X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=25e7fdf6f9aa96358c88f43f8177a92d64252007;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=537f2b787479810a562710359c25807726940c66;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 537f2b7..25e7fdf 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
- * 
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemabinding.version2;
 
@@ -52,24 +55,51 @@ 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.
@@ -92,13 +122,24 @@ public class StructureState implements java.io.Serializable
   private boolean _has_height;
 
   /**
-   * 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.
+   * Field _xpos.
    */
-  private java.lang.String _viewId;
+  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 -/
@@ -116,6 +157,27 @@ public class StructureState implements java.io.Serializable
 
   /**
      */
+  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;
@@ -150,6 +212,47 @@ 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 '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
    * 
@@ -178,6 +281,7 @@ public class StructureState implements java.io.Serializable
    * 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()
@@ -226,6 +330,36 @@ 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 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
@@ -276,6 +410,47 @@ 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 '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
@@ -340,6 +515,53 @@ 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 '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
    * 
@@ -371,6 +593,7 @@ public class StructureState implements java.io.Serializable
    * 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'.
    */