X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=39fea565b6f522b3e285960f27e3917c98caba14;hb=190a4893d444dde29d9bc2c825b483491fa0088d;hp=3e913cb6c712ae0f8515eaacb0cb5e00e1857bd8;hpb=6951479b7dc56bd022ce2c370b7f88b5571004fd;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 3e913cb..39fea56 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,6 +1,23 @@
+/*******************************************************************************
+ * 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.
  * $Id$
  */
@@ -11,15 +28,8 @@ package jalview.schemabinding.version2;
  //- 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.
@@ -39,7 +49,7 @@ public class StructureState implements java.io.Serializable {
     private java.lang.String _content = "";
 
     /**
-     * Field _visible
+     * Field _visible.
      */
     private boolean _visible;
 
@@ -49,27 +59,57 @@ public class StructureState implements java.io.Serializable {
     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;
 
@@ -79,7 +119,7 @@ public class StructureState implements java.io.Serializable {
     private boolean _has_width;
 
     /**
-     * Field _height
+     * Field _height.
      */
     private int _height;
 
@@ -88,6 +128,26 @@ public class StructureState implements java.io.Serializable {
      */
     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 -/
@@ -96,7 +156,7 @@ public class StructureState implements java.io.Serializable {
     public StructureState() {
         super();
         setContent("");
-    } //-- jalview.schemabinding.version2.StructureState()
+    }
 
 
       //-----------/
@@ -104,222 +164,416 @@ public class StructureState implements java.io.Serializable {
     //-----------/
 
     /**
-     * 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
@@ -327,89 +581,113 @@ public class StructureState implements java.io.Serializable {
      * 
      * @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() 
+    }
 
 }