+++ /dev/null
----
-version: 2.11.3
-date: 2022-12-12
-channel: "release"
----
-
-## New Features
-
-- <!-- JAL-4061 --> Find can search sequence features' type and description
-- <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
-JAL-4089 use selected columns for superposition
-JAL-4086 Highlight aligned positions on all associated structures when mousing over a column
-JAL-4083 Exceptions for multiple residue highlights in Jmol
-JAL-4075 Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
-JAL-4033 selections with visual feedback via contact matrix annotation
-JAL-4027 contact matrix datatype in Jalview
-JAL-3895 Alphafold red/orange/yellow/green colourscheme for structures
-JAL-3855 Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
-JAL-3416 FlatLAF default look and feel on Linux, OSX and everywhere else ?
-JAL-2961 Jmol view not always centred on structures when multiple structures are viewed
-JAL-2382 Import and display sequence-associated contact predictions in CASP-RR format
-JAL-2349 Contact prediction visualisation
-JAL-2348 modularise annotation renderer
-JAL-1551 Standard source code formatting and editing settings
---
## New Features
-JAL-4064 Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
-JAL-4054 Installers built with install4j10
-JAL-3676 Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
-JAL-3416 FlatLAF default look and feel on Linux, OSX and everywhere else ?
+- <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
+- <!-- JAL-4054 --> Installers built with install4j10
+- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
+- <!-- JAL-3416 --> FlatLAF default look and feel on Linux, OSX and everywhere else ?
-## Issues Resolved
-JAL-3776 Cancelling interactive calculation leaves empty progress bar.
-JAL-3772 Unsaved Alignment windows close without prompting to save, individually or at application quit.
-JAL-1988 Can quit Jalview while 'save project' is in progress
+- <!-- JAL-4019 --> Ambiguous Base Colourscheme
+- <!-- JAL-4061 --> Find can search sequence features' type and description
+- <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
+- <!-- JAL-4089 --> Use selected columns for superposition
+- <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
+
+- <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
+- <!-- JAL-4095 --> Interactive picking of low pAE score regions
+- <!-- JAL-4027 --> contact matrix datatype in Jalview
+- <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
+
+- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
+- <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
+
+- <!-- JAL-2961 --> Jmol view not always centred on structures when multiple structures are viewed
+
+- <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
+
+- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
+
+- <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
+- <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
+
+## Still in progress (delete on release)
+
+- <!-- JAL-2382 --> Import and display sequence-associated contact predictions in CASP-RR format
+- <!-- JAL-2349 --> Contact prediction visualisation
+- <!-- JAL-2348 --> modularise annotation renderer
+
+
+
+## Issues Resolved
+- <!-- JAL-3776 --> Cancelling interactive calculation leaves empty progress bar.
+- <!-- JAL-3772 --> Unsaved Alignment windows close without prompting to save, individually or at application quit.
+- <!-- JAL-1988 --> Can quit Jalview while 'save project' is in progress
+- <!-- JAL-4126 --> 'Use original colours' option of colour by annotation not honoured when restoring view from project
+- <!-- JAL-4116 --> PDB structures slow to view when Jalview Java Console is open (2.11.2.7 patch)
+- <!-- JAL-3784 --> Multiple overview windows can be opened for a particular alignment view when multiple views are present
+- <!-- JAL-3785 --> Overview windows opened automatically (due to preferences settings) lack title
+- <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
\ No newline at end of file
</xs:complexContent>
</xs:complexType>
</xs:element>
+ <xs:element name="overview" minOccurs="0">
+ <xs:complexType>
+ <xs:attributeGroup ref="jv:swingwindow" />
+ <xs:attribute name="showHidden" type="xs:boolean" />
+ <xs:attribute name="residueColour" type="xs:int" />
+ <xs:attribute name="gapColour" type="xs:int" />
+ <xs:attribute name="hiddenColour" type="xs:int" />
+ <xs:attribute name="title" type="xs:string" />
+ </xs:complexType>
+ </xs:element>
</xs:sequence>
<xs:attributeGroup ref="jv:swingwindow" />
<xs:attribute name="conservationSelected" type="xs:boolean" />
viewport.setGatherViewsHere(true);
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
return newap;
}
}
/**
- * DOCUMENT ME!
+ * Opens an Overview panel for the alignment, unless one is open already
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
+ boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ openOverviewPanel(showHiddenRegions);
+ }
+
+ public OverviewPanel openOverviewPanel(boolean showHidden)
+ {
if (alignPanel.overviewPanel != null)
{
- return;
+ return alignPanel.overviewPanel;
}
-
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager
- .formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+ Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
true, true);
frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ final AlignmentPanel thePanel = this.alignPanel;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
javax.swing.event.InternalFrameEvent evt)
{
overview.dispose();
- alignPanel.setOverviewPanel(null);
+ thePanel.setOverviewPanel(null);
}
});
if (getKeyListeners().length > 0)
}
alignPanel.setOverviewPanel(overview);
+ alignPanel.setOverviewTitle(this);
+
+ return overview;
}
@Override
{
if (index > -1)
{
+ /*
+ * update current Overview window title (if there is one)
+ * to add view name "Original" if necessary
+ */
+ alignPanel.setOverviewTitle(this);
+
+ /*
+ * switch panels and set Overview title (if there is one
+ * because it was opened automatically)
+ */
alignPanel = alignPanels.get(index);
+ alignPanel.setOverviewTitle(this);
+
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
return calculationDialog;
}
+ /**
+ * Constructs and sets the title for the Overview window (if there is one),
+ * including the align frame's title, and view name (if applicable). Returns
+ * the title, or null if this panel has no Overview window open.
+ *
+ * @param alignFrame
+ * @return
+ */
+ public String setOverviewTitle(AlignFrame alignFrame)
+ {
+ if (this.overviewPanel == null)
+ {
+ return null;
+ }
+ String overviewTitle = MessageManager
+ .formatMessage("label.overview_params", new Object[]
+ { alignFrame.getTitle() });
+ String viewName = getViewName();
+ if (viewName != null)
+ {
+ overviewTitle += (" " + viewName);
+ }
+ overviewPanel.setTitle(overviewTitle);
+ return overviewTitle;
+ }
+
+ /**
+ * If this alignment panel has an Overview panel open, closes it
+ */
+ public void closeOverviewPanel()
+ {
+ if (overviewPanel != null)
+ {
+ overviewPanel.close();
+ overviewPanel = null;
+ }
+ }
+
}
*/
package jalview.gui;
-import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
-import jalview.renderer.OverviewRenderer;
-import jalview.renderer.OverviewResColourFinder;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import javax.swing.JPanel;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
public class OverviewCanvas extends JPanel
{
+ public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+ public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+ public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white;
+
+ public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray;
+
+ public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+ .darker();
+
private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
// This is set true if the alignment view changes whilst
boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ OVERVIEW_DEFAULT_GAP);
Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
- cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+ OVERVIEW_DEFAULT_HIDDEN);
+ Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE;
+
+ cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
setSize(od.getWidth(), od.getHeight());
}
}
}
}
+
+ public Color getGapColour()
+ {
+ return cf.getGapColour();
+ }
+
+ public Color getHiddenColour()
+ {
+ return cf.getHiddenColour();
+ }
+
+ public Color getResidueColour()
+ {
+ return cf.getResidueColour();
+ }
+
+ /**
+ * Sets the colours to use for gaps, residues and hidden regions
+ *
+ * @param gaps
+ * @param residues
+ * @param hidden
+ */
+ public void setColours(Color gaps, Color residues, Color hidden)
+ {
+ cf = new OverviewResColourFinder(gaps, residues, hidden);
+ }
}
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.renderer.OverviewRenderer;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.viewmodel.OverviewDimensionsHideHidden;
-import jalview.viewmodel.OverviewDimensionsShowHidden;
-import jalview.viewmodel.ViewportListenerI;
-
import java.awt.BorderLayout;
import java.awt.Cursor;
import java.awt.Dimension;
+import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ComponentAdapter;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
+import jalview.renderer.OverviewRenderer;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsHideHidden;
+import jalview.viewmodel.OverviewDimensionsShowHidden;
+import jalview.viewmodel.ViewportListenerI;
+
/**
* Panel displaying an overview of the full alignment, with an interactive box
* representing the viewport onto the alignment.
private AlignmentPanel ap;
+ private JInternalFrame internalFrame;
+
protected JCheckBoxMenuItem displayToggle;
protected boolean showHidden = true;
*
* @param alPanel
* The alignment panel which is shown in the overview panel
+ * @param frame
+ * @param isShowHidden
+ * TODO
*/
- public OverviewPanel(AlignmentPanel alPanel)
+ public OverviewPanel(AlignmentPanel alPanel, JInternalFrame frame,
+ boolean isShowHidden)
{
this.av = alPanel.av;
this.ap = alPanel;
+ this.internalFrame = frame;
- showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- false);
+ showHidden = isShowHidden;
if (showHidden)
{
od = new OverviewDimensionsShowHidden(av.getRanges(),
oviewCanvas = null;
ap = null;
od = null;
+ internalFrame = null;
}
}
+
+ public boolean isShowHiddenRegions()
+ {
+ return showHidden;
+ }
+
+ public OverviewCanvas getCanvas()
+ {
+ return oviewCanvas;
+ }
+
+ /**
+ * Sets the title of the enclosing frame
+ *
+ * @param title
+ */
+ public void setTitle(String title)
+ {
+ internalFrame.setTitle(title);
+ }
+
+ /**
+ * Returns the title of the enclosing frame
+ *
+ * @return title
+ */
+ public String getTitle()
+ {
+ return internalFrame.getTitle();
+ }
+
+ /**
+ * Sets the bounds of the frame holding the Overview panel
+ *
+ * @param xpos
+ * @param ypos
+ * @param width
+ * @param height
+ */
+ public void setFrameBounds(int xpos, int ypos, int width, int height)
+ {
+ internalFrame.setBounds(xpos, ypos, width, height);
+ }
+
+ /**
+ * Returns the bounds of the enclosing frame
+ *
+ * @return
+ */
+ public Rectangle getFrameBounds()
+ {
+ return internalFrame.getBounds();
+ }
+
+ /**
+ * Closes the frame containing the overview panel
+ */
+ public void close()
+ {
+ internalFrame.dispose();
+ }
}
* Set overview panel defaults
*/
gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ OverviewCanvas.OVERVIEW_DEFAULT_GAP));
hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
gapLabel.setEnabled(!useLegacyGap.isSelected());
gapColour.setEnabled(!useLegacyGap.isSelected());
boolean enabled = useLegacyGap.isSelected();
if (enabled)
{
- gapColour.setBackground(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
+ gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
}
else
{
- gapColour.setBackground(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
}
gapColour.setEnabled(!enabled);
gapLabel.setEnabled(!enabled);
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
showHiddenAtStart.setSelected(false);
- hiddenColour.setBackground(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+ hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
}
@Override
// that perform queries to find the 'current working alignment'
Desktop.addInternalFrame(alignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * for an Overview automatically opened with alignment,
+ * set its title now alignFrame title has been set
+ */
+ alignFrame.alignPanel.setOverviewTitle(alignFrame);
}
try
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
+import jalview.gui.OverviewPanel;
import jalview.gui.PCAPanel;
import jalview.gui.PaintRefresher;
import jalview.gui.SplitFrame;
import jalview.xml.binding.jalview.JalviewModel.Viewport;
import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
view.setStartRes(vpRanges.getStartRes());
view.setStartSeq(vpRanges.getStartSeq());
+ OverviewPanel ov = ap.getOverviewPanel();
+ if (ov != null)
+ {
+ Overview overview = new Overview();
+ overview.setTitle(ov.getTitle());
+ Rectangle bounds = ov.getFrameBounds();
+ overview.setXpos(bounds.x);
+ overview.setYpos(bounds.y);
+ overview.setWidth(bounds.width);
+ overview.setHeight(bounds.height);
+ overview.setShowHidden(ov.isShowHiddenRegions());
+ overview.setGapColour(ov.getCanvas().getGapColour().getRGB());
+ overview.setResidueColour(
+ ov.getCanvas().getResidueColour().getRGB());
+ overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
+ view.setOverview(overview);
+ }
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
}
/*
- * Load any trees, PDB structures and viewers
+ * Load any trees, PDB structures and viewers, Overview
*
* Not done if flag is false (when this method is used for New View)
*/
loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
+ loadOverview(view, jalviewModel.getVersion(), af);
}
// and finally return.
return af;
}
/**
+ * Load Overview window, restoring colours, 'show hidden regions' flag, title
+ * and geometry as saved
+ *
+ * @param view
+ * @param af
+ */
+ protected void loadOverview(Viewport view, String version, AlignFrame af)
+ {
+ if (!isVersionStringLaterThan("2.11.3",
+ version) && view.getOverview()==null)
+ {
+ return;
+ }
+ /*
+ * first close any Overview that was opened automatically
+ * (if so configured in Preferences) so that the view is
+ * restored in the same state as saved
+ */
+ af.alignPanel.closeOverviewPanel();
+
+ Overview overview = view.getOverview();
+ if (overview != null)
+ {
+ OverviewPanel overviewPanel = af
+ .openOverviewPanel(overview.isShowHidden());
+ overviewPanel.setTitle(overview.getTitle());
+ overviewPanel.setFrameBounds(overview.getXpos(), overview.getYpos(),
+ overview.getWidth(), overview.getHeight());
+ Color gap = new Color(overview.getGapColour());
+ Color residue = new Color(overview.getResidueColour());
+ Color hidden = new Color(overview.getHiddenColour());
+ overviewPanel.getCanvas().setColours(gap, residue, hidden);
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
* - minimum version we are comparing against
* @param version
* - version of data being processsed
- * @return
+ * @return true if version is equal to or later than supported
*/
public static boolean isVersionStringLaterThan(String supported,
String version)
{
splitFrameCandidates.put(view, af);
}
+
return af;
}
int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,
int lastcol)
{
- Color color = resColFinder.GAP_COLOUR;
+ Color color = resColFinder.gapColour;
if ((seq != null) && (seq.getLength() > lastcol))
{
*/
package jalview.renderer;
+import java.awt.Color;
+
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
-import java.awt.Color;
-
public class OverviewResColourFinder extends ResidueColourFinder
{
- final Color GAP_COLOUR; // default colour to use at gaps
-
- final Color RESIDUE_COLOUR; // default colour to use at residues
-
- final Color HIDDEN_COLOUR; // colour for hidden regions
-
- boolean useLegacy = false;
-
- public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+ /*
+ * colour for gaps (unless overridden by colour scheme)
+ * - as set in Preferences, _or_ read from a project file
+ */
+ Color gapColour;
- public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+ /*
+ * colour for residues if no colour scheme set (before feature colouring)
+ * - as set in Preferences, _or_ read from a project file
+ */
+ Color residueColour;
- public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
- .darker();
+ /*
+ * colour for hidden regions
+ * - as set in Preferences, _or_ read from a project file
+ */
+ Color hiddenColour;
/**
* Constructor without colour settings (used by applet)
+ * @deprecated
*/
+ @Deprecated
public OverviewResColourFinder()
{
- this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
+ this(Color.lightGray, Color.white, Color.darkGray.darker());
}
/**
- * Constructor with colour settings
+ * Constructor given default colours for gaps, residues and hidden regions
*
- * @param useLegacyColouring
- * whether to use legacy gap colouring (white gaps, grey residues)
- * @param gapCol
- * gap colour if not legacy
- * @param hiddenCol
- * hidden region colour (transparency applied by rendering code)
+ * @param gaps
+ * @param residues
+ * @param hidden
*/
- public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
- Color hiddenCol)
+ public OverviewResColourFinder(Color gaps, Color residues, Color hidden)
{
- if (useLegacyColouring)
- {
- GAP_COLOUR = Color.white;
- RESIDUE_COLOUR = Color.lightGray;
- HIDDEN_COLOUR = hiddenCol;
- }
- else
- {
- GAP_COLOUR = gapCol;
- RESIDUE_COLOUR = Color.white;
- HIDDEN_COLOUR = hiddenCol;
- }
+ gapColour = gaps;
+ residueColour = residues;
+ hiddenColour = hidden;
}
@Override
public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
{
- Color resBoxColour = RESIDUE_COLOUR;
+ Color resBoxColour = residueColour;
char currentChar = seq.getCharAt(i);
// In the overview window, gaps are coloured grey, unless the colour scheme
if (Comparison.isGap(currentChar)
&& (!shader.getColourScheme().hasGapColour()))
{
- resBoxColour = GAP_COLOUR;
+ resBoxColour = gapColour;
}
else
{
}
else if (Comparison.isGap(currentChar))
{
- resBoxColour = GAP_COLOUR;
+ resBoxColour = gapColour;
}
return resBoxColour;
}
/**
- * Supply hidden colour
+ * Returns the colour used for hidden regions
+ *
+ * @return
+ */
+ public Color getHiddenColour()
+ {
+ return hiddenColour;
+ }
+
+ /**
+ * Returns the colour used for gaps, if not overridden by the alignment colour
+ * scheme
+ *
+ * @return
+ */
+ public Color getGapColour()
+ {
+ return gapColour;
+ }
+
+ /**
+ * Returns the colour used for residues (before applying any feature
+ * colouring) if there is no alignment colour scheme
*
- * @return colour of hidden regions
+ * @return
*/
- protected Color getHiddenColour()
+ public Color getResidueColour()
{
- return HIDDEN_COLOUR;
+ return residueColour;
}
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.14 at 02:46:00 PM BST
+// Generated on: 2023.01.31 at 04:07:09 PM GMT
//
+
package jalview.xml.binding.embl;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for EntrySetType complex type.
+ * <p>Java class for EntrySetType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="EntrySetType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = { "entry" })
-public class EntrySetType
-{
+@XmlType(name = "EntrySetType", propOrder = {
+ "entry"
+})
+public class EntrySetType {
- @XmlElement(required = true)
- protected List<EntryType> entry;
+ @XmlElement(required = true)
+ protected List<EntryType> entry;
- /**
- * Gets the value of the entry property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the entry property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEntry().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link EntryType }
- *
- *
- */
- public List<EntryType> getEntry()
- {
- if (entry == null)
- {
- entry = new ArrayList<EntryType>();
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType }
+ *
+ *
+ */
+ public List<EntryType> getEntry() {
+ if (entry == null) {
+ entry = new ArrayList<EntryType>();
+ }
+ return this.entry;
}
- return this.entry;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.14 at 02:46:00 PM BST
+// Generated on: 2023.01.31 at 04:07:09 PM GMT
//
+
package jalview.xml.binding.embl;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlType;
import javax.xml.datatype.XMLGregorianCalendar;
+
/**
- * <p>
- * Java class for EntryType complex type.
+ * <p>Java class for EntryType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="EntryType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "EntryType",
- propOrder =
- { "secondaryAccession", "projectAccession", "description", "comment",
- "keyword", "reference", "xref", "feature", "assembly", "contig",
- "sequence" })
-public class EntryType
-{
-
- protected List<String> secondaryAccession;
-
- protected List<String> projectAccession;
-
- @XmlElement(required = true)
- protected String description;
-
- protected String comment;
-
- protected List<String> keyword;
-
- protected List<EntryType.Reference> reference;
-
- protected List<XrefType> xref;
-
- protected List<EntryType.Feature> feature;
-
- protected EntryType.Assembly assembly;
-
- protected EntryType.Contig contig;
-
- protected String sequence;
-
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
-
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
-
- @XmlAttribute(name = "entryVersion")
- protected BigInteger entryVersion;
-
- @XmlAttribute(name = "dataClass", required = true)
- protected String dataClass;
-
- @XmlAttribute(name = "taxonomicDivision", required = true)
- protected String taxonomicDivision;
-
- @XmlAttribute(name = "moleculeType", required = true)
- protected String moleculeType;
-
- @XmlAttribute(name = "sequenceLength", required = true)
- protected BigInteger sequenceLength;
-
- @XmlAttribute(name = "topology", required = true)
- protected String topology;
-
- @XmlAttribute(name = "firstPublic")
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar firstPublic;
-
- @XmlAttribute(name = "firstPublicRelease")
- protected BigInteger firstPublicRelease;
-
- @XmlAttribute(name = "lastUpdated")
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar lastUpdated;
-
- @XmlAttribute(name = "lastUpdatedRelease")
- protected BigInteger lastUpdatedRelease;
-
- /**
- * Gets the value of the secondaryAccession property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the secondaryAccession property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSecondaryAccession().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getSecondaryAccession()
- {
- if (secondaryAccession == null)
- {
- secondaryAccession = new ArrayList<String>();
- }
- return this.secondaryAccession;
- }
-
- /**
- * Gets the value of the projectAccession property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the projectAccession property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getProjectAccession().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getProjectAccession()
- {
- if (projectAccession == null)
- {
- projectAccession = new ArrayList<String>();
- }
- return this.projectAccession;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the comment property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getComment()
- {
- return comment;
- }
-
- /**
- * Sets the value of the comment property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setComment(String value)
- {
- this.comment = value;
- }
-
- /**
- * Gets the value of the keyword property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the keyword property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getKeyword().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getKeyword()
- {
- if (keyword == null)
- {
- keyword = new ArrayList<String>();
- }
- return this.keyword;
- }
-
- /**
- * Gets the value of the reference property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the reference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Reference }
- *
- *
- */
- public List<EntryType.Reference> getReference()
- {
- if (reference == null)
- {
- reference = new ArrayList<EntryType.Reference>();
- }
- return this.reference;
- }
-
- /**
- * Gets the value of the xref property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the xref property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getXref().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link XrefType }
- *
- *
- */
- public List<XrefType> getXref()
- {
- if (xref == null)
- {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
- }
-
- /**
- * Gets the value of the feature property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the feature property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getFeature().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature }
- *
- *
- */
- public List<EntryType.Feature> getFeature()
- {
- if (feature == null)
- {
- feature = new ArrayList<EntryType.Feature>();
- }
- return this.feature;
- }
-
- /**
- * Gets the value of the assembly property.
- *
- * @return possible object is {@link EntryType.Assembly }
- *
- */
- public EntryType.Assembly getAssembly()
- {
- return assembly;
- }
-
- /**
- * Sets the value of the assembly property.
- *
- * @param value
- * allowed object is {@link EntryType.Assembly }
- *
- */
- public void setAssembly(EntryType.Assembly value)
- {
- this.assembly = value;
- }
-
- /**
- * Gets the value of the contig property.
- *
- * @return possible object is {@link EntryType.Contig }
- *
- */
- public EntryType.Contig getContig()
- {
- return contig;
- }
-
- /**
- * Sets the value of the contig property.
- *
- * @param value
- * allowed object is {@link EntryType.Contig }
- *
- */
- public void setContig(EntryType.Contig value)
- {
- this.contig = value;
- }
-
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequence()
- {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequence(String value)
- {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setAccession(String value)
- {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the entryVersion property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getEntryVersion()
- {
- return entryVersion;
- }
-
- /**
- * Sets the value of the entryVersion property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setEntryVersion(BigInteger value)
- {
- this.entryVersion = value;
- }
-
- /**
- * Gets the value of the dataClass property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDataClass()
- {
- return dataClass;
- }
-
- /**
- * Sets the value of the dataClass property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDataClass(String value)
- {
- this.dataClass = value;
- }
-
- /**
- * Gets the value of the taxonomicDivision property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTaxonomicDivision()
- {
- return taxonomicDivision;
- }
-
- /**
- * Sets the value of the taxonomicDivision property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTaxonomicDivision(String value)
- {
- this.taxonomicDivision = value;
- }
-
- /**
- * Gets the value of the moleculeType property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getMoleculeType()
- {
- return moleculeType;
- }
-
- /**
- * Sets the value of the moleculeType property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setMoleculeType(String value)
- {
- this.moleculeType = value;
- }
-
- /**
- * Gets the value of the sequenceLength property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getSequenceLength()
- {
- return sequenceLength;
- }
-
- /**
- * Sets the value of the sequenceLength property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setSequenceLength(BigInteger value)
- {
- this.sequenceLength = value;
- }
-
- /**
- * Gets the value of the topology property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTopology()
- {
- return topology;
- }
-
- /**
- * Sets the value of the topology property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTopology(String value)
- {
- this.topology = value;
- }
-
- /**
- * Gets the value of the firstPublic property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getFirstPublic()
- {
- return firstPublic;
- }
-
- /**
- * Sets the value of the firstPublic property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setFirstPublic(XMLGregorianCalendar value)
- {
- this.firstPublic = value;
- }
-
- /**
- * Gets the value of the firstPublicRelease property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getFirstPublicRelease()
- {
- return firstPublicRelease;
- }
-
- /**
- * Sets the value of the firstPublicRelease property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setFirstPublicRelease(BigInteger value)
- {
- this.firstPublicRelease = value;
- }
-
- /**
- * Gets the value of the lastUpdated property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getLastUpdated()
- {
- return lastUpdated;
- }
-
- /**
- * Sets the value of the lastUpdated property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setLastUpdated(XMLGregorianCalendar value)
- {
- this.lastUpdated = value;
- }
-
- /**
- * Gets the value of the lastUpdatedRelease property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getLastUpdatedRelease()
- {
- return lastUpdatedRelease;
- }
-
- /**
- * Sets the value of the lastUpdatedRelease property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setLastUpdatedRelease(BigInteger value)
- {
- this.lastUpdatedRelease = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="range" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "range" })
- public static class Assembly
- {
-
+@XmlType(name = "EntryType", propOrder = {
+ "secondaryAccession",
+ "projectAccession",
+ "description",
+ "comment",
+ "keyword",
+ "reference",
+ "xref",
+ "feature",
+ "assembly",
+ "contig",
+ "sequence"
+})
+public class EntryType {
+
+ protected List<String> secondaryAccession;
+ protected List<String> projectAccession;
@XmlElement(required = true)
- protected List<EntryType.Assembly.Range> range;
+ protected String description;
+ protected String comment;
+ protected List<String> keyword;
+ protected List<EntryType.Reference> reference;
+ protected List<XrefType> xref;
+ protected List<EntryType.Feature> feature;
+ protected EntryType.Assembly assembly;
+ protected EntryType.Contig contig;
+ protected String sequence;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "entryVersion")
+ protected BigInteger entryVersion;
+ @XmlAttribute(name = "dataClass", required = true)
+ protected String dataClass;
+ @XmlAttribute(name = "taxonomicDivision", required = true)
+ protected String taxonomicDivision;
+ @XmlAttribute(name = "moleculeType", required = true)
+ protected String moleculeType;
+ @XmlAttribute(name = "sequenceLength", required = true)
+ protected BigInteger sequenceLength;
+ @XmlAttribute(name = "topology", required = true)
+ protected String topology;
+ @XmlAttribute(name = "firstPublic")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar firstPublic;
+ @XmlAttribute(name = "firstPublicRelease")
+ protected BigInteger firstPublicRelease;
+ @XmlAttribute(name = "lastUpdated")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar lastUpdated;
+ @XmlAttribute(name = "lastUpdatedRelease")
+ protected BigInteger lastUpdatedRelease;
/**
- * Gets the value of the range property.
+ * Gets the value of the secondaryAccession property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the range property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getRange().add(newItem);
+ * getSecondaryAccession().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Assembly.Range }
+ * {@link String }
*
*
*/
- public List<EntryType.Assembly.Range> getRange()
- {
- if (range == null)
- {
- range = new ArrayList<EntryType.Assembly.Range>();
- }
- return this.range;
+ public List<String> getSecondaryAccession() {
+ if (secondaryAccession == null) {
+ secondaryAccession = new ArrayList<String>();
+ }
+ return this.secondaryAccession;
}
/**
- * <p>
- * Java class for anonymous complex type.
+ * Gets the value of the projectAccession property.
*
* <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
*
+ * <p>
+ * For example, to add a new item, do as follows:
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getProjectAccession().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Range
- {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
-
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
-
- @XmlAttribute(name = "primaryBegin")
- protected BigInteger primaryBegin;
-
- @XmlAttribute(name = "primaryEnd")
- protected BigInteger primaryEnd;
-
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
-
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
-
- @XmlAttribute(name = "complement")
- protected Boolean complement;
-
- /**
- * Gets the value of the begin property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getBegin()
- {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value)
- {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the primaryBegin property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPrimaryBegin()
- {
- return primaryBegin;
- }
-
- /**
- * Sets the value of the primaryBegin property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPrimaryBegin(BigInteger value)
- {
- this.primaryBegin = value;
- }
-
- /**
- * Gets the value of the primaryEnd property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPrimaryEnd()
- {
- return primaryEnd;
- }
-
- /**
- * Sets the value of the primaryEnd property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPrimaryEnd(BigInteger value)
- {
- this.primaryEnd = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setAccession(String value)
- {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the complement property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isComplement()
- {
- if (complement == null)
- {
- return false;
- }
- else
- {
- return complement;
+ public List<String> getProjectAccession() {
+ if (projectAccession == null) {
+ projectAccession = new ArrayList<String>();
}
- }
-
- /**
- * Sets the value of the complement property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setComplement(Boolean value)
- {
- this.complement = value;
- }
+ return this.projectAccession;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComment() {
+ return comment;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <choice maxOccurs="unbounded" minOccurs="0">
- * <element name="range">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="gap">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </choice>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "rangeOrGap" })
- public static class Contig
- {
-
- @XmlElements({
- @XmlElement(name = "range", type = EntryType.Contig.Range.class),
- @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) })
- protected List<Object> rangeOrGap;
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComment(String value) {
+ this.comment = value;
+ }
/**
- * Gets the value of the rangeOrGap property.
+ * Gets the value of the keyword property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the rangeOrGap property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the keyword property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getRangeOrGap().add(newItem);
+ * getKeyword().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
+ * {@link String }
*
*
*/
- public List<Object> getRangeOrGap()
- {
- if (rangeOrGap == null)
- {
- rangeOrGap = new ArrayList<Object>();
- }
- return this.rangeOrGap;
+ public List<String> getKeyword() {
+ if (keyword == null) {
+ keyword = new ArrayList<String>();
+ }
+ return this.keyword;
}
/**
- * <p>
- * Java class for anonymous complex type.
+ * Gets the value of the reference property.
*
* <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the reference property.
*
+ * <p>
+ * For example, to add a new item, do as follows:
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getReference().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Reference }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Gap
- {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
-
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
-
- @XmlAttribute(name = "length", required = true)
- protected BigInteger length;
-
- @XmlAttribute(name = "unknownLength")
- protected Boolean unknownLength;
-
- /**
- * Gets the value of the begin property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getBegin()
- {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value)
- {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the length property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getLength()
- {
- return length;
- }
-
- /**
- * Sets the value of the length property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setLength(BigInteger value)
- {
- this.length = value;
- }
-
- /**
- * Gets the value of the unknownLength property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isUnknownLength()
- {
- if (unknownLength == null)
- {
- return false;
+ public List<EntryType.Reference> getReference() {
+ if (reference == null) {
+ reference = new ArrayList<EntryType.Reference>();
}
- else
- {
- return unknownLength;
- }
- }
-
- /**
- * Sets the value of the unknownLength property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setUnknownLength(Boolean value)
- {
- this.unknownLength = value;
- }
-
+ return this.reference;
}
/**
- * <p>
- * Java class for anonymous complex type.
+ * Gets the value of the xref property.
*
* <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
*
+ * <p>
+ * For example, to add a new item, do as follows:
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getXref().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Range
- {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
-
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
-
- @XmlAttribute(name = "primaryBegin")
- protected BigInteger primaryBegin;
-
- @XmlAttribute(name = "primaryEnd")
- protected BigInteger primaryEnd;
-
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
-
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
-
- @XmlAttribute(name = "complement")
- protected Boolean complement;
-
- /**
- * Gets the value of the begin property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getBegin()
- {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value)
- {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the primaryBegin property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPrimaryBegin()
- {
- return primaryBegin;
- }
-
- /**
- * Sets the value of the primaryBegin property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPrimaryBegin(BigInteger value)
- {
- this.primaryBegin = value;
- }
-
- /**
- * Gets the value of the primaryEnd property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPrimaryEnd()
- {
- return primaryEnd;
- }
-
- /**
- * Sets the value of the primaryEnd property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPrimaryEnd(BigInteger value)
- {
- this.primaryEnd = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setAccession(String value)
- {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the complement property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isComplement()
- {
- if (complement == null)
- {
- return false;
- }
- else
- {
- return complement;
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
}
- }
-
- /**
- * Sets the value of the complement property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setComplement(Boolean value)
- {
- this.complement = value;
- }
-
+ return this.xref;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="lineage" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" })
- public static class Feature
- {
-
- protected EntryType.Feature.FeatureTaxon taxon;
-
- protected List<XrefType> xref;
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature }
+ *
+ *
+ */
+ public List<EntryType.Feature> getFeature() {
+ if (feature == null) {
+ feature = new ArrayList<EntryType.Feature>();
+ }
+ return this.feature;
+ }
- protected List<EntryType.Feature.Qualifier> qualifier;
+ /**
+ * Gets the value of the assembly property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly getAssembly() {
+ return assembly;
+ }
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ /**
+ * Sets the value of the assembly property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Assembly }
+ *
+ */
+ public void setAssembly(EntryType.Assembly value) {
+ this.assembly = value;
+ }
- @XmlAttribute(name = "location", required = true)
- protected String location;
+ /**
+ * Gets the value of the contig property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig getContig() {
+ return contig;
+ }
/**
- * Gets the value of the taxon property.
+ * Sets the value of the contig property.
*
- * @return possible object is {@link EntryType.Feature.FeatureTaxon }
+ * @param value
+ * allowed object is
+ * {@link EntryType.Contig }
+ *
+ */
+ public void setContig(EntryType.Contig value) {
+ this.contig = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public EntryType.Feature.FeatureTaxon getTaxon()
- {
- return taxon;
+ public String getSequence() {
+ return sequence;
}
/**
- * Sets the value of the taxon property.
+ * Sets the value of the sequence property.
*
* @param value
- * allowed object is {@link EntryType.Feature.FeatureTaxon }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setTaxon(EntryType.Feature.FeatureTaxon value)
- {
- this.taxon = value;
+ public String getAccession() {
+ return accession;
}
/**
- * Gets the value of the xref property.
+ * Sets the value of the accession property.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the xref property.
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
*
- * <p>
- * For example, to add a new item, do as follows:
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
*
- * <pre>
- * getXref().add(newItem);
- * </pre>
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the entryVersion property.
*
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEntryVersion() {
+ return entryVersion;
+ }
+
+ /**
+ * Sets the value of the entryVersion property.
*
- * <p>
- * Objects of the following type(s) are allowed in the list {@link XrefType
- * }
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEntryVersion(BigInteger value) {
+ this.entryVersion = value;
+ }
+
+ /**
+ * Gets the value of the dataClass property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDataClass() {
+ return dataClass;
+ }
+
+ /**
+ * Sets the value of the dataClass property.
*
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
*/
- public List<XrefType> getXref()
- {
- if (xref == null)
- {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
+ public void setDataClass(String value) {
+ this.dataClass = value;
}
/**
- * Gets the value of the qualifier property.
+ * Gets the value of the taxonomicDivision property.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the qualifier property.
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTaxonomicDivision() {
+ return taxonomicDivision;
+ }
+
+ /**
+ * Sets the value of the taxonomicDivision property.
*
- * <p>
- * For example, to add a new item, do as follows:
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTaxonomicDivision(String value) {
+ this.taxonomicDivision = value;
+ }
+
+ /**
+ * Gets the value of the moleculeType property.
*
- * <pre>
- * getQualifier().add(newItem);
- * </pre>
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMoleculeType() {
+ return moleculeType;
+ }
+
+ /**
+ * Sets the value of the moleculeType property.
*
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMoleculeType(String value) {
+ this.moleculeType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceLength property.
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature.Qualifier }
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getSequenceLength() {
+ return sequenceLength;
+ }
+
+ /**
+ * Sets the value of the sequenceLength property.
*
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setSequenceLength(BigInteger value) {
+ this.sequenceLength = value;
+ }
+
+ /**
+ * Gets the value of the topology property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public List<EntryType.Feature.Qualifier> getQualifier()
- {
- if (qualifier == null)
- {
- qualifier = new ArrayList<EntryType.Feature.Qualifier>();
- }
- return this.qualifier;
+ public String getTopology() {
+ return topology;
}
/**
- * Gets the value of the name property.
+ * Sets the value of the topology property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTopology(String value) {
+ this.topology = value;
+ }
+
+ /**
+ * Gets the value of the firstPublic property.
*
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
*/
- public String getName()
- {
- return name;
+ public XMLGregorianCalendar getFirstPublic() {
+ return firstPublic;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the firstPublic property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setFirstPublic(XMLGregorianCalendar value) {
+ this.firstPublic = value;
+ }
+
+ /**
+ * Gets the value of the firstPublicRelease property.
*
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
*/
- public void setName(String value)
- {
- this.name = value;
+ public BigInteger getFirstPublicRelease() {
+ return firstPublicRelease;
}
/**
- * Gets the value of the location property.
+ * Sets the value of the firstPublicRelease property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setFirstPublicRelease(BigInteger value) {
+ this.firstPublicRelease = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdated property.
*
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
*/
- public String getLocation()
- {
- return location;
+ public XMLGregorianCalendar getLastUpdated() {
+ return lastUpdated;
}
/**
- * Sets the value of the location property.
+ * Sets the value of the lastUpdated property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
*/
- public void setLocation(String value)
- {
- this.location = value;
+ public void setLastUpdated(XMLGregorianCalendar value) {
+ this.lastUpdated = value;
}
/**
- * <p>
- * Java class for anonymous complex type.
+ * Gets the value of the lastUpdatedRelease property.
*
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getLastUpdatedRelease() {
+ return lastUpdatedRelease;
+ }
+
+ /**
+ * Sets the value of the lastUpdatedRelease property.
*
- * <pre>
- * <complexType>
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setLastUpdatedRelease(BigInteger value) {
+ this.lastUpdatedRelease = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="lineage" minOccurs="0">
+ * <element name="range" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "lineage" })
- public static class FeatureTaxon
- {
-
- protected EntryType.Feature.FeatureTaxon.Lineage lineage;
-
- @XmlAttribute(name = "scientificName", required = true)
- protected String scientificName;
-
- @XmlAttribute(name = "commonName")
- protected String commonName;
-
- @XmlAttribute(name = "taxId")
- protected BigInteger taxId;
-
- /**
- * Gets the value of the lineage property.
- *
- * @return possible object is
- * {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage getLineage()
- {
- return lineage;
- }
-
- /**
- * Sets the value of the lineage property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
- {
- this.lineage = value;
- }
-
- /**
- * Gets the value of the scientificName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getScientificName()
- {
- return scientificName;
- }
-
- /**
- * Sets the value of the scientificName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setScientificName(String value)
- {
- this.scientificName = value;
- }
-
- /**
- * Gets the value of the commonName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCommonName()
- {
- return commonName;
- }
-
- /**
- * Sets the value of the commonName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCommonName(String value)
- {
- this.commonName = value;
- }
-
- /**
- * Gets the value of the taxId property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getTaxId()
- {
- return taxId;
- }
-
- /**
- * Sets the value of the taxId property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setTaxId(BigInteger value)
- {
- this.taxId = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "taxon" })
- public static class Lineage
- {
+ @XmlType(name = "", propOrder = {
+ "range"
+ })
+ public static class Assembly {
@XmlElement(required = true)
- protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
+ protected List<EntryType.Assembly.Range> range;
/**
- * Gets the value of the taxon property.
+ * Gets the value of the range property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list
- * will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the taxon property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the range property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getTaxon().add(newItem);
+ * getRange().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ * {@link EntryType.Assembly.Range }
+ *
+ *
+ */
+ public List<EntryType.Assembly.Range> getRange() {
+ if (range == null) {
+ range = new ArrayList<EntryType.Assembly.Range>();
+ }
+ return this.range;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
- public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon()
- {
- if (taxon == null)
- {
- taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
- }
- return this.taxon;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin() {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value) {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd() {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value) {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isComplement() {
+ if (complement == null) {
+ return false;
+ } else {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value) {
+ this.complement = value;
+ }
+
}
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "rangeOrGap"
+ })
+ public static class Contig {
+
+ @XmlElements({
+ @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+ @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
+ })
+ protected List<Object> rangeOrGap;
+
/**
+ * Gets the value of the rangeOrGap property.
+ *
* <p>
- * Java class for anonymous complex type.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
*
* <p>
- * The following schema fragment specifies the expected content
- * contained within this class.
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRangeOrGap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Contig.Range }
+ * {@link EntryType.Contig.Gap }
+ *
+ *
+ */
+ public List<Object> getRangeOrGap() {
+ if (rangeOrGap == null) {
+ rangeOrGap = new ArrayList<Object>();
+ }
+ return this.rangeOrGap;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
* </restriction>
* </complexContent>
* </complexType>
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "")
- public static class Taxon
- {
-
- @XmlAttribute(name = "scientificName", required = true)
- protected String scientificName;
-
- /**
- * Gets the value of the scientificName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getScientificName()
- {
- return scientificName;
- }
-
- /**
- * Sets the value of the scientificName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setScientificName(String value)
- {
- this.scientificName = value;
- }
+ public static class Gap {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "length", required = true)
+ protected BigInteger length;
+ @XmlAttribute(name = "unknownLength")
+ protected Boolean unknownLength;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getLength() {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setLength(BigInteger value) {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the unknownLength property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isUnknownLength() {
+ if (unknownLength == null) {
+ return false;
+ } else {
+ return unknownLength;
+ }
+ }
+
+ /**
+ * Sets the value of the unknownLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setUnknownLength(Boolean value) {
+ this.unknownLength = value;
+ }
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin() {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value) {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd() {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value) {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccession() {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccession(String value) {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isComplement() {
+ if (complement == null) {
+ return false;
+ } else {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value) {
+ this.complement = value;
+ }
+
+ }
}
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
* </sequence>
* <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class Qualifier
- {
-
- protected String value;
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- }
+ @XmlType(name = "", propOrder = {
+ "taxon",
+ "xref",
+ "qualifier"
+ })
+ public static class Feature {
+
+ protected EntryType.Feature.FeatureTaxon taxon;
+ protected List<XrefType> xref;
+ protected List<EntryType.Feature.Qualifier> qualifier;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "location", required = true)
+ protected String location;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
- * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="submission"/>
- * <enumeration value="book"/>
- * <enumeration value="article"/>
- * <enumeration value="patent"/>
- * <enumeration value="thesis"/>
- * <enumeration value="unpublished"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "title", "author", "applicant", "consortium", "submissionDate",
- "journal", "year", "volume", "issue", "firstPage", "lastPage",
- "comment", "referenceLocation", "xref" })
- public static class Reference
- {
-
- protected String title;
-
- protected List<String> author;
-
- protected List<String> applicant;
-
- protected String consortium;
+ /**
+ * Gets the value of the taxon property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon getTaxon() {
+ return taxon;
+ }
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar submissionDate;
+ /**
+ * Sets the value of the taxon property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public void setTaxon(EntryType.Feature.FeatureTaxon value) {
+ this.taxon = value;
+ }
- protected String journal;
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
- protected String year;
+ /**
+ * Gets the value of the qualifier property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the qualifier property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getQualifier().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.Qualifier }
+ *
+ *
+ */
+ public List<EntryType.Feature.Qualifier> getQualifier() {
+ if (qualifier == null) {
+ qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+ }
+ return this.qualifier;
+ }
- protected String volume;
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
- protected String issue;
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
- protected String firstPage;
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocation() {
+ return location;
+ }
- protected String lastPage;
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocation(String value) {
+ this.location = value;
+ }
- protected String comment;
- protected String referenceLocation;
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "lineage"
+ })
+ public static class FeatureTaxon {
+
+ protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+ @XmlAttribute(name = "commonName")
+ protected String commonName;
+ @XmlAttribute(name = "taxId")
+ protected BigInteger taxId;
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScientificName() {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScientificName(String value) {
+ this.scientificName = value;
+ }
+
+ /**
+ * Gets the value of the commonName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * Sets the value of the commonName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCommonName(String value) {
+ this.commonName = value;
+ }
+
+ /**
+ * Gets the value of the taxId property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getTaxId() {
+ return taxId;
+ }
+
+ /**
+ * Sets the value of the taxId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setTaxId(BigInteger value) {
+ this.taxId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon"
+ })
+ public static class Lineage {
+
+ @XmlElement(required = true)
+ protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the taxon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTaxon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ *
+ */
+ public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
+ if (taxon == null) {
+ taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+ }
+ return this.taxon;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Taxon {
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScientificName() {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScientificName(String value) {
+ this.scientificName = value;
+ }
+
+ }
+
+ }
- protected List<XrefType> xref;
+ }
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "number", required = true)
- protected BigInteger number;
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Qualifier {
+
+ protected String value;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
- @XmlAttribute(name = "location")
- protected String location;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
}
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
/**
- * Gets the value of the author property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the author property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getAuthor().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
*/
- public List<String> getAuthor()
- {
- if (author == null)
- {
- author = new ArrayList<String>();
- }
- return this.author;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "author",
+ "applicant",
+ "consortium",
+ "submissionDate",
+ "journal",
+ "year",
+ "volume",
+ "issue",
+ "firstPage",
+ "lastPage",
+ "comment",
+ "referenceLocation",
+ "xref"
+ })
+ public static class Reference {
+
+ protected String title;
+ protected List<String> author;
+ protected List<String> applicant;
+ protected String consortium;
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar submissionDate;
+ protected String journal;
+ protected String year;
+ protected String volume;
+ protected String issue;
+ protected String firstPage;
+ protected String lastPage;
+ protected String comment;
+ protected String referenceLocation;
+ protected List<XrefType> xref;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "number", required = true)
+ protected BigInteger number;
+ @XmlAttribute(name = "location")
+ protected String location;
- /**
- * Gets the value of the applicant property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the applicant property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getApplicant().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getApplicant()
- {
- if (applicant == null)
- {
- applicant = new ArrayList<String>();
- }
- return this.applicant;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- /**
- * Gets the value of the consortium property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getConsortium()
- {
- return consortium;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- /**
- * Sets the value of the consortium property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setConsortium(String value)
- {
- this.consortium = value;
- }
+ /**
+ * Gets the value of the author property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the author property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAuthor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAuthor() {
+ if (author == null) {
+ author = new ArrayList<String>();
+ }
+ return this.author;
+ }
- /**
- * Gets the value of the submissionDate property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getSubmissionDate()
- {
- return submissionDate;
- }
+ /**
+ * Gets the value of the applicant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the applicant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getApplicant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getApplicant() {
+ if (applicant == null) {
+ applicant = new ArrayList<String>();
+ }
+ return this.applicant;
+ }
- /**
- * Sets the value of the submissionDate property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setSubmissionDate(XMLGregorianCalendar value)
- {
- this.submissionDate = value;
- }
+ /**
+ * Gets the value of the consortium property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getConsortium() {
+ return consortium;
+ }
- /**
- * Gets the value of the journal property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getJournal()
- {
- return journal;
- }
+ /**
+ * Sets the value of the consortium property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setConsortium(String value) {
+ this.consortium = value;
+ }
- /**
- * Sets the value of the journal property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setJournal(String value)
- {
- this.journal = value;
- }
+ /**
+ * Gets the value of the submissionDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getSubmissionDate() {
+ return submissionDate;
+ }
- /**
- * Gets the value of the year property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getYear()
- {
- return year;
- }
+ /**
+ * Sets the value of the submissionDate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setSubmissionDate(XMLGregorianCalendar value) {
+ this.submissionDate = value;
+ }
- /**
- * Sets the value of the year property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setYear(String value)
- {
- this.year = value;
- }
+ /**
+ * Gets the value of the journal property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getJournal() {
+ return journal;
+ }
- /**
- * Gets the value of the volume property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVolume()
- {
- return volume;
- }
+ /**
+ * Sets the value of the journal property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setJournal(String value) {
+ this.journal = value;
+ }
- /**
- * Sets the value of the volume property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVolume(String value)
- {
- this.volume = value;
- }
+ /**
+ * Gets the value of the year property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getYear() {
+ return year;
+ }
- /**
- * Gets the value of the issue property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getIssue()
- {
- return issue;
- }
+ /**
+ * Sets the value of the year property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setYear(String value) {
+ this.year = value;
+ }
- /**
- * Sets the value of the issue property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setIssue(String value)
- {
- this.issue = value;
- }
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVolume() {
+ return volume;
+ }
- /**
- * Gets the value of the firstPage property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFirstPage()
- {
- return firstPage;
- }
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVolume(String value) {
+ this.volume = value;
+ }
- /**
- * Sets the value of the firstPage property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFirstPage(String value)
- {
- this.firstPage = value;
- }
+ /**
+ * Gets the value of the issue property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getIssue() {
+ return issue;
+ }
- /**
- * Gets the value of the lastPage property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLastPage()
- {
- return lastPage;
- }
+ /**
+ * Sets the value of the issue property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setIssue(String value) {
+ this.issue = value;
+ }
- /**
- * Sets the value of the lastPage property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLastPage(String value)
- {
- this.lastPage = value;
- }
+ /**
+ * Gets the value of the firstPage property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFirstPage() {
+ return firstPage;
+ }
- /**
- * Gets the value of the comment property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getComment()
- {
- return comment;
- }
+ /**
+ * Sets the value of the firstPage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFirstPage(String value) {
+ this.firstPage = value;
+ }
- /**
- * Sets the value of the comment property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setComment(String value)
- {
- this.comment = value;
- }
+ /**
+ * Gets the value of the lastPage property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLastPage() {
+ return lastPage;
+ }
- /**
- * Gets the value of the referenceLocation property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getReferenceLocation()
- {
- return referenceLocation;
- }
+ /**
+ * Sets the value of the lastPage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLastPage(String value) {
+ this.lastPage = value;
+ }
- /**
- * Sets the value of the referenceLocation property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setReferenceLocation(String value)
- {
- this.referenceLocation = value;
- }
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComment() {
+ return comment;
+ }
- /**
- * Gets the value of the xref property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the xref property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getXref().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link XrefType
- * }
- *
- *
- */
- public List<XrefType> getXref()
- {
- if (xref == null)
- {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
- }
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComment(String value) {
+ this.comment = value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the referenceLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getReferenceLocation() {
+ return referenceLocation;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the referenceLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setReferenceLocation(String value) {
+ this.referenceLocation = value;
+ }
- /**
- * Gets the value of the number property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getNumber()
- {
- return number;
- }
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref() {
+ if (xref == null) {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
- /**
- * Sets the value of the number property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setNumber(BigInteger value)
- {
- this.number = value;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Gets the value of the location property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLocation()
- {
- return location;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLocation(String value)
- {
- this.location = value;
- }
+ /**
+ * Gets the value of the number property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getNumber() {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setNumber(BigInteger value) {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocation() {
+ return location;
+ }
+
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocation(String value) {
+ this.location = value;
+ }
- }
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.14 at 02:46:00 PM BST
+// Generated on: 2023.01.31 at 04:07:09 PM GMT
//
+
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlRegistry;
+
/**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.embl package.
- * <p>
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.embl package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory
-{
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of
- * schema derived classes for package: jalview.xml.binding.embl
- *
- */
- public ObjectFactory()
- {
- }
-
- /**
- * Create an instance of {@link EntryType }
- *
- */
- public EntryType createEntryType()
- {
- return new EntryType();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig }
- *
- */
- public EntryType.Contig createEntryTypeContig()
- {
- return new EntryType.Contig();
- }
-
- /**
- * Create an instance of {@link EntryType.Assembly }
- *
- */
- public EntryType.Assembly createEntryTypeAssembly()
- {
- return new EntryType.Assembly();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature }
- *
- */
- public EntryType.Feature createEntryTypeFeature()
- {
- return new EntryType.Feature();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon()
- {
- return new EntryType.Feature.FeatureTaxon();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage()
- {
- return new EntryType.Feature.FeatureTaxon.Lineage();
- }
-
- /**
- * Create an instance of {@link ROOT }
- *
- */
- public ROOT createROOT()
- {
- return new ROOT();
- }
-
- /**
- * Create an instance of {@link EntrySetType }
- *
- */
- public EntrySetType createEntrySetType()
- {
- return new EntrySetType();
- }
-
- /**
- * Create an instance of {@link XrefType }
- *
- */
- public XrefType createXrefType()
- {
- return new XrefType();
- }
-
- /**
- * Create an instance of {@link EntryType.Reference }
- *
- */
- public EntryType.Reference createEntryTypeReference()
- {
- return new EntryType.Reference();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig.Range }
- *
- */
- public EntryType.Contig.Range createEntryTypeContigRange()
- {
- return new EntryType.Contig.Range();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig.Gap }
- *
- */
- public EntryType.Contig.Gap createEntryTypeContigGap()
- {
- return new EntryType.Contig.Gap();
- }
-
- /**
- * Create an instance of {@link EntryType.Assembly.Range }
- *
- */
- public EntryType.Assembly.Range createEntryTypeAssemblyRange()
- {
- return new EntryType.Assembly.Range();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.Qualifier }
- *
- */
- public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier()
- {
- return new EntryType.Feature.Qualifier();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon()
- {
- return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
- }
+public class ObjectFactory {
+
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link EntryType }
+ *
+ */
+ public EntryType createEntryType() {
+ return new EntryType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig createEntryTypeContig() {
+ return new EntryType.Contig();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly createEntryTypeAssembly() {
+ return new EntryType.Assembly();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature }
+ *
+ */
+ public EntryType.Feature createEntryTypeFeature() {
+ return new EntryType.Feature();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
+ return new EntryType.Feature.FeatureTaxon();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
+ return new EntryType.Feature.FeatureTaxon.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ROOT }
+ *
+ */
+ public ROOT createROOT() {
+ return new ROOT();
+ }
+
+ /**
+ * Create an instance of {@link EntrySetType }
+ *
+ */
+ public EntrySetType createEntrySetType() {
+ return new EntrySetType();
+ }
+
+ /**
+ * Create an instance of {@link XrefType }
+ *
+ */
+ public XrefType createXrefType() {
+ return new XrefType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Reference }
+ *
+ */
+ public EntryType.Reference createEntryTypeReference() {
+ return new EntryType.Reference();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Range }
+ *
+ */
+ public EntryType.Contig.Range createEntryTypeContigRange() {
+ return new EntryType.Contig.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Gap }
+ *
+ */
+ public EntryType.Contig.Gap createEntryTypeContigGap() {
+ return new EntryType.Contig.Gap();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly.Range }
+ *
+ */
+ public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
+ return new EntryType.Assembly.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.Qualifier }
+ *
+ */
+ public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
+ return new EntryType.Feature.Qualifier();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
+ return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.14 at 02:46:00 PM BST
+// Generated on: 2023.01.31 at 04:07:09 PM GMT
//
+
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "entrySet", "entry" })
+@XmlType(name = "", propOrder = {
+ "entrySet",
+ "entry"
+})
@XmlRootElement(name = "ROOT")
-public class ROOT
-{
-
- protected EntrySetType entrySet;
+public class ROOT {
- protected EntryType entry;
+ protected EntrySetType entrySet;
+ protected EntryType entry;
- /**
- * Gets the value of the entrySet property.
- *
- * @return possible object is {@link EntrySetType }
- *
- */
- public EntrySetType getEntrySet()
- {
- return entrySet;
- }
+ /**
+ * Gets the value of the entrySet property.
+ *
+ * @return
+ * possible object is
+ * {@link EntrySetType }
+ *
+ */
+ public EntrySetType getEntrySet() {
+ return entrySet;
+ }
- /**
- * Sets the value of the entrySet property.
- *
- * @param value
- * allowed object is {@link EntrySetType }
- *
- */
- public void setEntrySet(EntrySetType value)
- {
- this.entrySet = value;
- }
+ /**
+ * Sets the value of the entrySet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntrySetType }
+ *
+ */
+ public void setEntrySet(EntrySetType value) {
+ this.entrySet = value;
+ }
- /**
- * Gets the value of the entry property.
- *
- * @return possible object is {@link EntryType }
- *
- */
- public EntryType getEntry()
- {
- return entry;
- }
+ /**
+ * Gets the value of the entry property.
+ *
+ * @return
+ * possible object is
+ * {@link EntryType }
+ *
+ */
+ public EntryType getEntry() {
+ return entry;
+ }
- /**
- * Sets the value of the entry property.
- *
- * @param value
- * allowed object is {@link EntryType }
- *
- */
- public void setEntry(EntryType value)
- {
- this.entry = value;
- }
+ /**
+ * Sets the value of the entry property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType }
+ *
+ */
+ public void setEntry(EntryType value) {
+ this.entry = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.14 at 02:46:00 PM BST
+// Generated on: 2023.01.31 at 04:07:09 PM GMT
//
+
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
* Database cross-reference.
*
- * <p>
- * Java class for XrefType complex type.
+ * <p>Java class for XrefType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="XrefType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "XrefType")
-public class XrefType
-{
-
- @XmlAttribute(name = "db", required = true)
- protected String db;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
+public class XrefType {
- @XmlAttribute(name = "secondaryId")
- protected String secondaryId;
+ @XmlAttribute(name = "db", required = true)
+ protected String db;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "secondaryId")
+ protected String secondaryId;
- /**
- * Gets the value of the db property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDb()
- {
- return db;
- }
+ /**
+ * Gets the value of the db property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDb() {
+ return db;
+ }
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDb(String value)
- {
- this.db = value;
- }
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDb(String value) {
+ this.db = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the secondaryId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSecondaryId()
- {
- return secondaryId;
- }
+ /**
+ * Gets the value of the secondaryId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSecondaryId() {
+ return secondaryId;
+ }
- /**
- * Sets the value of the secondaryId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSecondaryId(String value)
- {
- this.secondaryId = value;
- }
+ /**
+ * Sets the value of the secondaryId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSecondaryId(String value) {
+ this.secondaryId = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="alcodon" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2"
- * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute
- * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ * </sequence>
+ * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+ "alcodon",
+ "alcodMap"
+})
@XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame
-{
-
- protected List<AlcodonFrame.Alcodon> alcodon;
-
- protected List<AlcodonFrame.AlcodMap> alcodMap;
+public class AlcodonFrame {
- /**
- * Gets the value of the alcodon property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the alcodon property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAlcodon().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.Alcodon }
- *
- *
- */
- public List<AlcodonFrame.Alcodon> getAlcodon()
- {
- if (alcodon == null)
- {
- alcodon = new ArrayList<AlcodonFrame.Alcodon>();
- }
- return this.alcodon;
- }
-
- /**
- * Gets the value of the alcodMap property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the alcodMap property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAlcodMap().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.AlcodMap }
- *
- *
- */
- public List<AlcodonFrame.AlcodMap> getAlcodMap()
- {
- if (alcodMap == null)
- {
- alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
- }
- return this.alcodMap;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "mapping" })
- public static class AlcodMap
- {
-
- @XmlElement(name = "Mapping", required = true)
- protected Mapping mapping;
-
- @XmlAttribute(name = "dnasq", required = true)
- protected String dnasq;
+ protected List<AlcodonFrame.Alcodon> alcodon;
+ protected List<AlcodonFrame.AlcodMap> alcodMap;
/**
+ * Gets the value of the alcodon property.
*
- * a Mapping entry and an associated protein sequence
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodon property.
*
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodon().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Mapping }
*
- */
- public Mapping getMapping()
- {
- return mapping;
- }
-
- /**
- * Sets the value of the mapping property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.Alcodon }
*
- * @param value
- * allowed object is {@link Mapping }
*
*/
- public void setMapping(Mapping value)
- {
- this.mapping = value;
+ public List<AlcodonFrame.Alcodon> getAlcodon() {
+ if (alcodon == null) {
+ alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+ }
+ return this.alcodon;
}
/**
- * Gets the value of the dnasq property.
+ * Gets the value of the alcodMap property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodMap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.AlcodMap }
*
- * @return possible object is {@link String }
*
*/
- public String getDnasq()
- {
- return dnasq;
+ public List<AlcodonFrame.AlcodMap> getAlcodMap() {
+ if (alcodMap == null) {
+ alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+ }
+ return this.alcodMap;
}
+
/**
- * Sets the value of the dnasq property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ * </sequence>
+ * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setDnasq(String value)
- {
- this.dnasq = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "mapping"
+ })
+ public static class AlcodMap {
- }
+ @XmlElement(name = "Mapping", required = true)
+ protected Mapping mapping;
+ @XmlAttribute(name = "dnasq", required = true)
+ protected String dnasq;
- /**
- *
- * specifies a series of aligned codons from an associated DNA sequence
- * alignment that when translated correspond to columns of a peptide
- * alignment. Element may have either all pos1,2,3 attributes specified, or
- * none at all (indicating a gapped column with no translated peptide).
- *
- *
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2"
- * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos3"
- * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Alcodon
- {
+ /**
+ *
+ * a Mapping entry and an associated protein sequence
+ *
+ *
+ * @return
+ * possible object is
+ * {@link Mapping }
+ *
+ */
+ public Mapping getMapping() {
+ return mapping;
+ }
- @XmlAttribute(name = "pos1")
- protected BigInteger pos1;
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value) {
+ this.mapping = value;
+ }
- @XmlAttribute(name = "pos2")
- protected BigInteger pos2;
+ /**
+ * Gets the value of the dnasq property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDnasq() {
+ return dnasq;
+ }
- @XmlAttribute(name = "pos3")
- protected BigInteger pos3;
+ /**
+ * Sets the value of the dnasq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDnasq(String value) {
+ this.dnasq = value;
+ }
- /**
- * Gets the value of the pos1 property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPos1()
- {
- return pos1;
}
- /**
- * Sets the value of the pos1 property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPos1(BigInteger value)
- {
- this.pos1 = value;
- }
/**
- * Gets the value of the pos2 property.
*
- * @return possible object is {@link BigInteger }
+ * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+ * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+ *
*
- */
- public BigInteger getPos2()
- {
- return pos2;
- }
-
- /**
- * Sets the value of the pos2 property.
+ * <p>Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link BigInteger }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public void setPos2(BigInteger value)
- {
- this.pos2 = value;
- }
-
- /**
- * Gets the value of the pos3 property.
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @return possible object is {@link BigInteger }
*
*/
- public BigInteger getPos3()
- {
- return pos3;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Alcodon {
- /**
- * Sets the value of the pos3 property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPos3(BigInteger value)
- {
- this.pos3 = value;
- }
+ @XmlAttribute(name = "pos1")
+ protected BigInteger pos1;
+ @XmlAttribute(name = "pos2")
+ protected BigInteger pos2;
+ @XmlAttribute(name = "pos3")
+ protected BigInteger pos3;
+
+ /**
+ * Gets the value of the pos1 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos1() {
+ return pos1;
+ }
- }
+ /**
+ * Sets the value of the pos1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos1(BigInteger value) {
+ this.pos1 = value;
+ }
+
+ /**
+ * Gets the value of the pos2 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos2() {
+ return pos2;
+ }
+
+ /**
+ * Sets the value of the pos2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos2(BigInteger value) {
+ this.pos2 = value;
+ }
+
+ /**
+ * Gets the value of the pos3 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos3() {
+ return pos3;
+ }
+
+ /**
+ * Sets the value of the pos3 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos3(BigInteger value) {
+ this.pos3 = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement"
- * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="label"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string"
- * minOccurs="0"/&gt; &lt;element name="thresholdLine"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="property" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="graph" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="graphColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="graphHeight"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreOnly"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="score"
- * type="{http://www.w3.org/2001/XMLSchema}double" /&gt; &lt;attribute
- * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showAllColLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="belowAlignment"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="calcId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="thresholdLine" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="property" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "annotationElement", "label", "description", "thresholdLine",
- "property" })
+@XmlType(name = "", propOrder = {
+ "annotationElement",
+ "label",
+ "description",
+ "thresholdLine",
+ "property"
+})
@XmlRootElement(name = "Annotation")
-public class Annotation
-{
+public class Annotation {
- protected List<AnnotationElement> annotationElement;
+ protected List<AnnotationElement> annotationElement;
+ @XmlElement(required = true)
+ protected String label;
+ protected String description;
+ protected Annotation.ThresholdLine thresholdLine;
+ protected List<Annotation.Property> property;
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+ @XmlAttribute(name = "score")
+ protected Double score;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
- @XmlElement(required = true)
- protected String label;
-
- protected String description;
-
- protected Annotation.ThresholdLine thresholdLine;
-
- protected List<Annotation.Property> property;
-
- @XmlAttribute(name = "graph", required = true)
- protected boolean graph;
-
- @XmlAttribute(name = "graphType")
- protected Integer graphType;
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
-
- @XmlAttribute(name = "groupRef")
- protected String groupRef;
-
- @XmlAttribute(name = "graphColour")
- protected Integer graphColour;
-
- @XmlAttribute(name = "graphGroup")
- protected Integer graphGroup;
-
- @XmlAttribute(name = "graphHeight")
- protected Integer graphHeight;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- @XmlAttribute(name = "scoreOnly")
- protected Boolean scoreOnly;
-
- @XmlAttribute(name = "score")
- protected Double score;
-
- @XmlAttribute(name = "visible")
- protected Boolean visible;
-
- @XmlAttribute(name = "centreColLabels")
- protected Boolean centreColLabels;
-
- @XmlAttribute(name = "scaleColLabels")
- protected Boolean scaleColLabels;
-
- @XmlAttribute(name = "showAllColLabels")
- protected Boolean showAllColLabels;
-
- @XmlAttribute(name = "autoCalculated")
- protected Boolean autoCalculated;
-
- @XmlAttribute(name = "belowAlignment")
- protected Boolean belowAlignment;
-
- @XmlAttribute(name = "calcId")
- protected String calcId;
-
- /**
- * Gets the value of the annotationElement property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the annotationElement property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAnnotationElement().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link AnnotationElement }
- *
- *
- */
- public List<AnnotationElement> getAnnotationElement()
- {
- if (annotationElement == null)
- {
- annotationElement = new ArrayList<AnnotationElement>();
- }
- return this.annotationElement;
- }
-
- /**
- * Gets the value of the label property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLabel()
- {
- return label;
- }
-
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLabel(String value)
- {
- this.label = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the thresholdLine property.
- *
- * @return possible object is {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine getThresholdLine()
- {
- return thresholdLine;
- }
-
- /**
- * Sets the value of the thresholdLine property.
- *
- * @param value
- * allowed object is {@link Annotation.ThresholdLine }
- *
- */
- public void setThresholdLine(Annotation.ThresholdLine value)
- {
- this.thresholdLine = value;
- }
-
- /**
- * Gets the value of the property property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the property property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getProperty().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Annotation.Property }
- *
- *
- */
- public List<Annotation.Property> getProperty()
- {
- if (property == null)
- {
- property = new ArrayList<Annotation.Property>();
- }
- return this.property;
- }
-
- /**
- * Gets the value of the graph property.
- *
- */
- public boolean isGraph()
- {
- return graph;
- }
-
- /**
- * Sets the value of the graph property.
- *
- */
- public void setGraph(boolean value)
- {
- this.graph = value;
- }
-
- /**
- * Gets the value of the graphType property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphType()
- {
- return graphType;
- }
-
- /**
- * Sets the value of the graphType property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphType(Integer value)
- {
- this.graphType = value;
- }
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceRef()
- {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceRef(String value)
- {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the groupRef property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getGroupRef()
- {
- return groupRef;
- }
-
- /**
- * Sets the value of the groupRef property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setGroupRef(String value)
- {
- this.groupRef = value;
- }
-
- /**
- * Gets the value of the graphColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphColour()
- {
- return graphColour;
- }
-
- /**
- * Sets the value of the graphColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphColour(Integer value)
- {
- this.graphColour = value;
- }
-
- /**
- * Gets the value of the graphGroup property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphGroup()
- {
- return graphGroup;
- }
-
- /**
- * Sets the value of the graphGroup property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphGroup(Integer value)
- {
- this.graphGroup = value;
- }
-
- /**
- * Gets the value of the graphHeight property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphHeight()
- {
- return graphHeight;
- }
-
- /**
- * Sets the value of the graphHeight property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphHeight(Integer value)
- {
- this.graphHeight = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the scoreOnly property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isScoreOnly()
- {
- if (scoreOnly == null)
- {
- return false;
- }
- else
- {
- return scoreOnly;
- }
- }
-
- /**
- * Sets the value of the scoreOnly property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScoreOnly(Boolean value)
- {
- this.scoreOnly = value;
- }
-
- /**
- * Gets the value of the score property.
- *
- * @return possible object is {@link Double }
- *
- */
- public Double getScore()
- {
- return score;
- }
-
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is {@link Double }
- *
- */
- public void setScore(Double value)
- {
- this.score = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isVisible()
- {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setVisible(Boolean value)
- {
- this.visible = value;
- }
-
- /**
- * Gets the value of the centreColLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isCentreColLabels()
- {
- return centreColLabels;
- }
-
- /**
- * Sets the value of the centreColLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCentreColLabels(Boolean value)
- {
- this.centreColLabels = value;
- }
-
- /**
- * Gets the value of the scaleColLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isScaleColLabels()
- {
- return scaleColLabels;
- }
-
- /**
- * Sets the value of the scaleColLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScaleColLabels(Boolean value)
- {
- this.scaleColLabels = value;
- }
-
- /**
- * Gets the value of the showAllColLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowAllColLabels()
- {
- return showAllColLabels;
- }
-
- /**
- * Sets the value of the showAllColLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowAllColLabels(Boolean value)
- {
- this.showAllColLabels = value;
- }
-
- /**
- * Gets the value of the autoCalculated property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isAutoCalculated()
- {
- if (autoCalculated == null)
- {
- return false;
- }
- else
- {
- return autoCalculated;
- }
- }
-
- /**
- * Sets the value of the autoCalculated property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoCalculated(Boolean value)
- {
- this.autoCalculated = value;
- }
-
- /**
- * Gets the value of the belowAlignment property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isBelowAlignment()
- {
- if (belowAlignment == null)
- {
- return true;
- }
- else
- {
- return belowAlignment;
- }
- }
-
- /**
- * Sets the value of the belowAlignment property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setBelowAlignment(Boolean value)
- {
- this.belowAlignment = value;
- }
-
- /**
- * Gets the value of the calcId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCalcId()
- {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCalcId(String value)
- {
- this.calcId = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property
- {
-
- @XmlAttribute(name = "name")
- protected String name;
-
- @XmlAttribute(name = "value")
- protected String value;
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
+ /**
+ * Gets the value of the annotationElement property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAnnotationElement().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AnnotationElement }
+ *
+ *
+ */
+ public List<AnnotationElement> getAnnotationElement() {
+ if (annotationElement == null) {
+ annotationElement = new ArrayList<AnnotationElement>();
+ }
+ return this.annotationElement;
+ }
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the description property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setName(String value)
- {
- this.name = value;
+ public String getDescription() {
+ return description;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the description property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the thresholdLine property.
*
+ * @return
+ * possible object is
+ * {@link Annotation.ThresholdLine }
+ *
*/
- public String getValue()
- {
- return value;
+ public Annotation.ThresholdLine getThresholdLine() {
+ return thresholdLine;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the thresholdLine property.
*
* @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
-
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class ThresholdLine
- {
-
- @XmlAttribute(name = "label")
- protected String label;
+ * allowed object is
+ * {@link Annotation.ThresholdLine }
+ *
+ */
+ public void setThresholdLine(Annotation.ThresholdLine value) {
+ this.thresholdLine = value;
+ }
- @XmlAttribute(name = "value")
- protected Float value;
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Annotation.Property }
+ *
+ *
+ */
+ public List<Annotation.Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Annotation.Property>();
+ }
+ return this.property;
+ }
- @XmlAttribute(name = "colour")
- protected Integer colour;
+ /**
+ * Gets the value of the graph property.
+ *
+ */
+ public boolean isGraph() {
+ return graph;
+ }
/**
- * Gets the value of the label property.
+ * Sets the value of the graph property.
*
- * @return possible object is {@link String }
+ */
+ public void setGraph(boolean value) {
+ this.graph = value;
+ }
+
+ /**
+ * Gets the value of the graphType property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getLabel()
- {
- return label;
+ public Integer getGraphType() {
+ return graphType;
}
/**
- * Sets the value of the label property.
+ * Sets the value of the graphType property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphType(Integer value) {
+ this.graphType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the groupRef property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getGroupRef() {
+ return groupRef;
+ }
+
+ /**
+ * Sets the value of the groupRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setLabel(String value)
- {
- this.label = value;
+ public void setGroupRef(String value) {
+ this.groupRef = value;
}
/**
- * Gets the value of the value property.
+ * Gets the value of the graphColour property.
*
- * @return possible object is {@link Float }
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGraphColour() {
+ return graphColour;
+ }
+
+ /**
+ * Sets the value of the graphColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphColour(Integer value) {
+ this.graphColour = value;
+ }
+
+ /**
+ * Gets the value of the graphGroup property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Float getValue()
- {
- return value;
+ public Integer getGraphGroup() {
+ return graphGroup;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the graphGroup property.
*
* @param value
- * allowed object is {@link Float }
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphGroup(Integer value) {
+ this.graphGroup = value;
+ }
+
+ /**
+ * Gets the value of the graphHeight property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public void setValue(Float value)
- {
- this.value = value;
+ public Integer getGraphHeight() {
+ return graphHeight;
}
/**
- * Gets the value of the colour property.
+ * Sets the value of the graphHeight property.
*
- * @return possible object is {@link Integer }
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphHeight(Integer value) {
+ this.graphHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public Integer getColour()
- {
- return colour;
+ public String getId() {
+ return id;
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the id property.
*
* @param value
- * allowed object is {@link Integer }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the scoreOnly property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public void setColour(Integer value)
- {
- this.colour = value;
+ public boolean isScoreOnly() {
+ if (scoreOnly == null) {
+ return false;
+ } else {
+ return scoreOnly;
+ }
}
- }
+ /**
+ * Sets the value of the scoreOnly property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScoreOnly(Boolean value) {
+ this.scoreOnly = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return
+ * possible object is
+ * {@link Double }
+ *
+ */
+ public Double getScore() {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Double }
+ *
+ */
+ public void setScore(Double value) {
+ this.score = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the centreColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCentreColLabels() {
+ return centreColLabels;
+ }
+
+ /**
+ * Sets the value of the centreColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColLabels(Boolean value) {
+ this.centreColLabels = value;
+ }
+
+ /**
+ * Gets the value of the scaleColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isScaleColLabels() {
+ return scaleColLabels;
+ }
+
+ /**
+ * Sets the value of the scaleColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleColLabels(Boolean value) {
+ this.scaleColLabels = value;
+ }
+
+ /**
+ * Gets the value of the showAllColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAllColLabels() {
+ return showAllColLabels;
+ }
+
+ /**
+ * Sets the value of the showAllColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAllColLabels(Boolean value) {
+ this.showAllColLabels = value;
+ }
+
+ /**
+ * Gets the value of the autoCalculated property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAutoCalculated() {
+ if (autoCalculated == null) {
+ return false;
+ } else {
+ return autoCalculated;
+ }
+ }
+
+ /**
+ * Sets the value of the autoCalculated property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoCalculated(Boolean value) {
+ this.autoCalculated = value;
+ }
+
+ /**
+ * Gets the value of the belowAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isBelowAlignment() {
+ if (belowAlignment == null) {
+ return true;
+ } else {
+ return belowAlignment;
+ }
+ }
+
+ /**
+ * Sets the value of the belowAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setBelowAlignment(Boolean value) {
+ this.belowAlignment = value;
+ }
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property {
+
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "value")
+ protected String value;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine {
+
+ @XmlAttribute(name = "label")
+ protected String label;
+ @XmlAttribute(name = "value")
+ protected Float value;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setValue(Float value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for AnnotationColourScheme complex type.
+ * <p>Java class for AnnotationColourScheme complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="AnnotationColourScheme"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="annotation"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="maxColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="predefinedColours"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="AnnotationColourScheme">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme
-{
-
- @XmlAttribute(name = "aboveThreshold")
- protected Integer aboveThreshold;
-
- @XmlAttribute(name = "annotation")
- protected String annotation;
-
- @XmlAttribute(name = "minColour")
- protected Integer minColour;
-
- @XmlAttribute(name = "maxColour")
- protected Integer maxColour;
-
- @XmlAttribute(name = "colourScheme")
- protected String colourScheme;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "perSequence")
- protected Boolean perSequence;
-
- @XmlAttribute(name = "predefinedColours")
- protected Boolean predefinedColours;
-
- /**
- * Gets the value of the aboveThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getAboveThreshold()
- {
- return aboveThreshold;
- }
-
- /**
- * Sets the value of the aboveThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setAboveThreshold(Integer value)
- {
- this.aboveThreshold = value;
- }
-
- /**
- * Gets the value of the annotation property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getAnnotation()
- {
- return annotation;
- }
-
- /**
- * Sets the value of the annotation property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setAnnotation(String value)
- {
- this.annotation = value;
- }
-
- /**
- * Gets the value of the minColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMinColour()
- {
- return minColour;
- }
-
- /**
- * Sets the value of the minColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMinColour(Integer value)
- {
- this.minColour = value;
- }
-
- /**
- * Gets the value of the maxColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMaxColour()
- {
- return maxColour;
- }
-
- /**
- * Sets the value of the maxColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMaxColour(Integer value)
- {
- this.maxColour = value;
- }
-
- /**
- * Gets the value of the colourScheme property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getColourScheme()
- {
- return colourScheme;
- }
-
- /**
- * Sets the value of the colourScheme property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setColourScheme(String value)
- {
- this.colourScheme = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the perSequence property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPerSequence()
- {
- return perSequence;
- }
-
- /**
- * Sets the value of the perSequence property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPerSequence(Boolean value)
- {
- this.perSequence = value;
- }
-
- /**
- * Gets the value of the predefinedColours property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPredefinedColours()
- {
- return predefinedColours;
- }
-
- /**
- * Sets the value of the predefinedColours property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPredefinedColours(Boolean value)
- {
- this.predefinedColours = value;
- }
+public class AnnotationColourScheme {
+
+ @XmlAttribute(name = "aboveThreshold")
+ protected Integer aboveThreshold;
+ @XmlAttribute(name = "annotation")
+ protected String annotation;
+ @XmlAttribute(name = "minColour")
+ protected Integer minColour;
+ @XmlAttribute(name = "maxColour")
+ protected Integer maxColour;
+ @XmlAttribute(name = "colourScheme")
+ protected String colourScheme;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "perSequence")
+ protected Boolean perSequence;
+ @XmlAttribute(name = "predefinedColours")
+ protected Boolean predefinedColours;
+
+ /**
+ * Gets the value of the aboveThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getAboveThreshold() {
+ return aboveThreshold;
+ }
+
+ /**
+ * Sets the value of the aboveThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setAboveThreshold(Integer value) {
+ this.aboveThreshold = value;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotation() {
+ return annotation;
+ }
+
+ /**
+ * Sets the value of the annotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotation(String value) {
+ this.annotation = value;
+ }
+
+ /**
+ * Gets the value of the minColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMinColour() {
+ return minColour;
+ }
+
+ /**
+ * Sets the value of the minColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMinColour(Integer value) {
+ this.minColour = value;
+ }
+
+ /**
+ * Gets the value of the maxColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMaxColour() {
+ return maxColour;
+ }
+
+ /**
+ * Sets the value of the maxColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMaxColour(Integer value) {
+ this.maxColour = value;
+ }
+
+ /**
+ * Gets the value of the colourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColourScheme() {
+ return colourScheme;
+ }
+
+ /**
+ * Sets the value of the colourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColourScheme(String value) {
+ this.colourScheme = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the perSequence property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPerSequence() {
+ return perSequence;
+ }
+
+ /**
+ * Sets the value of the perSequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPerSequence(Boolean value) {
+ this.perSequence = value;
+ }
+
+ /**
+ * Gets the value of the predefinedColours property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPredefinedColours() {
+ return predefinedColours;
+ }
+
+ /**
+ * Sets the value of the predefinedColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPredefinedColours(Boolean value) {
+ this.predefinedColours = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="displayCharacter"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="secondaryStructure" minOccurs="0"&gt;
- * &lt;simpleType&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;length
- * value="1"/&gt; &lt;/restriction&gt; &lt;/simpleType&gt;
- * &lt;/element&gt; &lt;element name="value"
- * type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="position" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="secondaryStructure" minOccurs="0">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <length value="1"/>
+ * </restriction>
+ * </simpleType>
+ * </element>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "displayCharacter", "description", "secondaryStructure", "value" })
+@XmlType(name = "", propOrder = {
+ "displayCharacter",
+ "description",
+ "secondaryStructure",
+ "value"
+})
@XmlRootElement(name = "annotationElement")
-public class AnnotationElement
-{
-
- protected String displayCharacter;
-
- protected String description;
-
- protected String secondaryStructure;
-
- protected Float value;
-
- @XmlAttribute(name = "position", required = true)
- protected int position;
-
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the displayCharacter property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDisplayCharacter()
- {
- return displayCharacter;
- }
-
- /**
- * Sets the value of the displayCharacter property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDisplayCharacter(String value)
- {
- this.displayCharacter = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSecondaryStructure()
- {
- return secondaryStructure;
- }
-
- /**
- * Sets the value of the secondaryStructure property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSecondaryStructure(String value)
- {
- this.secondaryStructure = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setValue(Float value)
- {
- this.value = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- */
- public int getPosition()
- {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- */
- public void setPosition(int value)
- {
- this.position = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColour(Integer value)
- {
- this.colour = value;
- }
+public class AnnotationElement {
+
+ protected String displayCharacter;
+ protected String description;
+ protected String secondaryStructure;
+ protected Float value;
+ @XmlAttribute(name = "position", required = true)
+ protected int position;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the displayCharacter property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDisplayCharacter() {
+ return displayCharacter;
+ }
+
+ /**
+ * Sets the value of the displayCharacter property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDisplayCharacter(String value) {
+ this.displayCharacter = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSecondaryStructure() {
+ return secondaryStructure;
+ }
+
+ /**
+ * Sets the value of the secondaryStructure property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSecondaryStructure(String value) {
+ this.secondaryStructure = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setValue(Float value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ */
+ public int getPosition() {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ */
+ public void setPosition(int value) {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for DoubleMatrix complex type.
+ * <p>Java class for DoubleMatrix complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="DoubleMatrix"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="row"
- * type="{www.jalview.org}DoubleVector" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="D"
- * type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt; &lt;element
- * name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="rows"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="DoubleMatrix">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ * <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "DoubleMatrix",
- namespace = "www.jalview.org",
- propOrder =
- { "row", "d", "e" })
-public class DoubleMatrix
-{
-
- protected List<DoubleVector> row;
-
- @XmlElement(name = "D")
- protected DoubleVector d;
-
- @XmlElement(name = "E")
- protected DoubleVector e;
-
- @XmlAttribute(name = "rows")
- protected Integer rows;
-
- @XmlAttribute(name = "columns")
- protected Integer columns;
-
- /**
- * Gets the value of the row property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the row property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getRow().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link DoubleVector }
- *
- *
- */
- public List<DoubleVector> getRow()
- {
- if (row == null)
- {
- row = new ArrayList<DoubleVector>();
+@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
+ "row",
+ "d",
+ "e"
+})
+public class DoubleMatrix {
+
+ protected List<DoubleVector> row;
+ @XmlElement(name = "D")
+ protected DoubleVector d;
+ @XmlElement(name = "E")
+ protected DoubleVector e;
+ @XmlAttribute(name = "rows")
+ protected Integer rows;
+ @XmlAttribute(name = "columns")
+ protected Integer columns;
+
+ /**
+ * Gets the value of the row property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the row property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRow().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DoubleVector }
+ *
+ *
+ */
+ public List<DoubleVector> getRow() {
+ if (row == null) {
+ row = new ArrayList<DoubleVector>();
+ }
+ return this.row;
+ }
+
+ /**
+ * Gets the value of the d property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleVector }
+ *
+ */
+ public DoubleVector getD() {
+ return d;
+ }
+
+ /**
+ * Sets the value of the d property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleVector }
+ *
+ */
+ public void setD(DoubleVector value) {
+ this.d = value;
+ }
+
+ /**
+ * Gets the value of the e property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleVector }
+ *
+ */
+ public DoubleVector getE() {
+ return e;
+ }
+
+ /**
+ * Sets the value of the e property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleVector }
+ *
+ */
+ public void setE(DoubleVector value) {
+ this.e = value;
+ }
+
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getRows() {
+ return rows;
+ }
+
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setRows(Integer value) {
+ this.rows = value;
+ }
+
+ /**
+ * Gets the value of the columns property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColumns() {
+ return columns;
+ }
+
+ /**
+ * Sets the value of the columns property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColumns(Integer value) {
+ this.columns = value;
}
- return this.row;
- }
-
- /**
- * Gets the value of the d property.
- *
- * @return possible object is {@link DoubleVector }
- *
- */
- public DoubleVector getD()
- {
- return d;
- }
-
- /**
- * Sets the value of the d property.
- *
- * @param value
- * allowed object is {@link DoubleVector }
- *
- */
- public void setD(DoubleVector value)
- {
- this.d = value;
- }
-
- /**
- * Gets the value of the e property.
- *
- * @return possible object is {@link DoubleVector }
- *
- */
- public DoubleVector getE()
- {
- return e;
- }
-
- /**
- * Sets the value of the e property.
- *
- * @param value
- * allowed object is {@link DoubleVector }
- *
- */
- public void setE(DoubleVector value)
- {
- this.e = value;
- }
-
- /**
- * Gets the value of the rows property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getRows()
- {
- return rows;
- }
-
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setRows(Integer value)
- {
- this.rows = value;
- }
-
- /**
- * Gets the value of the columns property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColumns()
- {
- return columns;
- }
-
- /**
- * Sets the value of the columns property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColumns(Integer value)
- {
- this.columns = value;
- }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for DoubleVector complex type.
+ * <p>Java class for DoubleVector complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="DoubleVector"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="v"
- * type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="DoubleVector">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "DoubleVector",
- namespace = "www.jalview.org",
- propOrder =
- { "v" })
-public class DoubleVector
-{
+@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
+ "v"
+})
+public class DoubleVector {
- @XmlElement(type = Double.class)
- protected List<Double> v;
+ @XmlElement(type = Double.class)
+ protected List<Double> v;
- /**
- * Gets the value of the v property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the v property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getV().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Double }
- *
- *
- */
- public List<Double> getV()
- {
- if (v == null)
- {
- v = new ArrayList<Double>();
+ /**
+ * Gets the value of the v property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the v property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getV().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Double }
+ *
+ *
+ */
+ public List<Double> getV() {
+ if (v == null) {
+ v = new ArrayList<Double>();
+ }
+ return this.v;
}
- return this.v;
- }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for feature complex type.
+ * <p>Java class for feature complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="feature"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="otherData"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="key2"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="begin" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="status"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="feature">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="otherData" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "feature",
- namespace = "www.jalview.org",
- propOrder =
- { "otherData" })
-public class Feature
-{
-
- protected List<Feature.OtherData> otherData;
-
- @XmlAttribute(name = "begin", required = true)
- protected int begin;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "description")
- protected String description;
-
- @XmlAttribute(name = "status")
- protected String status;
-
- @XmlAttribute(name = "featureGroup")
- protected String featureGroup;
-
- @XmlAttribute(name = "score")
- protected Float score;
-
- /**
- * Gets the value of the otherData property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the otherData property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getOtherData().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Feature.OtherData }
- *
- *
- */
- public List<Feature.OtherData> getOtherData()
- {
- if (otherData == null)
- {
- otherData = new ArrayList<Feature.OtherData>();
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+ "otherData"
+})
+public class Feature {
+
+ protected List<Feature.OtherData> otherData;
+ @XmlAttribute(name = "begin", required = true)
+ protected int begin;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "description")
+ protected String description;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "featureGroup")
+ protected String featureGroup;
+ @XmlAttribute(name = "score")
+ protected Float score;
+
+ /**
+ * Gets the value of the otherData property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the otherData property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOtherData().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature.OtherData }
+ *
+ *
+ */
+ public List<Feature.OtherData> getOtherData() {
+ if (otherData == null) {
+ otherData = new ArrayList<Feature.OtherData>();
+ }
+ return this.otherData;
}
- return this.otherData;
- }
-
- /**
- * Gets the value of the begin property.
- *
- */
- public int getBegin()
- {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- */
- public void setBegin(int value)
- {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getStatus()
- {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setStatus(String value)
- {
- this.status = value;
- }
-
- /**
- * Gets the value of the featureGroup property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFeatureGroup()
- {
- return featureGroup;
- }
-
- /**
- * Sets the value of the featureGroup property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFeatureGroup(String value)
- {
- this.featureGroup = value;
- }
-
- /**
- * Gets the value of the score property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getScore()
- {
- return score;
- }
-
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setScore(Float value)
- {
- this.score = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="key2"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class OtherData
- {
-
- @XmlAttribute(name = "key", required = true)
- protected String key;
-
- @XmlAttribute(name = "key2")
- protected String key2;
-
- @XmlAttribute(name = "value", required = true)
- protected String value;
/**
- * Gets the value of the key property.
+ * Gets the value of the begin property.
*
- * @return possible object is {@link String }
+ */
+ public int getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
*
*/
- public String getKey()
- {
- return key;
+ public void setBegin(int value) {
+ this.begin = value;
}
/**
- * Sets the value of the key property.
+ * Gets the value of the end property.
*
- * @param value
- * allowed object is {@link String }
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the type property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setKey(String value)
- {
- this.key = value;
+ public String getType() {
+ return type;
}
/**
- * Gets the value of the key2 property.
+ * Sets the value of the type property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the description property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getKey2()
- {
- return key2;
+ public String getDescription() {
+ return description;
}
/**
- * Sets the value of the key2 property.
+ * Sets the value of the description property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the status property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setKey2(String value)
- {
- this.key2 = value;
+ public String getStatus() {
+ return status;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the status property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the featureGroup property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getValue()
- {
- return value;
+ public String getFeatureGroup() {
+ return featureGroup;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the featureGroup property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFeatureGroup(String value) {
+ this.featureGroup = value;
+ }
+
+ /**
+ * Gets the value of the score property.
*
+ * @return
+ * possible object is
+ * {@link Float }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public Float getScore() {
+ return score;
}
- }
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setScore(Float value) {
+ this.score = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class OtherData {
+
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+ @XmlAttribute(name = "key2")
+ protected String key2;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+ /**
+ * Gets the value of the key2 property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey2() {
+ return key2;
+ }
+
+ /**
+ * Sets the value of the key2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey2(String value) {
+ this.key2 = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for FeatureMatcher complex type.
+ * <p>Java class for FeatureMatcher complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="FeatureMatcher"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="condition"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="by"
- * type="{www.jalview.org/colours}FilterBy" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="FeatureMatcher">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "FeatureMatcher",
- namespace = "www.jalview.org/colours",
- propOrder =
- { "attributeName", "condition", "value" })
-public class FeatureMatcher
-{
-
- @XmlElement(namespace = "")
- protected List<String> attributeName;
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+ "attributeName",
+ "condition",
+ "value"
+})
+public class FeatureMatcher {
- @XmlElement(namespace = "", required = true)
- protected String condition;
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "", required = true)
+ protected String condition;
+ @XmlElement(namespace = "", required = true)
+ protected String value;
+ @XmlAttribute(name = "by")
+ protected FilterBy by;
- @XmlElement(namespace = "", required = true)
- protected String value;
-
- @XmlAttribute(name = "by")
- protected FilterBy by;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAttributeName().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
}
- return this.attributeName;
- }
- /**
- * Gets the value of the condition property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCondition()
- {
- return condition;
- }
+ /**
+ * Gets the value of the condition property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCondition() {
+ return condition;
+ }
- /**
- * Sets the value of the condition property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCondition(String value)
- {
- this.condition = value;
- }
+ /**
+ * Sets the value of the condition property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCondition(String value) {
+ this.condition = value;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the by property.
- *
- * @return possible object is {@link FilterBy }
- *
- */
- public FilterBy getBy()
- {
- return by;
- }
+ /**
+ * Gets the value of the by property.
+ *
+ * @return
+ * possible object is
+ * {@link FilterBy }
+ *
+ */
+ public FilterBy getBy() {
+ return by;
+ }
- /**
- * Sets the value of the by property.
- *
- * @param value
- * allowed object is {@link FilterBy }
- *
- */
- public void setBy(FilterBy value)
- {
- this.by = value;
- }
+ /**
+ * Sets the value of the by property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FilterBy }
+ *
+ */
+ public void setBy(FilterBy value) {
+ this.by = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
* A feature match condition, which may be simple or compound
*
- * <p>Java class for FeatureMatcherSet complex type.
+ * <p>Java class for FeatureMatcherSet complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="FeatureMatcherSet"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;choice&gt; &lt;element name="matchCondition"
- * type="{www.jalview.org/colours}FeatureMatcher"/&gt; &lt;element
- * name="compoundMatcher"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
- * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute name="and"
- * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;/choice&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="FeatureMatcherSet">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <choice>
+ * <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
+ * <element name="compoundMatcher">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ * </sequence>
+ * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "FeatureMatcherSet",
- namespace = "www.jalview.org/colours",
- propOrder =
- { "matchCondition", "compoundMatcher" })
-public class FeatureMatcherSet
-{
-
- @XmlElement(namespace = "")
- protected FeatureMatcher matchCondition;
-
- @XmlElement(namespace = "")
- protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
-
- /**
- * Gets the value of the matchCondition property.
- *
- * @return possible object is {@link FeatureMatcher }
- *
- */
- public FeatureMatcher getMatchCondition()
- {
- return matchCondition;
- }
-
- /**
- * Sets the value of the matchCondition property.
- *
- * @param value
- * allowed object is {@link FeatureMatcher }
- *
- */
- public void setMatchCondition(FeatureMatcher value)
- {
- this.matchCondition = value;
- }
-
- /**
- * Gets the value of the compoundMatcher property.
- *
- * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
- {
- return compoundMatcher;
- }
-
- /**
- * Sets the value of the compoundMatcher property.
- *
- * @param value
- * allowed object is {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
- {
- this.compoundMatcher = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
- * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute
- * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "matcherSet" })
- public static class CompoundMatcher
- {
-
- @XmlElement(namespace = "", required = true)
- protected List<FeatureMatcherSet> matcherSet;
-
- @XmlAttribute(name = "and", required = true)
- protected boolean and;
+@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
+ "matchCondition",
+ "compoundMatcher"
+})
+public class FeatureMatcherSet {
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcher matchCondition;
+ @XmlElement(namespace = "")
+ protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
/**
- * Gets the value of the matcherSet property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the matcherSet property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getMatcherSet().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link FeatureMatcherSet }
+ * Gets the value of the matchCondition property.
*
+ * @return
+ * possible object is
+ * {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher getMatchCondition() {
+ return matchCondition;
+ }
+
+ /**
+ * Sets the value of the matchCondition property.
*
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcher }
+ *
*/
- public List<FeatureMatcherSet> getMatcherSet()
- {
- if (matcherSet == null)
- {
- matcherSet = new ArrayList<FeatureMatcherSet>();
- }
- return this.matcherSet;
+ public void setMatchCondition(FeatureMatcher value) {
+ this.matchCondition = value;
}
/**
- * Gets the value of the and property.
+ * Gets the value of the compoundMatcher property.
*
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet.CompoundMatcher }
+ *
*/
- public boolean isAnd()
- {
- return and;
+ public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
+ return compoundMatcher;
}
/**
- * Sets the value of the and property.
+ * Sets the value of the compoundMatcher property.
*
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet.CompoundMatcher }
+ *
*/
- public void setAnd(boolean value)
- {
- this.and = value;
+ public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
+ this.compoundMatcher = value;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ * </sequence>
+ * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "matcherSet"
+ })
+ public static class CompoundMatcher {
+
+ @XmlElement(namespace = "", required = true)
+ protected List<FeatureMatcherSet> matcherSet;
+ @XmlAttribute(name = "and", required = true)
+ protected boolean and;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMatcherSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link FeatureMatcherSet }
+ *
+ *
+ */
+ public List<FeatureMatcherSet> getMatcherSet() {
+ if (matcherSet == null) {
+ matcherSet = new ArrayList<FeatureMatcherSet>();
+ }
+ return this.matcherSet;
+ }
+
+ /**
+ * Gets the value of the and property.
+ *
+ */
+ public boolean isAnd() {
+ return and;
+ }
+
+ /**
+ * Sets the value of the and property.
+ *
+ */
+ public void setAnd(boolean value) {
+ this.and = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for FilterBy.
+ * <p>Java class for FilterBy.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class. <pre> &lt;simpleType
- * name="FilterBy"&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
- * value="byLabel"/&gt; &lt;enumeration value="byScore"/&gt;
- * &lt;enumeration value="byAttribute"/&gt; &lt;/restriction&gt;
- * &lt;/simpleType&gt; </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * <simpleType name="FilterBy">
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="byLabel"/>
+ * <enumeration value="byScore"/>
+ * <enumeration value="byAttribute"/>
+ * </restriction>
+ * </simpleType>
+ * </pre>
*
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum FilterBy
-{
-
- @XmlEnumValue("byLabel")
- BY_LABEL("byLabel"), @XmlEnumValue("byScore")
- BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
- BY_ATTRIBUTE("byAttribute");
-
- private final String value;
-
- FilterBy(String v)
- {
- value = v;
- }
-
- public String value()
- {
- return value;
- }
-
- public static FilterBy fromValue(String v)
- {
- for (FilterBy c : FilterBy.values())
- {
- if (c.value.equals(v))
- {
- return c;
- }
+public enum FilterBy {
+
+ @XmlEnumValue("byLabel")
+ BY_LABEL("byLabel"),
+ @XmlEnumValue("byScore")
+ BY_SCORE("byScore"),
+ @XmlEnumValue("byAttribute")
+ BY_ATTRIBUTE("byAttribute");
+ private final String value;
+
+ FilterBy(String v) {
+ value = v;
+ }
+
+ public String value() {
+ return value;
+ }
+
+ public static FilterBy fromValue(String v) {
+ for (FilterBy c: FilterBy.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
}
- throw new IllegalArgumentException(v);
- }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import javax.xml.datatype.XMLGregorianCalendar;
+
/**
- * <p>Java class for JalviewModel complex type.
+ * <p>Java class for JalviewModel complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="JalviewModel"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="creationDate"
- * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="vamsasModel"
- * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
- * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="features"
- * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;simpleContent&gt; &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/extension&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="hiddenSequences"
- * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="hidden"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="seq"
- * type="{http://www.w3.org/2001/XMLSchema}string"
- * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="showUnconserved"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="AnnotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="autoUpdate" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="pidSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="showBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="renderGaps"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showNPfeatureTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="followHighlight"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="showGroupConservation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="viewName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="gatheredViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute
- * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="UserColourScheme"
- * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt; &lt;element name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="markUnlinked"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequencePoint"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="seqPointMax"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="pcaData"
- * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; &lt;attGroup
- * ref="{www.jalview.org}SimilarityParams"/&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="zDim"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
- * default="Min" /&gt; &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="JalviewModel">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ * <sequence>
+ * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="FeatureSettings" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "JalviewModel",
- namespace = "www.jalview.org",
- propOrder =
- { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
- "userColours", "tree", "pcaViewer", "featureSettings" })
-public class JalviewModel
-{
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
-
- @XmlElement(required = true)
- protected String version;
-
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
-
- @XmlElement(name = "JSeq")
- protected List<JalviewModel.JSeq> jSeq;
-
- @XmlElement(name = "JGroup")
- protected List<JalviewModel.JGroup> jGroup;
-
- @XmlElement(name = "Viewport")
- protected List<JalviewModel.Viewport> viewport;
-
- @XmlElement(name = "UserColours")
- protected List<JalviewModel.UserColours> userColours;
-
- protected List<JalviewModel.Tree> tree;
-
- @XmlElement(name = "PcaViewer")
- protected List<JalviewModel.PcaViewer> pcaViewer;
-
- @XmlElement(name = "FeatureSettings")
- protected JalviewModel.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate()
- {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setCreationDate(XMLGregorianCalendar value)
- {
- this.creationDate = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return possible object is {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel()
- {
- return vamsasModel;
- }
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value)
- {
- this.vamsasModel = value;
- }
-
- /**
- * Gets the value of the jSeq property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the jSeq property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getJSeq().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
- *
- *
- */
- public List<JalviewModel.JSeq> getJSeq()
- {
- if (jSeq == null)
- {
- jSeq = new ArrayList<JalviewModel.JSeq>();
- }
- return this.jSeq;
- }
-
- /**
- * Gets the value of the jGroup property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the jGroup property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getJGroup().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
- *
- *
- */
- public List<JalviewModel.JGroup> getJGroup()
- {
- if (jGroup == null)
- {
- jGroup = new ArrayList<JalviewModel.JGroup>();
- }
- return this.jGroup;
- }
-
- /**
- * Gets the value of the viewport property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the viewport property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getViewport().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
- *
- *
- */
- public List<JalviewModel.Viewport> getViewport()
- {
- if (viewport == null)
- {
- viewport = new ArrayList<JalviewModel.Viewport>();
- }
- return this.viewport;
- }
-
- /**
- * Gets the value of the userColours property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the userColours property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getUserColours().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
- *
- *
- */
- public List<JalviewModel.UserColours> getUserColours()
- {
- if (userColours == null)
- {
- userColours = new ArrayList<JalviewModel.UserColours>();
- }
- return this.userColours;
- }
-
- /**
- * Gets the value of the tree property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the tree property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getTree().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
- *
- *
- */
- public List<JalviewModel.Tree> getTree()
- {
- if (tree == null)
- {
- tree = new ArrayList<JalviewModel.Tree>();
- }
- return this.tree;
- }
-
- /**
- * Gets the value of the pcaViewer property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the pcaViewer property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getPcaViewer().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
- *
- *
- */
- public List<JalviewModel.PcaViewer> getPcaViewer()
- {
- if (pcaViewer == null)
- {
- pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
- }
- return this.pcaViewer;
- }
-
- /**
- * Gets the value of the featureSettings property.
- *
- * @return possible object is {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings getFeatureSettings()
- {
- return featureSettings;
- }
-
- /**
- * Sets the value of the featureSettings property.
- *
- * @param value
- * allowed object is {@link JalviewModel.FeatureSettings }
- *
- */
- public void setFeatureSettings(JalviewModel.FeatureSettings value)
- {
- this.featureSettings = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="setting"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour"
- * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "setting", "group" })
- public static class FeatureSettings
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Setting> setting;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Group> group;
-
- /**
- * Gets the value of the setting property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the setting property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSetting().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Setting }
- *
- *
- */
- public List<JalviewModel.FeatureSettings.Setting> getSetting()
- {
- if (setting == null)
- {
- setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
- }
- return this.setting;
- }
-
- /**
- * Gets the value of the group property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the group property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getGroup().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Group }
- *
- *
- */
- public List<JalviewModel.FeatureSettings.Group> getGroup()
- {
- if (group == null)
- {
- group = new ArrayList<JalviewModel.FeatureSettings.Group>();
- }
- return this.group;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group
- {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay()
- {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value)
- {
- this.display = value;
- }
-
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
- * default="Min" /&gt; &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
- public static class Setting
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
-
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
-
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- @XmlAttribute(name = "order")
- protected Float order;
-
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
-
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
-
- @XmlAttribute(name = "max")
- protected Float max;
-
- @XmlAttribute(name = "min")
- protected Float min;
-
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
-
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p> This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the returned
- * list will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAttributeName().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return possible object is {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet()
- {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value)
- {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay()
- {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value)
- {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getOrder()
- {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setOrder(Float value)
- {
- this.order = value;
- }
-
- /**
- * Gets the value of the mincolour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMincolour()
- {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMincolour(Integer value)
- {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return possible object is {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour()
- {
- if (noValueColour == null)
- {
- return NoValueColour.MIN;
- }
- else
- {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value)
- {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the threshstate property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getThreshstate()
- {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setThreshstate(Integer value)
- {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMax()
- {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMax(Float value)
- {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMin()
- {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMin(Float value)
- {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isColourByLabel()
- {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value)
- {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isAutoScale()
- {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value)
- {
- this.autoScale = value;
- }
-
- }
-
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="seq"
- * type="{http://www.w3.org/2001/XMLSchema}string"
- * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="displayText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "seq", "annotationColours" })
- public static class JGroup
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<String> seq;
-
- @XmlElement(namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
-
- @XmlAttribute(name = "start")
- protected Integer start;
-
- @XmlAttribute(name = "end")
- protected Integer end;
-
- @XmlAttribute(name = "name")
- protected String name;
-
- @XmlAttribute(name = "colour")
- protected String colour;
-
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
-
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
-
- @XmlAttribute(name = "outlineColour")
- protected Integer outlineColour;
-
- @XmlAttribute(name = "displayBoxes")
- protected Boolean displayBoxes;
-
- @XmlAttribute(name = "displayText")
- protected Boolean displayText;
-
- @XmlAttribute(name = "colourText")
- protected Boolean colourText;
-
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
-
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
-
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
-
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
-
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
-
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
-
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
-
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the seq property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the seq property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSeq().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getSeq()
- {
- if (seq == null)
- {
- seq = new ArrayList<String>();
- }
- return this.seq;
- }
-
- /**
- * Gets the value of the annotationColours property.
- *
- * @return possible object is {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours()
- {
- return annotationColours;
- }
-
- /**
- * Sets the value of the annotationColours property.
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+ "creationDate",
+ "version",
+ "vamsasModel",
+ "jSeq",
+ "jGroup",
+ "viewport",
+ "userColours",
+ "tree",
+ "pcaViewer",
+ "featureSettings"
+})
+public class JalviewModel {
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+ @XmlElement(required = true)
+ protected String version;
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+ protected List<JalviewModel.Tree> tree;
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate() {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
*
* @param value
- * allowed object is {@link AnnotationColourScheme }
- *
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
*/
- public void setAnnotationColours(AnnotationColourScheme value)
- {
- this.annotationColours = value;
+ public void setCreationDate(XMLGregorianCalendar value) {
+ this.creationDate = value;
}
/**
- * Gets the value of the start property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the version property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public Integer getStart()
- {
- return start;
+ public String getVersion() {
+ return version;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setStart(Integer value)
- {
- this.start = value;
+ public void setVersion(String value) {
+ this.version = value;
}
/**
- * Gets the value of the end property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the vamsasModel property.
*
+ * @return
+ * possible object is
+ * {@link VAMSAS }
+ *
*/
- public Integer getEnd()
- {
- return end;
+ public VAMSAS getVamsasModel() {
+ return vamsasModel;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the vamsasModel property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link VAMSAS }
+ *
*/
- public void setEnd(Integer value)
- {
- this.end = value;
+ public void setVamsasModel(VAMSAS value) {
+ this.vamsasModel = value;
}
/**
- * Gets the value of the name property.
+ * Gets the value of the jSeq property.
*
- * @return possible object is {@link String }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
*
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the colour property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
*
- * @return possible object is {@link String }
*
*/
- public String getColour()
- {
- return colour;
+ public List<JalviewModel.JSeq> getJSeq() {
+ if (jSeq == null) {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
+ }
+ return this.jSeq;
}
/**
- * Sets the value of the colour property.
+ * Gets the value of the jGroup property.
*
- * @param value
- * allowed object is {@link String }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
*
- */
- public void setColour(String value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the consThreshold property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Integer }
*
- */
- public Integer getConsThreshold()
- {
- return consThreshold;
- }
-
- /**
- * Sets the value of the consThreshold property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
*
- * @param value
- * allowed object is {@link Integer }
*
*/
- public void setConsThreshold(Integer value)
- {
- this.consThreshold = value;
+ public List<JalviewModel.JGroup> getJGroup() {
+ if (jGroup == null) {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
+ }
+ return this.jGroup;
}
/**
- * Gets the value of the pidThreshold property.
+ * Gets the value of the viewport property.
*
- * @return possible object is {@link Integer }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
*
- */
- public Integer getPidThreshold()
- {
- return pidThreshold;
- }
-
- /**
- * Sets the value of the pidThreshold property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link Integer }
*
- */
- public void setPidThreshold(Integer value)
- {
- this.pidThreshold = value;
- }
-
- /**
- * Gets the value of the outlineColour property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
*
- * @return possible object is {@link Integer }
*
*/
- public Integer getOutlineColour()
- {
- return outlineColour;
+ public List<JalviewModel.Viewport> getViewport() {
+ if (viewport == null) {
+ viewport = new ArrayList<JalviewModel.Viewport>();
+ }
+ return this.viewport;
}
/**
- * Sets the value of the outlineColour property.
+ * Gets the value of the userColours property.
*
- * @param value
- * allowed object is {@link Integer }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
*
- */
- public void setOutlineColour(Integer value)
- {
- this.outlineColour = value;
- }
-
- /**
- * Gets the value of the displayBoxes property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
- */
- public Boolean isDisplayBoxes()
- {
- return displayBoxes;
- }
-
- /**
- * Sets the value of the displayBoxes property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
*
- * @param value
- * allowed object is {@link Boolean }
*
*/
- public void setDisplayBoxes(Boolean value)
- {
- this.displayBoxes = value;
+ public List<JalviewModel.UserColours> getUserColours() {
+ if (userColours == null) {
+ userColours = new ArrayList<JalviewModel.UserColours>();
+ }
+ return this.userColours;
}
/**
- * Gets the value of the displayText property.
+ * Gets the value of the tree property.
*
- * @return possible object is {@link Boolean }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- */
- public Boolean isDisplayText()
- {
- return displayText;
- }
-
- /**
- * Sets the value of the displayText property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link Boolean }
*
- */
- public void setDisplayText(Boolean value)
- {
- this.displayText = value;
- }
-
- /**
- * Gets the value of the colourText property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
*
- * @return possible object is {@link Boolean }
*
*/
- public Boolean isColourText()
- {
- return colourText;
+ public List<JalviewModel.Tree> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
}
/**
- * Sets the value of the colourText property.
+ * Gets the value of the pcaViewer property.
*
- * @param value
- * allowed object is {@link Boolean }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
*
- */
- public void setColourText(Boolean value)
- {
- this.colourText = value;
- }
-
- /**
- * Gets the value of the textCol1 property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPcaViewer().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Integer }
*
- */
- public Integer getTextCol1()
- {
- return textCol1;
- }
-
- /**
- * Sets the value of the textCol1 property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
*
- * @param value
- * allowed object is {@link Integer }
*
*/
- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
+ public List<JalviewModel.PcaViewer> getPcaViewer() {
+ if (pcaViewer == null) {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
}
/**
- * Gets the value of the textCol2 property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the featureSettings property.
*
+ * @return
+ * possible object is
+ * {@link JalviewModel.FeatureSettings }
+ *
*/
- public Integer getTextCol2()
- {
- return textCol2;
+ public JalviewModel.FeatureSettings getFeatureSettings() {
+ return featureSettings;
}
/**
- * Sets the value of the textCol2 property.
+ * Sets the value of the featureSettings property.
*
* @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
-
- /**
- * Gets the value of the textColThreshold property.
+ * allowed object is
+ * {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value) {
+ this.featureSettings = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @return possible object is {@link Integer }
*
*/
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "setting",
+ "group"
+ })
+ public static class FeatureSettings {
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowUnconserved()
- {
- return showUnconserved;
- }
+ /**
+ * Gets the value of the setting property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSetting().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Setting> getSetting() {
+ if (setting == null) {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
+ /**
+ * Gets the value of the group property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Group> getGroup() {
+ if (group == null) {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName",
+ "matcherSet"
+ })
+ public static class Setting {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+ @XmlAttribute(name = "order")
+ protected Float order;
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getOrder() {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setOrder(Float value) {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMincolour() {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value) {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getThreshstate() {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value) {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
}
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
/**
- * Gets the value of the id property.
+ * <p>Java class for anonymous complex type.
*
- * @return possible object is {@link String }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setId(String value)
- {
- this.id = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "seq",
+ "annotationColours"
+ })
+ public static class JGroup {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "colour")
+ protected String colour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "id")
+ protected String id;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="features"
- * type="{www.jalview.org}feature" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;simpleContent&gt; &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/extension&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="hiddenSequences"
- * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="rnaViewer"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="hidden"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "features", "pdbids", "hiddenSequences", "rnaViewer" })
- public static class JSeq
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids> pdbids;
-
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
-
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
-
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
-
- /**
- * Gets the value of the features property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the features property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getFeatures().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Feature }
- *
- *
- */
- public List<Feature> getFeatures()
- {
- if (features == null)
- {
- features = new ArrayList<Feature>();
- }
- return this.features;
- }
-
- /**
- * Gets the value of the pdbids property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the pdbids property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getPdbids().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids> getPdbids()
- {
- if (pdbids == null)
- {
- pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
- }
- return this.pdbids;
- }
-
- /**
- * Gets the value of the hiddenSequences property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the hiddenSequences property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getHiddenSequences().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getHiddenSequences()
- {
- if (hiddenSequences == null)
- {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
- }
-
- /**
- * Gets the value of the rnaViewer property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the rnaViewer property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getRnaViewer().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
- {
- if (rnaViewer == null)
- {
- rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColour(Integer value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the hidden property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isHidden()
- {
- return hidden;
- }
-
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setHidden(Boolean value)
- {
- this.hidden = value;
- }
-
- /**
- * Gets the value of the viewreference property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isViewreference()
- {
- return viewreference;
- }
-
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setViewreference(Boolean value)
- {
- this.viewreference = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt; &lt;element name="structureState"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;simpleContent&gt; &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/extension&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "structureState" })
- public static class Pdbids extends Pdbentry
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p> This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the returned
- * list will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the structureState property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getStructureState().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
- {
- if (structureState == null)
- {
- structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;simpleContent&gt;
- * &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
- * /&gt; &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
- * /&gt; &lt;attribute name="type"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class StructureState
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "visible")
- protected Boolean visible;
-
- @XmlAttribute(name = "viewId")
- protected String viewId;
-
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
-
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
-
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
-
- @XmlAttribute(name = "type")
- protected String type;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Gets the value of the seq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getSeq() {
+ if (seq == null) {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
+ }
/**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the annotationColours property.
*
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
*/
- public String getValue()
- {
- return value;
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the annotationColours property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
}
/**
- * Gets the value of the visible property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the start property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Boolean isVisible()
- {
- return visible;
+ public Integer getStart() {
+ return start;
}
/**
- * Sets the value of the visible property.
+ * Sets the value of the start property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setVisible(Boolean value)
- {
- this.visible = value;
+ public void setStart(Integer value) {
+ this.start = value;
}
/**
- * Gets the value of the viewId property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the end property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getViewId()
- {
- return viewId;
+ public Integer getEnd() {
+ return end;
}
/**
- * Sets the value of the viewId property.
+ * Sets the value of the end property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setViewId(String value)
- {
- this.viewId = value;
+ public void setEnd(Integer value) {
+ this.end = value;
}
/**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the name property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public boolean isAlignwithAlignPanel()
- {
- if (alignwithAlignPanel == null)
- {
- return true;
- }
- else
- {
- return alignwithAlignPanel;
- }
+ public String getName() {
+ return name;
}
/**
- * Sets the value of the alignwithAlignPanel property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setAlignwithAlignPanel(Boolean value)
- {
- this.alignwithAlignPanel = value;
+ public void setName(String value) {
+ this.name = value;
}
/**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the colour property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public boolean isColourwithAlignPanel()
- {
- if (colourwithAlignPanel == null)
- {
- return false;
- }
- else
- {
- return colourwithAlignPanel;
- }
+ public String getColour() {
+ return colour;
}
/**
- * Sets the value of the colourwithAlignPanel property.
+ * Sets the value of the colour property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setColourwithAlignPanel(Boolean value)
- {
- this.colourwithAlignPanel = value;
+ public void setColour(String value) {
+ this.colour = value;
}
/**
- * Gets the value of the colourByJmol property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the consThreshold property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public boolean isColourByJmol()
- {
- if (colourByJmol == null)
- {
- return true;
- }
- else
- {
- return colourByJmol;
- }
+ public Integer getConsThreshold() {
+ return consThreshold;
}
/**
- * Sets the value of the colourByJmol property.
+ * Sets the value of the consThreshold property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setColourByJmol(Boolean value)
- {
- this.colourByJmol = value;
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
}
/**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the pidThreshold property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getType()
- {
- return type;
+ public Integer getPidThreshold() {
+ return pidThreshold;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the pidThreshold property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setType(String value)
- {
- this.type = value;
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
}
/**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the outlineColour property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Integer getWidth()
- {
- return width;
+ public Integer getOutlineColour() {
+ return outlineColour;
}
/**
- * Sets the value of the width property.
+ * Sets the value of the outlineColour property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setWidth(Integer value)
- {
- this.width = value;
+ public void setOutlineColour(Integer value) {
+ this.outlineColour = value;
}
/**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the displayBoxes property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Integer getHeight()
- {
- return height;
+ public Boolean isDisplayBoxes() {
+ return displayBoxes;
}
/**
- * Sets the value of the height property.
+ * Sets the value of the displayBoxes property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setHeight(Integer value)
- {
- this.height = value;
+ public void setDisplayBoxes(Boolean value) {
+ this.displayBoxes = value;
}
/**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the displayText property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Integer getXpos()
- {
- return xpos;
+ public Boolean isDisplayText() {
+ return displayText;
}
/**
- * Sets the value of the xpos property.
+ * Sets the value of the displayText property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setXpos(Integer value)
- {
- this.xpos = value;
+ public void setDisplayText(Boolean value) {
+ this.displayText = value;
}
/**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the colourText property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Integer getYpos()
- {
- return ypos;
+ public Boolean isColourText() {
+ return colourText;
}
/**
- * Sets the value of the ypos property.
+ * Sets the value of the colourText property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setYpos(Integer value)
- {
- this.ypos = value;
+ public void setColourText(Boolean value) {
+ this.colourText = value;
}
- }
-
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "secondaryStructure" })
- public static class RnaViewer
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "viewId")
- protected String viewId;
-
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
-
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p> This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the returned
- * list will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the secondaryStructure
- * property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSecondaryStructure().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
- {
- if (secondaryStructure == null)
- {
- secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewId()
- {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewId(String value)
- {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getDividerLocation()
- {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setDividerLocation(Integer value)
- {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getSelectedRna()
- {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setSelectedRna(Integer value)
- {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure
- {
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
-
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
-
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
/**
- * Gets the value of the title property.
+ * Sets the value of the textCol1 property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
+
+ /**
+ * Gets the value of the textCol2 property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getTitle()
- {
- return title;
+ public Integer getTextCol2() {
+ return textCol2;
}
/**
- * Sets the value of the title property.
+ * Sets the value of the textCol2 property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public void setTitle(String value)
- {
- this.title = value;
+ public Integer getTextColThreshold() {
+ return textColThreshold;
}
/**
- * Gets the value of the annotationId property.
+ * Sets the value of the textColThreshold property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public String getAnnotationId()
- {
- return annotationId;
+ public Boolean isShowUnconserved() {
+ return showUnconserved;
}
/**
- * Sets the value of the annotationId property.
+ * Sets the value of the showUnconserved property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
+
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public void setAnnotationId(String value)
- {
- this.annotationId = value;
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
}
/**
- * Gets the value of the gapped property.
+ * Sets the value of the ignoreGapsinConsensus property.
*
- * @return possible object is {@link Boolean }
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
+
+ /**
+ * Gets the value of the showConsensusHistogram property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Boolean isGapped()
- {
- return gapped;
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
}
/**
- * Sets the value of the gapped property.
+ * Sets the value of the showConsensusHistogram property.
*
* @param value
- * allowed object is {@link Boolean }
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
+
+ /**
+ * Gets the value of the showSequenceLogo property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public void setGapped(Boolean value)
- {
- this.gapped = value;
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
}
/**
- * Gets the value of the viewerState property.
+ * Sets the value of the showSequenceLogo property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public String getViewerState()
- {
- return viewerState;
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
}
/**
- * Sets the value of the viewerState property.
+ * Sets the value of the normaliseSequenceLogo property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the id property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setViewerState(String value)
- {
- this.viewerState = value;
+ public String getId() {
+ return id;
}
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
}
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequencePoint"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute
- * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="pcaData"
- * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="xDim"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="bgColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
- public static class PcaViewer
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.Axis> axis;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected PcaDataType pcaData;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "scoreModelName")
- protected String scoreModelName;
-
- @XmlAttribute(name = "xDim")
- protected Integer xDim;
-
- @XmlAttribute(name = "yDim")
- protected Integer yDim;
-
- @XmlAttribute(name = "zDim")
- protected Integer zDim;
-
- @XmlAttribute(name = "bgColour")
- protected Integer bgColour;
-
- @XmlAttribute(name = "scaleFactor")
- protected Float scaleFactor;
-
- @XmlAttribute(name = "showLabels")
- protected Boolean showLabels;
-
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- @XmlAttribute(name = "includeGaps")
- protected Boolean includeGaps;
-
- @XmlAttribute(name = "matchGaps")
- protected Boolean matchGaps;
-
- @XmlAttribute(name = "includeGappedColumns")
- protected Boolean includeGappedColumns;
-
- @XmlAttribute(name = "denominateByShortestLength")
- protected Boolean denominateByShortestLength;
/**
- * Gets the value of the sequencePoint property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the sequencePoint property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSequencePoint().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.SequencePoint }
- *
- *
- */
- public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
- {
- if (sequencePoint == null)
- {
- sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
- }
- return this.sequencePoint;
- }
-
- /**
- * Gets the value of the axis property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the axis property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAxis().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.Axis }
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
- public List<JalviewModel.PcaViewer.Axis> getAxis()
- {
- if (axis == null)
- {
- axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
- }
- return this.axis;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "features",
+ "pdbids",
+ "hiddenSequences",
+ "rnaViewer"
+ })
+ public static class JSeq {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids> pdbids;
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
- /**
- * Gets the value of the seqPointMin property.
- *
- * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
- {
- return seqPointMin;
- }
+ /**
+ * Gets the value of the features property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature }
+ *
+ *
+ */
+ public List<Feature> getFeatures() {
+ if (features == null) {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
+ }
- /**
- * Sets the value of the seqPointMin property.
- *
- * @param value
- * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
- {
- this.seqPointMin = value;
- }
+ /**
+ * Gets the value of the pdbids property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPdbids().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids> getPdbids() {
+ if (pdbids == null) {
+ pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
- /**
- * Gets the value of the seqPointMax property.
- *
- * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
- {
- return seqPointMax;
- }
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getHiddenSequences() {
+ if (hiddenSequences == null) {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
- /**
- * Sets the value of the seqPointMax property.
- *
- * @param value
- * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
- {
- this.seqPointMax = value;
- }
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
+ if (rnaViewer == null) {
+ rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
- /**
- * Gets the value of the pcaData property.
- *
- * @return possible object is {@link PcaDataType }
- *
- */
- public PcaDataType getPcaData()
- {
- return pcaData;
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
- /**
- * Sets the value of the pcaData property.
- *
- * @param value
- * allowed object is {@link PcaDataType }
- *
- */
- public void setPcaData(PcaDataType value)
- {
- this.pcaData = value;
- }
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
- /**
- * Gets the value of the scoreModelName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getScoreModelName()
- {
- return scoreModelName;
- }
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
- /**
- * Sets the value of the scoreModelName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setScoreModelName(String value)
- {
- this.scoreModelName = value;
- }
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
- /**
- * Gets the value of the xDim property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXDim()
- {
- return xDim;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the xDim property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXDim(Integer value)
- {
- this.xDim = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the yDim property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYDim()
- {
- return yDim;
- }
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isHidden() {
+ return hidden;
+ }
- /**
- * Sets the value of the yDim property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYDim(Integer value)
- {
- this.yDim = value;
- }
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value) {
+ this.hidden = value;
+ }
- /**
- * Gets the value of the zDim property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getZDim()
- {
- return zDim;
- }
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isViewreference() {
+ return viewreference;
+ }
- /**
- * Sets the value of the zDim property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setZDim(Integer value)
- {
- this.zDim = value;
- }
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value) {
+ this.viewreference = value;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getBgColour()
- {
- return bgColour;
- }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setBgColour(Integer value)
- {
- this.bgColour = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "structureState"
+ })
+ public static class Pdbids
+ extends Pdbentry
+ {
- /**
- * Gets the value of the scaleFactor property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getScaleFactor()
- {
- return scaleFactor;
- }
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
+ if (structureState == null) {
+ structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class StructureState {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAlignwithAlignPanel() {
+ if (alignwithAlignPanel == null) {
+ return true;
+ } else {
+ return alignwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the alignwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAlignwithAlignPanel(Boolean value) {
+ this.alignwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourwithAlignPanel() {
+ if (colourwithAlignPanel == null) {
+ return false;
+ } else {
+ return colourwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the colourwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourwithAlignPanel(Boolean value) {
+ this.colourwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourByJmol property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourByJmol() {
+ if (colourByJmol == null) {
+ return true;
+ } else {
+ return colourByJmol;
+ }
+ }
+
+ /**
+ * Sets the value of the colourByJmol property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByJmol(Boolean value) {
+ this.colourByJmol = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
- /**
- * Sets the value of the scaleFactor property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setScaleFactor(Float value)
- {
- this.scaleFactor = value;
- }
+ }
- /**
- * Gets the value of the showLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowLabels()
- {
- return showLabels;
- }
- /**
- * Sets the value of the showLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value)
- {
- this.showLabels = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "secondaryStructure"
+ })
+ public static class RnaViewer {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+ if (secondaryStructure == null) {
+ secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getDividerLocation() {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value) {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getSelectedRna() {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value) {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the annotationId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotationId() {
+ return annotationId;
+ }
+
+ /**
+ * Sets the value of the annotationId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotationId(String value) {
+ this.annotationId = value;
+ }
+
+ /**
+ * Gets the value of the gapped property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGapped() {
+ return gapped;
+ }
+
+ /**
+ * Sets the value of the gapped property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGapped(Boolean value) {
+ this.gapped = value;
+ }
+
+ /**
+ * Gets the value of the viewerState property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewerState() {
+ return viewerState;
+ }
+
+ /**
+ * Sets the value of the viewerState property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewerState(String value) {
+ this.viewerState = value;
+ }
+
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isLinkToAllViews()
- {
- return linkToAllViews;
- }
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value)
- {
- this.linkToAllViews = value;
}
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
/**
- * Sets the value of the width property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link Integer }
*
*/
- public void setWidth(Integer value)
- {
- this.width = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "sequencePoint",
+ "axis",
+ "seqPointMin",
+ "seqPointMax",
+ "pcaData"
+ })
+ public static class PcaViewer {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.Axis> axis;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
+ /**
+ * Gets the value of the sequencePoint property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequencePoint().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
+ if (sequencePoint == null) {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
+ /**
+ * Gets the value of the axis property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAxis().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.Axis> getAxis() {
+ if (axis == null) {
+ axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+ }
+ return this.axis;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
+ /**
+ * Gets the value of the seqPointMin property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+ return seqPointMin;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
+ /**
+ * Sets the value of the seqPointMin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+ this.seqPointMin = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
+ /**
+ * Gets the value of the seqPointMax property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+ return seqPointMax;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+ this.seqPointMax = value;
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isIncludeGaps()
- {
- return includeGaps;
- }
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return
+ * possible object is
+ * {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData() {
+ return pcaData;
+ }
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value)
- {
- this.includeGaps = value;
- }
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value) {
+ this.pcaData = value;
+ }
- /**
- * Gets the value of the matchGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isMatchGaps()
- {
- return matchGaps;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value)
- {
- this.matchGaps = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns()
- {
- return includeGappedColumns;
- }
+ /**
+ * Gets the value of the scoreModelName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScoreModelName() {
+ return scoreModelName;
+ }
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value)
- {
- this.includeGappedColumns = value;
- }
+ /**
+ * Sets the value of the scoreModelName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScoreModelName(String value) {
+ this.scoreModelName = value;
+ }
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength()
- {
- return denominateByShortestLength;
- }
+ /**
+ * Gets the value of the xDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXDim() {
+ return xDim;
+ }
- /**
- * Sets the value of the denominateByShortestLength property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value)
- {
- this.denominateByShortestLength = value;
- }
+ /**
+ * Sets the value of the xDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXDim(Integer value) {
+ this.xDim = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis
- {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYDim() {
+ return yDim;
+ }
- }
+ /**
+ * Sets the value of the yDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYDim(Integer value) {
+ this.yDim = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax
- {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the zDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getZDim() {
+ return zDim;
+ }
- }
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setZDim(Integer value) {
+ this.zDim = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin
- {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getBgColour() {
+ return bgColour;
+ }
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value) {
+ this.bgColour = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute
- * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint
- {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceRef()
- {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceRef(String value)
- {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the scaleFactor property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getScaleFactor() {
+ return scaleFactor;
+ }
- }
+ /**
+ * Sets the value of the scaleFactor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setScaleFactor(Float value) {
+ this.scaleFactor = value;
+ }
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
- * minOccurs="0"&gt; &lt;element name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showDistances"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID"
- * /&gt; &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "title", "newick" })
- public static class Tree
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
-
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
-
- @XmlAttribute(name = "fontName")
- protected String fontName;
-
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
-
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
-
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
-
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
-
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
-
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
-
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
-
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels() {
+ return showLabels;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
+ /**
+ * Sets the value of the showLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowLabels(Boolean value) {
+ this.showLabels = value;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews() {
+ return linkToAllViews;
+ }
- /**
- * Gets the value of the newick property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getNewick()
- {
- return newick;
- }
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
- /**
- * Sets the value of the newick property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setNewick(String value)
- {
- this.newick = value;
- }
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps() {
+ return includeGaps;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFontName()
- {
- return fontName;
- }
+ /**
+ * Sets the value of the includeGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFontName(String value)
- {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps() {
+ return matchGaps;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontSize()
- {
- return fontSize;
- }
+ /**
+ * Sets the value of the matchGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontSize(Integer value)
- {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontStyle()
- {
- return fontStyle;
- }
+ /**
+ * Sets the value of the includeGappedColumns property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontStyle(Integer value)
- {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
+ }
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
+ }
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowBootstrap()
- {
- return showBootstrap;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value)
- {
- this.showBootstrap = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
- /**
- * Gets the value of the showDistances property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowDistances()
- {
- return showDistances;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value)
- {
- this.showDistances = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked()
- {
- return markUnlinked;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value)
- {
- this.markUnlinked = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isFitToWindow()
- {
- return fitToWindow;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value)
- {
- this.fitToWindow = value;
- }
- /**
- * Gets the value of the currentTree property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isCurrentTree()
- {
- return currentTree;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Axis {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value)
- {
- this.currentTree = value;
- }
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isLinkToAllViews()
- {
- if (linkToAllViews == null)
- {
- return false;
- }
- else
- {
- return linkToAllViews;
- }
- }
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value)
- {
- this.linkToAllViews = value;
}
+
/**
- * Gets the value of the width property.
+ * <p>Java class for anonymous complex type.
*
- * @return possible object is {@link Integer }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link Integer }
*
*/
- public void setWidth(Integer value)
- {
- this.width = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "newick"
+ })
+ public static class Tree {
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNewick() {
+ return newick;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNewick(String value) {
+ this.newick = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="UserColourScheme"
- * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "userColourScheme" })
- public static class UserColours
- {
-
- @XmlElement(
- name = "UserColourScheme",
- namespace = "www.jalview.org",
- required = true)
- protected JalviewUserColours userColourScheme;
-
- @XmlAttribute(name = "id")
- protected String id;
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return possible object is {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme()
- {
- return userColourScheme;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value)
- {
- this.userColourScheme = value;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="AnnotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="autoUpdate"
- * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="conservationSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="viewName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="gatheredViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="showComplementFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "annotationColours", "hiddenColumns", "calcIdParam" })
- public static class Viewport
- {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
-
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
-
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
-
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
-
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
-
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
-
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
-
- @XmlAttribute(name = "showText")
- protected Boolean showText;
-
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
-
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
-
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
-
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
-
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap() {
+ return showBootstrap;
+ }
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value) {
+ this.showBootstrap = value;
+ }
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances() {
+ return showDistances;
+ }
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value) {
+ this.showDistances = value;
+ }
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked() {
+ return markUnlinked;
+ }
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value) {
+ this.markUnlinked = value;
+ }
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow() {
+ return fitToWindow;
+ }
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value) {
+ this.fitToWindow = value;
+ }
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree() {
+ return currentTree;
+ }
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value) {
+ this.currentTree = value;
+ }
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews() {
+ if (linkToAllViews == null) {
+ return false;
+ } else {
+ return linkToAllViews;
+ }
+ }
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
- @XmlAttribute(name = "fontName")
- protected String fontName;
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
- @XmlAttribute(name = "viewName")
- protected String viewName;
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
+ }
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "userColourScheme"
+ })
+ public static class UserColours {
- @XmlAttribute(name = "complementId")
- protected String complementId;
+ @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+ protected JalviewUserColours userColourScheme;
+ @XmlAttribute(name = "id")
+ protected String id;
- @XmlAttribute(name = "showComplementFeatures")
- protected Boolean showComplementFeatures;
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme() {
+ return userColourScheme;
+ }
- @XmlAttribute(name = "showComplementFeaturesOnTop")
- protected Boolean showComplementFeaturesOnTop;
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value) {
+ this.userColourScheme = value;
+ }
- @XmlAttribute(name = "width")
- protected Integer width;
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- @XmlAttribute(name = "height")
- protected Integer height;
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
+ }
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
/**
- * Gets the value of the annotationColours property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @return possible object is {@link AnnotationColourScheme }
*
*/
- public AnnotationColourScheme getAnnotationColours()
- {
- return annotationColours;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "annotationColours",
+ "hiddenColumns",
+ "calcIdParam",
+ "overview"
+ })
+ public static class Viewport {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+ @XmlElement(namespace = "www.jalview.org")
+ protected JalviewModel.Viewport.Overview overview;
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value)
- {
- this.annotationColours = value;
- }
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
+ }
- /**
- * Gets the value of the hiddenColumns property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the hiddenColumns property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getHiddenColumns().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.HiddenColumns }
- *
- *
- */
- public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
- {
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
- }
- return this.hiddenColumns;
- }
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
- /**
- * Gets the value of the calcIdParam property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the calcIdParam property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getCalcIdParam().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.CalcIdParam }
- *
- *
- */
- public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
- {
- if (calcIdParam == null)
- {
- calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
- }
- return this.calcIdParam;
- }
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
+ if (hiddenColumns == null) {
+ hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isConservationSelected()
- {
- return conservationSelected;
- }
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
+ if (calcIdParam == null) {
+ calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value)
- {
- this.conservationSelected = value;
- }
+ /**
+ * Gets the value of the overview property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview getOverview() {
+ return overview;
+ }
- /**
- * Gets the value of the pidSelected property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPidSelected()
- {
- return pidSelected;
- }
+ /**
+ * Sets the value of the overview property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public void setOverview(JalviewModel.Viewport.Overview value) {
+ this.overview = value;
+ }
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value)
- {
- this.pidSelected = value;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected() {
+ return conservationSelected;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getBgColour()
- {
- return bgColour;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value) {
+ this.conservationSelected = value;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setBgColour(String value)
- {
- this.bgColour = value;
- }
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected() {
+ return pidSelected;
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getConsThreshold()
- {
- return consThreshold;
- }
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value) {
+ this.pidSelected = value;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setConsThreshold(Integer value)
- {
- this.consThreshold = value;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getBgColour() {
+ return bgColour;
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getPidThreshold()
- {
- return pidThreshold;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setBgColour(String value) {
+ this.bgColour = value;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setPidThreshold(Integer value)
- {
- this.pidThreshold = value;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getConsThreshold() {
+ return consThreshold;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getPidThreshold() {
+ return pidThreshold;
+ }
- /**
- * Gets the value of the showFullId property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowFullId()
- {
- return showFullId;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
+ }
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value)
- {
- this.showFullId = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isRightAlignIds()
- {
- return rightAlignIds;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value)
- {
- this.rightAlignIds = value;
- }
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId() {
+ return showFullId;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowText()
- {
- return showText;
- }
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value) {
+ this.showFullId = value;
+ }
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowText(Boolean value)
- {
- this.showText = value;
- }
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds() {
+ return rightAlignIds;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowColourText()
- {
- return showColourText;
- }
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value) {
+ this.rightAlignIds = value;
+ }
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value)
- {
- this.showColourText = value;
- }
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowText() {
+ return showText;
+ }
+
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value) {
+ this.showText = value;
+ }
+
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText() {
+ return showColourText;
+ }
+
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value) {
+ this.showColourText = value;
+ }
+
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved() {
+ if (showUnconserved == null) {
+ return false;
+ } else {
+ return showUnconserved;
+ }
+ }
+
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
+
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes() {
+ return showBoxes;
+ }
+
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value) {
+ this.showBoxes = value;
+ }
+
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment() {
+ return wrapAlignment;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowUnconserved()
- {
- if (showUnconserved == null)
- {
- return false;
- }
- else
- {
- return showUnconserved;
- }
- }
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value) {
+ this.wrapAlignment = value;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps() {
+ return renderGaps;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowBoxes()
- {
- return showBoxes;
- }
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value) {
+ this.renderGaps = value;
+ }
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value)
- {
- this.showBoxes = value;
- }
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures() {
+ return showSequenceFeatures;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isWrapAlignment()
- {
- return wrapAlignment;
- }
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value) {
+ this.showSequenceFeatures = value;
+ }
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value)
- {
- this.wrapAlignment = value;
- }
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip() {
+ return showNPfeatureTooltip;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isRenderGaps()
- {
- return renderGaps;
- }
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value) {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value)
- {
- this.renderGaps = value;
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip() {
+ return showDbRefTooltip;
+ }
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value) {
+ this.showDbRefTooltip = value;
+ }
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value)
- {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight() {
+ if (followHighlight == null) {
+ return true;
+ } else {
+ return followHighlight;
+ }
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip()
- {
- return showNPfeatureTooltip;
- }
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value) {
+ this.followHighlight = value;
+ }
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value)
- {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection() {
+ if (followSelection == null) {
+ return true;
+ } else {
+ return followSelection;
+ }
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip()
- {
- return showDbRefTooltip;
- }
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value) {
+ this.followSelection = value;
+ }
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value)
- {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation() {
+ return showAnnotation;
+ }
- /**
- * Gets the value of the followHighlight property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isFollowHighlight()
- {
- if (followHighlight == null)
- {
- return true;
- }
- else
- {
- return followHighlight;
- }
- }
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value) {
+ this.showAnnotation = value;
+ }
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value)
- {
- this.followHighlight = value;
- }
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels() {
+ if (centreColumnLabels == null) {
+ return false;
+ } else {
+ return centreColumnLabels;
+ }
+ }
- /**
- * Gets the value of the followSelection property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isFollowSelection()
- {
- if (followSelection == null)
- {
- return true;
- }
- else
- {
- return followSelection;
- }
- }
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value) {
+ this.centreColumnLabels = value;
+ }
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value)
- {
- this.followSelection = value;
- }
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation() {
+ if (showGroupConservation == null) {
+ return false;
+ } else {
+ return showGroupConservation;
+ }
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowAnnotation()
- {
- return showAnnotation;
- }
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value) {
+ this.showGroupConservation = value;
+ }
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value)
- {
- this.showAnnotation = value;
- }
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus() {
+ if (showGroupConsensus == null) {
+ return false;
+ } else {
+ return showGroupConsensus;
+ }
+ }
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels()
- {
- if (centreColumnLabels == null)
- {
- return false;
- }
- else
- {
- return centreColumnLabels;
- }
- }
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value) {
+ this.showGroupConsensus = value;
+ }
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value)
- {
- this.centreColumnLabels = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the showGroupConservation property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowGroupConservation()
- {
- if (showGroupConservation == null)
- {
- return false;
- }
- else
- {
- return showGroupConservation;
- }
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowGroupConservation(Boolean value)
- {
- this.showGroupConservation = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the showGroupConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus()
- {
- if (showGroupConsensus == null)
- {
- return false;
- }
- else
- {
- return showGroupConsensus;
- }
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowGroupConsensus(Boolean value)
- {
- this.showGroupConsensus = value;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartRes() {
+ return startRes;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value) {
+ this.startRes = value;
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartSeq() {
+ return startSeq;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value) {
+ this.startSeq = value;
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStartRes()
- {
- return startRes;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStartRes(Integer value)
- {
- this.startRes = value;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
- /**
- * Gets the value of the startSeq property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStartSeq()
- {
- return startSeq;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStartSeq(Integer value)
- {
- this.startSeq = value;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFontName()
- {
- return fontName;
- }
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna() {
+ if (scaleProteinAsCdna == null) {
+ return true;
+ } else {
+ return scaleProteinAsCdna;
+ }
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFontName(String value)
- {
- this.fontName = value;
- }
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value) {
+ this.scaleProteinAsCdna = value;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontSize()
- {
- return fontSize;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewName() {
+ return viewName;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontSize(Integer value)
- {
- this.fontSize = value;
- }
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewName(String value) {
+ this.viewName = value;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontStyle()
- {
- return fontStyle;
- }
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceSetId() {
+ return sequenceSetId;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontStyle(Integer value)
- {
- this.fontStyle = value;
- }
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceSetId(String value) {
+ this.sequenceSetId = value;
+ }
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna()
- {
- if (scaleProteinAsCdna == null)
- {
- return true;
- }
- else
- {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews() {
+ return gatheredViews;
+ }
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value)
- {
- this.scaleProteinAsCdna = value;
- }
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value) {
+ this.gatheredViews = value;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewName()
- {
- return viewName;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewName(String value)
- {
- this.viewName = value;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceSetId()
- {
- return sequenceSetId;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol2() {
+ return textCol2;
+ }
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceSetId(String value)
- {
- this.sequenceSetId = value;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isGatheredViews()
- {
- return gatheredViews;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold() {
+ return textColThreshold;
+ }
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value)
- {
- this.gatheredViews = value;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol1()
- {
- return textCol1;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol2()
- {
- return textCol2;
- }
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComplementId() {
+ return complementId;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComplementId(String value) {
+ this.complementId = value;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
+ /**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures() {
+ if (showComplementFeatures == null) {
+ return false;
+ } else {
+ return showComplementFeatures;
+ }
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value) {
+ this.showComplementFeatures = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop() {
+ if (showComplementFeaturesOnTop == null) {
+ return false;
+ } else {
+ return showComplementFeaturesOnTop;
+ }
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value) {
+ this.showComplementFeaturesOnTop = value;
+ }
- /**
- * Gets the value of the complementId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getComplementId()
- {
- return complementId;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setComplementId(String value)
- {
- this.complementId = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
- /**
- * Gets the value of the showComplementFeatures property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowComplementFeatures()
- {
- if (showComplementFeatures == null)
- {
- return false;
- }
- else
- {
- return showComplementFeatures;
- }
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
- /**
- * Sets the value of the showComplementFeatures property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowComplementFeatures(Boolean value)
- {
- this.showComplementFeatures = value;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
- /**
- * Gets the value of the showComplementFeaturesOnTop property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowComplementFeaturesOnTop()
- {
- if (showComplementFeaturesOnTop == null)
- {
- return false;
- }
- else
- {
- return showComplementFeaturesOnTop;
- }
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
- /**
- * Sets the value of the showComplementFeaturesOnTop property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowComplementFeaturesOnTop(Boolean value)
- {
- this.showComplementFeaturesOnTop = value;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam
+ extends WebServiceParameterSet
+ {
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate() {
+ if (needsUpdate == null) {
+ return false;
+ } else {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value) {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate() {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value) {
+ this.autoUpdate = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStart(Integer value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setEnd(Integer value) {
+ this.end = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="autoUpdate" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam extends WebServiceParameterSet
- {
-
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
-
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
-
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * Gets the value of the calcId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCalcId()
- {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCalcId(String value)
- {
- this.calcId = value;
- }
-
- /**
- * Gets the value of the needsUpdate property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNeedsUpdate()
- {
- if (needsUpdate == null)
- {
- return false;
}
- else
- {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNeedsUpdate(Boolean value)
- {
- this.needsUpdate = value;
- }
-
- /**
- * Gets the value of the autoUpdate property.
- *
- */
- public boolean isAutoUpdate()
- {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value)
- {
- this.autoUpdate = value;
- }
- }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns
- {
-
- @XmlAttribute(name = "start")
- protected Integer start;
-
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStart(Integer value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setEnd(Integer value)
- {
- this.end = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden() {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value) {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getResidueColour() {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value) {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGapColour() {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value) {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHiddenColour() {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value) {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- }
+ }
- }
+ }
}
+++ /dev/null
-//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
-// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.18 at 01:33:02 PM BST
-//
-
-package jalview.xml.binding.jalview;
-
-import java.util.ArrayList;
-import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlID;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
-import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-import javax.xml.datatype.XMLGregorianCalendar;
-
-/**
- * <p>
- * Java class for JalviewModelType complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
- *
- * <pre>
- * <complexType name="JalviewModelType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- * <sequence>
- * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="tree" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="FeatureSettings" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "JalviewModelType",
- namespace = "www.jalview.org",
- propOrder =
- { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
- "userColours", "tree", "featureSettings" })
-public class JalviewModelType
-{
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
-
- @XmlElement(required = true)
- protected String version;
-
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
-
- @XmlElement(name = "JSeq")
- protected List<JalviewModelType.JSeq> jSeq;
-
- @XmlElement(name = "JGroup")
- protected List<JalviewModelType.JGroup> jGroup;
-
- @XmlElement(name = "Viewport")
- protected List<JalviewModelType.Viewport> viewport;
-
- @XmlElement(name = "UserColours")
- protected List<JalviewModelType.UserColours> userColours;
-
- protected List<JalviewModelType.Tree> tree;
-
- @XmlElement(name = "FeatureSettings")
- protected JalviewModelType.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate()
- {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setCreationDate(XMLGregorianCalendar value)
- {
- this.creationDate = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return possible object is {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel()
- {
- return vamsasModel;
- }
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value)
- {
- this.vamsasModel = value;
- }
-
- /**
- * Gets the value of the jSeq property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the jSeq property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getJSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq }
- *
- *
- */
- public List<JalviewModelType.JSeq> getJSeq()
- {
- if (jSeq == null)
- {
- jSeq = new ArrayList<JalviewModelType.JSeq>();
- }
- return this.jSeq;
- }
-
- /**
- * Gets the value of the jGroup property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the jGroup property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getJGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JGroup }
- *
- *
- */
- public List<JalviewModelType.JGroup> getJGroup()
- {
- if (jGroup == null)
- {
- jGroup = new ArrayList<JalviewModelType.JGroup>();
- }
- return this.jGroup;
- }
-
- /**
- * Gets the value of the viewport property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the viewport property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getViewport().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport }
- *
- *
- */
- public List<JalviewModelType.Viewport> getViewport()
- {
- if (viewport == null)
- {
- viewport = new ArrayList<JalviewModelType.Viewport>();
- }
- return this.viewport;
- }
-
- /**
- * Gets the value of the userColours property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the userColours property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getUserColours().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.UserColours }
- *
- *
- */
- public List<JalviewModelType.UserColours> getUserColours()
- {
- if (userColours == null)
- {
- userColours = new ArrayList<JalviewModelType.UserColours>();
- }
- return this.userColours;
- }
-
- /**
- * Gets the value of the tree property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the tree property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getTree().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Tree }
- *
- *
- */
- public List<JalviewModelType.Tree> getTree()
- {
- if (tree == null)
- {
- tree = new ArrayList<JalviewModelType.Tree>();
- }
- return this.tree;
- }
-
- /**
- * Gets the value of the featureSettings property.
- *
- * @return possible object is {@link JalviewModelType.FeatureSettings }
- *
- */
- public JalviewModelType.FeatureSettings getFeatureSettings()
- {
- return featureSettings;
- }
-
- /**
- * Sets the value of the featureSettings property.
- *
- * @param value
- * allowed object is {@link JalviewModelType.FeatureSettings }
- *
- */
- public void setFeatureSettings(JalviewModelType.FeatureSettings value)
- {
- this.featureSettings = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "setting", "group" })
- public static class FeatureSettings
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.FeatureSettings.Setting> setting;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.FeatureSettings.Group> group;
-
- /**
- * Gets the value of the setting property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the setting property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSetting().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.FeatureSettings.Setting }
- *
- *
- */
- public List<JalviewModelType.FeatureSettings.Setting> getSetting()
- {
- if (setting == null)
- {
- setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
- }
- return this.setting;
- }
-
- /**
- * Gets the value of the group property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the group property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.FeatureSettings.Group }
- *
- *
- */
- public List<JalviewModelType.FeatureSettings.Group> getGroup()
- {
- if (group == null)
- {
- group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
- }
- return this.group;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group
- {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay()
- {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value)
- {
- this.display = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
- public static class Setting
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
-
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
-
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- @XmlAttribute(name = "order")
- protected Float order;
-
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
-
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
-
- @XmlAttribute(name = "max")
- protected Float max;
-
- @XmlAttribute(name = "min")
- protected Float min;
-
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
-
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String
- * }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return possible object is {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet()
- {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value)
- {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay()
- {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value)
- {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getOrder()
- {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setOrder(Float value)
- {
- this.order = value;
- }
-
- /**
- * Gets the value of the mincolour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMincolour()
- {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMincolour(Integer value)
- {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return possible object is {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour()
- {
- if (noValueColour == null)
- {
- return NoValueColour.MIN;
- }
- else
- {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value)
- {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the threshstate property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getThreshstate()
- {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setThreshstate(Integer value)
- {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMax()
- {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMax(Float value)
- {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMin()
- {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMin(Float value)
- {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isColourByLabel()
- {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value)
- {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isAutoScale()
- {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value)
- {
- this.autoScale = value;
- }
-
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "seq", "annotationColours" })
- public static class JGroup
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<String> seq;
-
- @XmlElement(namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
-
- @XmlAttribute(name = "start")
- protected Integer start;
-
- @XmlAttribute(name = "end")
- protected Integer end;
-
- @XmlAttribute(name = "name")
- protected String name;
-
- @XmlAttribute(name = "colour")
- protected String colour;
-
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
-
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
-
- @XmlAttribute(name = "outlineColour")
- protected Integer outlineColour;
-
- @XmlAttribute(name = "displayBoxes")
- protected Boolean displayBoxes;
-
- @XmlAttribute(name = "displayText")
- protected Boolean displayText;
-
- @XmlAttribute(name = "colourText")
- protected Boolean colourText;
-
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
-
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
-
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
-
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
-
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
-
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
-
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
-
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the seq property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the seq property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getSeq()
- {
- if (seq == null)
- {
- seq = new ArrayList<String>();
- }
- return this.seq;
- }
-
- /**
- * Gets the value of the annotationColours property.
- *
- * @return possible object is {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours()
- {
- return annotationColours;
- }
-
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value)
- {
- this.annotationColours = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStart(Integer value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setEnd(Integer value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setColour(String value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the consThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getConsThreshold()
- {
- return consThreshold;
- }
-
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setConsThreshold(Integer value)
- {
- this.consThreshold = value;
- }
-
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getPidThreshold()
- {
- return pidThreshold;
- }
-
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setPidThreshold(Integer value)
- {
- this.pidThreshold = value;
- }
-
- /**
- * Gets the value of the outlineColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getOutlineColour()
- {
- return outlineColour;
- }
-
- /**
- * Sets the value of the outlineColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setOutlineColour(Integer value)
- {
- this.outlineColour = value;
- }
-
- /**
- * Gets the value of the displayBoxes property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isDisplayBoxes()
- {
- return displayBoxes;
- }
-
- /**
- * Sets the value of the displayBoxes property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setDisplayBoxes(Boolean value)
- {
- this.displayBoxes = value;
- }
-
- /**
- * Gets the value of the displayText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isDisplayText()
- {
- return displayText;
- }
-
- /**
- * Sets the value of the displayText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setDisplayText(Boolean value)
- {
- this.displayText = value;
- }
-
- /**
- * Gets the value of the colourText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isColourText()
- {
- return colourText;
- }
-
- /**
- * Sets the value of the colourText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourText(Boolean value)
- {
- this.colourText = value;
- }
-
- /**
- * Gets the value of the textCol1 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol1()
- {
- return textCol1;
- }
-
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
- }
-
- /**
- * Gets the value of the textCol2 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol2()
- {
- return textCol2;
- }
-
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
-
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
-
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
-
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowUnconserved()
- {
- return showUnconserved;
- }
-
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
-
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
-
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
-
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
-
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
-
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
-
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "features", "pdbids", "hiddenSequences", "rnaViewer" })
- public static class JSeq
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.JSeq.Pdbids> pdbids;
-
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.JSeq.RnaViewer> rnaViewer;
-
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
-
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
-
- /**
- * Gets the value of the features property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the features property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getFeatures().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Feature }
- *
- *
- */
- public List<Feature> getFeatures()
- {
- if (features == null)
- {
- features = new ArrayList<Feature>();
- }
- return this.features;
- }
-
- /**
- * Gets the value of the pdbids property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the pdbids property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getPdbids().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.Pdbids }
- *
- *
- */
- public List<JalviewModelType.JSeq.Pdbids> getPdbids()
- {
- if (pdbids == null)
- {
- pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
- }
- return this.pdbids;
- }
-
- /**
- * Gets the value of the hiddenSequences property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the hiddenSequences property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getHiddenSequences().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getHiddenSequences()
- {
- if (hiddenSequences == null)
- {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
- }
-
- /**
- * Gets the value of the rnaViewer property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the rnaViewer property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getRnaViewer().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.RnaViewer }
- *
- *
- */
- public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer()
- {
- if (rnaViewer == null)
- {
- rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColour(Integer value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the hidden property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isHidden()
- {
- return hidden;
- }
-
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setHidden(Boolean value)
- {
- this.hidden = value;
- }
-
- /**
- * Gets the value of the viewreference property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isViewreference()
- {
- return viewreference;
- }
-
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setViewreference(Boolean value)
- {
- this.viewreference = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "structureState" })
- public static class Pdbids extends Pdbentry
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the structureState property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState()
- {
- if (structureState == null)
- {
- structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class StructureState
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "visible")
- protected Boolean visible;
-
- @XmlAttribute(name = "viewId")
- protected String viewId;
-
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
-
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
-
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
-
- @XmlAttribute(name = "type")
- protected String type;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isVisible()
- {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setVisible(Boolean value)
- {
- this.visible = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewId()
- {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewId(String value)
- {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isAlignwithAlignPanel()
- {
- if (alignwithAlignPanel == null)
- {
- return true;
- }
- else
- {
- return alignwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the alignwithAlignPanel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAlignwithAlignPanel(Boolean value)
- {
- this.alignwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isColourwithAlignPanel()
- {
- if (colourwithAlignPanel == null)
- {
- return false;
- }
- else
- {
- return colourwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the colourwithAlignPanel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourwithAlignPanel(Boolean value)
- {
- this.colourwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourByJmol property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isColourByJmol()
- {
- if (colourByJmol == null)
- {
- return true;
- }
- else
- {
- return colourByJmol;
- }
- }
-
- /**
- * Sets the value of the colourByJmol property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourByJmol(Boolean value)
- {
- this.colourByJmol = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
-
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "secondaryStructure" })
- public static class RnaViewer
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "viewId")
- protected String viewId;
-
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
-
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the secondaryStructure property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSecondaryStructure().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
- {
- if (secondaryStructure == null)
- {
- secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewId()
- {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewId(String value)
- {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getDividerLocation()
- {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setDividerLocation(Integer value)
- {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getSelectedRna()
- {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setSelectedRna(Integer value)
- {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure
- {
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
-
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
-
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the annotationId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getAnnotationId()
- {
- return annotationId;
- }
-
- /**
- * Sets the value of the annotationId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setAnnotationId(String value)
- {
- this.annotationId = value;
- }
-
- /**
- * Gets the value of the gapped property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isGapped()
- {
- return gapped;
- }
-
- /**
- * Sets the value of the gapped property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setGapped(Boolean value)
- {
- this.gapped = value;
- }
-
- /**
- * Gets the value of the viewerState property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewerState()
- {
- return viewerState;
- }
-
- /**
- * Sets the value of the viewerState property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewerState(String value)
- {
- this.viewerState = value;
- }
-
- }
-
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "title", "newick" })
- public static class Tree
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
-
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
-
- @XmlAttribute(name = "fontName")
- protected String fontName;
-
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
-
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
-
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
-
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
-
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
-
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
-
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the newick property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getNewick()
- {
- return newick;
- }
-
- /**
- * Sets the value of the newick property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setNewick(String value)
- {
- this.newick = value;
- }
-
- /**
- * Gets the value of the fontName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFontName()
- {
- return fontName;
- }
-
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFontName(String value)
- {
- this.fontName = value;
- }
-
- /**
- * Gets the value of the fontSize property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontSize()
- {
- return fontSize;
- }
-
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontSize(Integer value)
- {
- this.fontSize = value;
- }
-
- /**
- * Gets the value of the fontStyle property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontStyle()
- {
- return fontStyle;
- }
-
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontStyle(Integer value)
- {
- this.fontStyle = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowBootstrap()
- {
- return showBootstrap;
- }
-
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value)
- {
- this.showBootstrap = value;
- }
-
- /**
- * Gets the value of the showDistances property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowDistances()
- {
- return showDistances;
- }
-
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value)
- {
- this.showDistances = value;
- }
-
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked()
- {
- return markUnlinked;
- }
-
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value)
- {
- this.markUnlinked = value;
- }
-
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isFitToWindow()
- {
- return fitToWindow;
- }
-
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value)
- {
- this.fitToWindow = value;
- }
-
- /**
- * Gets the value of the currentTree property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isCurrentTree()
- {
- return currentTree;
- }
-
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value)
- {
- this.currentTree = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "userColourScheme" })
- public static class UserColours
- {
-
- @XmlElement(
- name = "UserColourScheme",
- namespace = "www.jalview.org",
- required = true)
- protected JalviewUserColours userColourScheme;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return possible object is {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme()
- {
- return userColourScheme;
- }
-
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value)
- {
- this.userColourScheme = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "annotationColours", "hiddenColumns", "calcIdParam" })
- public static class Viewport
- {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
-
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
-
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
-
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
-
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
-
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
-
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
-
- @XmlAttribute(name = "showText")
- protected Boolean showText;
-
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
-
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
-
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
-
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
-
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
-
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
-
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
-
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
-
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
-
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
-
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
-
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
-
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
-
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
-
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
-
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
-
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
-
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
-
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
-
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
-
- @XmlAttribute(name = "fontName")
- protected String fontName;
-
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
-
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
-
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
-
- @XmlAttribute(name = "viewName")
- protected String viewName;
-
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
-
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
-
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
-
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
-
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
-
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
-
- @XmlAttribute(name = "complementId")
- protected String complementId;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the annotationColours property.
- *
- * @return possible object is {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours()
- {
- return annotationColours;
- }
-
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value)
- {
- this.annotationColours = value;
- }
-
- /**
- * Gets the value of the hiddenColumns property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the hiddenColumns property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getHiddenColumns().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport.HiddenColumns }
- *
- *
- */
- public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns()
- {
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
- }
- return this.hiddenColumns;
- }
-
- /**
- * Gets the value of the calcIdParam property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the calcIdParam property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getCalcIdParam().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport.CalcIdParam }
- *
- *
- */
- public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam()
- {
- if (calcIdParam == null)
- {
- calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
- }
- return this.calcIdParam;
- }
-
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isConservationSelected()
- {
- return conservationSelected;
- }
-
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value)
- {
- this.conservationSelected = value;
- }
-
- /**
- * Gets the value of the pidSelected property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPidSelected()
- {
- return pidSelected;
- }
-
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value)
- {
- this.pidSelected = value;
- }
-
- /**
- * Gets the value of the bgColour property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getBgColour()
- {
- return bgColour;
- }
-
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setBgColour(String value)
- {
- this.bgColour = value;
- }
-
- /**
- * Gets the value of the consThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getConsThreshold()
- {
- return consThreshold;
- }
-
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setConsThreshold(Integer value)
- {
- this.consThreshold = value;
- }
-
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getPidThreshold()
- {
- return pidThreshold;
- }
-
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setPidThreshold(Integer value)
- {
- this.pidThreshold = value;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the showFullId property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowFullId()
- {
- return showFullId;
- }
-
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value)
- {
- this.showFullId = value;
- }
-
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isRightAlignIds()
- {
- return rightAlignIds;
- }
-
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value)
- {
- this.rightAlignIds = value;
- }
-
- /**
- * Gets the value of the showText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowText()
- {
- return showText;
- }
-
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowText(Boolean value)
- {
- this.showText = value;
- }
-
- /**
- * Gets the value of the showColourText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowColourText()
- {
- return showColourText;
- }
-
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value)
- {
- this.showColourText = value;
- }
-
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowUnconserved()
- {
- if (showUnconserved == null)
- {
- return false;
- }
- else
- {
- return showUnconserved;
- }
- }
-
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
-
- /**
- * Gets the value of the showBoxes property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowBoxes()
- {
- return showBoxes;
- }
-
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value)
- {
- this.showBoxes = value;
- }
-
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isWrapAlignment()
- {
- return wrapAlignment;
- }
-
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value)
- {
- this.wrapAlignment = value;
- }
-
- /**
- * Gets the value of the renderGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isRenderGaps()
- {
- return renderGaps;
- }
-
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value)
- {
- this.renderGaps = value;
- }
-
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
-
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value)
- {
- this.showSequenceFeatures = value;
- }
-
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip()
- {
- return showNPfeatureTooltip;
- }
-
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value)
- {
- this.showNPfeatureTooltip = value;
- }
-
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip()
- {
- return showDbRefTooltip;
- }
-
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value)
- {
- this.showDbRefTooltip = value;
- }
-
- /**
- * Gets the value of the followHighlight property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isFollowHighlight()
- {
- if (followHighlight == null)
- {
- return true;
- }
- else
- {
- return followHighlight;
- }
- }
-
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value)
- {
- this.followHighlight = value;
- }
-
- /**
- * Gets the value of the followSelection property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isFollowSelection()
- {
- if (followSelection == null)
- {
- return true;
- }
- else
- {
- return followSelection;
- }
- }
-
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value)
- {
- this.followSelection = value;
- }
-
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowAnnotation()
- {
- return showAnnotation;
- }
-
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value)
- {
- this.showAnnotation = value;
- }
-
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels()
- {
- if (centreColumnLabels == null)
- {
- return false;
- }
- else
- {
- return centreColumnLabels;
- }
- }
-
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value)
- {
- this.centreColumnLabels = value;
- }
-
- /**
- * Gets the value of the showGroupConservation property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowGroupConservation()
- {
- if (showGroupConservation == null)
- {
- return false;
- }
- else
- {
- return showGroupConservation;
- }
- }
-
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowGroupConservation(Boolean value)
- {
- this.showGroupConservation = value;
- }
-
- /**
- * Gets the value of the showGroupConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus()
- {
- if (showGroupConsensus == null)
- {
- return false;
- }
- else
- {
- return showGroupConsensus;
- }
- }
-
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowGroupConsensus(Boolean value)
- {
- this.showGroupConsensus = value;
- }
-
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
-
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
-
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
-
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
-
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
-
- /**
- * Gets the value of the startRes property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStartRes()
- {
- return startRes;
- }
-
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStartRes(Integer value)
- {
- this.startRes = value;
- }
-
- /**
- * Gets the value of the startSeq property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStartSeq()
- {
- return startSeq;
- }
-
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStartSeq(Integer value)
- {
- this.startSeq = value;
- }
-
- /**
- * Gets the value of the fontName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFontName()
- {
- return fontName;
- }
-
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFontName(String value)
- {
- this.fontName = value;
- }
-
- /**
- * Gets the value of the fontSize property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontSize()
- {
- return fontSize;
- }
-
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontSize(Integer value)
- {
- this.fontSize = value;
- }
-
- /**
- * Gets the value of the fontStyle property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontStyle()
- {
- return fontStyle;
- }
-
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontStyle(Integer value)
- {
- this.fontStyle = value;
- }
-
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna()
- {
- if (scaleProteinAsCdna == null)
- {
- return true;
- }
- else
- {
- return scaleProteinAsCdna;
- }
- }
-
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value)
- {
- this.scaleProteinAsCdna = value;
- }
-
- /**
- * Gets the value of the viewName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewName()
- {
- return viewName;
- }
-
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewName(String value)
- {
- this.viewName = value;
- }
-
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceSetId()
- {
- return sequenceSetId;
- }
-
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceSetId(String value)
- {
- this.sequenceSetId = value;
- }
-
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isGatheredViews()
- {
- return gatheredViews;
- }
-
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value)
- {
- this.gatheredViews = value;
- }
-
- /**
- * Gets the value of the textCol1 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol1()
- {
- return textCol1;
- }
-
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
- }
-
- /**
- * Gets the value of the textCol2 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol2()
- {
- return textCol2;
- }
-
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
-
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
-
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the complementId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getComplementId()
- {
- return complementId;
- }
-
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setComplementId(String value)
- {
- this.complementId = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam extends WebServiceParameterSet
- {
-
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
-
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
-
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * Gets the value of the calcId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCalcId()
- {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCalcId(String value)
- {
- this.calcId = value;
- }
-
- /**
- * Gets the value of the needsUpdate property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNeedsUpdate()
- {
- if (needsUpdate == null)
- {
- return false;
- }
- else
- {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNeedsUpdate(Boolean value)
- {
- this.needsUpdate = value;
- }
-
- /**
- * Gets the value of the autoUpdate property.
- *
- */
- public boolean isAutoUpdate()
- {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value)
- {
- this.autoUpdate = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns
- {
-
- @XmlAttribute(name = "start")
- protected Integer start;
-
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStart(Integer value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setEnd(Integer value)
- {
- this.end = value;
- }
-
- }
-
- }
-
-}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for JalviewUserColours complex type.
+ * <p>Java class for JalviewUserColours complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="JalviewUserColours"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="Version"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
- * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour"
- * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType"
- * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="featureType" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="schemeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="JalviewUserColours">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="colour" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="filter" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ * </sequence>
+ * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "JalviewUserColours",
- namespace = "www.jalview.org/colours",
- propOrder =
- { "version", "colour", "filter" })
-public class JalviewUserColours
-{
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
-
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Colour> colour;
-
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Filter> filter;
-
- @XmlAttribute(name = "schemeName")
- protected String schemeName;
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the colour property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getColour().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Colour }
- *
- *
- */
- public List<JalviewUserColours.Colour> getColour()
- {
- if (colour == null)
- {
- colour = new ArrayList<JalviewUserColours.Colour>();
- }
- return this.colour;
- }
-
- /**
- * Gets the value of the filter property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the filter property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getFilter().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Filter }
- *
- *
- */
- public List<JalviewUserColours.Filter> getFilter()
- {
- if (filter == null)
- {
- filter = new ArrayList<JalviewUserColours.Filter>();
- }
- return this.filter;
- }
-
- /**
- * Gets the value of the schemeName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSchemeName()
- {
- return schemeName;
- }
-
- /**
- * Sets the value of the schemeName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSchemeName(String value)
- {
- this.schemeName = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
- * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour"
- * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType"
- * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "attributeName" })
- public static class Colour
- {
-
+@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
+ "version",
+ "colour",
+ "filter"
+})
+public class JalviewUserColours {
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
@XmlElement(namespace = "")
- protected List<String> attributeName;
-
- @XmlAttribute(name = "Name")
- protected String name;
-
- @XmlAttribute(name = "RGB", required = true)
- protected String rgb;
-
- @XmlAttribute(name = "minRGB")
- protected String minRGB;
-
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
-
- @XmlAttribute(name = "threshType")
- protected ThresholdType threshType;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "max")
- protected Float max;
-
- @XmlAttribute(name = "min")
- protected Float min;
-
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
-
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAttributeName().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the rgb property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getRGB()
- {
- return rgb;
- }
-
- /**
- * Sets the value of the rgb property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setRGB(String value)
- {
- this.rgb = value;
- }
-
- /**
- * Gets the value of the minRGB property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getMinRGB()
- {
- return minRGB;
- }
-
- /**
- * Sets the value of the minRGB property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setMinRGB(String value)
- {
- this.minRGB = value;
- }
+ protected List<JalviewUserColours.Colour> colour;
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Filter> filter;
+ @XmlAttribute(name = "schemeName")
+ protected String schemeName;
/**
- * Gets the value of the noValueColour property.
- *
- * @return possible object is {@link NoValueColour }
+ * Gets the value of the version property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public NoValueColour getNoValueColour()
- {
- if (noValueColour == null)
- {
- return NoValueColour.MIN;
- }
- else
- {
- return noValueColour;
- }
+ public String getVersion() {
+ return version;
}
/**
- * Sets the value of the noValueColour property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is {@link NoValueColour }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setNoValueColour(NoValueColour value)
- {
- this.noValueColour = value;
+ public void setVersion(String value) {
+ this.version = value;
}
/**
- * Gets the value of the threshType property.
+ * Gets the value of the colour property.
*
- * @return possible object is {@link ThresholdType }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the colour property.
*
- */
- public ThresholdType getThreshType()
- {
- return threshType;
- }
-
- /**
- * Sets the value of the threshType property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getColour().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link ThresholdType }
*
- */
- public void setThreshType(ThresholdType value)
- {
- this.threshType = value;
- }
-
- /**
- * Gets the value of the threshold property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Colour }
*
- * @return possible object is {@link Float }
*
*/
- public Float getThreshold()
- {
- return threshold;
+ public List<JalviewUserColours.Colour> getColour() {
+ if (colour == null) {
+ colour = new ArrayList<JalviewUserColours.Colour>();
+ }
+ return this.colour;
}
/**
- * Sets the value of the threshold property.
+ * Gets the value of the filter property.
*
- * @param value
- * allowed object is {@link Float }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the filter property.
*
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the max property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFilter().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Float }
*
- */
- public Float getMax()
- {
- return max;
- }
-
- /**
- * Sets the value of the max property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Filter }
*
- * @param value
- * allowed object is {@link Float }
*
*/
- public void setMax(Float value)
- {
- this.max = value;
+ public List<JalviewUserColours.Filter> getFilter() {
+ if (filter == null) {
+ filter = new ArrayList<JalviewUserColours.Filter>();
+ }
+ return this.filter;
}
/**
- * Gets the value of the min property.
- *
- * @return possible object is {@link Float }
+ * Gets the value of the schemeName property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public Float getMin()
- {
- return min;
+ public String getSchemeName() {
+ return schemeName;
}
/**
- * Sets the value of the min property.
+ * Sets the value of the schemeName property.
*
* @param value
- * allowed object is {@link Float }
- *
- */
- public void setMin(Float value)
- {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return possible object is {@link Boolean }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public Boolean isColourByLabel()
- {
- return colourByLabel;
+ public void setSchemeName(String value) {
+ this.schemeName = value;
}
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value)
- {
- this.colourByLabel = value;
- }
/**
- * Gets the value of the autoScale property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
*/
- public Boolean isAutoScale()
- {
- return autoScale;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName"
+ })
+ public static class Colour {
+
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
+ @XmlAttribute(name = "Name")
+ protected String name;
+ @XmlAttribute(name = "RGB", required = true)
+ protected String rgb;
+ @XmlAttribute(name = "minRGB")
+ protected String minRGB;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshType")
+ protected ThresholdType threshType;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the rgb property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRGB() {
+ return rgb;
+ }
+
+ /**
+ * Sets the value of the rgb property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRGB(String value) {
+ this.rgb = value;
+ }
+
+ /**
+ * Gets the value of the minRGB property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMinRGB() {
+ return minRGB;
+ }
+
+ /**
+ * Sets the value of the minRGB property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMinRGB(String value) {
+ this.minRGB = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshType property.
+ *
+ * @return
+ * possible object is
+ * {@link ThresholdType }
+ *
+ */
+ public ThresholdType getThreshType() {
+ return threshType;
+ }
+
+ /**
+ * Sets the value of the threshType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ThresholdType }
+ *
+ */
+ public void setThreshType(ThresholdType value) {
+ this.threshType = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value)
- {
- this.autoScale = value;
}
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="featureType"
- * use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "matcherSet" })
- public static class Filter
- {
-
- @XmlElement(namespace = "", required = true)
- protected FeatureMatcherSet matcherSet;
-
- @XmlAttribute(name = "featureType", required = true)
- protected String featureType;
/**
- * Gets the value of the matcherSet property.
+ * <p>Java class for anonymous complex type.
*
- * @return possible object is {@link FeatureMatcherSet }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public FeatureMatcherSet getMatcherSet()
- {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ * </sequence>
+ * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link FeatureMatcherSet }
*
*/
- public void setMatcherSet(FeatureMatcherSet value)
- {
- this.matcherSet = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "matcherSet"
+ })
+ public static class Filter {
+
+ @XmlElement(namespace = "", required = true)
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "featureType", required = true)
+ protected String featureType;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the featureType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFeatureType() {
+ return featureType;
+ }
+
+ /**
+ * Sets the value of the featureType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFeatureType(String value) {
+ this.featureType = value;
+ }
- /**
- * Gets the value of the featureType property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFeatureType()
- {
- return featureType;
}
- /**
- * Sets the value of the featureType property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFeatureType(String value)
- {
- this.featureType = value;
- }
-
- }
-
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
*
- * This effectively represents a java.util.MapList object
+ * This effectively represents a java.util.MapList object
+ *
*
+ * <p>Java class for mapListType complex type.
*
- * <p>Java class for mapListType complex type.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType name="mapListType"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="mapListFrom"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="mapFromUnit" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;attribute name="mapToUnit" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="mapListType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ * <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
-@XmlSeeAlso({ Mapping.class })
-public class MapListType
-{
-
- protected List<MapListType.MapListFrom> mapListFrom;
-
- protected List<MapListType.MapListTo> mapListTo;
-
- @XmlAttribute(name = "mapFromUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapFromUnit;
-
- @XmlAttribute(name = "mapToUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapToUnit;
-
- /**
- * Gets the value of the mapListFrom property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the mapListFrom property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getMapListFrom().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListFrom }
- *
- *
- */
- public List<MapListType.MapListFrom> getMapListFrom()
- {
- if (mapListFrom == null)
- {
- mapListFrom = new ArrayList<MapListType.MapListFrom>();
- }
- return this.mapListFrom;
- }
-
- /**
- * Gets the value of the mapListTo property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the mapListTo property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getMapListTo().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListTo }
- *
- *
- */
- public List<MapListType.MapListTo> getMapListTo()
- {
- if (mapListTo == null)
- {
- mapListTo = new ArrayList<MapListType.MapListTo>();
- }
- return this.mapListTo;
- }
-
- /**
- * Gets the value of the mapFromUnit property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getMapFromUnit()
- {
- return mapFromUnit;
- }
-
- /**
- * Sets the value of the mapFromUnit property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setMapFromUnit(BigInteger value)
- {
- this.mapFromUnit = value;
- }
+@XmlType(name = "mapListType", propOrder = {
+ "mapListFrom",
+ "mapListTo"
+})
+@XmlSeeAlso({
+ Mapping.class
+})
+public class MapListType {
- /**
- * Gets the value of the mapToUnit property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getMapToUnit()
- {
- return mapToUnit;
- }
-
- /**
- * Sets the value of the mapToUnit property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setMapToUnit(BigInteger value)
- {
- this.mapToUnit = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListFrom
- {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
+ protected List<MapListType.MapListFrom> mapListFrom;
+ protected List<MapListType.MapListTo> mapListTo;
+ @XmlAttribute(name = "mapFromUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapFromUnit;
+ @XmlAttribute(name = "mapToUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapToUnit;
/**
- * Gets the value of the start property.
+ * Gets the value of the mapListFrom property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMapListFrom().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListFrom }
+ *
*
*/
- public int getStart()
- {
- return start;
+ public List<MapListType.MapListFrom> getMapListFrom() {
+ if (mapListFrom == null) {
+ mapListFrom = new ArrayList<MapListType.MapListFrom>();
+ }
+ return this.mapListFrom;
}
/**
- * Sets the value of the start property.
+ * Gets the value of the mapListTo property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMapListTo().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListTo }
+ *
*
*/
- public void setStart(int value)
- {
- this.start = value;
+ public List<MapListType.MapListTo> getMapListTo() {
+ if (mapListTo == null) {
+ mapListTo = new ArrayList<MapListType.MapListTo>();
+ }
+ return this.mapListTo;
}
/**
- * Gets the value of the end property.
+ * Gets the value of the mapFromUnit property.
*
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
*/
- public int getEnd()
- {
- return end;
+ public BigInteger getMapFromUnit() {
+ return mapFromUnit;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the mapFromUnit property.
*
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
*/
- public void setEnd(int value)
- {
- this.end = value;
+ public void setMapFromUnit(BigInteger value) {
+ this.mapFromUnit = value;
}
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListTo
- {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
/**
- * Gets the value of the start property.
+ * Gets the value of the mapToUnit property.
*
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
*/
- public int getStart()
- {
- return start;
+ public BigInteger getMapToUnit() {
+ return mapToUnit;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the mapToUnit property.
*
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
*/
- public void setStart(int value)
- {
- this.start = value;
+ public void setMapToUnit(BigInteger value) {
+ this.mapToUnit = value;
}
+
/**
- * Gets the value of the end property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
*
*/
- public int getEnd()
- {
- return end;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListFrom {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
}
+
/**
- * Sets the value of the end property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
*
*/
- public void setEnd(int value)
- {
- this.end = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListTo {
- }
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
*
- * Represent the jalview.datamodel.Mapping object - it also provides a way of
- * storing sequences that are mapped 'to' without adding them to the sequence
- * set (which will mean they are then added to the alignment too).
- *
+ * Represent the jalview.datamodel.Mapping object - it also provides
+ * a way of storing sequences that are mapped 'to' without adding them
+ * to the sequence set (which will mean they are then added to the alignment too).
+ *
*
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
- * &lt;sequence&gt; &lt;choice minOccurs="0"&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt; &lt;element
- * name="dseqFor"&gt; &lt;simpleType&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;/restriction&gt; &lt;/simpleType&gt;
- * &lt;/element&gt; &lt;/choice&gt; &lt;/sequence&gt;
- * &lt;attribute name="mappingType"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
+ * <sequence>
+ * <choice minOccurs="0">
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
+ * <element name="dseqFor">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * </restriction>
+ * </simpleType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
+@XmlType(name = "", propOrder = {
+ "sequence",
+ "dseqFor"
+})
@XmlRootElement(name = "Mapping")
-public class Mapping extends MapListType
+public class Mapping
+ extends MapListType
{
- @XmlElement(name = "Sequence")
- protected Sequence sequence;
-
- protected String dseqFor;
-
- @XmlAttribute(name = "mappingType")
- protected String mappingType;
+ @XmlElement(name = "Sequence")
+ protected Sequence sequence;
+ protected String dseqFor;
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link Sequence }
- *
- */
- public Sequence getSequence()
- {
- return sequence;
- }
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link Sequence }
+ *
+ */
+ public Sequence getSequence() {
+ return sequence;
+ }
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link Sequence }
- *
- */
- public void setSequence(Sequence value)
- {
- this.sequence = value;
- }
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Sequence }
+ *
+ */
+ public void setSequence(Sequence value) {
+ this.sequence = value;
+ }
- /**
- * Gets the value of the dseqFor property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDseqFor()
- {
- return dseqFor;
- }
+ /**
+ * Gets the value of the dseqFor property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDseqFor() {
+ return dseqFor;
+ }
- /**
- * Sets the value of the dseqFor property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDseqFor(String value)
- {
- this.dseqFor = value;
- }
+ /**
+ * Sets the value of the dseqFor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDseqFor(String value) {
+ this.dseqFor = value;
+ }
- /**
- * Gets the value of the mappingType property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getMappingType()
- {
- return mappingType;
- }
+ /**
+ * Gets the value of the mappingType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMappingType() {
+ return mappingType;
+ }
- /**
- * Sets the value of the mappingType property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setMappingType(String value)
- {
- this.mappingType = value;
- }
+ /**
+ * Sets the value of the mappingType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMappingType(String value) {
+ this.mappingType = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for NoValueColour.
+ * <p>Java class for NoValueColour.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class. <pre> &lt;simpleType
- * name="NoValueColour"&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
- * value="None"/&gt; &lt;enumeration value="Min"/&gt;
- * &lt;enumeration value="Max"/&gt; &lt;/restriction&gt;
- * &lt;/simpleType&gt; </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * <simpleType name="NoValueColour">
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="None"/>
+ * <enumeration value="Min"/>
+ * <enumeration value="Max"/>
+ * </restriction>
+ * </simpleType>
+ * </pre>
*
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum NoValueColour
-{
-
- @XmlEnumValue("None")
- NONE("None"), @XmlEnumValue("Min")
- MIN("Min"), @XmlEnumValue("Max")
- MAX("Max");
-
- private final String value;
-
- NoValueColour(String v)
- {
- value = v;
- }
-
- public String value()
- {
- return value;
- }
-
- public static NoValueColour fromValue(String v)
- {
- for (NoValueColour c : NoValueColour.values())
- {
- if (c.value.equals(v))
- {
- return c;
- }
+public enum NoValueColour {
+
+ @XmlEnumValue("None")
+ NONE("None"),
+ @XmlEnumValue("Min")
+ MIN("Min"),
+ @XmlEnumValue("Max")
+ MAX("Max");
+ private final String value;
+
+ NoValueColour(String v) {
+ value = v;
+ }
+
+ public String value() {
+ return value;
+ }
+
+ public static NoValueColour fromValue(String v) {
+ for (NoValueColour c: NoValueColour.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
}
- throw new IllegalArgumentException(v);
- }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlRegistry;
import javax.xml.namespace.QName;
+
/**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.jalview package.
- * <p>An ObjectFactory allows you to programatically construct new
- * instances of the Java representation for XML content. The Java representation
- * of XML content can consist of schema derived interfaces and classes
- * representing the binding of schema type definitions, element declarations and
- * model groups. Factory methods for each of these are provided in this class.
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.jalview package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory
-{
-
- private final static QName _JalviewModel_QNAME = new QName(
- "www.jalview.org", "JalviewModel");
-
- private final static QName _JalviewUserColours_QNAME = new QName(
- "www.jalview.org/colours", "JalviewUserColours");
-
- private final static QName _WebServiceParameterSet_QNAME = new QName(
- "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of
- * schema derived classes for package: jalview.xml.binding.jalview
- *
- */
- public ObjectFactory()
- {
- }
-
- /**
- * Create an instance of {@link MapListType }
- *
- */
- public MapListType createMapListType()
- {
- return new MapListType();
- }
-
- /**
- * Create an instance of {@link Sequence }
- *
- */
- public Sequence createSequence()
- {
- return new Sequence();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame()
- {
- return new AlcodonFrame();
- }
-
- /**
- * Create an instance of {@link Annotation }
- *
- */
- public Annotation createAnnotation()
- {
- return new Annotation();
- }
-
- /**
- * Create an instance of {@link SequenceSet }
- *
- */
- public SequenceSet createSequenceSet()
- {
- return new SequenceSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet createFeatureMatcherSet()
- {
- return new FeatureMatcherSet();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours }
- *
- */
- public JalviewUserColours createJalviewUserColours()
- {
- return new JalviewUserColours();
- }
-
- /**
- * Create an instance of {@link Pdbentry }
- *
- */
- public Pdbentry createPdbentry()
- {
- return new Pdbentry();
- }
-
- /**
- * Create an instance of {@link Feature }
- *
- */
- public Feature createFeature()
- {
- return new Feature();
- }
-
- /**
- * Create an instance of {@link JalviewModel }
- *
- */
- public JalviewModel createJalviewModel()
- {
- return new JalviewModel();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
- {
- return new JalviewModel.FeatureSettings();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer }
- *
- */
- public JalviewModel.PcaViewer createJalviewModelPcaViewer()
- {
- return new JalviewModel.PcaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport }
- *
- */
- public JalviewModel.Viewport createJalviewModelViewport()
- {
- return new JalviewModel.Viewport();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq }
- *
- */
- public JalviewModel.JSeq createJalviewModelJSeq()
- {
- return new JalviewModel.JSeq();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
- *
- */
- public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
- {
- return new JalviewModel.JSeq.RnaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids }
- *
- */
- public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
- {
- return new JalviewModel.JSeq.Pdbids();
- }
-
- /**
- * Create an instance of {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme createAnnotationColourScheme()
- {
- return new AnnotationColourScheme();
- }
-
- /**
- * Create an instance of {@link PcaDataType }
- *
- */
- public PcaDataType createPcaDataType()
- {
- return new PcaDataType();
- }
-
- /**
- * Create an instance of {@link DoubleVector }
- *
- */
- public DoubleVector createDoubleVector()
- {
- return new DoubleVector();
- }
-
- /**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix()
- {
- return new DoubleMatrix();
- }
-
- /**
- * Create an instance of {@link Mapping }
- *
- */
- public Mapping createMapping()
- {
- return new Mapping();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListFrom }
- *
- */
- public MapListType.MapListFrom createMapListTypeMapListFrom()
- {
- return new MapListType.MapListFrom();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListTo }
- *
- */
- public MapListType.MapListTo createMapListTypeMapListTo()
- {
- return new MapListType.MapListTo();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType()
- {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Sequence.DBRef }
- *
- */
- public Sequence.DBRef createSequenceDBRef()
- {
- return new Sequence.DBRef();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.Alcodon }
- *
- */
- public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
- {
- return new AlcodonFrame.Alcodon();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.AlcodMap }
- *
- */
- public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
- {
- return new AlcodonFrame.AlcodMap();
- }
-
- /**
- * Create an instance of {@link AnnotationElement }
- *
- */
- public AnnotationElement createAnnotationElement()
- {
- return new AnnotationElement();
- }
-
- /**
- * Create an instance of {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine createAnnotationThresholdLine()
- {
- return new Annotation.ThresholdLine();
- }
-
- /**
- * Create an instance of {@link Annotation.Property }
- *
- */
- public Annotation.Property createAnnotationProperty()
- {
- return new Annotation.Property();
- }
-
- /**
- * Create an instance of {@link SequenceSet.SequenceSetProperties }
- *
- */
- public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
- {
- return new SequenceSet.SequenceSetProperties();
- }
-
- /**
- * Create an instance of {@link VAMSAS }
- *
- */
- public VAMSAS createVAMSAS()
- {
- return new VAMSAS();
- }
-
- /**
- * Create an instance of {@link FeatureMatcher }
- *
- */
- public FeatureMatcher createFeatureMatcher()
- {
- return new FeatureMatcher();
- }
-
- /**
- * Create an instance of {@link WebServiceParameterSet }
- *
- */
- public WebServiceParameterSet createWebServiceParameterSet()
- {
- return new WebServiceParameterSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
- {
- return new FeatureMatcherSet.CompoundMatcher();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Colour }
- *
- */
- public JalviewUserColours.Colour createJalviewUserColoursColour()
- {
- return new JalviewUserColours.Colour();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Filter }
- *
- */
- public JalviewUserColours.Filter createJalviewUserColoursFilter()
- {
- return new JalviewUserColours.Filter();
- }
-
- /**
- * Create an instance of {@link Pdbentry.Property }
- *
- */
- public Pdbentry.Property createPdbentryProperty()
- {
- return new Pdbentry.Property();
- }
-
- /**
- * Create an instance of {@link Feature.OtherData }
- *
- */
- public Feature.OtherData createFeatureOtherData()
- {
- return new Feature.OtherData();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JGroup }
- *
- */
- public JalviewModel.JGroup createJalviewModelJGroup()
- {
- return new JalviewModel.JGroup();
- }
-
- /**
- * Create an instance of {@link JalviewModel.UserColours }
- *
- */
- public JalviewModel.UserColours createJalviewModelUserColours()
- {
- return new JalviewModel.UserColours();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Tree }
- *
- */
- public JalviewModel.Tree createJalviewModelTree()
- {
- return new JalviewModel.Tree();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
- *
- */
- public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
- {
- return new JalviewModel.FeatureSettings.Setting();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Group }
- *
- */
- public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
- {
- return new JalviewModel.FeatureSettings.Group();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
- *
- */
- public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
- {
- return new JalviewModel.PcaViewer.SequencePoint();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.Axis }
- *
- */
- public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
- {
- return new JalviewModel.PcaViewer.Axis();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
- {
- return new JalviewModel.PcaViewer.SeqPointMin();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
- {
- return new JalviewModel.PcaViewer.SeqPointMax();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
- *
- */
- public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
- {
- return new JalviewModel.Viewport.HiddenColumns();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
- *
- */
- public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
- {
- return new JalviewModel.Viewport.CalcIdParam();
- }
-
- /**
- * Create an instance of
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- */
- public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
- {
- return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- */
- public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
- {
- return new JalviewModel.JSeq.Pdbids.StructureState();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
- * }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return the new instance of {@link JAXBElement
- * }{@code <}{@link JalviewModel }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
- public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
- {
- return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
- JalviewModel.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement
- * }{@code <}{@link JalviewUserColours }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return the new instance of {@link JAXBElement
- * }{@code <}{@link JalviewUserColours }{@code >}
- */
- @XmlElementDecl(
- namespace = "www.jalview.org/colours",
- name = "JalviewUserColours")
- public JAXBElement<JalviewUserColours> createJalviewUserColours(
- JalviewUserColours value)
- {
- return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
- JalviewUserColours.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement
- * }{@code <}{@link WebServiceParameterSet }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return the new instance of {@link JAXBElement
- * }{@code <}{@link WebServiceParameterSet }{@code >}
- */
- @XmlElementDecl(
- namespace = "www.jalview.org/xml/wsparamset",
- name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
- WebServiceParameterSet value)
- {
- return new JAXBElement<WebServiceParameterSet>(
- _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
- null, value);
- }
+public class ObjectFactory {
+
+ private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+ private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
+ private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame() {
+ return new AlcodonFrame();
+ }
+
+ /**
+ * Create an instance of {@link MapListType }
+ *
+ */
+ public MapListType createMapListType() {
+ return new MapListType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence }
+ *
+ */
+ public Sequence createSequence() {
+ return new Sequence();
+ }
+
+ /**
+ * Create an instance of {@link Annotation }
+ *
+ */
+ public Annotation createAnnotation() {
+ return new Annotation();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet }
+ *
+ */
+ public SequenceSet createSequenceSet() {
+ return new SequenceSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet createFeatureMatcherSet() {
+ return new FeatureMatcherSet();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours createJalviewUserColours() {
+ return new JalviewUserColours();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry }
+ *
+ */
+ public Pdbentry createPdbentry() {
+ return new Pdbentry();
+ }
+
+ /**
+ * Create an instance of {@link Feature }
+ *
+ */
+ public Feature createFeature() {
+ return new Feature();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel }
+ *
+ */
+ public JalviewModel createJalviewModel() {
+ return new JalviewModel();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
+ return new JalviewModel.FeatureSettings();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer }
+ *
+ */
+ public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+ return new JalviewModel.PcaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport }
+ *
+ */
+ public JalviewModel.Viewport createJalviewModelViewport() {
+ return new JalviewModel.Viewport();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq }
+ *
+ */
+ public JalviewModel.JSeq createJalviewModelJSeq() {
+ return new JalviewModel.JSeq();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
+ return new JalviewModel.JSeq.RnaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
+ return new JalviewModel.JSeq.Pdbids();
+ }
+
+ /**
+ * Create an instance of {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix createDoubleMatrix() {
+ return new DoubleMatrix();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme createAnnotationColourScheme() {
+ return new AnnotationColourScheme();
+ }
+
+ /**
+ * Create an instance of {@link PcaDataType }
+ *
+ */
+ public PcaDataType createPcaDataType() {
+ return new PcaDataType();
+ }
+
+ /**
+ * Create an instance of {@link DoubleVector }
+ *
+ */
+ public DoubleVector createDoubleVector() {
+ return new DoubleVector();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement() {
+ return new AnnotationElement();
+ }
+
+ /**
+ * Create an instance of {@link Mapping }
+ *
+ */
+ public Mapping createMapping() {
+ return new Mapping();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListFrom }
+ *
+ */
+ public MapListType.MapListFrom createMapListTypeMapListFrom() {
+ return new MapListType.MapListFrom();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListTo }
+ *
+ */
+ public MapListType.MapListTo createMapListTypeMapListTo() {
+ return new MapListType.MapListTo();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType() {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence.DBRef }
+ *
+ */
+ public Sequence.DBRef createSequenceDBRef() {
+ return new Sequence.DBRef();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine createAnnotationThresholdLine() {
+ return new Annotation.ThresholdLine();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.Property }
+ *
+ */
+ public Annotation.Property createAnnotationProperty() {
+ return new Annotation.Property();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet.SequenceSetProperties }
+ *
+ */
+ public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
+ return new SequenceSet.SequenceSetProperties();
+ }
+
+ /**
+ * Create an instance of {@link VAMSAS }
+ *
+ */
+ public VAMSAS createVAMSAS() {
+ return new VAMSAS();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher createFeatureMatcher() {
+ return new FeatureMatcher();
+ }
+
+ /**
+ * Create an instance of {@link WebServiceParameterSet }
+ *
+ */
+ public WebServiceParameterSet createWebServiceParameterSet() {
+ return new WebServiceParameterSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
+ return new FeatureMatcherSet.CompoundMatcher();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Colour }
+ *
+ */
+ public JalviewUserColours.Colour createJalviewUserColoursColour() {
+ return new JalviewUserColours.Colour();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Filter }
+ *
+ */
+ public JalviewUserColours.Filter createJalviewUserColoursFilter() {
+ return new JalviewUserColours.Filter();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry.Property }
+ *
+ */
+ public Pdbentry.Property createPdbentryProperty() {
+ return new Pdbentry.Property();
+ }
+
+ /**
+ * Create an instance of {@link Feature.OtherData }
+ *
+ */
+ public Feature.OtherData createFeatureOtherData() {
+ return new Feature.OtherData();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JGroup }
+ *
+ */
+ public JalviewModel.JGroup createJalviewModelJGroup() {
+ return new JalviewModel.JGroup();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.UserColours }
+ *
+ */
+ public JalviewModel.UserColours createJalviewModelUserColours() {
+ return new JalviewModel.UserColours();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Tree }
+ *
+ */
+ public JalviewModel.Tree createJalviewModelTree() {
+ return new JalviewModel.Tree();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+ *
+ */
+ public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
+ return new JalviewModel.FeatureSettings.Setting();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+ *
+ */
+ public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
+ return new JalviewModel.FeatureSettings.Group();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ */
+ public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
+ return new JalviewModel.PcaViewer.SequencePoint();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+ *
+ */
+ public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
+ return new JalviewModel.PcaViewer.Axis();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
+ return new JalviewModel.PcaViewer.SeqPointMin();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
+ return new JalviewModel.PcaViewer.SeqPointMax();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ */
+ public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
+ return new JalviewModel.Viewport.HiddenColumns();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ */
+ public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
+ return new JalviewModel.Viewport.CalcIdParam();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
+ return new JalviewModel.Viewport.Overview();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
+ return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
+ return new JalviewModel.JSeq.Pdbids.StructureState();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+ return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+ public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
+ return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
+ public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
+ return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
*
- * The results of a PCA calculation
- *
+ * The results of a PCA calculation
+ *
*
- * <p>Java class for PcaDataType complex type.
+ * <p>Java class for PcaDataType complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="PcaDataType"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="pairwiseMatrix"
- * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;element
- * name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;element name="eigenMatrix"
- * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;/sequence&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="PcaDataType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ * <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ * <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "PcaDataType",
- namespace = "www.jalview.org",
- propOrder =
- { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
-public class PcaDataType
-{
-
- @XmlElement(required = true)
- protected DoubleMatrix pairwiseMatrix;
-
- @XmlElement(required = true)
- protected DoubleMatrix tridiagonalMatrix;
+@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
+ "pairwiseMatrix",
+ "tridiagonalMatrix",
+ "eigenMatrix"
+})
+public class PcaDataType {
- @XmlElement(required = true)
- protected DoubleMatrix eigenMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix pairwiseMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix tridiagonalMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix eigenMatrix;
- /**
- * Gets the value of the pairwiseMatrix property.
- *
- * @return possible object is {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getPairwiseMatrix()
- {
- return pairwiseMatrix;
- }
+ /**
+ * Gets the value of the pairwiseMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getPairwiseMatrix() {
+ return pairwiseMatrix;
+ }
- /**
- * Sets the value of the pairwiseMatrix property.
- *
- * @param value
- * allowed object is {@link DoubleMatrix }
- *
- */
- public void setPairwiseMatrix(DoubleMatrix value)
- {
- this.pairwiseMatrix = value;
- }
+ /**
+ * Sets the value of the pairwiseMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setPairwiseMatrix(DoubleMatrix value) {
+ this.pairwiseMatrix = value;
+ }
- /**
- * Gets the value of the tridiagonalMatrix property.
- *
- * @return possible object is {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getTridiagonalMatrix()
- {
- return tridiagonalMatrix;
- }
+ /**
+ * Gets the value of the tridiagonalMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getTridiagonalMatrix() {
+ return tridiagonalMatrix;
+ }
- /**
- * Sets the value of the tridiagonalMatrix property.
- *
- * @param value
- * allowed object is {@link DoubleMatrix }
- *
- */
- public void setTridiagonalMatrix(DoubleMatrix value)
- {
- this.tridiagonalMatrix = value;
- }
+ /**
+ * Sets the value of the tridiagonalMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setTridiagonalMatrix(DoubleMatrix value) {
+ this.tridiagonalMatrix = value;
+ }
- /**
- * Gets the value of the eigenMatrix property.
- *
- * @return possible object is {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getEigenMatrix()
- {
- return eigenMatrix;
- }
+ /**
+ * Gets the value of the eigenMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getEigenMatrix() {
+ return eigenMatrix;
+ }
- /**
- * Sets the value of the eigenMatrix property.
- *
- * @param value
- * allowed object is {@link DoubleMatrix }
- *
- */
- public void setEigenMatrix(DoubleMatrix value)
- {
- this.eigenMatrix = value;
- }
+ /**
+ * Sets the value of the eigenMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setEigenMatrix(DoubleMatrix value) {
+ this.eigenMatrix = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for pdbentry complex type.
+ * <p>Java class for pdbentry complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="pdbentry"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;element name="property"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="value" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="id" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="pdbentry">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence maxOccurs="unbounded" minOccurs="0">
+ * <element name="property" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "pdbentry",
- namespace = "www.jalview.org",
- propOrder =
- { "property" })
-@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
-public class Pdbentry
-{
-
- protected List<Pdbentry.Property> property;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "type")
- protected String type;
-
- @XmlAttribute(name = "file")
- protected String file;
-
- /**
- * Gets the value of the property property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the property property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getProperty().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Pdbentry.Property }
- *
- *
- */
- public List<Pdbentry.Property> getProperty()
- {
- if (property == null)
- {
- property = new ArrayList<Pdbentry.Property>();
- }
- return this.property;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the file property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFile()
- {
- return file;
- }
-
- /**
- * Sets the value of the file property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFile(String value)
- {
- this.file = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="value" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property
- {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- @XmlAttribute(name = "value", required = true)
- protected String value;
+@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
+ "property"
+})
+@XmlSeeAlso({
+ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
+})
+public class Pdbentry {
+
+ protected List<Pdbentry.Property> property;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "file")
+ protected String file;
/**
- * Gets the value of the name property.
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Pdbentry.Property }
+ *
*
- * @return possible object is {@link String }
+ */
+ public List<Pdbentry.Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Pdbentry.Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the id property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getName()
- {
- return name;
+ public String getId() {
+ return id;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the id property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the type property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setName(String value)
- {
- this.name = value;
+ public String getType() {
+ return type;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the type property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the file property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getValue()
- {
- return value;
+ public String getFile() {
+ return file;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the file property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public void setFile(String value) {
+ this.file = value;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
- * &lt;sequence&gt; &lt;element name="DBRef" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="source"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="canonical"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="dsseqid"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ * <sequence>
+ * <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "dbRef" })
+@XmlType(name = "", propOrder = {
+ "dbRef"
+})
@XmlRootElement(name = "Sequence")
-public class Sequence extends SequenceType
+public class Sequence
+ extends SequenceType
{
- @XmlElement(name = "DBRef")
- protected List<Sequence.DBRef> dbRef;
-
- @XmlAttribute(name = "dsseqid")
- protected String dsseqid;
-
- @XmlAttribute(name = "biotype")
- protected String biotype;
-
- /**
- * Gets the value of the dbRef property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the dbRef property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getDBRef().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Sequence.DBRef }
- *
- *
- */
- public List<Sequence.DBRef> getDBRef()
- {
- if (dbRef == null)
- {
- dbRef = new ArrayList<Sequence.DBRef>();
- }
- return this.dbRef;
- }
-
- /**
- * Gets the value of the dsseqid property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDsseqid()
- {
- return dsseqid;
- }
-
- /**
- * Sets the value of the dsseqid property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDsseqid(String value)
- {
- this.dsseqid = value;
- }
-
- /**
- * Gets the value of the biotype property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getBiotype()
- {
- return biotype;
- }
-
- /**
- * Sets the value of the biotype property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setBiotype(String value)
- {
- this.biotype = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="source"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="canonical"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "mapping" })
- public static class DBRef
- {
-
- @XmlElement(name = "Mapping")
- protected Mapping mapping;
-
- @XmlAttribute(name = "source")
- protected String source;
-
- @XmlAttribute(name = "version")
- protected String version;
-
- @XmlAttribute(name = "accessionId")
- protected String accessionId;
-
- @XmlAttribute(name = "locus")
- protected Boolean locus;
-
- @XmlAttribute(name = "canonical")
- protected Boolean canonical;
+ @XmlElement(name = "DBRef")
+ protected List<Sequence.DBRef> dbRef;
+ @XmlAttribute(name = "dsseqid")
+ protected String dsseqid;
+ @XmlAttribute(name = "biotype")
+ protected String biotype;
/**
- * Gets the value of the mapping property.
+ * Gets the value of the dbRef property.
*
- * @return possible object is {@link Mapping }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbRef property.
*
- */
- public Mapping getMapping()
- {
- return mapping;
- }
-
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is {@link Mapping }
- *
- */
- public void setMapping(Mapping value)
- {
- this.mapping = value;
- }
-
- /**
- * Gets the value of the source property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDBRef().add(newItem);
+ * </pre>
*
- * @return possible object is {@link String }
*
- */
- public String getSource()
- {
- return source;
- }
-
- /**
- * Sets the value of the source property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence.DBRef }
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setSource(String value)
- {
- this.source = value;
+ public List<Sequence.DBRef> getDBRef() {
+ if (dbRef == null) {
+ dbRef = new ArrayList<Sequence.DBRef>();
+ }
+ return this.dbRef;
}
/**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the dsseqid property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getVersion()
- {
- return version;
+ public String getDsseqid() {
+ return dsseqid;
}
/**
- * Sets the value of the version property.
+ * Sets the value of the dsseqid property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setVersion(String value)
- {
- this.version = value;
+ public void setDsseqid(String value) {
+ this.dsseqid = value;
}
/**
- * Gets the value of the accessionId property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the biotype property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getAccessionId()
- {
- return accessionId;
+ public String getBiotype() {
+ return biotype;
}
/**
- * Sets the value of the accessionId property.
+ * Sets the value of the biotype property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setAccessionId(String value)
- {
- this.accessionId = value;
+ public void setBiotype(String value) {
+ this.biotype = value;
}
- /**
- * Gets the value of the locus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isLocus()
- {
- if (locus == null)
- {
- return false;
- }
- else
- {
- return locus;
- }
- }
/**
- * Sets the value of the locus property.
+ * <p>Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link Boolean }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public void setLocus(Boolean value)
- {
- this.locus = value;
- }
-
- /**
- * Gets the value of the canonical property.
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
*/
- public boolean isCanonical()
- {
- if (canonical == null)
- {
- return false;
- }
- else
- {
- return canonical;
- }
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "mapping"
+ })
+ public static class DBRef {
+
+ @XmlElement(name = "Mapping")
+ protected Mapping mapping;
+ @XmlAttribute(name = "source")
+ protected String source;
+ @XmlAttribute(name = "version")
+ protected String version;
+ @XmlAttribute(name = "accessionId")
+ protected String accessionId;
+ @XmlAttribute(name = "locus")
+ protected Boolean locus;
+ @XmlAttribute(name = "canonical")
+ protected Boolean canonical;
+
+ /**
+ * Gets the value of the mapping property.
+ *
+ * @return
+ * possible object is
+ * {@link Mapping }
+ *
+ */
+ public Mapping getMapping() {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value) {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSource() {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSource(String value) {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the accessionId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccessionId() {
+ return accessionId;
+ }
+
+ /**
+ * Sets the value of the accessionId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccessionId(String value) {
+ this.accessionId = value;
+ }
+
+ /**
+ * Gets the value of the locus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLocus() {
+ if (locus == null) {
+ return false;
+ } else {
+ return locus;
+ }
+ }
+
+ /**
+ * Sets the value of the locus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLocus(Boolean value) {
+ this.locus = value;
+ }
+
+ /**
+ * Gets the value of the canonical property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCanonical() {
+ if (canonical == null) {
+ return false;
+ } else {
+ return canonical;
+ }
+ }
+
+ /**
+ * Sets the value of the canonical property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCanonical(Boolean value) {
+ this.canonical = value;
+ }
- /**
- * Sets the value of the canonical property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCanonical(Boolean value)
- {
- this.canonical = value;
}
- }
-
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="sequenceSetProperties"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
- * name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="datasetId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+@XmlType(name = "", propOrder = {
+ "sequence",
+ "annotation",
+ "sequenceSetProperties",
+ "alcodonFrame"
+})
@XmlRootElement(name = "SequenceSet")
-public class SequenceSet
-{
-
- @XmlElement(name = "Sequence")
- protected List<Sequence> sequence;
-
- @XmlElement(name = "Annotation")
- protected List<Annotation> annotation;
+public class SequenceSet {
- protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+ @XmlElement(name = "Sequence")
+ protected List<Sequence> sequence;
+ @XmlElement(name = "Annotation")
+ protected List<Annotation> annotation;
+ protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+ @XmlElement(name = "AlcodonFrame")
+ protected List<AlcodonFrame> alcodonFrame;
+ @XmlAttribute(name = "gapChar", required = true)
+ protected String gapChar;
+ @XmlAttribute(name = "datasetId")
+ protected String datasetId;
- @XmlElement(name = "AlcodonFrame")
- protected List<AlcodonFrame> alcodonFrame;
-
- @XmlAttribute(name = "gapChar", required = true)
- protected String gapChar;
-
- @XmlAttribute(name = "datasetId")
- protected String datasetId;
-
- /**
- * Gets the value of the sequence property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the sequence property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSequence().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Sequence }
- *
- *
- */
- public List<Sequence> getSequence()
- {
- if (sequence == null)
- {
- sequence = new ArrayList<Sequence>();
+ /**
+ * Gets the value of the sequence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence }
+ *
+ *
+ */
+ public List<Sequence> getSequence() {
+ if (sequence == null) {
+ sequence = new ArrayList<Sequence>();
+ }
+ return this.sequence;
}
- return this.sequence;
- }
- /**
- * Gets the value of the annotation property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the annotation property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAnnotation().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Annotation }
- *
- *
- */
- public List<Annotation> getAnnotation()
- {
- if (annotation == null)
- {
- annotation = new ArrayList<Annotation>();
+ /**
+ * Gets the value of the annotation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the annotation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAnnotation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Annotation }
+ *
+ *
+ */
+ public List<Annotation> getAnnotation() {
+ if (annotation == null) {
+ annotation = new ArrayList<Annotation>();
+ }
+ return this.annotation;
}
- return this.annotation;
- }
- /**
- * Gets the value of the sequenceSetProperties property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the sequenceSetProperties property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSequenceSetProperties().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link SequenceSet.SequenceSetProperties }
- *
- *
- */
- public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
- {
- if (sequenceSetProperties == null)
- {
- sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+ /**
+ * Gets the value of the sequenceSetProperties property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequenceSetProperties().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet.SequenceSetProperties }
+ *
+ *
+ */
+ public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
+ if (sequenceSetProperties == null) {
+ sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+ }
+ return this.sequenceSetProperties;
}
- return this.sequenceSetProperties;
- }
- /**
- * Gets the value of the alcodonFrame property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the alcodonFrame property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getAlcodonFrame().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame }
- *
- *
- */
- public List<AlcodonFrame> getAlcodonFrame()
- {
- if (alcodonFrame == null)
- {
- alcodonFrame = new ArrayList<AlcodonFrame>();
+ /**
+ * Gets the value of the alcodonFrame property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodonFrame().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame }
+ *
+ *
+ */
+ public List<AlcodonFrame> getAlcodonFrame() {
+ if (alcodonFrame == null) {
+ alcodonFrame = new ArrayList<AlcodonFrame>();
+ }
+ return this.alcodonFrame;
}
- return this.alcodonFrame;
- }
-
- /**
- * Gets the value of the gapChar property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getGapChar()
- {
- return gapChar;
- }
-
- /**
- * Sets the value of the gapChar property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setGapChar(String value)
- {
- this.gapChar = value;
- }
-
- /**
- * Gets the value of the datasetId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDatasetId()
- {
- return datasetId;
- }
-
- /**
- * Sets the value of the datasetId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDatasetId(String value)
- {
- this.datasetId = value;
- }
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequenceSetProperties
- {
-
- @XmlAttribute(name = "key")
- protected String key;
-
- @XmlAttribute(name = "value")
- protected String value;
/**
- * Gets the value of the key property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the gapChar property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getKey()
- {
- return key;
+ public String getGapChar() {
+ return gapChar;
}
/**
- * Sets the value of the key property.
+ * Sets the value of the gapChar property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setKey(String value)
- {
- this.key = value;
+ public void setGapChar(String value) {
+ this.gapChar = value;
}
/**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the datasetId property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getValue()
- {
- return value;
+ public String getDatasetId() {
+ return datasetId;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the datasetId property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public void setDatasetId(String value) {
+ this.datasetId = value;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequenceSetProperties {
+
+ @XmlAttribute(name = "key")
+ protected String key;
+ @XmlAttribute(name = "value")
+ protected String value;
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for SequenceType complex type.
+ * <p>Java class for SequenceType complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="SequenceType"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequence"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="SequenceType">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
-@XmlSeeAlso({ Sequence.class })
-public class SequenceType
-{
-
- protected String sequence;
-
- protected String name;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- @XmlAttribute(name = "description")
- protected String description;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequence()
- {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequence(String value)
- {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
+@XmlType(name = "SequenceType", propOrder = {
+ "sequence",
+ "name"
+})
+@XmlSeeAlso({
+ Sequence.class
+})
+public class SequenceType {
+
+ protected String sequence;
+ protected String name;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for ThresholdType.
+ * <p>Java class for ThresholdType.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class. <pre> &lt;simpleType
- * name="ThresholdType"&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
- * value="NONE"/&gt; &lt;enumeration value="ABOVE"/&gt;
- * &lt;enumeration value="BELOW"/&gt; &lt;/restriction&gt;
- * &lt;/simpleType&gt; </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * <simpleType name="ThresholdType">
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="NONE"/>
+ * <enumeration value="ABOVE"/>
+ * <enumeration value="BELOW"/>
+ * </restriction>
+ * </simpleType>
+ * </pre>
*
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum ThresholdType
-{
+public enum ThresholdType {
- NONE, ABOVE, BELOW;
+ NONE,
+ ABOVE,
+ BELOW;
- public String value()
- {
- return name();
- }
+ public String value() {
+ return name();
+ }
- public static ThresholdType fromValue(String v)
- {
- return valueOf(v);
- }
+ public static ThresholdType fromValue(String v) {
+ return valueOf(v);
+ }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for VAMSAS complex type.
+ * <p>Java class for VAMSAS complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="VAMSAS"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="Tree"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element
- * ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="VAMSAS">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
-public class VAMSAS
-{
-
- @XmlElement(name = "Tree")
- protected List<String> tree;
+@XmlType(name = "VAMSAS", propOrder = {
+ "tree",
+ "sequenceSet"
+})
+public class VAMSAS {
- @XmlElement(name = "SequenceSet")
- protected List<SequenceSet> sequenceSet;
+ @XmlElement(name = "Tree")
+ protected List<String> tree;
+ @XmlElement(name = "SequenceSet")
+ protected List<SequenceSet> sequenceSet;
- /**
- * Gets the value of the tree property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the tree property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getTree().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getTree()
- {
- if (tree == null)
- {
- tree = new ArrayList<String>();
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<String>();
+ }
+ return this.tree;
}
- return this.tree;
- }
- /**
- * Gets the value of the sequenceSet property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the sequenceSet property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getSequenceSet().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link SequenceSet }
- *
- *
- */
- public List<SequenceSet> getSequenceSet()
- {
- if (sequenceSet == null)
- {
- sequenceSet = new ArrayList<SequenceSet>();
+ /**
+ * Gets the value of the sequenceSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequenceSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet }
+ *
+ *
+ */
+ public List<SequenceSet> getSequenceSet() {
+ if (sequenceSet == null) {
+ sequenceSet = new ArrayList<SequenceSet>();
+ }
+ return this.sequenceSet;
}
- return this.sequenceSet;
- }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for WebServiceParameterSet complex type.
+ * <p>Java class for WebServiceParameterSet complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre> &lt;complexType name="WebServiceParameterSet"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="Version"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description"
- * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="serviceURL"
- * type="{http://www.w3.org/2001/XMLSchema}anyURI"
- * maxOccurs="unbounded"/&gt; &lt;element name="parameters"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="WebServiceParameterSet">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
+ * <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "WebServiceParameterSet",
- namespace = "www.jalview.org/xml/wsparamset",
- propOrder =
- { "version", "description", "serviceURL", "parameters" })
+@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
+ "version",
+ "description",
+ "serviceURL",
+ "parameters"
+})
@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
-public class WebServiceParameterSet
-{
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
-
- @XmlElement(namespace = "")
- protected String description;
-
- @XmlElement(namespace = "", required = true)
- @XmlSchemaType(name = "anyURI")
- protected List<String> serviceURL;
-
- @XmlElement(namespace = "", required = true)
- protected String parameters;
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the serviceURL property.
- *
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the serviceURL property.
- *
- * <p> For example, to add a new item, do as follows: <pre>
- * getServiceURL().add(newItem); </pre>
- *
- *
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getServiceURL()
- {
- if (serviceURL == null)
- {
- serviceURL = new ArrayList<String>();
+ jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
+})
+public class WebServiceParameterSet {
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+ @XmlElement(namespace = "")
+ protected String description;
+ @XmlElement(namespace = "", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected List<String> serviceURL;
+ @XmlElement(namespace = "", required = true)
+ protected String parameters;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the serviceURL property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getServiceURL().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getServiceURL() {
+ if (serviceURL == null) {
+ serviceURL = new ArrayList<String>();
+ }
+ return this.serviceURL;
+ }
+
+ /**
+ * Gets the value of the parameters property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getParameters() {
+ return parameters;
+ }
+
+ /**
+ * Sets the value of the parameters property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setParameters(String value) {
+ this.parameters = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
}
- return this.serviceURL;
- }
-
- /**
- * Gets the value of the parameters property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getParameters()
- {
- return parameters;
- }
-
- /**
- * Sets the value of the parameters property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setParameters(String value)
- {
- this.parameters = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
}
//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
-@javax.xml.bind.annotation.XmlSchema(
- namespace = "www.vamsas.ac.uk/jalview/version2",
- elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.jalview;
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes different types of citations. Equivalent to the flat file RX-, RG-,
- * RA-, RT- and RL-lines.
+ * Describes different types of citations.
+ * Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
*
- * <p>
- * Java class for citationType complex type.
+ * <p>Java class for citationType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="citationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "citationType",
- propOrder =
- { "title", "editorList", "authorList", "locator", "dbReference" })
-public class CitationType
-{
-
- protected String title;
-
- protected NameListType editorList;
-
- protected NameListType authorList;
-
- protected String locator;
-
- protected List<DbReferenceType> dbReference;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "date")
- protected String date;
-
- @XmlAttribute(name = "name")
- protected String name;
-
- @XmlAttribute(name = "volume")
- protected String volume;
-
- @XmlAttribute(name = "first")
- protected String first;
-
- @XmlAttribute(name = "last")
- protected String last;
-
- @XmlAttribute(name = "publisher")
- protected String publisher;
-
- @XmlAttribute(name = "city")
- protected String city;
-
- @XmlAttribute(name = "db")
- protected String db;
-
- @XmlAttribute(name = "number")
- protected String number;
-
- @XmlAttribute(name = "institute")
- protected String institute;
-
- @XmlAttribute(name = "country")
- protected String country;
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the editorList property.
- *
- * @return possible object is {@link NameListType }
- *
- */
- public NameListType getEditorList()
- {
- return editorList;
- }
-
- /**
- * Sets the value of the editorList property.
- *
- * @param value
- * allowed object is {@link NameListType }
- *
- */
- public void setEditorList(NameListType value)
- {
- this.editorList = value;
- }
-
- /**
- * Gets the value of the authorList property.
- *
- * @return possible object is {@link NameListType }
- *
- */
- public NameListType getAuthorList()
- {
- return authorList;
- }
-
- /**
- * Sets the value of the authorList property.
- *
- * @param value
- * allowed object is {@link NameListType }
- *
- */
- public void setAuthorList(NameListType value)
- {
- this.authorList = value;
- }
-
- /**
- * Gets the value of the locator property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLocator()
- {
- return locator;
- }
-
- /**
- * Sets the value of the locator property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLocator(String value)
- {
- this.locator = value;
- }
-
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference()
- {
- if (dbReference == null)
- {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the date property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDate()
- {
- return date;
- }
-
- /**
- * Sets the value of the date property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDate(String value)
- {
- this.date = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the volume property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVolume()
- {
- return volume;
- }
-
- /**
- * Sets the value of the volume property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVolume(String value)
- {
- this.volume = value;
- }
-
- /**
- * Gets the value of the first property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFirst()
- {
- return first;
- }
-
- /**
- * Sets the value of the first property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFirst(String value)
- {
- this.first = value;
- }
-
- /**
- * Gets the value of the last property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLast()
- {
- return last;
- }
-
- /**
- * Sets the value of the last property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLast(String value)
- {
- this.last = value;
- }
-
- /**
- * Gets the value of the publisher property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getPublisher()
- {
- return publisher;
- }
-
- /**
- * Sets the value of the publisher property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setPublisher(String value)
- {
- this.publisher = value;
- }
-
- /**
- * Gets the value of the city property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCity()
- {
- return city;
- }
-
- /**
- * Sets the value of the city property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCity(String value)
- {
- this.city = value;
- }
-
- /**
- * Gets the value of the db property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDb()
- {
- return db;
- }
-
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDb(String value)
- {
- this.db = value;
- }
-
- /**
- * Gets the value of the number property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getNumber()
- {
- return number;
- }
-
- /**
- * Sets the value of the number property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setNumber(String value)
- {
- this.number = value;
- }
-
- /**
- * Gets the value of the institute property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getInstitute()
- {
- return institute;
- }
-
- /**
- * Sets the value of the institute property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setInstitute(String value)
- {
- this.institute = value;
- }
-
- /**
- * Gets the value of the country property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCountry()
- {
- return country;
- }
-
- /**
- * Sets the value of the country property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCountry(String value)
- {
- this.country = value;
- }
+@XmlType(name = "citationType", propOrder = {
+ "title",
+ "editorList",
+ "authorList",
+ "locator",
+ "dbReference"
+})
+public class CitationType {
+
+ protected String title;
+ protected NameListType editorList;
+ protected NameListType authorList;
+ protected String locator;
+ protected List<DbReferenceType> dbReference;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "date")
+ protected String date;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "volume")
+ protected String volume;
+ @XmlAttribute(name = "first")
+ protected String first;
+ @XmlAttribute(name = "last")
+ protected String last;
+ @XmlAttribute(name = "publisher")
+ protected String publisher;
+ @XmlAttribute(name = "city")
+ protected String city;
+ @XmlAttribute(name = "db")
+ protected String db;
+ @XmlAttribute(name = "number")
+ protected String number;
+ @XmlAttribute(name = "institute")
+ protected String institute;
+ @XmlAttribute(name = "country")
+ protected String country;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the editorList property.
+ *
+ * @return
+ * possible object is
+ * {@link NameListType }
+ *
+ */
+ public NameListType getEditorList() {
+ return editorList;
+ }
+
+ /**
+ * Sets the value of the editorList property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NameListType }
+ *
+ */
+ public void setEditorList(NameListType value) {
+ this.editorList = value;
+ }
+
+ /**
+ * Gets the value of the authorList property.
+ *
+ * @return
+ * possible object is
+ * {@link NameListType }
+ *
+ */
+ public NameListType getAuthorList() {
+ return authorList;
+ }
+
+ /**
+ * Sets the value of the authorList property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NameListType }
+ *
+ */
+ public void setAuthorList(NameListType value) {
+ this.authorList = value;
+ }
+
+ /**
+ * Gets the value of the locator property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLocator() {
+ return locator;
+ }
+
+ /**
+ * Sets the value of the locator property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocator(String value) {
+ this.locator = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the date property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDate() {
+ return date;
+ }
+
+ /**
+ * Sets the value of the date property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDate(String value) {
+ this.date = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVolume() {
+ return volume;
+ }
+
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVolume(String value) {
+ this.volume = value;
+ }
+
+ /**
+ * Gets the value of the first property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFirst() {
+ return first;
+ }
+
+ /**
+ * Sets the value of the first property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFirst(String value) {
+ this.first = value;
+ }
+
+ /**
+ * Gets the value of the last property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLast() {
+ return last;
+ }
+
+ /**
+ * Sets the value of the last property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLast(String value) {
+ this.last = value;
+ }
+
+ /**
+ * Gets the value of the publisher property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getPublisher() {
+ return publisher;
+ }
+
+ /**
+ * Sets the value of the publisher property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setPublisher(String value) {
+ this.publisher = value;
+ }
+
+ /**
+ * Gets the value of the city property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCity() {
+ return city;
+ }
+
+ /**
+ * Sets the value of the city property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCity(String value) {
+ this.city = value;
+ }
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDb() {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDb(String value) {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the number property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNumber() {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNumber(String value) {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the institute property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getInstitute() {
+ return institute;
+ }
+
+ /**
+ * Sets the value of the institute property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setInstitute(String value) {
+ this.institute = value;
+ }
+
+ /**
+ * Gets the value of the country property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCountry() {
+ return country;
+ }
+
+ /**
+ * Sets the value of the country property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCountry(String value) {
+ this.country = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
* Describes a cofactor.
*
- * <p>
- * Java class for cofactorType complex type.
+ * <p>Java class for cofactorType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="cofactorType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
-public class CofactorType
-{
-
- @XmlElement(required = true)
- protected String name;
-
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
+@XmlType(name = "cofactorType", propOrder = {
+ "name",
+ "dbReference"
+})
+public class CofactorType {
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected String name;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
- /**
- * Gets the value of the dbReference property.
- *
- * @return possible object is {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference()
- {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value)
- {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes different types of general annotations. Equivalent to the flat file
- * CC-line.
+ * Describes different types of general annotations.
+ * Equivalent to the flat file CC-line.
*
- * <p>
- * Java class for commentType complex type.
+ * <p>Java class for commentType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="commentType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "commentType",
- propOrder =
- { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
- "temperatureDependence", "reaction", "physiologicalReaction",
- "cofactor", "subcellularLocation", "conflict", "link", "event",
- "isoform", "interactant", "organismsDiffer", "experiments", "disease",
- "location", "text" })
-public class CommentType
-{
-
- protected MoleculeType molecule;
-
- protected CommentType.Absorption absorption;
-
- protected CommentType.Kinetics kinetics;
-
- protected CommentType.PhDependence phDependence;
-
- protected CommentType.RedoxPotential redoxPotential;
-
- protected CommentType.TemperatureDependence temperatureDependence;
-
- protected ReactionType reaction;
-
- protected List<PhysiologicalReactionType> physiologicalReaction;
-
- protected List<CofactorType> cofactor;
-
- protected List<SubcellularLocationType> subcellularLocation;
-
- protected CommentType.Conflict conflict;
-
- protected List<CommentType.Link> link;
+@XmlType(name = "commentType", propOrder = {
+ "molecule",
+ "absorption",
+ "kinetics",
+ "phDependence",
+ "redoxPotential",
+ "temperatureDependence",
+ "reaction",
+ "physiologicalReaction",
+ "cofactor",
+ "subcellularLocation",
+ "conflict",
+ "link",
+ "event",
+ "isoform",
+ "interactant",
+ "organismsDiffer",
+ "experiments",
+ "disease",
+ "location",
+ "text"
+})
+public class CommentType {
+
+ protected MoleculeType molecule;
+ protected CommentType.Absorption absorption;
+ protected CommentType.Kinetics kinetics;
+ protected CommentType.PhDependence phDependence;
+ protected CommentType.RedoxPotential redoxPotential;
+ protected CommentType.TemperatureDependence temperatureDependence;
+ protected ReactionType reaction;
+ protected List<PhysiologicalReactionType> physiologicalReaction;
+ protected List<CofactorType> cofactor;
+ protected List<SubcellularLocationType> subcellularLocation;
+ protected CommentType.Conflict conflict;
+ protected List<CommentType.Link> link;
+ protected List<EventType> event;
+ protected List<IsoformType> isoform;
+ protected List<InteractantType> interactant;
+ @XmlElement(defaultValue = "false")
+ protected Boolean organismsDiffer;
+ protected Integer experiments;
+ protected CommentType.Disease disease;
+ protected List<LocationType> location;
+ protected List<EvidencedStringType> text;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "locationType")
+ protected String locationType;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "mass")
+ protected Float mass;
+ @XmlAttribute(name = "error")
+ protected String error;
+ @XmlAttribute(name = "method")
+ protected String method;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- protected List<EventType> event;
-
- protected List<IsoformType> isoform;
-
- protected List<InteractantType> interactant;
-
- @XmlElement(defaultValue = "false")
- protected Boolean organismsDiffer;
-
- protected Integer experiments;
-
- protected CommentType.Disease disease;
-
- protected List<LocationType> location;
-
- protected List<EvidencedStringType> text;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "locationType")
- protected String locationType;
-
- @XmlAttribute(name = "name")
- protected String name;
-
- @XmlAttribute(name = "mass")
- protected Float mass;
-
- @XmlAttribute(name = "error")
- protected String error;
-
- @XmlAttribute(name = "method")
- protected String method;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the molecule property.
- *
- * @return possible object is {@link MoleculeType }
- *
- */
- public MoleculeType getMolecule()
- {
- return molecule;
- }
-
- /**
- * Sets the value of the molecule property.
- *
- * @param value
- * allowed object is {@link MoleculeType }
- *
- */
- public void setMolecule(MoleculeType value)
- {
- this.molecule = value;
- }
-
- /**
- * Gets the value of the absorption property.
- *
- * @return possible object is {@link CommentType.Absorption }
- *
- */
- public CommentType.Absorption getAbsorption()
- {
- return absorption;
- }
-
- /**
- * Sets the value of the absorption property.
- *
- * @param value
- * allowed object is {@link CommentType.Absorption }
- *
- */
- public void setAbsorption(CommentType.Absorption value)
- {
- this.absorption = value;
- }
-
- /**
- * Gets the value of the kinetics property.
- *
- * @return possible object is {@link CommentType.Kinetics }
- *
- */
- public CommentType.Kinetics getKinetics()
- {
- return kinetics;
- }
-
- /**
- * Sets the value of the kinetics property.
- *
- * @param value
- * allowed object is {@link CommentType.Kinetics }
- *
- */
- public void setKinetics(CommentType.Kinetics value)
- {
- this.kinetics = value;
- }
-
- /**
- * Gets the value of the phDependence property.
- *
- * @return possible object is {@link CommentType.PhDependence }
- *
- */
- public CommentType.PhDependence getPhDependence()
- {
- return phDependence;
- }
-
- /**
- * Sets the value of the phDependence property.
- *
- * @param value
- * allowed object is {@link CommentType.PhDependence }
- *
- */
- public void setPhDependence(CommentType.PhDependence value)
- {
- this.phDependence = value;
- }
-
- /**
- * Gets the value of the redoxPotential property.
- *
- * @return possible object is {@link CommentType.RedoxPotential }
- *
- */
- public CommentType.RedoxPotential getRedoxPotential()
- {
- return redoxPotential;
- }
-
- /**
- * Sets the value of the redoxPotential property.
- *
- * @param value
- * allowed object is {@link CommentType.RedoxPotential }
- *
- */
- public void setRedoxPotential(CommentType.RedoxPotential value)
- {
- this.redoxPotential = value;
- }
-
- /**
- * Gets the value of the temperatureDependence property.
- *
- * @return possible object is {@link CommentType.TemperatureDependence }
- *
- */
- public CommentType.TemperatureDependence getTemperatureDependence()
- {
- return temperatureDependence;
- }
-
- /**
- * Sets the value of the temperatureDependence property.
- *
- * @param value
- * allowed object is {@link CommentType.TemperatureDependence }
- *
- */
- public void setTemperatureDependence(
- CommentType.TemperatureDependence value)
- {
- this.temperatureDependence = value;
- }
-
- /**
- * Gets the value of the reaction property.
- *
- * @return possible object is {@link ReactionType }
- *
- */
- public ReactionType getReaction()
- {
- return reaction;
- }
-
- /**
- * Sets the value of the reaction property.
- *
- * @param value
- * allowed object is {@link ReactionType }
- *
- */
- public void setReaction(ReactionType value)
- {
- this.reaction = value;
- }
-
- /**
- * Gets the value of the physiologicalReaction property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the physiologicalReaction property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getPhysiologicalReaction().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link PhysiologicalReactionType }
- *
- *
- */
- public List<PhysiologicalReactionType> getPhysiologicalReaction()
- {
- if (physiologicalReaction == null)
- {
- physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return
+ * possible object is
+ * {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule() {
+ return molecule;
}
- return this.physiologicalReaction;
- }
-
- /**
- * Gets the value of the cofactor property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the cofactor property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getCofactor().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CofactorType }
- *
- *
- */
- public List<CofactorType> getCofactor()
- {
- if (cofactor == null)
- {
- cofactor = new ArrayList<CofactorType>();
+
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is
+ * {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value) {
+ this.molecule = value;
}
- return this.cofactor;
- }
-
- /**
- * Gets the value of the subcellularLocation property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the subcellularLocation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSubcellularLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SubcellularLocationType }
- *
- *
- */
- public List<SubcellularLocationType> getSubcellularLocation()
- {
- if (subcellularLocation == null)
- {
- subcellularLocation = new ArrayList<SubcellularLocationType>();
+
+ /**
+ * Gets the value of the absorption property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption getAbsorption() {
+ return absorption;
}
- return this.subcellularLocation;
- }
-
- /**
- * Gets the value of the conflict property.
- *
- * @return possible object is {@link CommentType.Conflict }
- *
- */
- public CommentType.Conflict getConflict()
- {
- return conflict;
- }
-
- /**
- * Sets the value of the conflict property.
- *
- * @param value
- * allowed object is {@link CommentType.Conflict }
- *
- */
- public void setConflict(CommentType.Conflict value)
- {
- this.conflict = value;
- }
-
- /**
- * Gets the value of the link property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the link property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getLink().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CommentType.Link }
- *
- *
- */
- public List<CommentType.Link> getLink()
- {
- if (link == null)
- {
- link = new ArrayList<CommentType.Link>();
+
+ /**
+ * Sets the value of the absorption property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Absorption }
+ *
+ */
+ public void setAbsorption(CommentType.Absorption value) {
+ this.absorption = value;
}
- return this.link;
- }
-
- /**
- * Gets the value of the event property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the event property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvent().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link EventType }
- *
- *
- */
- public List<EventType> getEvent()
- {
- if (event == null)
- {
- event = new ArrayList<EventType>();
+
+ /**
+ * Gets the value of the kinetics property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics getKinetics() {
+ return kinetics;
}
- return this.event;
- }
-
- /**
- * Gets the value of the isoform property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the isoform property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getIsoform().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link IsoformType
- * }
- *
- *
- */
- public List<IsoformType> getIsoform()
- {
- if (isoform == null)
- {
- isoform = new ArrayList<IsoformType>();
+
+ /**
+ * Sets the value of the kinetics property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Kinetics }
+ *
+ */
+ public void setKinetics(CommentType.Kinetics value) {
+ this.kinetics = value;
}
- return this.isoform;
- }
-
- /**
- * Gets the value of the interactant property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the interactant property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getInteractant().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link InteractantType }
- *
- *
- */
- public List<InteractantType> getInteractant()
- {
- if (interactant == null)
- {
- interactant = new ArrayList<InteractantType>();
+
+ /**
+ * Gets the value of the phDependence property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence getPhDependence() {
+ return phDependence;
}
- return this.interactant;
- }
-
- /**
- * Gets the value of the organismsDiffer property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isOrganismsDiffer()
- {
- return organismsDiffer;
- }
-
- /**
- * Sets the value of the organismsDiffer property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setOrganismsDiffer(Boolean value)
- {
- this.organismsDiffer = value;
- }
-
- /**
- * Gets the value of the experiments property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getExperiments()
- {
- return experiments;
- }
-
- /**
- * Sets the value of the experiments property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setExperiments(Integer value)
- {
- this.experiments = value;
- }
-
- /**
- * Gets the value of the disease property.
- *
- * @return possible object is {@link CommentType.Disease }
- *
- */
- public CommentType.Disease getDisease()
- {
- return disease;
- }
-
- /**
- * Sets the value of the disease property.
- *
- * @param value
- * allowed object is {@link CommentType.Disease }
- *
- */
- public void setDisease(CommentType.Disease value)
- {
- this.disease = value;
- }
-
- /**
- * Gets the value of the location property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the location property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link LocationType }
- *
- *
- */
- public List<LocationType> getLocation()
- {
- if (location == null)
- {
- location = new ArrayList<LocationType>();
+
+ /**
+ * Sets the value of the phDependence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.PhDependence }
+ *
+ */
+ public void setPhDependence(CommentType.PhDependence value) {
+ this.phDependence = value;
}
- return this.location;
- }
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
+
+ /**
+ * Gets the value of the redoxPotential property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential getRedoxPotential() {
+ return redoxPotential;
}
- return this.text;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the locationType property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLocationType()
- {
- return locationType;
- }
-
- /**
- * Sets the value of the locationType property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLocationType(String value)
- {
- this.locationType = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the mass property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMass()
- {
- return mass;
- }
-
- /**
- * Sets the value of the mass property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMass(Float value)
- {
- this.mass = value;
- }
-
- /**
- * Gets the value of the error property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getError()
- {
- return error;
- }
-
- /**
- * Sets the value of the error property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setError(String value)
- {
- this.error = value;
- }
-
- /**
- * Gets the value of the method property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getMethod()
- {
- return method;
- }
-
- /**
- * Sets the value of the method property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setMethod(String value)
- {
- this.method = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+
+ /**
+ * Sets the value of the redoxPotential property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.RedoxPotential }
+ *
+ */
+ public void setRedoxPotential(CommentType.RedoxPotential value) {
+ this.redoxPotential = value;
}
- return this.evidence;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "max", "text" })
- public static class Absorption
- {
-
- protected EvidencedStringType max;
- protected List<EvidencedStringType> text;
+ /**
+ * Gets the value of the temperatureDependence property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence getTemperatureDependence() {
+ return temperatureDependence;
+ }
/**
- * Gets the value of the max property.
+ * Sets the value of the temperatureDependence property.
*
- * @return possible object is {@link EvidencedStringType }
+ * @param value
+ * allowed object is
+ * {@link CommentType.TemperatureDependence }
+ *
+ */
+ public void setTemperatureDependence(CommentType.TemperatureDependence value) {
+ this.temperatureDependence = value;
+ }
+
+ /**
+ * Gets the value of the reaction property.
*
+ * @return
+ * possible object is
+ * {@link ReactionType }
+ *
*/
- public EvidencedStringType getMax()
- {
- return max;
+ public ReactionType getReaction() {
+ return reaction;
}
/**
- * Sets the value of the max property.
+ * Sets the value of the reaction property.
*
* @param value
- * allowed object is {@link EvidencedStringType }
- *
+ * allowed object is
+ * {@link ReactionType }
+ *
*/
- public void setMax(EvidencedStringType value)
- {
- this.max = value;
+ public void setReaction(ReactionType value) {
+ this.reaction = value;
}
/**
- * Gets the value of the text property.
+ * Gets the value of the physiologicalReaction property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the text property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getText().add(newItem);
+ * getPhysiologicalReaction().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ * {@link PhysiologicalReactionType }
*
*
*/
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ public List<PhysiologicalReactionType> getPhysiologicalReaction() {
+ if (physiologicalReaction == null) {
+ physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+ }
+ return this.physiologicalReaction;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequence" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="resource" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="EMBL-CDS"/>
- * <enumeration value="EMBL"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="frameshift"/>
- * <enumeration value="erroneous initiation"/>
- * <enumeration value="erroneous termination"/>
- * <enumeration value="erroneous gene model prediction"/>
- * <enumeration value="erroneous translation"/>
- * <enumeration value="miscellaneous discrepancy"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "sequence" })
- public static class Conflict
- {
-
- protected CommentType.Conflict.Sequence sequence;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "ref")
- protected String ref;
-
/**
- * Gets the value of the sequence property.
+ * Gets the value of the cofactor property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cofactor property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCofactor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CofactorType }
*
- * @return possible object is {@link CommentType.Conflict.Sequence }
*
*/
- public CommentType.Conflict.Sequence getSequence()
- {
- return sequence;
+ public List<CofactorType> getCofactor() {
+ if (cofactor == null) {
+ cofactor = new ArrayList<CofactorType>();
+ }
+ return this.cofactor;
}
/**
- * Sets the value of the sequence property.
+ * Gets the value of the subcellularLocation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubcellularLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SubcellularLocationType }
*
- * @param value
- * allowed object is {@link CommentType.Conflict.Sequence }
*
*/
- public void setSequence(CommentType.Conflict.Sequence value)
- {
- this.sequence = value;
+ public List<SubcellularLocationType> getSubcellularLocation() {
+ if (subcellularLocation == null) {
+ subcellularLocation = new ArrayList<SubcellularLocationType>();
+ }
+ return this.subcellularLocation;
}
/**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the conflict property.
*
+ * @return
+ * possible object is
+ * {@link CommentType.Conflict }
+ *
*/
- public String getType()
- {
- return type;
+ public CommentType.Conflict getConflict() {
+ return conflict;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the conflict property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link CommentType.Conflict }
+ *
*/
- public void setType(String value)
- {
- this.type = value;
+ public void setConflict(CommentType.Conflict value) {
+ this.conflict = value;
}
/**
- * Gets the value of the ref property.
+ * Gets the value of the link property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the link property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getLink().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CommentType.Link }
*
- * @return possible object is {@link String }
*
*/
- public String getRef()
- {
- return ref;
+ public List<CommentType.Link> getLink() {
+ if (link == null) {
+ link = new ArrayList<CommentType.Link>();
+ }
+ return this.link;
}
/**
- * Sets the value of the ref property.
+ * Gets the value of the event property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the event property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EventType }
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setRef(String value)
- {
- this.ref = value;
+ public List<EventType> getEvent() {
+ if (event == null) {
+ event = new ArrayList<EventType>();
+ }
+ return this.event;
}
/**
- * <p>
- * Java class for anonymous complex type.
+ * Gets the value of the isoform property.
*
* <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the isoform property.
*
+ * <p>
+ * For example, to add a new item, do as follows:
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="resource" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="EMBL-CDS"/>
- * <enumeration value="EMBL"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getIsoform().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link IsoformType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Sequence
- {
-
- @XmlAttribute(name = "resource", required = true)
- protected String resource;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "version")
- protected Integer version;
-
- /**
- * Gets the value of the resource property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getResource()
- {
- return resource;
- }
-
- /**
- * Sets the value of the resource property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setResource(String value)
- {
- this.resource = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setVersion(Integer value)
- {
- this.version = value;
- }
-
+ public List<IsoformType> getIsoform() {
+ if (isoform == null) {
+ isoform = new ArrayList<IsoformType>();
+ }
+ return this.isoform;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
- * </sequence>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "name", "acronym", "description", "dbReference" })
- public static class Disease
- {
-
- @XmlElement(required = true)
- protected String name;
-
- @XmlElement(required = true)
- protected String acronym;
+ /**
+ * Gets the value of the interactant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the interactant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInteractant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link InteractantType }
+ *
+ *
+ */
+ public List<InteractantType> getInteractant() {
+ if (interactant == null) {
+ interactant = new ArrayList<InteractantType>();
+ }
+ return this.interactant;
+ }
- @XmlElement(required = true)
- protected String description;
+ /**
+ * Gets the value of the organismsDiffer property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isOrganismsDiffer() {
+ return organismsDiffer;
+ }
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
+ /**
+ * Sets the value of the organismsDiffer property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setOrganismsDiffer(Boolean value) {
+ this.organismsDiffer = value;
+ }
- @XmlAttribute(name = "id", required = true)
- protected String id;
+ /**
+ * Gets the value of the experiments property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getExperiments() {
+ return experiments;
+ }
/**
- * Gets the value of the name property.
+ * Sets the value of the experiments property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setExperiments(Integer value) {
+ this.experiments = value;
+ }
+
+ /**
+ * Gets the value of the disease property.
*
+ * @return
+ * possible object is
+ * {@link CommentType.Disease }
+ *
*/
- public String getName()
- {
- return name;
+ public CommentType.Disease getDisease() {
+ return disease;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the disease property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link CommentType.Disease }
+ *
*/
- public void setName(String value)
- {
- this.name = value;
+ public void setDisease(CommentType.Disease value) {
+ this.disease = value;
}
/**
- * Gets the value of the acronym property.
+ * Gets the value of the location property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link LocationType }
*
- * @return possible object is {@link String }
*
*/
- public String getAcronym()
- {
- return acronym;
+ public List<LocationType> getLocation() {
+ if (location == null) {
+ location = new ArrayList<LocationType>();
+ }
+ return this.location;
}
/**
- * Sets the value of the acronym property.
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setAcronym(String value)
- {
- this.acronym = value;
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
/**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the type property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getDescription()
- {
- return description;
+ public String getType() {
+ return type;
}
/**
- * Sets the value of the description property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the locationType property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setDescription(String value)
- {
- this.description = value;
+ public String getLocationType() {
+ return locationType;
}
/**
- * Gets the value of the dbReference property.
+ * Sets the value of the locationType property.
*
- * @return possible object is {@link DbReferenceType }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLocationType(String value) {
+ this.locationType = value;
+ }
+
+ /**
+ * Gets the value of the name property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public DbReferenceType getDbReference()
- {
- return dbReference;
+ public String getName() {
+ return name;
}
/**
- * Sets the value of the dbReference property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is {@link DbReferenceType }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
*
+ * @return
+ * possible object is
+ * {@link Float }
+ *
*/
- public void setDbReference(DbReferenceType value)
- {
- this.dbReference = value;
+ public Float getMass() {
+ return mass;
}
/**
- * Gets the value of the id property.
+ * Sets the value of the mass property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMass(Float value) {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the error property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getId()
- {
- return id;
+ public String getError() {
+ return error;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the error property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setId(String value)
- {
- this.id = value;
+ public void setError(String value) {
+ this.error = value;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "km", "vmax", "text" })
- public static class Kinetics
- {
-
- @XmlElement(name = "KM")
- protected List<EvidencedStringType> km;
-
- @XmlElement(name = "Vmax")
- protected List<EvidencedStringType> vmax;
+ /**
+ * Gets the value of the method property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMethod() {
+ return method;
+ }
- protected List<EvidencedStringType> text;
+ /**
+ * Sets the value of the method property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMethod(String value) {
+ this.method = value;
+ }
/**
- * Gets the value of the km property.
+ * Gets the value of the evidence property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the km property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getKM().add(newItem);
+ * getEvidence().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ * {@link Integer }
*
*
*/
- public List<EvidencedStringType> getKM()
- {
- if (km == null)
- {
- km = new ArrayList<EvidencedStringType>();
- }
- return this.km;
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+
/**
- * Gets the value of the vmax property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the vmax property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getVmax().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getVmax()
- {
- if (vmax == null)
- {
- vmax = new ArrayList<EvidencedStringType>();
- }
- return this.vmax;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "max",
+ "text"
+ })
+ public static class Absorption {
+
+ protected EvidencedStringType max;
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setMax(EvidencedStringType value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
}
+
/**
- * Gets the value of the text property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getText().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequence" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="frameshift"/>
+ * <enumeration value="erroneous initiation"/>
+ * <enumeration value="erroneous termination"/>
+ * <enumeration value="erroneous gene model prediction"/>
+ * <enumeration value="erroneous translation"/>
+ * <enumeration value="miscellaneous discrepancy"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "sequence"
+ })
+ public static class Conflict {
+
+ protected CommentType.Conflict.Sequence sequence;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public CommentType.Conflict.Sequence getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public void setSequence(CommentType.Conflict.Sequence value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRef() {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRef(String value) {
+ this.ref = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence {
+
+ @XmlAttribute(name = "resource", required = true)
+ protected String resource;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "version")
+ protected Integer version;
+
+ /**
+ * Gets the value of the resource property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getResource() {
+ return resource;
+ }
+
+ /**
+ * Sets the value of the resource property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setResource(String value) {
+ this.resource = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setVersion(Integer value) {
+ this.version = value;
+ }
+
+ }
+
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Link
- {
-
- @XmlAttribute(name = "uri", required = true)
- @XmlSchemaType(name = "anyURI")
- protected String uri;
/**
- * Gets the value of the uri property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @return possible object is {@link String }
*
*/
- public String getUri()
- {
- return uri;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "name",
+ "acronym",
+ "description",
+ "dbReference"
+ })
+ public static class Disease {
+
+ @XmlElement(required = true)
+ protected String name;
+ @XmlElement(required = true)
+ protected String acronym;
+ @XmlElement(required = true)
+ protected String description;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the acronym property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAcronym() {
+ return acronym;
+ }
+
+ /**
+ * Sets the value of the acronym property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAcronym(String value) {
+ this.acronym = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
}
+
/**
- * Sets the value of the uri property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setUri(String value)
- {
- this.uri = value;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "km",
+ "vmax",
+ "text"
+ })
+ public static class Kinetics {
+
+ @XmlElement(name = "KM")
+ protected List<EvidencedStringType> km;
+ @XmlElement(name = "Vmax")
+ protected List<EvidencedStringType> vmax;
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the km property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the km property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getKM().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getKM() {
+ if (km == null) {
+ km = new ArrayList<EvidencedStringType>();
+ }
+ return this.km;
+ }
+
+ /**
+ * Gets the value of the vmax property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the vmax property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getVmax().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getVmax() {
+ if (vmax == null) {
+ vmax = new ArrayList<EvidencedStringType>();
+ }
+ return this.vmax;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "text" })
- public static class PhDependence
- {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
/**
- * Gets the value of the text property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getText().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Link {
+
+ @XmlAttribute(name = "uri", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected String uri;
+
+ /**
+ * Gets the value of the uri property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getUri() {
+ return uri;
+ }
+
+ /**
+ * Sets the value of the uri property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setUri(String value) {
+ this.uri = value;
+ }
+
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "text" })
- public static class RedoxPotential
- {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
/**
- * Gets the value of the text property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getText().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "text"
+ })
+ public static class PhDependence {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "text" })
- public static class TemperatureDependence
- {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
/**
- * Gets the value of the text property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getText().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "text"
+ })
+ public static class RedoxPotential {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "text"
+ })
+ public static class TemperatureDependence {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
- }
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the authors of a citation when these are represented by a
- * consortium. Equivalent to the flat file RG-line.
+ * Describes the authors of a citation when these are represented by a consortium.
+ * Equivalent to the flat file RG-line.
*
- * <p>
- * Java class for consortiumType complex type.
+ * <p>Java class for consortiumType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="consortiumType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "consortiumType")
-public class ConsortiumType
-{
+public class ConsortiumType {
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes a database cross-reference. Equivalent to the flat file DR-line.
+ * Describes a database cross-reference.
+ * Equivalent to the flat file DR-line.
+ *
*
+ * <p>Java class for dbReferenceType complex type.
*
- * <p>
- * Java class for dbReferenceType complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="dbReferenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
-public class DbReferenceType
-{
-
- protected MoleculeType molecule;
-
- protected List<PropertyType> property;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the molecule property.
- *
- * @return possible object is {@link MoleculeType }
- *
- */
- public MoleculeType getMolecule()
- {
- return molecule;
- }
+@XmlType(name = "dbReferenceType", propOrder = {
+ "molecule",
+ "property"
+})
+public class DbReferenceType {
+
+ protected MoleculeType molecule;
+ protected List<PropertyType> property;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return
+ * possible object is
+ * {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule() {
+ return molecule;
+ }
- /**
- * Sets the value of the molecule property.
- *
- * @param value
- * allowed object is {@link MoleculeType }
- *
- */
- public void setMolecule(MoleculeType value)
- {
- this.molecule = value;
- }
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is
+ * {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value) {
+ this.molecule = value;
+ }
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link PropertyType }
- *
- *
- */
- public List<PropertyType> getProperty()
- {
- if (property == null)
- {
- property = new ArrayList<PropertyType>();
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link PropertyType }
+ *
+ *
+ */
+ public List<PropertyType> getProperty() {
+ if (property == null) {
+ property = new ArrayList<PropertyType>();
+ }
+ return this.property;
}
- return this.property;
- }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.datatype.XMLGregorianCalendar;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "accession", "name", "protein", "gene", "organism", "organismHost",
- "geneLocation", "reference", "comment", "dbReference",
- "proteinExistence", "keyword", "feature", "evidence", "sequence" })
+@XmlType(name = "", propOrder = {
+ "accession",
+ "name",
+ "protein",
+ "gene",
+ "organism",
+ "organismHost",
+ "geneLocation",
+ "reference",
+ "comment",
+ "dbReference",
+ "proteinExistence",
+ "keyword",
+ "feature",
+ "evidence",
+ "sequence"
+})
@XmlRootElement(name = "entry")
-public class Entry
-{
-
- @XmlElement(required = true)
- protected List<String> accession;
-
- @XmlElement(required = true)
- protected List<String> name;
-
- @XmlElement(required = true)
- protected ProteinType protein;
-
- protected List<GeneType> gene;
+public class Entry {
+
+ @XmlElement(required = true)
+ protected List<String> accession;
+ @XmlElement(required = true)
+ protected List<String> name;
+ @XmlElement(required = true)
+ protected ProteinType protein;
+ protected List<GeneType> gene;
+ @XmlElement(required = true)
+ protected OrganismType organism;
+ protected List<OrganismType> organismHost;
+ protected List<GeneLocationType> geneLocation;
+ @XmlElement(required = true)
+ protected List<ReferenceType> reference;
+ @XmlElement(nillable = true)
+ protected List<CommentType> comment;
+ protected List<DbReferenceType> dbReference;
+ @XmlElement(required = true)
+ protected ProteinExistenceType proteinExistence;
+ protected List<KeywordType> keyword;
+ protected List<FeatureType> feature;
+ protected List<EvidenceType> evidence;
+ @XmlElement(required = true)
+ protected SequenceType sequence;
+ @XmlAttribute(name = "dataset", required = true)
+ protected String dataset;
+ @XmlAttribute(name = "created", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar created;
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the accession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAccession() {
+ if (accession == null) {
+ accession = new ArrayList<String>();
+ }
+ return this.accession;
+ }
- @XmlElement(required = true)
- protected OrganismType organism;
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getName() {
+ if (name == null) {
+ name = new ArrayList<String>();
+ }
+ return this.name;
+ }
- protected List<OrganismType> organismHost;
+ /**
+ * Gets the value of the protein property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType }
+ *
+ */
+ public ProteinType getProtein() {
+ return protein;
+ }
- protected List<GeneLocationType> geneLocation;
+ /**
+ * Sets the value of the protein property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType }
+ *
+ */
+ public void setProtein(ProteinType value) {
+ this.protein = value;
+ }
- @XmlElement(required = true)
- protected List<ReferenceType> reference;
+ /**
+ * Gets the value of the gene property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the gene property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGene().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneType }
+ *
+ *
+ */
+ public List<GeneType> getGene() {
+ if (gene == null) {
+ gene = new ArrayList<GeneType>();
+ }
+ return this.gene;
+ }
- @XmlElement(nillable = true)
- protected List<CommentType> comment;
+ /**
+ * Gets the value of the organism property.
+ *
+ * @return
+ * possible object is
+ * {@link OrganismType }
+ *
+ */
+ public OrganismType getOrganism() {
+ return organism;
+ }
- protected List<DbReferenceType> dbReference;
+ /**
+ * Sets the value of the organism property.
+ *
+ * @param value
+ * allowed object is
+ * {@link OrganismType }
+ *
+ */
+ public void setOrganism(OrganismType value) {
+ this.organism = value;
+ }
- @XmlElement(required = true)
- protected ProteinExistenceType proteinExistence;
+ /**
+ * Gets the value of the organismHost property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the organismHost property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOrganismHost().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismType }
+ *
+ *
+ */
+ public List<OrganismType> getOrganismHost() {
+ if (organismHost == null) {
+ organismHost = new ArrayList<OrganismType>();
+ }
+ return this.organismHost;
+ }
- protected List<KeywordType> keyword;
+ /**
+ * Gets the value of the geneLocation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGeneLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneLocationType }
+ *
+ *
+ */
+ public List<GeneLocationType> getGeneLocation() {
+ if (geneLocation == null) {
+ geneLocation = new ArrayList<GeneLocationType>();
+ }
+ return this.geneLocation;
+ }
- protected List<FeatureType> feature;
+ /**
+ * Gets the value of the reference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ReferenceType }
+ *
+ *
+ */
+ public List<ReferenceType> getReference() {
+ if (reference == null) {
+ reference = new ArrayList<ReferenceType>();
+ }
+ return this.reference;
+ }
- protected List<EvidenceType> evidence;
+ /**
+ * Gets the value of the comment property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the comment property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getComment().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CommentType }
+ *
+ *
+ */
+ public List<CommentType> getComment() {
+ if (comment == null) {
+ comment = new ArrayList<CommentType>();
+ }
+ return this.comment;
+ }
- @XmlElement(required = true)
- protected SequenceType sequence;
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
- @XmlAttribute(name = "dataset", required = true)
- protected String dataset;
+ /**
+ * Gets the value of the proteinExistence property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType getProteinExistence() {
+ return proteinExistence;
+ }
- @XmlAttribute(name = "created", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar created;
+ /**
+ * Sets the value of the proteinExistence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinExistenceType }
+ *
+ */
+ public void setProteinExistence(ProteinExistenceType value) {
+ this.proteinExistence = value;
+ }
- @XmlAttribute(name = "modified", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar modified;
+ /**
+ * Gets the value of the keyword property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link KeywordType }
+ *
+ *
+ */
+ public List<KeywordType> getKeyword() {
+ if (keyword == null) {
+ keyword = new ArrayList<KeywordType>();
+ }
+ return this.keyword;
+ }
- @XmlAttribute(name = "version", required = true)
- protected int version;
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link FeatureType }
+ *
+ *
+ */
+ public List<FeatureType> getFeature() {
+ if (feature == null) {
+ feature = new ArrayList<FeatureType>();
+ }
+ return this.feature;
+ }
- /**
- * Gets the value of the accession property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the accession property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAccession().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getAccession()
- {
- if (accession == null)
- {
- accession = new ArrayList<String>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidenceType }
+ *
+ *
+ */
+ public List<EvidenceType> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<EvidenceType>();
+ }
+ return this.evidence;
}
- return this.accession;
- }
-
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getName()
- {
- if (name == null)
- {
- name = new ArrayList<String>();
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link SequenceType }
+ *
+ */
+ public SequenceType getSequence() {
+ return sequence;
}
- return this.name;
- }
-
- /**
- * Gets the value of the protein property.
- *
- * @return possible object is {@link ProteinType }
- *
- */
- public ProteinType getProtein()
- {
- return protein;
- }
-
- /**
- * Sets the value of the protein property.
- *
- * @param value
- * allowed object is {@link ProteinType }
- *
- */
- public void setProtein(ProteinType value)
- {
- this.protein = value;
- }
-
- /**
- * Gets the value of the gene property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the gene property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getGene().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link GeneType }
- *
- *
- */
- public List<GeneType> getGene()
- {
- if (gene == null)
- {
- gene = new ArrayList<GeneType>();
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link SequenceType }
+ *
+ */
+ public void setSequence(SequenceType value) {
+ this.sequence = value;
}
- return this.gene;
- }
-
- /**
- * Gets the value of the organism property.
- *
- * @return possible object is {@link OrganismType }
- *
- */
- public OrganismType getOrganism()
- {
- return organism;
- }
-
- /**
- * Sets the value of the organism property.
- *
- * @param value
- * allowed object is {@link OrganismType }
- *
- */
- public void setOrganism(OrganismType value)
- {
- this.organism = value;
- }
-
- /**
- * Gets the value of the organismHost property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the organismHost property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getOrganismHost().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link OrganismType }
- *
- *
- */
- public List<OrganismType> getOrganismHost()
- {
- if (organismHost == null)
- {
- organismHost = new ArrayList<OrganismType>();
+
+ /**
+ * Gets the value of the dataset property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDataset() {
+ return dataset;
}
- return this.organismHost;
- }
-
- /**
- * Gets the value of the geneLocation property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the geneLocation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getGeneLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneLocationType }
- *
- *
- */
- public List<GeneLocationType> getGeneLocation()
- {
- if (geneLocation == null)
- {
- geneLocation = new ArrayList<GeneLocationType>();
+
+ /**
+ * Sets the value of the dataset property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDataset(String value) {
+ this.dataset = value;
}
- return this.geneLocation;
- }
-
- /**
- * Gets the value of the reference property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the reference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ReferenceType }
- *
- *
- */
- public List<ReferenceType> getReference()
- {
- if (reference == null)
- {
- reference = new ArrayList<ReferenceType>();
+
+ /**
+ * Gets the value of the created property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreated() {
+ return created;
}
- return this.reference;
- }
-
- /**
- * Gets the value of the comment property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the comment property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getComment().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link CommentType
- * }
- *
- *
- */
- public List<CommentType> getComment()
- {
- if (comment == null)
- {
- comment = new ArrayList<CommentType>();
+
+ /**
+ * Sets the value of the created property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreated(XMLGregorianCalendar value) {
+ this.created = value;
}
- return this.comment;
- }
-
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference()
- {
- if (dbReference == null)
- {
- dbReference = new ArrayList<DbReferenceType>();
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified() {
+ return modified;
}
- return this.dbReference;
- }
-
- /**
- * Gets the value of the proteinExistence property.
- *
- * @return possible object is {@link ProteinExistenceType }
- *
- */
- public ProteinExistenceType getProteinExistence()
- {
- return proteinExistence;
- }
-
- /**
- * Sets the value of the proteinExistence property.
- *
- * @param value
- * allowed object is {@link ProteinExistenceType }
- *
- */
- public void setProteinExistence(ProteinExistenceType value)
- {
- this.proteinExistence = value;
- }
-
- /**
- * Gets the value of the keyword property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the keyword property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getKeyword().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link KeywordType
- * }
- *
- *
- */
- public List<KeywordType> getKeyword()
- {
- if (keyword == null)
- {
- keyword = new ArrayList<KeywordType>();
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value) {
+ this.modified = value;
}
- return this.keyword;
- }
-
- /**
- * Gets the value of the feature property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the feature property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getFeature().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link FeatureType
- * }
- *
- *
- */
- public List<FeatureType> getFeature()
- {
- if (feature == null)
- {
- feature = new ArrayList<FeatureType>();
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion() {
+ return version;
}
- return this.feature;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidenceType }
- *
- *
- */
- public List<EvidenceType> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<EvidenceType>();
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value) {
+ this.version = value;
}
- return this.evidence;
- }
-
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link SequenceType }
- *
- */
- public SequenceType getSequence()
- {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link SequenceType }
- *
- */
- public void setSequence(SequenceType value)
- {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the dataset property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDataset()
- {
- return dataset;
- }
-
- /**
- * Sets the value of the dataset property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDataset(String value)
- {
- this.dataset = value;
- }
-
- /**
- * Gets the value of the created property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreated()
- {
- return created;
- }
-
- /**
- * Sets the value of the created property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setCreated(XMLGregorianCalendar value)
- {
- this.created = value;
- }
-
- /**
- * Gets the value of the modified property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getModified()
- {
- return modified;
- }
-
- /**
- * Sets the value of the modified property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setModified(XMLGregorianCalendar value)
- {
- this.modified = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- */
- public int getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- */
- public void setVersion(int value)
- {
- this.version = value;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
* Describes the type of events that cause alternative products.
*
- * <p>
- * Java class for eventType complex type.
+ * <p>Java class for eventType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="eventType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "eventType")
-public class EventType
-{
+public class EventType {
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the evidence for an annotation. No flat file equivalent.
+ * Describes the evidence for an annotation.
+ * No flat file equivalent.
*
- * <p>
- * Java class for evidenceType complex type.
+ * <p>Java class for evidenceType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="evidenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
-public class EvidenceType
-{
-
- protected SourceType source;
-
- protected ImportedFromType importedFrom;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "key", required = true)
- protected BigInteger key;
-
- /**
- * Gets the value of the source property.
- *
- * @return possible object is {@link SourceType }
- *
- */
- public SourceType getSource()
- {
- return source;
- }
-
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is {@link SourceType }
- *
- */
- public void setSource(SourceType value)
- {
- this.source = value;
- }
-
- /**
- * Gets the value of the importedFrom property.
- *
- * @return possible object is {@link ImportedFromType }
- *
- */
- public ImportedFromType getImportedFrom()
- {
- return importedFrom;
- }
-
- /**
- * Sets the value of the importedFrom property.
- *
- * @param value
- * allowed object is {@link ImportedFromType }
- *
- */
- public void setImportedFrom(ImportedFromType value)
- {
- this.importedFrom = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the key property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getKey()
- {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setKey(BigInteger value)
- {
- this.key = value;
- }
+@XmlType(name = "evidenceType", propOrder = {
+ "source",
+ "importedFrom"
+})
+public class EvidenceType {
+
+ protected SourceType source;
+ protected ImportedFromType importedFrom;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "key", required = true)
+ protected BigInteger key;
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link SourceType }
+ *
+ */
+ public SourceType getSource() {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link SourceType }
+ *
+ */
+ public void setSource(SourceType value) {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the importedFrom property.
+ *
+ * @return
+ * possible object is
+ * {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType getImportedFrom() {
+ return importedFrom;
+ }
+
+ /**
+ * Sets the value of the importedFrom property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ImportedFromType }
+ *
+ */
+ public void setImportedFrom(ImportedFromType value) {
+ this.importedFrom = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setKey(BigInteger value) {
+ this.key = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
- * <p>
- * Java class for evidencedStringType complex type.
+ * <p>Java class for evidencedStringType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="evidencedStringType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = { "value" })
-public class EvidencedStringType
-{
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+@XmlType(name = "evidencedStringType", propOrder = {
+ "value"
+})
+public class EvidencedStringType {
- @XmlAttribute(name = "status")
- protected String status;
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
- /**
- * Gets the value of the status property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getStatus()
- {
- return status;
- }
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ return status;
+ }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setStatus(String value)
- {
- this.status = value;
- }
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes different types of sequence annotations. Equivalent to the flat
- * file FT-line.
+ * Describes different types of sequence annotations.
+ * Equivalent to the flat file FT-line.
*
- * <p>
- * Java class for featureType complex type.
+ * <p>Java class for featureType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="featureType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "featureType",
- propOrder =
- { "original", "variation", "location" })
-public class FeatureType
-{
-
- protected String original;
-
- protected List<String> variation;
-
- @XmlElement(required = true)
- protected LocationType location;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
+@XmlType(name = "featureType", propOrder = {
+ "original",
+ "variation",
+ "location"
+})
+public class FeatureType {
- @XmlAttribute(name = "status")
- protected String status;
+ protected String original;
+ protected List<String> variation;
+ @XmlElement(required = true)
+ protected LocationType location;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "description")
+ protected String description;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "ref")
+ protected String ref;
- @XmlAttribute(name = "id")
- protected String id;
-
- @XmlAttribute(name = "description")
- protected String description;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- @XmlAttribute(name = "ref")
- protected String ref;
-
- /**
- * Gets the value of the original property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getOriginal()
- {
- return original;
- }
+ /**
+ * Gets the value of the original property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getOriginal() {
+ return original;
+ }
- /**
- * Sets the value of the original property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setOriginal(String value)
- {
- this.original = value;
- }
+ /**
+ * Sets the value of the original property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setOriginal(String value) {
+ this.original = value;
+ }
- /**
- * Gets the value of the variation property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the variation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getVariation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getVariation()
- {
- if (variation == null)
- {
- variation = new ArrayList<String>();
+ /**
+ * Gets the value of the variation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the variation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getVariation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getVariation() {
+ if (variation == null) {
+ variation = new ArrayList<String>();
+ }
+ return this.variation;
}
- return this.variation;
- }
- /**
- * Gets the value of the location property.
- *
- * @return possible object is {@link LocationType }
- *
- */
- public LocationType getLocation()
- {
- return location;
- }
+ /**
+ * Gets the value of the location property.
+ *
+ * @return
+ * possible object is
+ * {@link LocationType }
+ *
+ */
+ public LocationType getLocation() {
+ return location;
+ }
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is {@link LocationType }
- *
- */
- public void setLocation(LocationType value)
- {
- this.location = value;
- }
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is
+ * {@link LocationType }
+ *
+ */
+ public void setLocation(LocationType value) {
+ this.location = value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getStatus()
- {
- return status;
- }
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ return status;
+ }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setStatus(String value)
- {
- this.status = value;
- }
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
- /**
- * Gets the value of the ref property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getRef()
- {
- return ref;
- }
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRef() {
+ return ref;
+ }
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setRef(String value)
- {
- this.ref = value;
- }
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRef(String value) {
+ this.ref = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to
- * the flat file OG-line.
+ * Describes non-nuclear gene locations (organelles and plasmids).
+ * Equivalent to the flat file OG-line.
*
- * <p>
- * Java class for geneLocationType complex type.
+ * <p>Java class for geneLocationType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="geneLocationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = { "name" })
-public class GeneLocationType
-{
-
- protected List<StatusType> name;
+@XmlType(name = "geneLocationType", propOrder = {
+ "name"
+})
+public class GeneLocationType {
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ protected List<StatusType> name;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link StatusType
- * }
- *
- *
- */
- public List<StatusType> getName()
- {
- if (name == null)
- {
- name = new ArrayList<StatusType>();
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link StatusType }
+ *
+ *
+ */
+ public List<StatusType> getName() {
+ if (name == null) {
+ name = new ArrayList<StatusType>();
+ }
+ return this.name;
}
- return this.name;
- }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
- * Describes different types of gene designations. Equivalent to the flat file
- * GN-line.
+ * Describes different types of gene designations.
+ * Equivalent to the flat file GN-line.
*
- * <p>
- * Java class for geneNameType complex type.
+ * <p>Java class for geneNameType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="geneNameType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = { "value" })
-public class GeneNameType
-{
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+@XmlType(name = "geneNameType", propOrder = {
+ "value"
+})
+public class GeneNameType {
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes a gene. Equivalent to the flat file GN-line.
+ * Describes a gene.
+ * Equivalent to the flat file GN-line.
*
- * <p>
- * Java class for geneType complex type.
+ * <p>Java class for geneType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="geneType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = { "name" })
-public class GeneType
-{
+@XmlType(name = "geneType", propOrder = {
+ "name"
+})
+public class GeneType {
- @XmlElement(required = true)
- protected List<GeneNameType> name;
+ @XmlElement(required = true)
+ protected List<GeneNameType> name;
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneNameType }
- *
- *
- */
- public List<GeneNameType> getName()
- {
- if (name == null)
- {
- name = new ArrayList<GeneNameType>();
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneNameType }
+ *
+ *
+ */
+ public List<GeneNameType> getName() {
+ if (name == null) {
+ name = new ArrayList<GeneNameType>();
+ }
+ return this.name;
}
- return this.name;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the source of the evidence, when it is not assigned by UniProt, but
- * imported from an external database.
+ * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
*
- * <p>
- * Java class for importedFromType complex type.
+ * <p>Java class for importedFromType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="importedFromType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = { "dbReference" })
-public class ImportedFromType
-{
+@XmlType(name = "importedFromType", propOrder = {
+ "dbReference"
+})
+public class ImportedFromType {
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Gets the value of the dbReference property.
- *
- * @return possible object is {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference()
- {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value)
- {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for interactantType complex type.
+ * <p>Java class for interactantType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="interactantType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = { "id", "label" })
-public class InteractantType
-{
-
- protected String id;
-
- protected String label;
+@XmlType(name = "interactantType", propOrder = {
+ "id",
+ "label"
+})
+public class InteractantType {
- @XmlAttribute(name = "intactId", required = true)
- protected String intactId;
+ protected String id;
+ protected String label;
+ @XmlAttribute(name = "intactId", required = true)
+ protected String intactId;
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the label property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLabel()
- {
- return label;
- }
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLabel(String value)
- {
- this.label = value;
- }
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
- /**
- * Gets the value of the intactId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getIntactId()
- {
- return intactId;
- }
+ /**
+ * Gets the value of the intactId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getIntactId() {
+ return intactId;
+ }
- /**
- * Sets the value of the intactId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setIntactId(String value)
- {
- this.intactId = value;
- }
+ /**
+ * Sets the value of the intactId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setIntactId(String value) {
+ this.intactId = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
* Describes isoforms in 'alternative products' annotations.
*
- * <p>
- * Java class for isoformType complex type.
+ * <p>Java class for isoformType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="isoformType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "isoformType",
- propOrder =
- { "id", "name", "sequence", "text" })
-public class IsoformType
-{
-
- @XmlElement(required = true)
- protected List<String> id;
-
- @XmlElement(required = true)
- protected List<IsoformType.Name> name;
-
- @XmlElement(required = true)
- protected IsoformType.Sequence sequence;
-
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the id property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the id property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getId().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getId()
- {
- if (id == null)
- {
- id = new ArrayList<String>();
- }
- return this.id;
- }
-
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link IsoformType.Name }
- *
- *
- */
- public List<IsoformType.Name> getName()
- {
- if (name == null)
- {
- name = new ArrayList<IsoformType.Name>();
- }
- return this.name;
- }
+@XmlType(name = "isoformType", propOrder = {
+ "id",
+ "name",
+ "sequence",
+ "text"
+})
+public class IsoformType {
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link IsoformType.Sequence }
- *
- */
- public IsoformType.Sequence getSequence()
- {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link IsoformType.Sequence }
- *
- */
- public void setSequence(IsoformType.Sequence value)
- {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText()
- {
- if (text == null)
- {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class Name
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected List<String> id;
+ @XmlElement(required = true)
+ protected List<IsoformType.Name> name;
+ @XmlElement(required = true)
+ protected IsoformType.Sequence sequence;
+ protected List<EvidencedStringType> text;
/**
- * Gets the value of the value property.
+ * Gets the value of the id property.
*
- * @return possible object is {@link String }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the id property.
*
- */
- public String getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getId().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setValue(String value)
- {
- this.value = value;
+ public List<String> getId() {
+ if (id == null) {
+ id = new ArrayList<String>();
+ }
+ return this.id;
}
/**
- * Gets the value of the evidence property.
+ * Gets the value of the name property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the evidence property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getEvidence().add(newItem);
+ * getName().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
+ * Objects of the following type(s) are allowed in the list
+ * {@link IsoformType.Name }
*
*
*/
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ public List<IsoformType.Name> getName() {
+ if (name == null) {
+ name = new ArrayList<IsoformType.Name>();
+ }
+ return this.name;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="not described"/>
- * <enumeration value="described"/>
- * <enumeration value="displayed"/>
- * <enumeration value="external"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Sequence
- {
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "ref")
- protected String ref;
-
/**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the sequence property.
*
+ * @return
+ * possible object is
+ * {@link IsoformType.Sequence }
+ *
*/
- public String getType()
- {
- return type;
+ public IsoformType.Sequence getSequence() {
+ return sequence;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the sequence property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link IsoformType.Sequence }
+ *
*/
- public void setType(String value)
- {
- this.type = value;
+ public void setSequence(IsoformType.Sequence value) {
+ this.sequence = value;
}
/**
- * Gets the value of the ref property.
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
*
- * @return possible object is {@link String }
*
*/
- public String getRef()
- {
- return ref;
+ public List<EvidencedStringType> getText() {
+ if (text == null) {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+
/**
- * Sets the value of the ref property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setRef(String value)
- {
- this.ref = value;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Name {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="not described"/>
+ * <enumeration value="described"/>
+ * <enumeration value="displayed"/>
+ * <enumeration value="external"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRef() {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRef(String value) {
+ this.ref = value;
+ }
+
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
- * <p>
- * Java class for keywordType complex type.
+ * <p>Java class for keywordType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="keywordType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = { "value" })
-public class KeywordType
-{
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+@XmlType(name = "keywordType", propOrder = {
+ "value"
+})
+public class KeywordType {
- @XmlAttribute(name = "id", required = true)
- protected String id;
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes a sequence location as either a range with a begin and end or as a
- * position. The 'sequence' attribute is only used when the location is not on
- * the canonical sequence displayed in the current entry.
+ * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
*
- * <p>
- * Java class for locationType complex type.
+ * <p>Java class for locationType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="locationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
-public class LocationType
-{
-
- protected PositionType begin;
-
- protected PositionType end;
-
- protected PositionType position;
-
- @XmlAttribute(name = "sequence")
- protected String sequence;
-
- /**
- * Gets the value of the begin property.
- *
- * @return possible object is {@link PositionType }
- *
- */
- public PositionType getBegin()
- {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is {@link PositionType }
- *
- */
- public void setBegin(PositionType value)
- {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link PositionType }
- *
- */
- public PositionType getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link PositionType }
- *
- */
- public void setEnd(PositionType value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- * @return possible object is {@link PositionType }
- *
- */
- public PositionType getPosition()
- {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is {@link PositionType }
- *
- */
- public void setPosition(PositionType value)
- {
- this.position = value;
- }
-
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequence()
- {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequence(String value)
- {
- this.sequence = value;
- }
+@XmlType(name = "locationType", propOrder = {
+ "begin",
+ "end",
+ "position"
+})
+public class LocationType {
+
+ protected PositionType begin;
+ protected PositionType end;
+ protected PositionType position;
+ @XmlAttribute(name = "sequence")
+ protected String sequence;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return
+ * possible object is
+ * {@link PositionType }
+ *
+ */
+ public PositionType getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PositionType }
+ *
+ */
+ public void setBegin(PositionType value) {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link PositionType }
+ *
+ */
+ public PositionType getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PositionType }
+ *
+ */
+ public void setEnd(PositionType value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ * @return
+ * possible object is
+ * {@link PositionType }
+ *
+ */
+ public PositionType getPosition() {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PositionType }
+ *
+ */
+ public void setPosition(PositionType value) {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
* Describes a molecule by name or unique identifier.
*
- * <p>
- * Java class for moleculeType complex type.
+ * <p>Java class for moleculeType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="moleculeType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = { "value" })
-public class MoleculeType
-{
-
- @XmlValue
- protected String value;
+@XmlType(name = "moleculeType", propOrder = {
+ "value"
+})
+public class MoleculeType {
- @XmlAttribute(name = "id")
- protected String id;
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElements;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for nameListType complex type.
+ * <p>Java class for nameListType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="nameListType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
-public class NameListType
-{
+@XmlType(name = "nameListType", propOrder = {
+ "consortiumOrPerson"
+})
+public class NameListType {
- @XmlElements({
- @XmlElement(name = "consortium", type = ConsortiumType.class),
- @XmlElement(name = "person", type = PersonType.class) })
- protected List<Object> consortiumOrPerson;
+ @XmlElements({
+ @XmlElement(name = "consortium", type = ConsortiumType.class),
+ @XmlElement(name = "person", type = PersonType.class)
+ })
+ protected List<Object> consortiumOrPerson;
- /**
- * Gets the value of the consortiumOrPerson property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the consortiumOrPerson property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getConsortiumOrPerson().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ConsortiumType } {@link PersonType }
- *
- *
- */
- public List<Object> getConsortiumOrPerson()
- {
- if (consortiumOrPerson == null)
- {
- consortiumOrPerson = new ArrayList<Object>();
+ /**
+ * Gets the value of the consortiumOrPerson property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getConsortiumOrPerson().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ConsortiumType }
+ * {@link PersonType }
+ *
+ *
+ */
+ public List<Object> getConsortiumOrPerson() {
+ if (consortiumOrPerson == null) {
+ consortiumOrPerson = new ArrayList<Object>();
+ }
+ return this.consortiumOrPerson;
}
- return this.consortiumOrPerson;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlRegistry;
import javax.xml.namespace.QName;
+
/**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.uniprot package.
- * <p>
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.uniprot package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory
-{
-
- private final static QName _Copyright_QNAME = new QName(
- "http://uniprot.org/uniprot", "copyright");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of
- * schema derived classes for package: jalview.xml.binding.uniprot
- *
- */
- public ObjectFactory()
- {
- }
-
- /**
- * Create an instance of {@link SourceDataType }
- *
- */
- public SourceDataType createSourceDataType()
- {
- return new SourceDataType();
- }
-
- /**
- * Create an instance of {@link IsoformType }
- *
- */
- public IsoformType createIsoformType()
- {
- return new IsoformType();
- }
-
- /**
- * Create an instance of {@link CommentType }
- *
- */
- public CommentType createCommentType()
- {
- return new CommentType();
- }
-
- /**
- * Create an instance of {@link CommentType.Conflict }
- *
- */
- public CommentType.Conflict createCommentTypeConflict()
- {
- return new CommentType.Conflict();
- }
-
- /**
- * Create an instance of {@link OrganismType }
- *
- */
- public OrganismType createOrganismType()
- {
- return new OrganismType();
- }
-
- /**
- * Create an instance of {@link ProteinType }
- *
- */
- public ProteinType createProteinType()
- {
- return new ProteinType();
- }
-
- /**
- * Create an instance of {@link Entry }
- *
- */
- public Entry createEntry()
- {
- return new Entry();
- }
-
- /**
- * Create an instance of {@link GeneType }
- *
- */
- public GeneType createGeneType()
- {
- return new GeneType();
- }
-
- /**
- * Create an instance of {@link GeneLocationType }
- *
- */
- public GeneLocationType createGeneLocationType()
- {
- return new GeneLocationType();
- }
-
- /**
- * Create an instance of {@link ReferenceType }
- *
- */
- public ReferenceType createReferenceType()
- {
- return new ReferenceType();
- }
-
- /**
- * Create an instance of {@link DbReferenceType }
- *
- */
- public DbReferenceType createDbReferenceType()
- {
- return new DbReferenceType();
- }
-
- /**
- * Create an instance of {@link ProteinExistenceType }
- *
- */
- public ProteinExistenceType createProteinExistenceType()
- {
- return new ProteinExistenceType();
- }
-
- /**
- * Create an instance of {@link KeywordType }
- *
- */
- public KeywordType createKeywordType()
- {
- return new KeywordType();
- }
-
- /**
- * Create an instance of {@link FeatureType }
- *
- */
- public FeatureType createFeatureType()
- {
- return new FeatureType();
- }
-
- /**
- * Create an instance of {@link EvidenceType }
- *
- */
- public EvidenceType createEvidenceType()
- {
- return new EvidenceType();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType()
- {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Uniprot }
- *
- */
- public Uniprot createUniprot()
- {
- return new Uniprot();
- }
-
- /**
- * Create an instance of {@link StatusType }
- *
- */
- public StatusType createStatusType()
- {
- return new StatusType();
- }
-
- /**
- * Create an instance of {@link PositionType }
- *
- */
- public PositionType createPositionType()
- {
- return new PositionType();
- }
-
- /**
- * Create an instance of {@link ConsortiumType }
- *
- */
- public ConsortiumType createConsortiumType()
- {
- return new ConsortiumType();
- }
-
- /**
- * Create an instance of {@link GeneNameType }
- *
- */
- public GeneNameType createGeneNameType()
- {
- return new GeneNameType();
- }
-
- /**
- * Create an instance of {@link LocationType }
- *
- */
- public LocationType createLocationType()
- {
- return new LocationType();
- }
-
- /**
- * Create an instance of {@link CitationType }
- *
- */
- public CitationType createCitationType()
- {
- return new CitationType();
- }
-
- /**
- * Create an instance of {@link PropertyType }
- *
- */
- public PropertyType createPropertyType()
- {
- return new PropertyType();
- }
-
- /**
- * Create an instance of {@link PhysiologicalReactionType }
- *
- */
- public PhysiologicalReactionType createPhysiologicalReactionType()
- {
- return new PhysiologicalReactionType();
- }
-
- /**
- * Create an instance of {@link CofactorType }
- *
- */
- public CofactorType createCofactorType()
- {
- return new CofactorType();
- }
-
- /**
- * Create an instance of {@link EvidencedStringType }
- *
- */
- public EvidencedStringType createEvidencedStringType()
- {
- return new EvidencedStringType();
- }
-
- /**
- * Create an instance of {@link PersonType }
- *
- */
- public PersonType createPersonType()
- {
- return new PersonType();
- }
-
- /**
- * Create an instance of {@link ImportedFromType }
- *
- */
- public ImportedFromType createImportedFromType()
- {
- return new ImportedFromType();
- }
-
- /**
- * Create an instance of {@link EventType }
- *
- */
- public EventType createEventType()
- {
- return new EventType();
- }
-
- /**
- * Create an instance of {@link InteractantType }
- *
- */
- public InteractantType createInteractantType()
- {
- return new InteractantType();
- }
-
- /**
- * Create an instance of {@link NameListType }
- *
- */
- public NameListType createNameListType()
- {
- return new NameListType();
- }
-
- /**
- * Create an instance of {@link ReactionType }
- *
- */
- public ReactionType createReactionType()
- {
- return new ReactionType();
- }
-
- /**
- * Create an instance of {@link SourceType }
- *
- */
- public SourceType createSourceType()
- {
- return new SourceType();
- }
-
- /**
- * Create an instance of {@link MoleculeType }
- *
- */
- public MoleculeType createMoleculeType()
- {
- return new MoleculeType();
- }
-
- /**
- * Create an instance of {@link OrganismNameType }
- *
- */
- public OrganismNameType createOrganismNameType()
- {
- return new OrganismNameType();
- }
-
- /**
- * Create an instance of {@link SubcellularLocationType }
- *
- */
- public SubcellularLocationType createSubcellularLocationType()
- {
- return new SubcellularLocationType();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Strain }
- *
- */
- public SourceDataType.Strain createSourceDataTypeStrain()
- {
- return new SourceDataType.Strain();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Plasmid }
- *
- */
- public SourceDataType.Plasmid createSourceDataTypePlasmid()
- {
- return new SourceDataType.Plasmid();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Transposon }
- *
- */
- public SourceDataType.Transposon createSourceDataTypeTransposon()
- {
- return new SourceDataType.Transposon();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Tissue }
- *
- */
- public SourceDataType.Tissue createSourceDataTypeTissue()
- {
- return new SourceDataType.Tissue();
- }
-
- /**
- * Create an instance of {@link IsoformType.Name }
- *
- */
- public IsoformType.Name createIsoformTypeName()
- {
- return new IsoformType.Name();
- }
-
- /**
- * Create an instance of {@link IsoformType.Sequence }
- *
- */
- public IsoformType.Sequence createIsoformTypeSequence()
- {
- return new IsoformType.Sequence();
- }
-
- /**
- * Create an instance of {@link CommentType.Absorption }
- *
- */
- public CommentType.Absorption createCommentTypeAbsorption()
- {
- return new CommentType.Absorption();
- }
-
- /**
- * Create an instance of {@link CommentType.Kinetics }
- *
- */
- public CommentType.Kinetics createCommentTypeKinetics()
- {
- return new CommentType.Kinetics();
- }
-
- /**
- * Create an instance of {@link CommentType.PhDependence }
- *
- */
- public CommentType.PhDependence createCommentTypePhDependence()
- {
- return new CommentType.PhDependence();
- }
-
- /**
- * Create an instance of {@link CommentType.RedoxPotential }
- *
- */
- public CommentType.RedoxPotential createCommentTypeRedoxPotential()
- {
- return new CommentType.RedoxPotential();
- }
-
- /**
- * Create an instance of {@link CommentType.TemperatureDependence }
- *
- */
- public CommentType.TemperatureDependence createCommentTypeTemperatureDependence()
- {
- return new CommentType.TemperatureDependence();
- }
-
- /**
- * Create an instance of {@link CommentType.Link }
- *
- */
- public CommentType.Link createCommentTypeLink()
- {
- return new CommentType.Link();
- }
-
- /**
- * Create an instance of {@link CommentType.Disease }
- *
- */
- public CommentType.Disease createCommentTypeDisease()
- {
- return new CommentType.Disease();
- }
-
- /**
- * Create an instance of {@link CommentType.Conflict.Sequence }
- *
- */
- public CommentType.Conflict.Sequence createCommentTypeConflictSequence()
- {
- return new CommentType.Conflict.Sequence();
- }
-
- /**
- * Create an instance of {@link OrganismType.Lineage }
- *
- */
- public OrganismType.Lineage createOrganismTypeLineage()
- {
- return new OrganismType.Lineage();
- }
-
- /**
- * Create an instance of {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName createProteinTypeRecommendedName()
- {
- return new ProteinType.RecommendedName();
- }
-
- /**
- * Create an instance of {@link ProteinType.AlternativeName }
- *
- */
- public ProteinType.AlternativeName createProteinTypeAlternativeName()
- {
- return new ProteinType.AlternativeName();
- }
-
- /**
- * Create an instance of {@link ProteinType.SubmittedName }
- *
- */
- public ProteinType.SubmittedName createProteinTypeSubmittedName()
- {
- return new ProteinType.SubmittedName();
- }
-
- /**
- * Create an instance of {@link ProteinType.Domain }
- *
- */
- public ProteinType.Domain createProteinTypeDomain()
- {
- return new ProteinType.Domain();
- }
-
- /**
- * Create an instance of {@link ProteinType.Component }
- *
- */
- public ProteinType.Component createProteinTypeComponent()
- {
- return new ProteinType.Component();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link String
- * }{@code >}}
- *
- */
- @XmlElementDecl(
- namespace = "http://uniprot.org/uniprot",
- name = "copyright")
- public JAXBElement<String> createCopyright(String value)
- {
- return new JAXBElement<String>(_Copyright_QNAME, String.class, null,
- value);
- }
+public class ObjectFactory {
+
+ private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType }
+ *
+ */
+ public SourceDataType createSourceDataType() {
+ return new SourceDataType();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType }
+ *
+ */
+ public IsoformType createIsoformType() {
+ return new IsoformType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType }
+ *
+ */
+ public CommentType createCommentType() {
+ return new CommentType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict createCommentTypeConflict() {
+ return new CommentType.Conflict();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType }
+ *
+ */
+ public OrganismType createOrganismType() {
+ return new OrganismType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType }
+ *
+ */
+ public ProteinType createProteinType() {
+ return new ProteinType();
+ }
+
+ /**
+ * Create an instance of {@link Entry }
+ *
+ */
+ public Entry createEntry() {
+ return new Entry();
+ }
+
+ /**
+ * Create an instance of {@link GeneType }
+ *
+ */
+ public GeneType createGeneType() {
+ return new GeneType();
+ }
+
+ /**
+ * Create an instance of {@link GeneLocationType }
+ *
+ */
+ public GeneLocationType createGeneLocationType() {
+ return new GeneLocationType();
+ }
+
+ /**
+ * Create an instance of {@link ReferenceType }
+ *
+ */
+ public ReferenceType createReferenceType() {
+ return new ReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType createDbReferenceType() {
+ return new DbReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType createProteinExistenceType() {
+ return new ProteinExistenceType();
+ }
+
+ /**
+ * Create an instance of {@link KeywordType }
+ *
+ */
+ public KeywordType createKeywordType() {
+ return new KeywordType();
+ }
+
+ /**
+ * Create an instance of {@link FeatureType }
+ *
+ */
+ public FeatureType createFeatureType() {
+ return new FeatureType();
+ }
+
+ /**
+ * Create an instance of {@link EvidenceType }
+ *
+ */
+ public EvidenceType createEvidenceType() {
+ return new EvidenceType();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType() {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Uniprot }
+ *
+ */
+ public Uniprot createUniprot() {
+ return new Uniprot();
+ }
+
+ /**
+ * Create an instance of {@link StatusType }
+ *
+ */
+ public StatusType createStatusType() {
+ return new StatusType();
+ }
+
+ /**
+ * Create an instance of {@link PositionType }
+ *
+ */
+ public PositionType createPositionType() {
+ return new PositionType();
+ }
+
+ /**
+ * Create an instance of {@link ConsortiumType }
+ *
+ */
+ public ConsortiumType createConsortiumType() {
+ return new ConsortiumType();
+ }
+
+ /**
+ * Create an instance of {@link GeneNameType }
+ *
+ */
+ public GeneNameType createGeneNameType() {
+ return new GeneNameType();
+ }
+
+ /**
+ * Create an instance of {@link LocationType }
+ *
+ */
+ public LocationType createLocationType() {
+ return new LocationType();
+ }
+
+ /**
+ * Create an instance of {@link CitationType }
+ *
+ */
+ public CitationType createCitationType() {
+ return new CitationType();
+ }
+
+ /**
+ * Create an instance of {@link PropertyType }
+ *
+ */
+ public PropertyType createPropertyType() {
+ return new PropertyType();
+ }
+
+ /**
+ * Create an instance of {@link PhysiologicalReactionType }
+ *
+ */
+ public PhysiologicalReactionType createPhysiologicalReactionType() {
+ return new PhysiologicalReactionType();
+ }
+
+ /**
+ * Create an instance of {@link CofactorType }
+ *
+ */
+ public CofactorType createCofactorType() {
+ return new CofactorType();
+ }
+
+ /**
+ * Create an instance of {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType createEvidencedStringType() {
+ return new EvidencedStringType();
+ }
+
+ /**
+ * Create an instance of {@link PersonType }
+ *
+ */
+ public PersonType createPersonType() {
+ return new PersonType();
+ }
+
+ /**
+ * Create an instance of {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType createImportedFromType() {
+ return new ImportedFromType();
+ }
+
+ /**
+ * Create an instance of {@link EventType }
+ *
+ */
+ public EventType createEventType() {
+ return new EventType();
+ }
+
+ /**
+ * Create an instance of {@link InteractantType }
+ *
+ */
+ public InteractantType createInteractantType() {
+ return new InteractantType();
+ }
+
+ /**
+ * Create an instance of {@link NameListType }
+ *
+ */
+ public NameListType createNameListType() {
+ return new NameListType();
+ }
+
+ /**
+ * Create an instance of {@link ReactionType }
+ *
+ */
+ public ReactionType createReactionType() {
+ return new ReactionType();
+ }
+
+ /**
+ * Create an instance of {@link SourceType }
+ *
+ */
+ public SourceType createSourceType() {
+ return new SourceType();
+ }
+
+ /**
+ * Create an instance of {@link MoleculeType }
+ *
+ */
+ public MoleculeType createMoleculeType() {
+ return new MoleculeType();
+ }
+
+ /**
+ * Create an instance of {@link OrganismNameType }
+ *
+ */
+ public OrganismNameType createOrganismNameType() {
+ return new OrganismNameType();
+ }
+
+ /**
+ * Create an instance of {@link SubcellularLocationType }
+ *
+ */
+ public SubcellularLocationType createSubcellularLocationType() {
+ return new SubcellularLocationType();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Strain }
+ *
+ */
+ public SourceDataType.Strain createSourceDataTypeStrain() {
+ return new SourceDataType.Strain();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Plasmid }
+ *
+ */
+ public SourceDataType.Plasmid createSourceDataTypePlasmid() {
+ return new SourceDataType.Plasmid();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Transposon }
+ *
+ */
+ public SourceDataType.Transposon createSourceDataTypeTransposon() {
+ return new SourceDataType.Transposon();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Tissue }
+ *
+ */
+ public SourceDataType.Tissue createSourceDataTypeTissue() {
+ return new SourceDataType.Tissue();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Name }
+ *
+ */
+ public IsoformType.Name createIsoformTypeName() {
+ return new IsoformType.Name();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence createIsoformTypeSequence() {
+ return new IsoformType.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption createCommentTypeAbsorption() {
+ return new CommentType.Absorption();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics createCommentTypeKinetics() {
+ return new CommentType.Kinetics();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence createCommentTypePhDependence() {
+ return new CommentType.PhDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
+ return new CommentType.RedoxPotential();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
+ return new CommentType.TemperatureDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Link }
+ *
+ */
+ public CommentType.Link createCommentTypeLink() {
+ return new CommentType.Link();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease createCommentTypeDisease() {
+ return new CommentType.Disease();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
+ return new CommentType.Conflict.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage createOrganismTypeLineage() {
+ return new OrganismType.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName createProteinTypeRecommendedName() {
+ return new ProteinType.RecommendedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.AlternativeName }
+ *
+ */
+ public ProteinType.AlternativeName createProteinTypeAlternativeName() {
+ return new ProteinType.AlternativeName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.SubmittedName }
+ *
+ */
+ public ProteinType.SubmittedName createProteinTypeSubmittedName() {
+ return new ProteinType.SubmittedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Domain }
+ *
+ */
+ public ProteinType.Domain createProteinTypeDomain() {
+ return new ProteinType.Domain();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Component }
+ *
+ */
+ public ProteinType.Component createProteinTypeComponent() {
+ return new ProteinType.Component();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
+ *
+ */
+ @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
+ public JAXBElement<String> createCopyright(String value) {
+ return new JAXBElement<String>(_Copyright_QNAME, String.class, null, value);
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
* Describes different types of source organism names.
*
- * <p>
- * Java class for organismNameType complex type.
+ * <p>Java class for organismNameType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="organismNameType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = { "value" })
-public class OrganismNameType
-{
-
- @XmlValue
- protected String value;
+@XmlType(name = "organismNameType", propOrder = {
+ "value"
+})
+public class OrganismNameType {
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
* Describes the source organism.
*
- * <p>
- * Java class for organismType complex type.
+ * <p>Java class for organismType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="organismType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "organismType",
- propOrder =
- { "name", "dbReference", "lineage" })
-public class OrganismType
-{
-
- @XmlElement(required = true)
- protected List<OrganismNameType> name;
-
- @XmlElement(required = true)
- protected List<DbReferenceType> dbReference;
-
- protected OrganismType.Lineage lineage;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link OrganismNameType }
- *
- *
- */
- public List<OrganismNameType> getName()
- {
- if (name == null)
- {
- name = new ArrayList<OrganismNameType>();
+@XmlType(name = "organismType", propOrder = {
+ "name",
+ "dbReference",
+ "lineage"
+})
+public class OrganismType {
+
+ @XmlElement(required = true)
+ protected List<OrganismNameType> name;
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
+ protected OrganismType.Lineage lineage;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismNameType }
+ *
+ *
+ */
+ public List<OrganismNameType> getName() {
+ if (name == null) {
+ name = new ArrayList<OrganismNameType>();
+ }
+ return this.name;
}
- return this.name;
- }
-
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference()
- {
- if (dbReference == null)
- {
- dbReference = new ArrayList<DbReferenceType>();
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
}
- return this.dbReference;
- }
-
- /**
- * Gets the value of the lineage property.
- *
- * @return possible object is {@link OrganismType.Lineage }
- *
- */
- public OrganismType.Lineage getLineage()
- {
- return lineage;
- }
-
- /**
- * Sets the value of the lineage property.
- *
- * @param value
- * allowed object is {@link OrganismType.Lineage }
- *
- */
- public void setLineage(OrganismType.Lineage value)
- {
- this.lineage = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return
+ * possible object is
+ * {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage getLineage() {
+ return lineage;
}
- return this.evidence;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "taxon" })
- public static class Lineage
- {
- @XmlElement(required = true)
- protected List<String> taxon;
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link OrganismType.Lineage }
+ *
+ */
+ public void setLineage(OrganismType.Lineage value) {
+ this.lineage = value;
+ }
/**
- * Gets the value of the taxon property.
+ * Gets the value of the evidence property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the taxon property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getTaxon().add(newItem);
+ * getEvidence().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list {@link String }
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
*
*
*/
- public List<String> getTaxon()
- {
- if (taxon == null)
- {
- taxon = new ArrayList<String>();
- }
- return this.taxon;
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "taxon"
+ })
+ public static class Lineage {
+
+ @XmlElement(required = true)
+ protected List<String> taxon;
+
+ /**
+ * Gets the value of the taxon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the taxon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTaxon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getTaxon() {
+ if (taxon == null) {
+ taxon = new ArrayList<String>();
+ }
+ return this.taxon;
+ }
+
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for personType complex type.
+ * <p>Java class for personType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="personType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "personType")
-public class PersonType
-{
+public class PersonType {
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
* Describes a physiological reaction.
*
- * <p>
- * Java class for physiologicalReactionType complex type.
+ * <p>Java class for physiologicalReactionType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="physiologicalReactionType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
-public class PhysiologicalReactionType
-{
-
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
-
- @XmlAttribute(name = "direction", required = true)
- protected String direction;
+@XmlType(name = "physiologicalReactionType", propOrder = {
+ "dbReference"
+})
+public class PhysiologicalReactionType {
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "direction", required = true)
+ protected String direction;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the dbReference property.
- *
- * @return possible object is {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference()
- {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value)
- {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the direction property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDirection()
- {
- return direction;
- }
+ /**
+ * Gets the value of the direction property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDirection() {
+ return direction;
+ }
- /**
- * Sets the value of the direction property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDirection(String value)
- {
- this.direction = value;
- }
+ /**
+ * Sets the value of the direction property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDirection(String value) {
+ this.direction = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for positionType complex type.
+ * <p>Java class for positionType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="positionType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "positionType")
-public class PositionType
-{
-
- @XmlAttribute(name = "position")
- @XmlSchemaType(name = "unsignedLong")
- protected BigInteger position;
-
- @XmlAttribute(name = "status")
- protected String status;
+public class PositionType {
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlAttribute(name = "position")
+ @XmlSchemaType(name = "unsignedLong")
+ protected BigInteger position;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the position property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPosition()
- {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPosition(BigInteger value)
- {
- this.position = value;
- }
+ /**
+ * Gets the value of the position property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPosition() {
+ return position;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getStatus()
- {
- if (status == null)
- {
- return "certain";
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPosition(BigInteger value) {
+ this.position = value;
}
- else
- {
- return status;
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ if (status == null) {
+ return "certain";
+ } else {
+ return status;
+ }
}
- }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setStatus(String value)
- {
- this.status = value;
- }
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for propertyType complex type.
+ * <p>Java class for propertyType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="propertyType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "propertyType")
-public class PropertyType
-{
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
+public class PropertyType {
- @XmlAttribute(name = "value", required = true)
- protected String value;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the evidence for the protein's existence. Equivalent to the flat
- * file PE-line.
+ * Describes the evidence for the protein's existence.
+ * Equivalent to the flat file PE-line.
*
- * <p>
- * Java class for proteinExistenceType complex type.
+ * <p>Java class for proteinExistenceType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="proteinExistenceType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType
-{
+public class ProteinExistenceType {
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the names for the protein and parts thereof. Equivalent to the flat
- * file DE-line.
+ * Describes the names for the protein and parts thereof.
+ * Equivalent to the flat file DE-line.
*
- * <p>
- * Java class for proteinType complex type.
+ * <p>Java class for proteinType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="proteinType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "proteinType",
- propOrder =
- { "recommendedName", "alternativeName", "submittedName", "allergenName",
- "biotechName", "cdAntigenName", "innName", "domain", "component" })
-public class ProteinType
-{
-
- protected ProteinType.RecommendedName recommendedName;
-
- protected List<ProteinType.AlternativeName> alternativeName;
-
- protected List<ProteinType.SubmittedName> submittedName;
-
- protected EvidencedStringType allergenName;
-
- protected EvidencedStringType biotechName;
-
- protected List<EvidencedStringType> cdAntigenName;
-
- protected List<EvidencedStringType> innName;
-
- protected List<ProteinType.Domain> domain;
-
- protected List<ProteinType.Component> component;
-
- /**
- * Gets the value of the recommendedName property.
- *
- * @return possible object is {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName getRecommendedName()
- {
- return recommendedName;
- }
-
- /**
- * Sets the value of the recommendedName property.
- *
- * @param value
- * allowed object is {@link ProteinType.RecommendedName }
- *
- */
- public void setRecommendedName(ProteinType.RecommendedName value)
- {
- this.recommendedName = value;
- }
-
- /**
- * Gets the value of the alternativeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the alternativeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAlternativeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.AlternativeName }
- *
- *
- */
- public List<ProteinType.AlternativeName> getAlternativeName()
- {
- if (alternativeName == null)
- {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
- }
-
- /**
- * Gets the value of the submittedName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the submittedName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSubmittedName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.SubmittedName }
- *
- *
- */
- public List<ProteinType.SubmittedName> getSubmittedName()
- {
- if (submittedName == null)
- {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
- }
-
- /**
- * Gets the value of the allergenName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getAllergenName()
- {
- return allergenName;
- }
-
- /**
- * Sets the value of the allergenName property.
- *
- * @param value
- * allowed object is {@link EvidencedStringType }
- *
- */
- public void setAllergenName(EvidencedStringType value)
- {
- this.allergenName = value;
- }
-
- /**
- * Gets the value of the biotechName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getBiotechName()
- {
- return biotechName;
- }
-
- /**
- * Sets the value of the biotechName property.
- *
- * @param value
- * allowed object is {@link EvidencedStringType }
- *
- */
- public void setBiotechName(EvidencedStringType value)
- {
- this.biotechName = value;
- }
-
- /**
- * Gets the value of the cdAntigenName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the cdAntigenName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getCdAntigenName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getCdAntigenName()
- {
- if (cdAntigenName == null)
- {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
- }
-
- /**
- * Gets the value of the innName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the innName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getInnName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getInnName()
- {
- if (innName == null)
- {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
-
- /**
- * Gets the value of the domain property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the domain property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getDomain().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.Domain }
- *
- *
- */
- public List<ProteinType.Domain> getDomain()
- {
- if (domain == null)
- {
- domain = new ArrayList<ProteinType.Domain>();
- }
- return this.domain;
- }
-
- /**
- * Gets the value of the component property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the component property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getComponent().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.Component }
- *
- *
- */
- public List<ProteinType.Component> getComponent()
- {
- if (component == null)
- {
- component = new ArrayList<ProteinType.Component>();
- }
- return this.component;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
- * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
- public static class AlternativeName
- {
-
- protected EvidencedStringType fullName;
-
- protected List<EvidencedStringType> shortName;
-
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName()
- {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value)
- {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the shortName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the shortName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getShortName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getShortName()
- {
- if (shortName == null)
- {
- shortName = new ArrayList<EvidencedStringType>();
- }
- return this.shortName;
- }
-
- /**
- * Gets the value of the ecNumber property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber()
- {
- if (ecNumber == null)
- {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "recommendedName", "alternativeName", "submittedName", "allergenName",
- "biotechName", "cdAntigenName", "innName" })
- public static class Component
- {
+@XmlType(name = "proteinType", propOrder = {
+ "recommendedName",
+ "alternativeName",
+ "submittedName",
+ "allergenName",
+ "biotechName",
+ "cdAntigenName",
+ "innName",
+ "domain",
+ "component"
+})
+public class ProteinType {
protected ProteinType.RecommendedName recommendedName;
-
protected List<ProteinType.AlternativeName> alternativeName;
-
protected List<ProteinType.SubmittedName> submittedName;
-
protected EvidencedStringType allergenName;
-
protected EvidencedStringType biotechName;
-
protected List<EvidencedStringType> cdAntigenName;
-
protected List<EvidencedStringType> innName;
+ protected List<ProteinType.Domain> domain;
+ protected List<ProteinType.Component> component;
/**
* Gets the value of the recommendedName property.
*
- * @return possible object is {@link ProteinType.RecommendedName }
- *
+ * @return
+ * possible object is
+ * {@link ProteinType.RecommendedName }
+ *
*/
- public ProteinType.RecommendedName getRecommendedName()
- {
- return recommendedName;
+ public ProteinType.RecommendedName getRecommendedName() {
+ return recommendedName;
}
/**
* Sets the value of the recommendedName property.
*
* @param value
- * allowed object is {@link ProteinType.RecommendedName }
- *
+ * allowed object is
+ * {@link ProteinType.RecommendedName }
+ *
*/
- public void setRecommendedName(ProteinType.RecommendedName value)
- {
- this.recommendedName = value;
+ public void setRecommendedName(ProteinType.RecommendedName value) {
+ this.recommendedName = value;
}
/**
* Gets the value of the alternativeName property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the alternativeName property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getAlternativeName().add(newItem);
+ * getAlternativeName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<ProteinType.AlternativeName> getAlternativeName()
- {
- if (alternativeName == null)
- {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
+ public List<ProteinType.AlternativeName> getAlternativeName() {
+ if (alternativeName == null) {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
}
/**
* Gets the value of the submittedName property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the submittedName property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getSubmittedName().add(newItem);
+ * getSubmittedName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<ProteinType.SubmittedName> getSubmittedName()
- {
- if (submittedName == null)
- {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
+ public List<ProteinType.SubmittedName> getSubmittedName() {
+ if (submittedName == null) {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
}
/**
* Gets the value of the allergenName property.
*
- * @return possible object is {@link EvidencedStringType }
- *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
*/
- public EvidencedStringType getAllergenName()
- {
- return allergenName;
+ public EvidencedStringType getAllergenName() {
+ return allergenName;
}
/**
* Sets the value of the allergenName property.
*
* @param value
- * allowed object is {@link EvidencedStringType }
- *
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
*/
- public void setAllergenName(EvidencedStringType value)
- {
- this.allergenName = value;
+ public void setAllergenName(EvidencedStringType value) {
+ this.allergenName = value;
}
/**
* Gets the value of the biotechName property.
*
- * @return possible object is {@link EvidencedStringType }
- *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
*/
- public EvidencedStringType getBiotechName()
- {
- return biotechName;
+ public EvidencedStringType getBiotechName() {
+ return biotechName;
}
/**
* Sets the value of the biotechName property.
*
* @param value
- * allowed object is {@link EvidencedStringType }
- *
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
*/
- public void setBiotechName(EvidencedStringType value)
- {
- this.biotechName = value;
+ public void setBiotechName(EvidencedStringType value) {
+ this.biotechName = value;
}
/**
* Gets the value of the cdAntigenName property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the cdAntigenName property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getCdAntigenName().add(newItem);
+ * getCdAntigenName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<EvidencedStringType> getCdAntigenName()
- {
- if (cdAntigenName == null)
- {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
+ public List<EvidencedStringType> getCdAntigenName() {
+ if (cdAntigenName == null) {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
}
/**
* Gets the value of the innName property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the innName property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the innName property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getInnName().add(newItem);
+ * getInnName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<EvidencedStringType> getInnName()
- {
- if (innName == null)
- {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "recommendedName", "alternativeName", "submittedName", "allergenName",
- "biotechName", "cdAntigenName", "innName" })
- public static class Domain
- {
-
- protected ProteinType.RecommendedName recommendedName;
-
- protected List<ProteinType.AlternativeName> alternativeName;
-
- protected List<ProteinType.SubmittedName> submittedName;
-
- protected EvidencedStringType allergenName;
-
- protected EvidencedStringType biotechName;
-
- protected List<EvidencedStringType> cdAntigenName;
-
- protected List<EvidencedStringType> innName;
-
- /**
- * Gets the value of the recommendedName property.
- *
- * @return possible object is {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName getRecommendedName()
- {
- return recommendedName;
+ public List<EvidencedStringType> getInnName() {
+ if (innName == null) {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
}
/**
- * Sets the value of the recommendedName property.
- *
- * @param value
- * allowed object is {@link ProteinType.RecommendedName }
- *
- */
- public void setRecommendedName(ProteinType.RecommendedName value)
- {
- this.recommendedName = value;
- }
-
- /**
- * Gets the value of the alternativeName property.
+ * Gets the value of the domain property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the alternativeName property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the domain property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getAlternativeName().add(newItem);
+ * getDomain().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link ProteinType.AlternativeName }
+ * {@link ProteinType.Domain }
*
*
*/
- public List<ProteinType.AlternativeName> getAlternativeName()
- {
- if (alternativeName == null)
- {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
+ public List<ProteinType.Domain> getDomain() {
+ if (domain == null) {
+ domain = new ArrayList<ProteinType.Domain>();
+ }
+ return this.domain;
}
/**
- * Gets the value of the submittedName property.
+ * Gets the value of the component property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the submittedName property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the component property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getSubmittedName().add(newItem);
+ * getComponent().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link ProteinType.SubmittedName }
- *
- *
- */
- public List<ProteinType.SubmittedName> getSubmittedName()
- {
- if (submittedName == null)
- {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
- }
-
- /**
- * Gets the value of the allergenName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getAllergenName()
- {
- return allergenName;
- }
-
- /**
- * Sets the value of the allergenName property.
+ * {@link ProteinType.Component }
*
- * @param value
- * allowed object is {@link EvidencedStringType }
*
*/
- public void setAllergenName(EvidencedStringType value)
- {
- this.allergenName = value;
+ public List<ProteinType.Component> getComponent() {
+ if (component == null) {
+ component = new ArrayList<ProteinType.Component>();
+ }
+ return this.component;
}
- /**
- * Gets the value of the biotechName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getBiotechName()
- {
- return biotechName;
- }
/**
- * Sets the value of the biotechName property.
+ * <p>Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link EvidencedStringType }
- *
- */
- public void setBiotechName(EvidencedStringType value)
- {
- this.biotechName = value;
- }
-
- /**
- * Gets the value of the cdAntigenName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the cdAntigenName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getCdAntigenName().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getCdAntigenName()
- {
- if (cdAntigenName == null)
- {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "fullName",
+ "shortName",
+ "ecNumber"
+ })
+ public static class AlternativeName {
+
+ protected EvidencedStringType fullName;
+ protected List<EvidencedStringType> shortName;
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName() {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value) {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the shortName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getShortName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getShortName() {
+ if (shortName == null) {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber() {
+ if (ecNumber == null) {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
}
+
/**
- * Gets the value of the innName property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the innName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getInnName().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getInnName()
- {
- if (innName == null)
- {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "recommendedName",
+ "alternativeName",
+ "submittedName",
+ "allergenName",
+ "biotechName",
+ "cdAntigenName",
+ "innName"
+ })
+ public static class Component {
+
+ protected ProteinType.RecommendedName recommendedName;
+ protected List<ProteinType.AlternativeName> alternativeName;
+ protected List<ProteinType.SubmittedName> submittedName;
+ protected EvidencedStringType allergenName;
+ protected EvidencedStringType biotechName;
+ protected List<EvidencedStringType> cdAntigenName;
+ protected List<EvidencedStringType> innName;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName() {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value) {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName() {
+ if (alternativeName == null) {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName() {
+ if (submittedName == null) {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName() {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value) {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName() {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value) {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName() {
+ if (cdAntigenName == null) {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName() {
+ if (innName == null) {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
- * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
- public static class RecommendedName
- {
-
- @XmlElement(required = true)
- protected EvidencedStringType fullName;
-
- protected List<EvidencedStringType> shortName;
-
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName()
- {
- return fullName;
}
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value)
- {
- this.fullName = value;
- }
/**
- * Gets the value of the shortName property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the shortName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getShortName().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getShortName()
- {
- if (shortName == null)
- {
- shortName = new ArrayList<EvidencedStringType>();
- }
- return this.shortName;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "recommendedName",
+ "alternativeName",
+ "submittedName",
+ "allergenName",
+ "biotechName",
+ "cdAntigenName",
+ "innName"
+ })
+ public static class Domain {
+
+ protected ProteinType.RecommendedName recommendedName;
+ protected List<ProteinType.AlternativeName> alternativeName;
+ protected List<ProteinType.SubmittedName> submittedName;
+ protected EvidencedStringType allergenName;
+ protected EvidencedStringType biotechName;
+ protected List<EvidencedStringType> cdAntigenName;
+ protected List<EvidencedStringType> innName;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return
+ * possible object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName() {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value) {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName() {
+ if (alternativeName == null) {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName() {
+ if (submittedName == null) {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName() {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value) {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName() {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value) {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName() {
+ if (cdAntigenName == null) {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName() {
+ if (innName == null) {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
}
+
/**
- * Gets the value of the ecNumber property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the ecNumber property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getEcNumber().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getEcNumber()
- {
- if (ecNumber == null)
- {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
- public static class SubmittedName
- {
-
- @XmlElement(required = true)
- protected EvidencedStringType fullName;
-
- protected List<EvidencedStringType> ecNumber;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "fullName",
+ "shortName",
+ "ecNumber"
+ })
+ public static class RecommendedName {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+ protected List<EvidencedStringType> shortName;
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName() {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value) {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the shortName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getShortName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getShortName() {
+ if (shortName == null) {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber() {
+ if (ecNumber == null) {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
- /**
- * Gets the value of the fullName property.
- *
- * @return possible object is {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName()
- {
- return fullName;
}
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value)
- {
- this.fullName = value;
- }
/**
- * Gets the value of the ecNumber property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getEcNumber().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
*/
- public List<EvidencedStringType> getEcNumber()
- {
- if (ecNumber == null)
- {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "fullName",
+ "ecNumber"
+ })
+ public static class SubmittedName {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return
+ * possible object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName() {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value) {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber() {
+ if (ecNumber == null) {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
- }
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
* Describes a chemical reaction.
*
- * <p>
- * Java class for reactionType complex type.
+ * <p>Java class for reactionType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="reactionType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
-public class ReactionType
-{
-
- @XmlElement(required = true)
- protected String text;
+@XmlType(name = "reactionType", propOrder = {
+ "text",
+ "dbReference"
+})
+public class ReactionType {
- @XmlElement(required = true)
- protected List<DbReferenceType> dbReference;
+ @XmlElement(required = true)
+ protected String text;
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the text property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getText()
- {
- return text;
- }
+ /**
+ * Gets the value of the text property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getText() {
+ return text;
+ }
- /**
- * Sets the value of the text property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setText(String value)
- {
- this.text = value;
- }
+ /**
+ * Sets the value of the text property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setText(String value) {
+ this.text = value;
+ }
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference()
- {
- if (dbReference == null)
- {
- dbReference = new ArrayList<DbReferenceType>();
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference() {
+ if (dbReference == null) {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
}
- return this.dbReference;
- }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes a citation and a summary of its content. Equivalent to the flat
- * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ * Describes a citation and a summary of its content.
+ * Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
*
- * <p>
- * Java class for referenceType complex type.
+ * <p>Java class for referenceType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="referenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "referenceType",
- propOrder =
- { "citation", "scope", "source" })
-public class ReferenceType
-{
-
- @XmlElement(required = true)
- protected CitationType citation;
-
- @XmlElement(required = true)
- protected List<String> scope;
-
- protected SourceDataType source;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- @XmlAttribute(name = "key", required = true)
- protected String key;
-
- /**
- * Gets the value of the citation property.
- *
- * @return possible object is {@link CitationType }
- *
- */
- public CitationType getCitation()
- {
- return citation;
- }
+@XmlType(name = "referenceType", propOrder = {
+ "citation",
+ "scope",
+ "source"
+})
+public class ReferenceType {
+
+ @XmlElement(required = true)
+ protected CitationType citation;
+ @XmlElement(required = true)
+ protected List<String> scope;
+ protected SourceDataType source;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+
+ /**
+ * Gets the value of the citation property.
+ *
+ * @return
+ * possible object is
+ * {@link CitationType }
+ *
+ */
+ public CitationType getCitation() {
+ return citation;
+ }
- /**
- * Sets the value of the citation property.
- *
- * @param value
- * allowed object is {@link CitationType }
- *
- */
- public void setCitation(CitationType value)
- {
- this.citation = value;
- }
+ /**
+ * Sets the value of the citation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link CitationType }
+ *
+ */
+ public void setCitation(CitationType value) {
+ this.citation = value;
+ }
- /**
- * Gets the value of the scope property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the scope property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getScope().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getScope()
- {
- if (scope == null)
- {
- scope = new ArrayList<String>();
+ /**
+ * Gets the value of the scope property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the scope property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getScope().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getScope() {
+ if (scope == null) {
+ scope = new ArrayList<String>();
+ }
+ return this.scope;
}
- return this.scope;
- }
- /**
- * Gets the value of the source property.
- *
- * @return possible object is {@link SourceDataType }
- *
- */
- public SourceDataType getSource()
- {
- return source;
- }
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link SourceDataType }
+ *
+ */
+ public SourceDataType getSource() {
+ return source;
+ }
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is {@link SourceDataType }
- *
- */
- public void setSource(SourceDataType value)
- {
- this.source = value;
- }
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link SourceDataType }
+ *
+ */
+ public void setSource(SourceDataType value) {
+ this.source = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
- return this.evidence;
- }
- /**
- * Gets the value of the key property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getKey()
- {
- return key;
- }
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setKey(String value)
- {
- this.key = value;
- }
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlValue;
import javax.xml.datatype.XMLGregorianCalendar;
+
/**
- * <p>
- * Java class for sequenceType complex type.
+ * <p>Java class for sequenceType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="sequenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = { "value" })
-public class SequenceType
-{
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "length", required = true)
- protected int length;
-
- @XmlAttribute(name = "mass", required = true)
- protected int mass;
-
- @XmlAttribute(name = "checksum", required = true)
- protected String checksum;
-
- @XmlAttribute(name = "modified", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar modified;
-
- @XmlAttribute(name = "version", required = true)
- protected int version;
-
- @XmlAttribute(name = "precursor")
- protected Boolean precursor;
-
- @XmlAttribute(name = "fragment")
- protected String fragment;
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
-
- /**
- * Gets the value of the length property.
- *
- */
- public int getLength()
- {
- return length;
- }
-
- /**
- * Sets the value of the length property.
- *
- */
- public void setLength(int value)
- {
- this.length = value;
- }
-
- /**
- * Gets the value of the mass property.
- *
- */
- public int getMass()
- {
- return mass;
- }
-
- /**
- * Sets the value of the mass property.
- *
- */
- public void setMass(int value)
- {
- this.mass = value;
- }
-
- /**
- * Gets the value of the checksum property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getChecksum()
- {
- return checksum;
- }
-
- /**
- * Sets the value of the checksum property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setChecksum(String value)
- {
- this.checksum = value;
- }
-
- /**
- * Gets the value of the modified property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getModified()
- {
- return modified;
- }
-
- /**
- * Sets the value of the modified property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setModified(XMLGregorianCalendar value)
- {
- this.modified = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- */
- public int getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- */
- public void setVersion(int value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the precursor property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPrecursor()
- {
- return precursor;
- }
-
- /**
- * Sets the value of the precursor property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPrecursor(Boolean value)
- {
- this.precursor = value;
- }
-
- /**
- * Gets the value of the fragment property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFragment()
- {
- return fragment;
- }
-
- /**
- * Sets the value of the fragment property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFragment(String value)
- {
- this.fragment = value;
- }
+@XmlType(name = "sequenceType", propOrder = {
+ "value"
+})
+public class SequenceType {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "length", required = true)
+ protected int length;
+ @XmlAttribute(name = "mass", required = true)
+ protected int mass;
+ @XmlAttribute(name = "checksum", required = true)
+ protected String checksum;
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
+ @XmlAttribute(name = "precursor")
+ protected Boolean precursor;
+ @XmlAttribute(name = "fragment")
+ protected String fragment;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ */
+ public int getLength() {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ */
+ public void setLength(int value) {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
+ *
+ */
+ public int getMass() {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ */
+ public void setMass(int value) {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the checksum property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getChecksum() {
+ return checksum;
+ }
+
+ /**
+ * Sets the value of the checksum property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setChecksum(String value) {
+ this.checksum = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified() {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value) {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the precursor property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPrecursor() {
+ return precursor;
+ }
+
+ /**
+ * Sets the value of the precursor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPrecursor(Boolean value) {
+ this.precursor = value;
+ }
+
+ /**
+ * Gets the value of the fragment property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFragment() {
+ return fragment;
+ }
+
+ /**
+ * Sets the value of the fragment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFragment(String value) {
+ this.fragment = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
- * Describes the source of the sequence according to the citation. Equivalent to
- * the flat file RC-line.
+ * Describes the source of the sequence according to the citation.
+ * Equivalent to the flat file RC-line.
*
- * <p>
- * Java class for sourceDataType complex type.
+ * <p>Java class for sourceDataType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="sourceDataType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "sourceDataType",
- propOrder =
- { "strainOrPlasmidOrTransposon" })
-public class SourceDataType
-{
-
- @XmlElements({
- @XmlElement(name = "strain", type = SourceDataType.Strain.class),
- @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
- @XmlElement(
- name = "transposon",
- type = SourceDataType.Transposon.class),
- @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
- protected List<Object> strainOrPlasmidOrTransposon;
-
- /**
- * Gets the value of the strainOrPlasmidOrTransposon property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the strainOrPlasmidOrTransposon property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getStrainOrPlasmidOrTransposon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid }
- * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue }
- *
- *
- */
- public List<Object> getStrainOrPlasmidOrTransposon()
- {
- if (strainOrPlasmidOrTransposon == null)
- {
- strainOrPlasmidOrTransposon = new ArrayList<Object>();
- }
- return this.strainOrPlasmidOrTransposon;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class Plasmid
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+@XmlType(name = "sourceDataType", propOrder = {
+ "strainOrPlasmidOrTransposon"
+})
+public class SourceDataType {
+
+ @XmlElements({
+ @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+ @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+ @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
+ @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
+ })
+ protected List<Object> strainOrPlasmidOrTransposon;
/**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
-
- /**
- * Gets the value of the evidence property.
+ * Gets the value of the strainOrPlasmidOrTransposon property.
*
* <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the evidence property.
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property.
*
* <p>
* For example, to add a new item, do as follows:
- *
* <pre>
- * getEvidence().add(newItem);
+ * getStrainOrPlasmidOrTransposon().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
+ * Objects of the following type(s) are allowed in the list
+ * {@link SourceDataType.Strain }
+ * {@link SourceDataType.Plasmid }
+ * {@link SourceDataType.Transposon }
+ * {@link SourceDataType.Tissue }
*
*
*/
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ public List<Object> getStrainOrPlasmidOrTransposon() {
+ if (strainOrPlasmidOrTransposon == null) {
+ strainOrPlasmidOrTransposon = new ArrayList<Object>();
+ }
+ return this.strainOrPlasmidOrTransposon;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class Strain
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
/**
- * Gets the value of the value property.
+ * <p>Java class for anonymous complex type.
*
- * @return possible object is {@link String }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public String getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setValue(String value)
- {
- this.value = value;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Plasmid {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
}
+
/**
- * Gets the value of the evidence property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getEvidence().add(newItem);
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
*/
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class Tissue
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Strain {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
}
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
/**
- * Gets the value of the evidence property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getEvidence().add(newItem);
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
*/
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Tissue {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class Transposon
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
}
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
/**
- * Gets the value of the evidence property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
- * getEvidence().add(newItem);
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
*/
- public List<Integer> getEvidence()
- {
- if (evidence == null)
- {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class Transposon {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence() {
+ if (evidence == null) {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
- }
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the source of the data using a database cross-reference (or a 'ref'
- * attribute when the source cannot be found in a public data source, such as
- * PubMed, and is cited only within the UniProtKB entry).
+ * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
*
- * <p>
- * Java class for sourceType complex type.
+ * <p>Java class for sourceType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="sourceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = { "dbReference" })
-public class SourceType
-{
-
- protected DbReferenceType dbReference;
+@XmlType(name = "sourceType", propOrder = {
+ "dbReference"
+})
+public class SourceType {
- @XmlAttribute(name = "ref")
- protected BigInteger ref;
+ protected DbReferenceType dbReference;
+ @XmlAttribute(name = "ref")
+ protected BigInteger ref;
- /**
- * Gets the value of the dbReference property.
- *
- * @return possible object is {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference()
- {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return
+ * possible object is
+ * {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference() {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value)
- {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value) {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the ref property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getRef()
- {
- return ref;
- }
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getRef() {
+ return ref;
+ }
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setRef(BigInteger value)
- {
- this.ref = value;
- }
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setRef(BigInteger value) {
+ this.ref = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
+
/**
* Indicates whether the name of a plasmid is known or unknown.
*
- * <p>
- * Java class for statusType complex type.
+ * <p>Java class for statusType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="statusType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = { "value" })
-public class StatusType
-{
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "status")
- protected String status;
+@XmlType(name = "statusType", propOrder = {
+ "value"
+})
+public class StatusType {
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getStatus()
- {
- if (status == null)
- {
- return "known";
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
}
- else
- {
- return status;
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getStatus() {
+ if (status == null) {
+ return "known";
+ } else {
+ return status;
+ }
}
- }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setStatus(String value)
- {
- this.status = value;
- }
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * Describes the subcellular location and optionally the topology and
- * orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and orientation of a molecule.
*
- * <p>
- * Java class for subcellularLocationType complex type.
+ * <p>Java class for subcellularLocationType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType name="subcellularLocationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "subcellularLocationType",
- propOrder =
- { "location", "topology", "orientation" })
-public class SubcellularLocationType
-{
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> location;
-
- protected List<EvidencedStringType> topology;
+@XmlType(name = "subcellularLocationType", propOrder = {
+ "location",
+ "topology",
+ "orientation"
+})
+public class SubcellularLocationType {
- protected List<EvidencedStringType> orientation;
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> location;
+ protected List<EvidencedStringType> topology;
+ protected List<EvidencedStringType> orientation;
- /**
- * Gets the value of the location property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the location property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getLocation()
- {
- if (location == null)
- {
- location = new ArrayList<EvidencedStringType>();
+ /**
+ * Gets the value of the location property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getLocation() {
+ if (location == null) {
+ location = new ArrayList<EvidencedStringType>();
+ }
+ return this.location;
}
- return this.location;
- }
- /**
- * Gets the value of the topology property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the topology property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getTopology().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getTopology()
- {
- if (topology == null)
- {
- topology = new ArrayList<EvidencedStringType>();
+ /**
+ * Gets the value of the topology property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the topology property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTopology().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getTopology() {
+ if (topology == null) {
+ topology = new ArrayList<EvidencedStringType>();
+ }
+ return this.topology;
}
- return this.topology;
- }
- /**
- * Gets the value of the orientation property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the orientation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getOrientation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getOrientation()
- {
- if (orientation == null)
- {
- orientation = new ArrayList<EvidencedStringType>();
+ /**
+ * Gets the value of the orientation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the orientation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOrientation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getOrientation() {
+ if (orientation == null) {
+ orientation = new ArrayList<EvidencedStringType>();
+ }
+ return this.orientation;
}
- return this.orientation;
- }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
+
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "entry", "copyright" })
+@XmlType(name = "", propOrder = {
+ "entry",
+ "copyright"
+})
@XmlRootElement(name = "uniprot")
-public class Uniprot
-{
-
- @XmlElement(required = true)
- protected List<Entry> entry;
+public class Uniprot {
- protected String copyright;
+ @XmlElement(required = true)
+ protected List<Entry> entry;
+ protected String copyright;
- /**
- * Gets the value of the entry property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the entry property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getEntry().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Entry }
- *
- *
- */
- public List<Entry> getEntry()
- {
- if (entry == null)
- {
- entry = new ArrayList<Entry>();
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry }
+ *
+ *
+ */
+ public List<Entry> getEntry() {
+ if (entry == null) {
+ entry = new ArrayList<Entry>();
+ }
+ return this.entry;
}
- return this.entry;
- }
- /**
- * Gets the value of the copyright property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCopyright()
- {
- return copyright;
- }
+ /**
+ * Gets the value of the copyright property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCopyright() {
+ return copyright;
+ }
- /**
- * Sets the value of the copyright property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCopyright(String value)
- {
- this.copyright = value;
- }
+ /**
+ * Sets the value of the copyright property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCopyright(String value) {
+ this.copyright = value;
+ }
}
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2019.04.05 at 08:01:44 AM BST
+// Generated on: 2023.01.31 at 04:07:10 PM GMT
//
-@javax.xml.bind.annotation.XmlSchema(
- namespace = "http://uniprot.org/uniprot",
- elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.uniprot;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotEquals;
+import static org.testng.Assert.assertNotNull;
import java.awt.Dimension;
import java.awt.Font;
Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
}
-}
+
+ @Test(groups = "Functional")
+ public void testSetOverviewTitle()
+ {
+ OverviewPanel ov1 = this.af.openOverviewPanel(true);
+ String alignFrameTitle = af.getTitle();
+ assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
+
+ /*
+ * on New View, existing overview should get " Original" added to title
+ * and new view's overview should get " View 1" added
+ */
+ af.newView_actionPerformed(null);
+ assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+ OverviewPanel ov2 = this.af.openOverviewPanel(true);
+ assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetOverviewTitle_automaticOverview()
+ {
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
+ assertNotNull(ov1);
+ String alignFrameTitle = alignFrame.getTitle();
+ assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
+
+ /*
+ * on New View, existing overview should get " Original" added to title
+ * and new view's automatic overview should have " View 1" added
+ */
+ alignFrame.newView_actionPerformed(null);
+ assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+ OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
+ assertNotNull(ov2);
+ assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
+ }
+}
\ No newline at end of file
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
import java.awt.Color;
+import java.awt.Rectangle;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
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.Annotation;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewPanel;
import jalview.gui.PCAPanel;
import jalview.gui.PopupMenu;
+import jalview.gui.Preferences;
import jalview.gui.SliderPanel;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+ /*
+ * test for patch release versions
+ */
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0","2.11.4"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.0b1","2.12.2.0"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.3","2.12.2.2"));
+
}
/**
assertTrue(dbRef instanceof GeneLocus);
assertEquals(dbRef, dbref3);
}
+
+ /**
+ * test store and recovery of Overview windows
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testStoreAndRecoverOverview() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ Cache.setProperty("SHOW_OVERVIEW", "false");
+ Cache.setProperty(Preferences.USE_LEGACY_GAP, "false");
+ Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green);
+ Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow);
+ Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true");
+
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+
+ /*
+ * open and resize / reposition overview
+ */
+ af.overviewMenuItem_actionPerformed(null);
+ OverviewPanel ov1 = af.alignPanel.getOverviewPanel();
+ assertNotNull(ov1);
+ ov1.setFrameBounds(20, 30, 200, 400);
+ assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa");
+ assertTrue(ov1.isShowHiddenRegions());
+
+ /*
+ * open a New View and its Overview and reposition it
+ */
+ af.newView_actionPerformed(null);
+ af.overviewMenuItem_actionPerformed(null);
+ OverviewPanel ov2 = af.alignPanel.getOverviewPanel();
+ assertNotNull(ov2);
+ assertNotSame(ov1, ov2);
+ ov2.setFrameBounds(25, 35, 205, 405);
+ assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+ assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+
+ File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ /*
+ * change preferences (should _not_ affect reloaded Overviews)
+ */
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ Cache.setProperty(Preferences.USE_LEGACY_GAP, "true");
+ Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue);
+ Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange);
+ Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false");
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+
+ /*
+ * workaround: explicitly select View 1 (not in focus after restore)
+ */
+ af.tabSelectionChanged(1);
+
+ /*
+ * verify restored overview for View 1
+ */
+ ov2 = af.alignPanel.getOverviewPanel();
+ assertEquals(ov2.getCanvas().getGapColour(), Color.green);
+ // 'non-legacy' colouring uses white for non-gapped residues
+ assertEquals(ov2.getCanvas().getResidueColour(), Color.white);
+ assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow);
+ assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+ assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405));
+ assertTrue(ov2.isShowHiddenRegions());
+
+ /*
+ * verify restored overview for Original view
+ */
+ af.tabSelectionChanged(0);
+ ov1 = af.alignPanel.getOverviewPanel();
+ assertEquals(ov1.getCanvas().getGapColour(), Color.green);
+ // 'non-legacy' colouring uses white for non-gapped residues
+ assertEquals(ov1.getCanvas().getResidueColour(), Color.white);
+ assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow);
+ assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+ assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400));
+ assertTrue(ov1.isShowHiddenRegions());
+ }
+
+ /**
+ * Test that a view with no Overview is restored with no Overview, even if
+ * 'Open Overview' is selected in Preferences
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testStoreAndRecoverNoOverview() throws Exception
+ {
+ Cache.setProperty("SHOW_OVERVIEW", "false");
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+
+ File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+
+ assertNull(af.alignPanel.getOverviewPanel());
+ }
+
+ /**
+ * Test that a view from an older version of Jalview is restored with Overview automatically shown when the preference is set
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testAutoShowOverviewForLegacyProjects() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile.jvp", DataSourceType.FILE);
+
+ Cache.setProperty("SHOW_OVERVIEW", "false");
+ assertNotNull(af.alignPanel.getOverviewPanel());
+ }
+
+ /**
+ * Test that loading example.jvp, doing some stuff, then hitting reload
+ * doesn't leave the modified window still open
+ *
+ * See JAL-4127 - interactively performing the same actions and reloading
+ * works fine, but programmatically they do not
+ *
+ * @throws Exception
+ */
+ @Test(groups = {"Functional"}, enabled=false)
+ public void testReloadActuallyReloads() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile.jvp", DataSourceType.FILE);
+ af.getViewport().getColumnSelection().addElement(3);
+ af.hideSelColumns_actionPerformed(null);
+ af.newView("new", true);
+ af.reload_actionPerformed(null);
+ Thread.sleep(30);
+ // af exists still but isn't shown
+ assertTrue(af.isClosed());
+ }
}
@Test
public void testGetColumnColourFromSequence()
{
- OverviewResColourFinder cf = new OverviewResColourFinder(false,
- Color.PINK, Color.green); // gapColour, hiddenColour
+ // gapColour, residueColour, hiddenColour
+ OverviewResColourFinder cf = new OverviewResColourFinder(
+ Color.PINK, Color.white, Color.green);
Sequence seq1 = new Sequence("seq1", "PQ-RL-");
Sequence seq2 = new Sequence("seq2", "FVE");
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
import static org.testng.AssertJUnit.assertEquals;
+import java.awt.Color;
+import java.util.ArrayList;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewCanvas;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import java.awt.Color;
-import java.util.ArrayList;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class OverviewResColourFinderTest
{
av.getResidueShading(), groups, seq, 2, null));
// use legacy colouring
- rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
// G in group specified as magenta in Zappo
assertEquals(Color.magenta, rcf.getResidueColour(false,
av.getResidueShading(), groups, seq, 2, null));
// use new colouring
- rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
// G in group specified as magenta in Zappo
assertEquals(Color.magenta, rcf.getResidueColour(false,
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
- c);
+ assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
// legacy colouring set explicitly via constructor
- rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
shader = new ResidueShader();
// residues light gray
// gaps gap colour
c = rcf.getBoxColour(shader, seq, 3);
- assertEquals(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
- c);
+ assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
// non legacy colouring with colour scheme
- rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.blue, Color.white, Color.red);
shader = new ResidueShader(new ZappoColourScheme());
// M residue pink
assertEquals(Color.blue, c);
// legacy colouring with colour scheme
- rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+ rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
// M residue pink
c = rcf.getBoxColour(shader, seq, 0);
git://source.jalview.org / jalview.git / commitdiff