/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
******************************************************************************/
/*
* 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);
}
}