X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=86d789e502b2b9ffd3972779792961a697c30983;hb=cb7c4a276c52b0bb3e448e6761886fecc0e9d05c;hp=c27e0836c2b08f1b08fbcb2ccc23291d93a1a1b0;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index c27e083..86d789e 100644
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,20 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 1.1</a>, using an XML
@@ -204,8 +187,19 @@ 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;
@@ -215,6 +209,11 @@ public class JGroup implements java.io.Serializable {
      */
     private java.util.Vector _seqList;
 
+    /**
+     * Field _annotationColours.
+     */
+    private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
 
       //----------------/
      //- Constructors -/
@@ -302,6 +301,13 @@ public class JGroup implements java.io.Serializable {
 
     /**
      */
+    public void deleteNormaliseSequenceLogo(
+    ) {
+        this._has_normaliseSequenceLogo= false;
+    }
+
+    /**
+     */
     public void deleteOutlineColour(
     ) {
         this._has_outlineColour= false;
@@ -374,6 +380,16 @@ 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'.
@@ -436,7 +452,8 @@ 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'.
@@ -467,6 +484,16 @@ 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'.
@@ -662,6 +689,17 @@ 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
@@ -793,6 +831,16 @@ 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'.
@@ -901,6 +949,17 @@ 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'.
@@ -968,7 +1027,8 @@ 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'.
@@ -1001,6 +1061,18 @@ 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'.