X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=b7056c4214468152636898062e9e577e1d200188;hb=0233fbee0ff0d7fad302aa2da743c51fd64be101;hp=884f15905c4d2d82e940c95aedda5484787e991b;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 884f159..b7056c4 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (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
@@ -63,6 +63,11 @@ public class Annotation implements java.io.Serializable {
     private java.lang.String _sequenceRef;
 
     /**
+     * Field _groupRef.
+     */
+    private java.lang.String _groupRef;
+
+    /**
      * Field _graphColour.
      */
     private int _graphColour;
@@ -118,6 +123,46 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_visible;
 
     /**
+     * Field _centreColLabels.
+     */
+    private boolean _centreColLabels;
+
+    /**
+     * keeps track of state for field: _centreColLabels
+     */
+    private boolean _has_centreColLabels;
+
+    /**
+     * Field _scaleColLabels.
+     */
+    private boolean _scaleColLabels;
+
+    /**
+     * keeps track of state for field: _scaleColLabels
+     */
+    private boolean _has_scaleColLabels;
+
+    /**
+     * Field _showAllColLabels.
+     */
+    private boolean _showAllColLabels;
+
+    /**
+     * keeps track of state for field: _showAllColLabels
+     */
+    private boolean _has_showAllColLabels;
+
+    /**
+     * is an autocalculated annotation row
+     */
+    private boolean _autoCalculated = false;
+
+    /**
+     * keeps track of state for field: _autoCalculated
+     */
+    private boolean _has_autoCalculated;
+
+    /**
      * Field _annotationElementList.
      */
     private java.util.Vector _annotationElementList;
@@ -182,6 +227,20 @@ public class Annotation implements java.io.Serializable {
 
     /**
      */
+    public void deleteAutoCalculated(
+    ) {
+        this._has_autoCalculated= false;
+    }
+
+    /**
+     */
+    public void deleteCentreColLabels(
+    ) {
+        this._has_centreColLabels= false;
+    }
+
+    /**
+     */
     public void deleteGraph(
     ) {
         this._has_graph= false;
@@ -210,6 +269,13 @@ public class Annotation implements java.io.Serializable {
 
     /**
      */
+    public void deleteScaleColLabels(
+    ) {
+        this._has_scaleColLabels= false;
+    }
+
+    /**
+     */
     public void deleteScore(
     ) {
         this._has_score= false;
@@ -224,6 +290,13 @@ public class Annotation implements java.io.Serializable {
 
     /**
      */
+    public void deleteShowAllColLabels(
+    ) {
+        this._has_showAllColLabels= false;
+    }
+
+    /**
+     */
     public void deleteVisible(
     ) {
         this._has_visible= false;
@@ -288,6 +361,28 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'autoCalculated'. The field
+     * 'autoCalculated' has the following description: is an
+     * autocalculated annotation row
+     * 
+     * @return the value of field 'AutoCalculated'.
+     */
+    public boolean getAutoCalculated(
+    ) {
+        return this._autoCalculated;
+    }
+
+    /**
+     * Returns the value of field 'centreColLabels'.
+     * 
+     * @return the value of field 'CentreColLabels'.
+     */
+    public boolean getCentreColLabels(
+    ) {
+        return this._centreColLabels;
+    }
+
+    /**
      * Returns the value of field 'description'.
      * 
      * @return the value of field 'Description'.
@@ -338,6 +433,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'groupRef'.
+     * 
+     * @return the value of field 'GroupRef'.
+     */
+    public java.lang.String getGroupRef(
+    ) {
+        return this._groupRef;
+    }
+
+    /**
      * Returns the value of field 'id'.
      * 
      * @return the value of field 'Id'.
@@ -358,6 +463,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'scaleColLabels'.
+     * 
+     * @return the value of field 'ScaleColLabels'.
+     */
+    public boolean getScaleColLabels(
+    ) {
+        return this._scaleColLabels;
+    }
+
+    /**
      * Returns the value of field 'score'.
      * 
      * @return the value of field 'Score'.
@@ -388,6 +503,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'showAllColLabels'.
+     * 
+     * @return the value of field 'ShowAllColLabels'.
+     */
+    public boolean getShowAllColLabels(
+    ) {
+        return this._showAllColLabels;
+    }
+
+    /**
      * Returns the value of field 'thresholdLine'.
      * 
      * @return the value of field 'ThresholdLine'.
@@ -408,6 +533,26 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Method hasAutoCalculated.
+     * 
+     * @return true if at least one AutoCalculated has been added
+     */
+    public boolean hasAutoCalculated(
+    ) {
+        return this._has_autoCalculated;
+    }
+
+    /**
+     * Method hasCentreColLabels.
+     * 
+     * @return true if at least one CentreColLabels has been added
+     */
+    public boolean hasCentreColLabels(
+    ) {
+        return this._has_centreColLabels;
+    }
+
+    /**
      * Method hasGraph.
      * 
      * @return true if at least one Graph has been added
@@ -448,6 +593,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Method hasScaleColLabels.
+     * 
+     * @return true if at least one ScaleColLabels has been added
+     */
+    public boolean hasScaleColLabels(
+    ) {
+        return this._has_scaleColLabels;
+    }
+
+    /**
      * Method hasScore.
      * 
      * @return true if at least one Score has been added
@@ -468,6 +623,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Method hasShowAllColLabels.
+     * 
+     * @return true if at least one ShowAllColLabels has been added
+     */
+    public boolean hasShowAllColLabels(
+    ) {
+        return this._has_showAllColLabels;
+    }
+
+    /**
      * Method hasVisible.
      * 
      * @return true if at least one Visible has been added
@@ -478,6 +643,28 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'autoCalculated'. The field
+     * 'autoCalculated' has the following description: is an
+     * autocalculated annotation row
+     * 
+     * @return the value of field 'AutoCalculated'.
+     */
+    public boolean isAutoCalculated(
+    ) {
+        return this._autoCalculated;
+    }
+
+    /**
+     * Returns the value of field 'centreColLabels'.
+     * 
+     * @return the value of field 'CentreColLabels'.
+     */
+    public boolean isCentreColLabels(
+    ) {
+        return this._centreColLabels;
+    }
+
+    /**
      * Returns the value of field 'graph'.
      * 
      * @return the value of field 'Graph'.
@@ -488,6 +675,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'scaleColLabels'.
+     * 
+     * @return the value of field 'ScaleColLabels'.
+     */
+    public boolean isScaleColLabels(
+    ) {
+        return this._scaleColLabels;
+    }
+
+    /**
      * Returns the value of field 'scoreOnly'.
      * 
      * @return the value of field 'ScoreOnly'.
@@ -498,6 +695,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'showAllColLabels'.
+     * 
+     * @return the value of field 'ShowAllColLabels'.
+     */
+    public boolean isShowAllColLabels(
+    ) {
+        return this._showAllColLabels;
+    }
+
+    /**
      * Method isValid.
      * 
      * @return true if this object is valid according to the schema
@@ -621,6 +828,30 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'autoCalculated'. The field
+     * 'autoCalculated' has the following description: is an
+     * autocalculated annotation row
+     * 
+     * @param autoCalculated the value of field 'autoCalculated'.
+     */
+    public void setAutoCalculated(
+            final boolean autoCalculated) {
+        this._autoCalculated = autoCalculated;
+        this._has_autoCalculated = true;
+    }
+
+    /**
+     * Sets the value of field 'centreColLabels'.
+     * 
+     * @param centreColLabels the value of field 'centreColLabels'.
+     */
+    public void setCentreColLabels(
+            final boolean centreColLabels) {
+        this._centreColLabels = centreColLabels;
+        this._has_centreColLabels = true;
+    }
+
+    /**
      * Sets the value of field 'description'.
      * 
      * @param description the value of field 'description'.
@@ -675,6 +906,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'groupRef'.
+     * 
+     * @param groupRef the value of field 'groupRef'.
+     */
+    public void setGroupRef(
+            final java.lang.String groupRef) {
+        this._groupRef = groupRef;
+    }
+
+    /**
      * Sets the value of field 'id'.
      * 
      * @param id the value of field 'id'.
@@ -695,6 +936,17 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'scaleColLabels'.
+     * 
+     * @param scaleColLabels the value of field 'scaleColLabels'.
+     */
+    public void setScaleColLabels(
+            final boolean scaleColLabels) {
+        this._scaleColLabels = scaleColLabels;
+        this._has_scaleColLabels = true;
+    }
+
+    /**
      * Sets the value of field 'score'.
      * 
      * @param score the value of field 'score'.
@@ -727,6 +979,17 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'showAllColLabels'.
+     * 
+     * @param showAllColLabels the value of field 'showAllColLabels'
+     */
+    public void setShowAllColLabels(
+            final boolean showAllColLabels) {
+        this._showAllColLabels = showAllColLabels;
+        this._has_showAllColLabels = true;
+    }
+
+    /**
      * Sets the value of field 'thresholdLine'.
      * 
      * @param thresholdLine the value of field 'thresholdLine'.