X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewport.java;h=136a3b350d738f427a57c75c600bbf01f3ae7f8c;hb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;hp=000844e93f095aa9af65d19ef60d2b834969c3dc;hpb=a2094092396efa4d6736b11f3b1e1415098c3d12;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 000844e..136a3b3 100644
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -267,6 +267,16 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showSequenceLogo;
 
     /**
+     * Field _normaliseSequenceLogo.
+     */
+    private boolean _normaliseSequenceLogo = false;
+
+    /**
+     * keeps track of state for field: _normaliseSequenceLogo
+     */
+    private boolean _has_normaliseSequenceLogo;
+
+    /**
      * Field _ignoreGapsinConsensus.
      */
     private boolean _ignoreGapsinConsensus = true;
@@ -373,13 +383,21 @@ public class Viewport implements java.io.Serializable {
 
     /**
      * unique id used by jalview to
-     *  synchronize between stored and
+     *  synchronize
+     *  between stored and
      *  instantiated views
      *  
      */
     private java.lang.String _id;
 
     /**
+     * The viewport id of this viewport's
+     *  (cdna/protein) coding complement, if any
+     *  
+     */
+    private java.lang.String _complementId;
+
+    /**
      * Field _width.
      */
     private int _width;
@@ -578,6 +596,13 @@ public class Viewport implements java.io.Serializable {
 
     /**
      */
+    public void deleteNormaliseSequenceLogo(
+    ) {
+        this._has_normaliseSequenceLogo= false;
+    }
+
+    /**
+     */
     public void deletePidSelected(
     ) {
         this._has_pidSelected= false;
@@ -856,6 +881,20 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'complementId'. The field
+     * 'complementId' has the following description: The viewport
+     * id of this viewport's
+     *  (cdna/protein) coding complement, if any
+     *  
+     * 
+     * @return the value of field 'ComplementId'.
+     */
+    public java.lang.String getComplementId(
+    ) {
+        return this._complementId;
+    }
+
+    /**
      * Returns the value of field 'consThreshold'.
      * 
      * @return the value of field 'ConsThreshold'.
@@ -995,7 +1034,8 @@ public class Viewport implements java.io.Serializable {
     /**
      * Returns the value of field 'id'. The field 'id' has the
      * following description: unique id used by jalview to
-     *  synchronize between stored and
+     *  synchronize
+     *  between stored and
      *  instantiated views
      *  
      * 
@@ -1017,6 +1057,16 @@ public class Viewport 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 'pidSelected'.
      * 
      * @return the value of field 'PidSelected'.
@@ -1409,6 +1459,17 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Method hasNormaliseSequenceLogo.
+     * 
+     * @return true if at least one NormaliseSequenceLogo has been
+     * added
+     */
+    public boolean hasNormaliseSequenceLogo(
+    ) {
+        return this._has_normaliseSequenceLogo;
+    }
+
+    /**
      * Method hasPidSelected.
      * 
      * @return true if at least one PidSelected has been added
@@ -1733,6 +1794,16 @@ public class Viewport 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 'pidSelected'.
      * 
      * @return the value of field 'PidSelected'.
@@ -2080,6 +2151,20 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'complementId'. The field
+     * 'complementId' has the following description: The viewport
+     * id of this viewport's
+     *  (cdna/protein) coding complement, if any
+     *  
+     * 
+     * @param complementId the value of field 'complementId'.
+     */
+    public void setComplementId(
+            final java.lang.String complementId) {
+        this._complementId = complementId;
+    }
+
+    /**
      * Sets the value of field 'consThreshold'.
      * 
      * @param consThreshold the value of field 'consThreshold'.
@@ -2216,7 +2301,8 @@ public class Viewport implements java.io.Serializable {
     /**
      * Sets the value of field 'id'. The field 'id' has the
      * following description: unique id used by jalview to
-     *  synchronize between stored and
+     *  synchronize
+     *  between stored and
      *  instantiated views
      *  
      * 
@@ -2240,6 +2326,18 @@ public class Viewport 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 'pidSelected'.
      * 
      * @param pidSelected the value of field 'pidSelected'.