toString());
+ }
+
+ @Test(groups = "Functional")
+ public void testGetApplicableScoreModels()
+ {
+ ScoreModels models = ScoreModels.getInstance();
+ ScoreModelI blosum62 = models.getBlosum62();
+ ScoreModelI pam250 = models.getPam250();
+ ScoreModelI dna = models.getDefaultModel(false);
+
+ /*
+ * peptide models for PCA
+ */
+ List<ScoreModelI> filtered = CalculationChooser
+ .getApplicableScoreModels(false, true);
+ assertEquals(filtered.size(), 4);
+ assertSame(filtered.get(0), blosum62);
+ assertSame(filtered.get(1), pam250);
+ assertEquals(filtered.get(2).getName(), "PID");
+ assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+
+ /*
+ * peptide models for Tree are the same
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(false, false);
+ assertEquals(filtered.size(), 4);
+ assertSame(filtered.get(0), blosum62);
+ assertSame(filtered.get(1), pam250);
+ assertEquals(filtered.get(2).getName(), "PID");
+ assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+
+ /*
+ * nucleotide models for PCA
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, true);
+ assertEquals(filtered.size(), 3);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+ /*
+ * nucleotide models for Tree are the same
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, false);
+ assertEquals(filtered.size(), 3);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+ /*
+ * enable inclusion of BLOSUM62 for nucleotide PCA (JAL-2962)
+ */
+ Cache.applicationProperties.setProperty("BLOSUM62_PCA_FOR_NUCLEOTIDE",
+ Boolean.TRUE.toString());
+
+ /*
+ * nucleotide models for Tree are unchanged
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, false);
+ assertEquals(filtered.size(), 3);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+
+ /*
+ * nucleotide models for PCA add BLOSUM62 as last option
+ */
+ filtered = CalculationChooser.getApplicableScoreModels(true, true);
+ assertEquals(filtered.size(), 4);
+ assertSame(filtered.get(0), dna);
+ assertEquals(filtered.get(1).getName(), "PID");
+ assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
+ assertSame(filtered.get(3), blosum62);
+ }
+}
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+import jalview.analysis.PCA;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Point;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
import jalview.gui.FeatureRenderer;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
+import jalview.gui.PCAPanel;
import jalview.gui.PopupMenu;
+import jalview.gui.RotatableCanvas;
import jalview.gui.SliderPanel;
+import jalview.math.MatrixTest;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.BuriedColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
import java.awt.Color;
import java.io.File;
import java.util.List;
import java.util.Map;
+import javax.swing.JInternalFrame;
+import javax.swing.JRadioButton;
+
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUpMethod()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
@Override
@BeforeClass(alwaysRun = true)
addFeature(seq, featureType, score++);
addFeature(seq, featureType, score);
}
+
+ /**
+ * Test save and reload of a PCA viewer
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testSaveLoadPCA() throws IOException
+ {
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ assertEquals(af.getViewport().getAlignment().getHeight(), 15);
+
+ /*
+ * calculate and open PCA (calculates in a separate thread)
+ */
+ CalculationChooser chooser = new CalculationChooser(af);
+ ((JRadioButton) PA.getValue(chooser, "pca")).setSelected(true);
+ PA.invokeMethod(chooser, "calculate_actionPerformed()");
+ PCAPanel pcaPanel = (PCAPanel) PA.getValue(chooser, "pcaPanel");
+ assertNotNull(pcaPanel);
+ waitFor(50); // let it get started!!
+ while (pcaPanel.isWorking())
+ {
+ waitFor(50);
+ }
+ PA.invokeMethod(chooser, "close_actionPerformed()");
+
+ /*
+ * rotate, zoom in, change background colour
+ */
+ RotatableCanvas rc = (RotatableCanvas) PA.getValue(pcaPanel, "rc");
+ PA.setValue(rc, "bgColour", Color.PINK);
+ rc.zoom(1.9f);
+ rc.rotate(20, 40f);
+
+ /*
+ * save as Jalview project
+ */
+ File tfile = File.createTempFile("JalviewTest", ".jvp");
+ tfile.deleteOnExit();
+ String filePath = tfile.getAbsolutePath();
+ assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+ "Failed to store as a project.");
+
+ /*
+ * load the saved project and locate the restored PCA panel
+ */
+ new FileLoader().LoadFileWaitTillLoaded(filePath, DataSourceType.FILE);
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ PCAPanel pcaPanel2 = null;
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof PCAPanel && frame != pcaPanel)
+ {
+ pcaPanel2 = (PCAPanel) frame;
+ }
+ }
+ assertNotNull(pcaPanel2);
+
+ /*
+ * compare restored and original PCA
+ */
+ PCAModel pcaModel = (PCAModel) PA.getValue(pcaPanel, "pcaModel");
+ PCAModel pcaModel2 = (PCAModel) PA.getValue(pcaPanel2, "pcaModel");
+ RotatableCanvas rc2 = (RotatableCanvas) PA.getValue(pcaPanel2, "rc");
+ assertNotNull(pcaModel);
+ assertNotNull(pcaModel2);
+ assertNotNull(rc2);
+ assertEquals(rc2.getBackgroundColour(), Color.PINK);
+ assertEquals(PA.getValue(rc2, "scaleFactor"), 1.9f);
+
+ // original has input data
+ assertNotNull(pcaModel.getInputData());
+ // restored has no input data (JAL-2647 to do)
+ assertNull(pcaModel2.getInputData());
+
+ // verify sequence points are at the same positions
+ List<SequencePoint> seqPts = pcaModel.getSequencePoints();
+ List<SequencePoint> seqPts2 = pcaModel2.getSequencePoints();
+ assertEquals(seqPts.size(), seqPts2.size());
+ for (int i = 0; i < seqPts.size(); i++)
+ {
+ SequencePoint sp = seqPts.get(i);
+ SequencePoint sp2 = seqPts2.get(i);
+ assertEquals(sp.getSequence().getName(), sp2.getSequence().getName());
+ assertEquals(sp.coord, sp2.coord);
+ }
+
+ // verify axis end points are at the same positions
+ Point[] axes = (Point[]) PA.getValue(rc, "axisEndPoints");
+ Point[] axes2 = (Point[]) PA.getValue(rc2, "axisEndPoints");
+ assertEquals(axes.length, 3);
+ assertEquals(axes2.length, 3);
+ for (int i = 0; i < 3; i++)
+ {
+ assertEquals(axes[i], axes2[i]);
+ }
+
+ // compare PCA data
+ PCA pca = (PCA) PA.getValue(pcaModel, "pca");
+ PCA pca2 = (PCA) PA.getValue(pcaModel2, "pca");
+ assertNotNull(pca);
+ assertNotNull(pca2);
+ // same (BLOSUM62) score model (a singleton object)
+ assertSame(PA.getValue(pca, "scoreModel"),
+ PA.getValue(pca2, "scoreModel"));
+ assertEquals(PA.getValue(pca, "similarityParams"),
+ PA.getValue(pca2, "similarityParams"));
+ MatrixTest.assertMatricesMatch(pca.getPairwiseScores(),
+ pca2.getPairwiseScores());
+ MatrixTest.assertMatricesMatch(pca.getTridiagonal(),
+ pca2.getTridiagonal());
+ MatrixTest.assertMatricesMatch(pca.getEigenmatrix(),
+ pca2.getEigenmatrix());
+ }
+
+ protected void waitFor(long t)
+ {
+ synchronized (this)
+ {
+ try
+ {
+ wait(t);
+ } catch (InterruptedException e)
+ {
+ fail(e.getMessage());
+ }
+ }
+ }
}
}
}
Matrix m1 = new Matrix(in);
+
Matrix m2 = (Matrix) m1.copy();
assertNotSame(m1, m2);
assertTrue(matrixEquals(m1, m2));
+ assertNull(m2.d);
+ assertNull(m2.e);
+
+ /*
+ * now add d and e vectors and recopy
+ */
+ m1.d = Arrays.copyOf(in[2], in[2].length);
+ m1.e = Arrays.copyOf(in[4], in[4].length);
+ m2 = (Matrix) m1.copy();
+ assertNotSame(m2.d, m1.d);
+ assertNotSame(m2.e, m1.e);
+ assertEquals(m2.d, m1.d);
+ assertEquals(m2.e, m1.e);
}
/**
assertMatricesMatch(m1, m2);
}
- private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+ public static void assertMatricesMatch(MatrixI m1, MatrixI m2)
{
if (m1.height() != m2.height())
{
}
}
}
- ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
- ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
+ ArrayAsserts.assertArrayEquals("D vector", m1.getD(), m2.getD(),
+ 0.00001d);
+ ArrayAsserts.assertArrayEquals("E vector", m1.getE(), m2.getE(),
+ 0.00001d);
}
@Test(groups = "Functional")
--- /dev/null
+package jalview.math;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.math.RotatableMatrix.Axis;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class RotatableMatrixTest
+{
+ private RotatableMatrix rm;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ rm = new RotatableMatrix();
+
+ /*
+ * 0.5 1.0 1.5
+ * 1.0 2.0 3.0
+ * 1.5 3.0 4.5
+ */
+ for (int i = 1; i <= 3; i++)
+ {
+ for (int j = 1; j <= 3; j++)
+ {
+ rm.setValue(i - 1, j - 1, i * j / 2f);
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testPreMultiply()
+ {
+ float[][] pre = new float[3][3];
+ int i = 1;
+ for (int j = 0; j < 3; j++)
+ {
+ for (int k = 0; k < 3; k++)
+ {
+ pre[j][k] = i++;
+ }
+ }
+
+ rm.preMultiply(pre);
+
+ /*
+ * check rm[i, j] is now the product of the i'th row of pre
+ * and the j'th column of (original) rm
+ */
+ for (int j = 0; j < 3; j++)
+ {
+ for (int k = 0; k < 3; k++)
+ {
+ float expected = 0f;
+ for (int l = 0; l < 3; l++)
+ {
+ float rm_l_k = (l + 1) * (k + 1) / 2f;
+ expected += pre[j][l] * rm_l_k;
+ }
+ assertEquals(rm.getValue(j, k), expected,
+ String.format("[%d, %d]", j, k));
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testVectorMultiply()
+ {
+ float[] result = rm.vectorMultiply(new float[] { 2f, 3f, 4.5f });
+
+ // vector times first column of matrix
+ assertEquals(result[0], 2f * 0.5f + 3f * 1f + 4.5f * 1.5f);
+
+ // vector times second column of matrix
+ assertEquals(result[1], 2f * 1.0f + 3f * 2f + 4.5f * 3f);
+
+ // vector times third column of matrix
+ assertEquals(result[2], 2f * 1.5f + 3f * 3f + 4.5f * 4.5f);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetRotation()
+ {
+ float theta = 60f;
+ double cosTheta = Math.cos((theta * Math.PI / 180f));
+ double sinTheta = Math.sin((theta * Math.PI / 180f));
+
+ /*
+ * sanity check that sin(60) = sqrt(3) / 2, cos(60) = 1/2
+ */
+ double delta = 0.0001d;
+ assertEquals(cosTheta, 0.5f, delta);
+ assertEquals(sinTheta, Math.sqrt(3d) / 2d, delta);
+
+ /*
+ * so far so good, now verify rotations
+ * @see https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations
+ */
+
+ /*
+ * 60 degrees about X axis should be
+ * 1 0 0
+ * 0 cos -sin
+ * 0 sin cos
+ * but code applies the negative of this
+ * nb cos(-x) = cos(x), sin(-x) = -sin(x)
+ */
+ float[][] rot = RotatableMatrix.getRotation(theta, Axis.X);
+ assertEquals(rot[0][0], 1f, delta);
+ assertEquals(rot[0][1], 0f, delta);
+ assertEquals(rot[0][2], 0f, delta);
+ assertEquals(rot[1][0], 0f, delta);
+ assertEquals(rot[1][1], cosTheta, delta);
+ assertEquals(rot[1][2], sinTheta, delta);
+ assertEquals(rot[2][0], 0f, delta);
+ assertEquals(rot[2][1], -sinTheta, delta);
+ assertEquals(rot[2][2], cosTheta, delta);
+
+ /*
+ * 60 degrees about Y axis should be
+ * cos 0 sin
+ * 0 1 0
+ * -sin 0 cos
+ * but code applies the negative of this
+ */
+ rot = RotatableMatrix.getRotation(theta, Axis.Y);
+ assertEquals(rot[0][0], cosTheta, delta);
+ assertEquals(rot[0][1], 0f, delta);
+ assertEquals(rot[0][2], -sinTheta, delta);
+ assertEquals(rot[1][0], 0f, delta);
+ assertEquals(rot[1][1], 1f, delta);
+ assertEquals(rot[1][2], 0f, delta);
+ assertEquals(rot[2][0], sinTheta, delta);
+ assertEquals(rot[2][1], 0f, delta);
+ assertEquals(rot[2][2], cosTheta, delta);
+
+ /*
+ * 60 degrees about Z axis should be
+ * cos -sin 0
+ * sin cos 0
+ * 0 0 1
+ * - and it is!
+ */
+ rot = RotatableMatrix.getRotation(theta, Axis.Z);
+ assertEquals(rot[0][0], cosTheta, delta);
+ assertEquals(rot[0][1], -sinTheta, delta);
+ assertEquals(rot[0][2], 0f, delta);
+ assertEquals(rot[1][0], sinTheta, delta);
+ assertEquals(rot[1][1], cosTheta, delta);
+ assertEquals(rot[1][2], 0f, delta);
+ assertEquals(rot[2][0], 0f, delta);
+ assertEquals(rot[2][1], 0f, delta);
+ assertEquals(rot[2][2], 1f, delta);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff