+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ *******************************************************************************/
/*
* This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
* Schema.
* $Id$
*/
//- Imported classes and packages -/
//---------------------------------/
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
/**
* Class StructureState.
private java.lang.String _content = "";
/**
- * Field _visible
+ * Field _visible.
*/
private boolean _visible;
private boolean _has_visible;
/**
- * Field _xpos
+ * 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 int _xpos;
+ private java.lang.String _viewId;
/**
- * keeps track of state for field: _xpos
+ * 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 _has_xpos;
+ private boolean _alignwithAlignPanel = true;
/**
- * Field _ypos
+ * keeps track of state for field: _alignwithAlignPanel
*/
- private int _ypos;
+ private boolean _has_alignwithAlignPanel;
/**
- * keeps track of state for field: _ypos
+ * 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 _has_ypos;
+ 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
+ * Field _width.
*/
private int _width;
private boolean _has_width;
/**
- * Field _height
+ * Field _height.
*/
private int _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("");
- } //-- jalview.schemabinding.version2.StructureState()
+ }
//-----------/
//-----------/
/**
- * Method deleteHeight
- *
*/
- public void deleteHeight()
- {
+ 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;
- } //-- void deleteHeight()
+ }
/**
- * Method deleteVisible
- *
*/
- public void deleteVisible()
- {
+ public void deleteVisible(
+ ) {
this._has_visible= false;
- } //-- void deleteVisible()
+ }
/**
- * Method deleteWidth
- *
*/
- public void deleteWidth()
- {
+ public void deleteWidth(
+ ) {
this._has_width= false;
- } //-- void deleteWidth()
+ }
/**
- * Method deleteXpos
- *
*/
- public void deleteXpos()
- {
+ public void deleteXpos(
+ ) {
this._has_xpos= false;
- } //-- void deleteXpos()
+ }
/**
- * Method deleteYpos
- *
*/
- public void deleteYpos()
- {
+ public void deleteYpos(
+ ) {
this._has_ypos= false;
- } //-- void deleteYpos()
+ }
+
+ /**
+ * 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 String
- * @return the value of field 'content'.
+ * @return the value of field 'Content'.
*/
- public java.lang.String getContent()
- {
+ public java.lang.String getContent(
+ ) {
return this._content;
- } //-- java.lang.String getContent()
+ }
/**
* Returns the value of field 'height'.
*
- * @return int
- * @return the value of field 'height'.
+ * @return the value of field 'Height'.
*/
- public int getHeight()
- {
+ public int getHeight(
+ ) {
return this._height;
- } //-- int getHeight()
+ }
+
+ /**
+ * 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 boolean
- * @return the value of field 'visible'.
+ * @return the value of field 'Visible'.
*/
- public boolean getVisible()
- {
+ public boolean getVisible(
+ ) {
return this._visible;
- } //-- boolean getVisible()
+ }
/**
* Returns the value of field 'width'.
*
- * @return int
- * @return the value of field 'width'.
+ * @return the value of field 'Width'.
*/
- public int getWidth()
- {
+ public int getWidth(
+ ) {
return this._width;
- } //-- int getWidth()
+ }
/**
* Returns the value of field 'xpos'.
*
- * @return int
- * @return the value of field 'xpos'.
+ * @return the value of field 'Xpos'.
*/
- public int getXpos()
- {
+ public int getXpos(
+ ) {
return this._xpos;
- } //-- int getXpos()
+ }
/**
* Returns the value of field 'ypos'.
*
- * @return int
- * @return the value of field 'ypos'.
+ * @return the value of field 'Ypos'.
*/
- public int getYpos()
- {
+ public int getYpos(
+ ) {
return this._ypos;
- } //-- int getYpos()
+ }
/**
- * Method hasHeight
- *
+ * Method hasAlignwithAlignPanel.
*
+ * @return true if at least one AlignwithAlignPanel has been
+ * added
+ */
+ public boolean hasAlignwithAlignPanel(
+ ) {
+ return this._has_alignwithAlignPanel;
+ }
+
+ /**
+ * Method hasColourByJmol.
*
- * @return boolean
+ * @return true if at least one ColourByJmol has been added
*/
- public boolean hasHeight()
- {
- return this._has_height;
- } //-- boolean hasHeight()
+ public boolean hasColourByJmol(
+ ) {
+ return this._has_colourByJmol;
+ }
/**
- * Method hasVisible
+ * 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 boolean
+ * @return true if at least one Visible has been added
*/
- public boolean hasVisible()
- {
+ public boolean hasVisible(
+ ) {
return this._has_visible;
- } //-- boolean hasVisible()
+ }
/**
- * Method hasWidth
+ * Method hasWidth.
*
- *
- *
- * @return boolean
+ * @return true if at least one Width has been added
*/
- public boolean hasWidth()
- {
+ public boolean hasWidth(
+ ) {
return this._has_width;
- } //-- boolean hasWidth()
+ }
/**
- * Method hasXpos
- *
- *
+ * Method hasXpos.
*
- * @return boolean
+ * @return true if at least one Xpos has been added
*/
- public boolean hasXpos()
- {
+ public boolean hasXpos(
+ ) {
return this._has_xpos;
- } //-- boolean hasXpos()
+ }
/**
- * Method hasYpos
+ * Method hasYpos.
*
- *
- *
- * @return boolean
+ * @return true if at least one Ypos has been added
*/
- public boolean hasYpos()
- {
+ public boolean hasYpos(
+ ) {
return this._has_ypos;
- } //-- boolean hasYpos()
+ }
/**
- * Method isValid
+ * 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 boolean
+ * @return true if this object is valid according to the schema
*/
- public boolean isValid()
- {
+ public boolean isValid(
+ ) {
try {
validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ } catch (org.exolab.castor.xml.ValidationException vex) {
return false;
}
return true;
- } //-- boolean isValid()
+ }
/**
- * Method marshal
+ * Returns the value of field 'visible'.
*
+ * @return the value of field 'Visible'.
+ */
+ public boolean isVisible(
+ ) {
+ return this._visible;
+ }
+
+ /**
*
*
* @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
+ * @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);
- } //-- void marshal(java.io.Writer)
+ }
/**
- * Method marshal
- *
*
*
* @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
+ * @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);
- } //-- void marshal(org.xml.sax.ContentHandler)
+ }
+
+ /**
+ * 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
*
* @param content the value of field 'content'.
*/
- public void setContent(java.lang.String content)
- {
+ public void setContent(
+ final java.lang.String content) {
this._content = content;
- } //-- void setContent(java.lang.String)
+ }
/**
* Sets the value of field 'height'.
*
* @param height the value of field 'height'.
*/
- public void setHeight(int height)
- {
+ public void setHeight(
+ final int height) {
this._height = height;
this._has_height = true;
- } //-- void setHeight(int)
+ }
+
+ /**
+ * 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(boolean visible)
- {
+ public void setVisible(
+ final boolean visible) {
this._visible = visible;
this._has_visible = true;
- } //-- void setVisible(boolean)
+ }
/**
* Sets the value of field 'width'.
*
* @param width the value of field 'width'.
*/
- public void setWidth(int width)
- {
+ public void setWidth(
+ final int width) {
this._width = width;
this._has_width = true;
- } //-- void setWidth(int)
+ }
/**
* Sets the value of field 'xpos'.
*
* @param xpos the value of field 'xpos'.
*/
- public void setXpos(int xpos)
- {
+ public void setXpos(
+ final int xpos) {
this._xpos = xpos;
this._has_xpos = true;
- } //-- void setXpos(int)
+ }
/**
* Sets the value of field 'ypos'.
*
* @param ypos the value of field 'ypos'.
*/
- public void setYpos(int ypos)
- {
+ public void setYpos(
+ final int ypos) {
this._ypos = ypos;
this._has_ypos = true;
- } //-- void setYpos(int)
+ }
/**
- * Method unmarshal
- *
- *
+ * Method unmarshal.
*
* @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
+ * @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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
+ }
/**
- * Method validate
*
+ *
+ * @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
- {
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
validator.validate(this);
- } //-- void validate()
+ }
}
git://source.jalview.org / jalview.git / blobdiff