updated schema to store and recover belowAlignment and calcId for JAL-1109 and JAL...

[jalview.git] / src / jalview / schemabinding / version2 / Annotation.java

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 9fd0802..039c227 100644 (file)
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -1,20 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, 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
@@ -180,6 +163,25 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_autoCalculated;
 
     /**
+     * is to be shown below the alignment - introduced in Jalview
+     * 2.8 for visualizing T-COFFEE alignment scores
+     */
+    private boolean _belowAlignment = true;
+
+    /**
+     * keeps track of state for field: _belowAlignment
+     */
+    private boolean _has_belowAlignment;
+
+    /**
+     * Optional string identifier used to group sets of annotation
+     * produced by a particular calculation. Values are opaque
+     * strings but have semantic meaning to Jalview's renderer,
+     * data importer and calculation system.
+     */
+    private java.lang.String _calcId;
+
+    /**
      * Field _annotationElementList.
      */
     private java.util.Vector _annotationElementList;
@@ -251,6 +253,13 @@ public class Annotation implements java.io.Serializable {
 
     /**
      */
+    public void deleteBelowAlignment(
+    ) {
+        this._has_belowAlignment= false;
+    }
+
+    /**
+     */
     public void deleteCentreColLabels(
     ) {
         this._has_centreColLabels= false;
@@ -397,6 +406,34 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'belowAlignment'. The field
+     * 'belowAlignment' has the following description: is to be
+     * shown below the alignment - introduced in Jalview 2.8 for
+     * visualizing T-COFFEE alignment scores
+     * 
+     * @return the value of field 'BelowAlignment'.
+     */
+    public boolean getBelowAlignment(
+    ) {
+        return this._belowAlignment;
+    }
+
+    /**
+     * Returns the value of field 'calcId'. The field 'calcId' has
+     * the following description: Optional string identifier used
+     * to group sets of annotation produced by a particular
+     * calculation. Values are opaque strings but have semantic
+     * meaning to Jalview's renderer, data importer and calculation
+     * system.
+     * 
+     * @return the value of field 'CalcId'.
+     */
+    public java.lang.String getCalcId(
+    ) {
+        return this._calcId;
+    }
+
+    /**
      * Returns the value of field 'centreColLabels'.
      * 
      * @return the value of field 'CentreColLabels'.
@@ -579,6 +616,16 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Method hasBelowAlignment.
+     * 
+     * @return true if at least one BelowAlignment has been added
+     */
+    public boolean hasBelowAlignment(
+    ) {
+        return this._has_belowAlignment;
+    }
+
+    /**
      * Method hasCentreColLabels.
      * 
      * @return true if at least one CentreColLabels has been added
@@ -701,6 +748,19 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'belowAlignment'. The field
+     * 'belowAlignment' has the following description: is to be
+     * shown below the alignment - introduced in Jalview 2.8 for
+     * visualizing T-COFFEE alignment scores
+     * 
+     * @return the value of field 'BelowAlignment'.
+     */
+    public boolean isBelowAlignment(
+    ) {
+        return this._belowAlignment;
+    }
+
+    /**
      * Returns the value of field 'centreColLabels'.
      * 
      * @return the value of field 'CentreColLabels'.
@@ -887,6 +947,35 @@ public class Annotation implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'belowAlignment'. The field
+     * 'belowAlignment' has the following description: is to be
+     * shown below the alignment - introduced in Jalview 2.8 for
+     * visualizing T-COFFEE alignment scores
+     * 
+     * @param belowAlignment the value of field 'belowAlignment'.
+     */
+    public void setBelowAlignment(
+            final boolean belowAlignment) {
+        this._belowAlignment = belowAlignment;
+        this._has_belowAlignment = true;
+    }
+
+    /**
+     * Sets the value of field 'calcId'. The field 'calcId' has the
+     * following description: Optional string identifier used to
+     * group sets of annotation produced by a particular
+     * calculation. Values are opaque strings but have semantic
+     * meaning to Jalview's renderer, data importer and calculation
+     * system.
+     * 
+     * @param calcId the value of field 'calcId'.
+     */
+    public void setCalcId(
+            final java.lang.String calcId) {
+        this._calcId = calcId;
+    }
+
+    /**
      * Sets the value of field 'centreColLabels'.
      * 
      * @param centreColLabels the value of field 'centreColLabels'.