X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=602473f5ec4f0a8400c3344151afb3e37696effd;hb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;hp=fda18025ba4b719ac742e0d1a204be43b7c2f554;hpb=9adf6bc4eac154c1f96a2be5867ce24d7c6470f1;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index fda1802..602473f 100644
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -187,8 +187,20 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_showSequenceLogo;
 
     /**
-     * Optional sequence group ID (only needs to be unique for this
-     * alignment)
+     * Field _normaliseSequenceLogo.
+     */
+    private boolean _normaliseSequenceLogo = false;
+
+    /**
+     * keeps track of state for field: _normaliseSequenceLogo
+     */
+    private boolean _has_normaliseSequenceLogo;
+
+    /**
+     * Optional sequence group ID (only
+     *  needs to be
+     *  unique for this
+     *  alignment)
      *  
      */
     private java.lang.String _id;
@@ -198,6 +210,11 @@ public class JGroup implements java.io.Serializable {
      */
     private java.util.Vector _seqList;
 
+    /**
+     * Field _annotationColours.
+     */
+    private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
 
       //----------------/
      //- Constructors -/
@@ -285,6 +302,13 @@ public class JGroup implements java.io.Serializable {
 
     /**
      */
+    public void deleteNormaliseSequenceLogo(
+    ) {
+        this._has_normaliseSequenceLogo= false;
+    }
+
+    /**
+     */
     public void deleteOutlineColour(
     ) {
         this._has_outlineColour= false;
@@ -357,6 +381,16 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'annotationColours'.
+     * 
+     * @return the value of field 'AnnotationColours'.
+     */
+    public jalview.schemabinding.version2.AnnotationColours getAnnotationColours(
+    ) {
+        return this._annotationColours;
+    }
+
+    /**
      * Returns the value of field 'colour'.
      * 
      * @return the value of field 'Colour'.
@@ -419,7 +453,9 @@ public class JGroup implements java.io.Serializable {
     /**
      * Returns the value of field 'id'. The field 'id' has the
      * following description: Optional sequence group ID (only
-     * needs to be unique for this alignment)
+     *  needs to be
+     *  unique for this
+     *  alignment)
      *  
      * 
      * @return the value of field 'Id'.
@@ -450,6 +486,16 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'normaliseSequenceLogo'.
+     * 
+     * @return the value of field 'NormaliseSequenceLogo'.
+     */
+    public boolean getNormaliseSequenceLogo(
+    ) {
+        return this._normaliseSequenceLogo;
+    }
+
+    /**
      * Returns the value of field 'outlineColour'.
      * 
      * @return the value of field 'OutlineColour'.
@@ -645,6 +691,17 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Method hasNormaliseSequenceLogo.
+     * 
+     * @return true if at least one NormaliseSequenceLogo has been
+     * added
+     */
+    public boolean hasNormaliseSequenceLogo(
+    ) {
+        return this._has_normaliseSequenceLogo;
+    }
+
+    /**
      * Method hasOutlineColour.
      * 
      * @return true if at least one OutlineColour has been added
@@ -776,6 +833,16 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'normaliseSequenceLogo'.
+     * 
+     * @return the value of field 'NormaliseSequenceLogo'.
+     */
+    public boolean isNormaliseSequenceLogo(
+    ) {
+        return this._normaliseSequenceLogo;
+    }
+
+    /**
      * Returns the value of field 'showConsensusHistogram'.
      * 
      * @return the value of field 'ShowConsensusHistogram'.
@@ -884,6 +951,17 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'annotationColours'.
+     * 
+     * @param annotationColours the value of field
+     * 'annotationColours'.
+     */
+    public void setAnnotationColours(
+            final jalview.schemabinding.version2.AnnotationColours annotationColours) {
+        this._annotationColours = annotationColours;
+    }
+
+    /**
      * Sets the value of field 'colour'.
      * 
      * @param colour the value of field 'colour'.
@@ -951,7 +1029,9 @@ public class JGroup implements java.io.Serializable {
     /**
      * Sets the value of field 'id'. The field 'id' has the
      * following description: Optional sequence group ID (only
-     * needs to be unique for this alignment)
+     *  needs to be
+     *  unique for this
+     *  alignment)
      *  
      * 
      * @param id the value of field 'id'.
@@ -984,6 +1064,18 @@ public class JGroup implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'normaliseSequenceLogo'.
+     * 
+     * @param normaliseSequenceLogo the value of field
+     * 'normaliseSequenceLogo'.
+     */
+    public void setNormaliseSequenceLogo(
+            final boolean normaliseSequenceLogo) {
+        this._normaliseSequenceLogo = normaliseSequenceLogo;
+        this._has_normaliseSequenceLogo = true;
+    }
+
+    /**
      * Sets the value of field 'outlineColour'.
      * 
      * @param outlineColour the value of field 'outlineColour'.