X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=443297149df0c989348d8a348efd83290eea7f50;hb=022166d52c42285e0d414f6f3f7c550f4ab65974;hp=6f4310838f101855145cd5b04ad413d2354fa218;hpb=cd07a161a10680208029f76aa46710c1032aae46;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 6f43108..4432971 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -82,10 +82,43 @@ public class StructureState implements java.io.Serializable {
     private boolean _has_height;
 
     /**
-     * Field _viewId.
+     * 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 = true;
+
+    /**
+     * keeps track of state for field: _colourwithAlignPanel
+     */
+    private boolean _has_colourwithAlignPanel;
+
 
       //----------------/
      //- Constructors -/
@@ -103,6 +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;
@@ -137,6 +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
      * 
@@ -158,7 +235,16 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
-     * Returns the value of field 'viewId'.
+     * 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'.
      */
@@ -208,6 +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
@@ -258,6 +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
@@ -315,6 +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
      * 
@@ -337,7 +509,16 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
-     * Sets the value of field 'viewId'.
+     * 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'.
      */