/*******************************************************************************
* 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 .
*******************************************************************************/
/*
* This class was automatically generated with
* Castor 1.1, using an XML
* Schema.
* $Id$
*/
package jalview.schemabinding.version2;
//---------------------------------/
//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
/**
* Class StructureState.
*
* @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;
/**
* 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);
}
}