/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class StructureState implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * internal content storage
- */
- private java.lang.String _content = "";
-
- /**
- * Field _visible.
- */
- private boolean _visible;
-
- /**
- * keeps track of state for field: _visible
- */
- private boolean _has_visible;
-
- /**
- * Field _xpos.
- */
- private int _xpos;
-
- /**
- * keeps track of state for field: _xpos
- */
- private boolean _has_xpos;
-
- /**
- * Field _ypos.
- */
- private int _ypos;
-
- /**
- * keeps track of state for field: _ypos
- */
- private boolean _has_ypos;
-
- /**
- * Field _width.
- */
- private int _width;
-
- /**
- * keeps track of state for field: _width
- */
- private boolean _has_width;
-
- /**
- * Field _height.
- */
- private int _height;
-
- /**
- * keeps track of state for field: _height
- */
- private boolean _has_height;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public StructureState() {
- super();
- setContent("");
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteHeight(
- ) {
- this._has_height= false;
- }
-
- /**
- */
- public void deleteVisible(
- ) {
- this._has_visible= false;
- }
-
- /**
- */
- public void deleteWidth(
- ) {
- this._has_width= false;
- }
-
- /**
- */
- public void deleteXpos(
- ) {
- this._has_xpos= false;
- }
-
- /**
- */
- public void deleteYpos(
- ) {
- this._has_ypos= false;
- }
-
- /**
- * Returns the value of field 'content'. The field 'content'
- * has the following description: internal content storage
- *
- * @return the value of field 'Content'.
- */
- public java.lang.String getContent(
- ) {
- return this._content;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight(
- ) {
- return this._height;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean getVisible(
- ) {
- return this._visible;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth(
- ) {
- return this._width;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos(
- ) {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos(
- ) {
- return this._ypos;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight(
- ) {
- return this._has_height;
- }
-
- /**
- * Method hasVisible.
- *
- * @return true if at least one Visible has been added
- */
- public boolean hasVisible(
- ) {
- return this._has_visible;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth(
- ) {
- return this._has_width;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos(
- ) {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos(
- ) {
- return this._has_ypos;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'visible'.
- *
- * @return the value of field 'Visible'.
- */
- public boolean isVisible(
- ) {
- return this._visible;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'content'. The field 'content' has
- * the following description: internal content storage
- *
- * @param content the value of field 'content'.
- */
- public void setContent(
- final java.lang.String content) {
- this._content = content;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height the value of field 'height'.
- */
- public void setHeight(
- final int height) {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'visible'.
- *
- * @param visible the value of field 'visible'.
- */
- public void setVisible(
- final boolean visible) {
- this._visible = visible;
- this._has_visible = true;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width the value of field 'width'.
- */
- public void setWidth(
- final int width) {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos the value of field 'xpos'.
- */
- public void setXpos(
- final int xpos) {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos the value of field 'ypos'.
- */
- public void setYpos(
- final int ypos) {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.StructureState
- */
- public static jalview.schemabinding.version2.StructureState unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+public class StructureState implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+ /**
+ * Field _visible.
+ */
+ private boolean _visible;
+
+ /**
+ * keeps track of state for field: _visible
+ */
+ private boolean _has_visible;
+
+ /**
+ * additional identifier which properly disambiguates the structure view from
+ * any other view with the same attributes. This is not an ID, because it is
+ * possible to have many references to the same physical structure view from
+ * different sequences in an alignment. A structureState element citing the
+ * same viewId will appear for each instance.
+ *
+ */
+ private java.lang.String _viewId;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should be included in
+ * those used to perform a structure superposition (since Jalview 2.7).
+ *
+ */
+ private boolean _alignwithAlignPanel = true;
+
+ /**
+ * keeps track of state for field: _alignwithAlignPanel
+ */
+ private boolean _has_alignwithAlignPanel;
+
+ /**
+ * Flag set if the alignment panel containing this JSeq should be included in
+ * those used to colour its associated sequences in this structureState(since
+ * Jalview 2.7).
+ *
+ */
+ private boolean _colourwithAlignPanel = false;
+
+ /**
+ * keeps track of state for field: _colourwithAlignPanel
+ */
+ private boolean _has_colourwithAlignPanel;
+
+ /**
+ * Flag set if the structure display is coloured by the Jmol state, rather
+ * than by one or more linked alignment views.
+ *
+ */
+ private boolean _colourByJmol = true;
+
+ /**
+ * keeps track of state for field: _colourByJmol
+ */
+ private boolean _has_colourByJmol;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public StructureState()
+ {
+ super();
+ setContent("");
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ */
+ public void deleteAlignwithAlignPanel()
+ {
+ this._has_alignwithAlignPanel = false;
+ }
+
+ /**
+ */
+ public void deleteColourByJmol()
+ {
+ this._has_colourByJmol = false;
+ }
+
+ /**
+ */
+ public void deleteColourwithAlignPanel()
+ {
+ this._has_colourwithAlignPanel = false;
+ }
+
+ /**
+ */
+ public void deleteHeight()
+ {
+ this._has_height = false;
+ }
+
+ /**
+ */
+ public void deleteVisible()
+ {
+ this._has_visible = false;
+ }
+
+ /**
+ */
+ public void deleteWidth()
+ {
+ this._has_width = false;
+ }
+
+ /**
+ */
+ public void deleteXpos()
+ {
+ this._has_xpos = false;
+ }
+
+ /**
+ */
+ public void deleteYpos()
+ {
+ this._has_ypos = false;
+ }
+
+ /**
+ * Returns the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * perform a structure superposition (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean getAlignwithAlignPanel()
+ {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+ * following description: Flag set if the structure display is coloured by the
+ * Jmol state, rather than by one or more linked alignment views.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean getColourByJmol()
+ {
+ return this._colourByJmol;
+ }
+
+ /**
+ * Returns the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * colour its associated sequences in this structureState(since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean getColourwithAlignPanel()
+ {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @return the value of field 'Content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight()
+ {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'viewId'. The field 'viewId' has the following
+ * description: additional identifier which properly disambiguates the
+ * structure view from any other view with the same attributes. This is not an
+ * ID, because it is possible to have many references to the same physical
+ * structure view from different sequences in an alignment. A structureState
+ * element citing the same viewId will appear for each instance.
+ *
+ *
+ * @return the value of field 'ViewId'.
+ */
+ public java.lang.String getViewId()
+ {
+ return this._viewId;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean getVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth()
+ {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos()
+ {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos()
+ {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasAlignwithAlignPanel.
+ *
+ * @return true if at least one AlignwithAlignPanel has been added
+ */
+ public boolean hasAlignwithAlignPanel()
+ {
+ return this._has_alignwithAlignPanel;
+ }
+
+ /**
+ * Method hasColourByJmol.
+ *
+ * @return true if at least one ColourByJmol has been added
+ */
+ public boolean hasColourByJmol()
+ {
+ return this._has_colourByJmol;
+ }
+
+ /**
+ * Method hasColourwithAlignPanel.
+ *
+ * @return true if at least one ColourwithAlignPanel has been added
+ */
+ public boolean hasColourwithAlignPanel()
+ {
+ return this._has_colourwithAlignPanel;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight()
+ {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasVisible.
+ *
+ * @return true if at least one Visible has been added
+ */
+ public boolean hasVisible()
+ {
+ return this._has_visible;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth()
+ {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos()
+ {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos()
+ {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * perform a structure superposition (since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'AlignwithAlignPanel'.
+ */
+ public boolean isAlignwithAlignPanel()
+ {
+ return this._alignwithAlignPanel;
+ }
+
+ /**
+ * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+ * following description: Flag set if the structure display is coloured by the
+ * Jmol state, rather than by one or more linked alignment views.
+ *
+ *
+ * @return the value of field 'ColourByJmol'.
+ */
+ public boolean isColourByJmol()
+ {
+ return this._colourByJmol;
+ }
+
+ /**
+ * Returns the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * colour its associated sequences in this structureState(since Jalview 2.7).
+ *
+ *
+ * @return the value of field 'ColourwithAlignPanel'.
+ */
+ public boolean isColourwithAlignPanel()
+ {
+ return this._colourwithAlignPanel;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'visible'.
+ *
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible()
+ {
+ return this._visible;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'alignwithAlignPanel'. The field
+ * 'alignwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * perform a structure superposition (since Jalview 2.7).
+ *
+ *
+ * @param alignwithAlignPanel
+ * the value of field 'alignwithAlignPanel'.
+ */
+ public void setAlignwithAlignPanel(final boolean alignwithAlignPanel)
+ {
+ this._alignwithAlignPanel = alignwithAlignPanel;
+ this._has_alignwithAlignPanel = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the
+ * following description: Flag set if the structure display is coloured by the
+ * Jmol state, rather than by one or more linked alignment views.
+ *
+ *
+ * @param colourByJmol
+ * the value of field 'colourByJmol'.
+ */
+ public void setColourByJmol(final boolean colourByJmol)
+ {
+ this._colourByJmol = colourByJmol;
+ this._has_colourByJmol = true;
+ }
+
+ /**
+ * Sets the value of field 'colourwithAlignPanel'. The field
+ * 'colourwithAlignPanel' has the following description: Flag set if the
+ * alignment panel containing this JSeq should be included in those used to
+ * colour its associated sequences in this structureState(since Jalview 2.7).
+ *
+ *
+ * @param colourwithAlignPanel
+ * the value of field 'colourwithAlignPanel'.
+ */
+ public void setColourwithAlignPanel(final boolean colourwithAlignPanel)
+ {
+ this._colourwithAlignPanel = colourwithAlignPanel;
+ this._has_colourwithAlignPanel = true;
+ }
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has the following
+ * description: internal content storage
+ *
+ * @param content
+ * the value of field 'content'.
+ */
+ public void setContent(final java.lang.String content)
+ {
+ this._content = content;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height
+ * the value of field 'height'.
+ */
+ public void setHeight(final int height)
+ {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'viewId'. The field 'viewId' has the following
+ * description: additional identifier which properly disambiguates the
+ * structure view from any other view with the same attributes. This is not an
+ * ID, because it is possible to have many references to the same physical
+ * structure view from different sequences in an alignment. A structureState
+ * element citing the same viewId will appear for each instance.
+ *
+ *
+ * @param viewId
+ * the value of field 'viewId'.
+ */
+ public void setViewId(final java.lang.String viewId)
+ {
+ this._viewId = viewId;
+ }
+
+ /**
+ * Sets the value of field 'visible'.
+ *
+ * @param visible
+ * the value of field 'visible'.
+ */
+ public void setVisible(final boolean visible)
+ {
+ this._visible = visible;
+ this._has_visible = true;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width
+ * the value of field 'width'.
+ */
+ public void setWidth(final int width)
+ {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos
+ * the value of field 'xpos'.
+ */
+ public void setXpos(final int xpos)
+ {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos
+ * the value of field 'ypos'.
+ */
+ public void setYpos(final int ypos)
+ {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.schemabinding.version2.StructureState
+ */
+ public static jalview.schemabinding.version2.StructureState unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.StructureState) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.StructureState.class,
+ reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
git://source.jalview.org / jalview.git / blobdiff