X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=443297149df0c989348d8a348efd83290eea7f50;hb=022166d52c42285e0d414f6f3f7c550f4ab65974;hp=fa22401b5cf3b3c41d6b7625dad9404ecb0520eb;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index fa22401..4432971 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,21 +1,10 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program 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 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
  */
+
 package jalview.schemabinding.version2;
 
   //---------------------------------/
@@ -104,6 +93,32 @@ public class StructureState implements java.io.Serializable {
      */
     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 = true;
+
+    /**
+     * keeps track of state for field: _colourwithAlignPanel
+     */
+    private boolean _has_colourwithAlignPanel;
+
 
       //----------------/
      //- Constructors -/
@@ -121,6 +136,20 @@ public class StructureState implements java.io.Serializable {
 
     /**
      */
+    public void deleteAlignwithAlignPanel(
+    ) {
+        this._has_alignwithAlignPanel= false;
+    }
+
+    /**
+     */
+    public void deleteColourwithAlignPanel(
+    ) {
+        this._has_colourwithAlignPanel= false;
+    }
+
+    /**
+     */
     public void deleteHeight(
     ) {
         this._has_height= false;
@@ -155,6 +184,36 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
+     * 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 '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
      * 
@@ -235,6 +294,28 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
+     * Method hasAlignwithAlignPanel.
+     * 
+     * @return true if at least one AlignwithAlignPanel has been
+     * added
+     */
+    public boolean hasAlignwithAlignPanel(
+    ) {
+        return this._has_alignwithAlignPanel;
+    }
+
+    /**
+     * 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
@@ -285,6 +366,36 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
+     * 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 '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
@@ -342,6 +453,40 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
+     * 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 '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
      *