X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=82773a3de0f256ea0156f376c84409c070261d6c;hp=72b9c916f770679df33ac34499fab643370fde73;hb=cb7c4a276c52b0bb3e448e6761886fecc0e9d05c;hpb=a394f0df3650d5b1e0b76e0319b650fe8ac98e41 diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 72b9c91..82773a3 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -1,27 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ 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 -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -32,655 +19,1064 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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; + + /** + * An identifier for the viewer type, currently either + * JMOL or CHIMERA + * + */ + private java.lang.String _type; + + /** + * 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 'type'. The field 'type' has the + * following description: An identifier for the viewer type, + * currently either + * JMOL or CHIMERA + * + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * 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 'type'. The field 'type' has the + * following description: An identifier for the viewer type, + * currently either + * JMOL or CHIMERA + * + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * 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); + } }