JAL-1863 allow RNA secondary structure rows exported by Jalview to be imported again

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

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 000844e..e3a19de 100644 (file)
--- 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;
@@ -322,6 +332,16 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontStyle;
 
     /**
+     * Field _scaleProteinAsCdna.
+     */
+    private boolean _scaleProteinAsCdna = true;
+
+    /**
+     * keeps track of state for field: _scaleProteinAsCdna
+     */
+    private boolean _has_scaleProteinAsCdna;
+
+    /**
      * Field _viewName.
      */
     private java.lang.String _viewName;
@@ -373,13 +393,21 @@ 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 +606,13 @@ public class Viewport implements java.io.Serializable {
 
     /**
      */
+    public void deleteNormaliseSequenceLogo(
+    ) {
+        this._has_normaliseSequenceLogo= false;
+    }
+
+    /**
+     */
     public void deletePidSelected(
     ) {
         this._has_pidSelected= false;
@@ -606,6 +641,13 @@ public class Viewport implements java.io.Serializable {
 
     /**
      */
+    public void deleteScaleProteinAsCdna(
+    ) {
+        this._has_scaleProteinAsCdna= false;
+    }
+
+    /**
+     */
     public void deleteShowAnnotation(
     ) {
         this._has_showAnnotation= false;
@@ -856,6 +898,20 @@ 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 +1051,8 @@ 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 +1074,16 @@ 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'.
@@ -1057,6 +1124,16 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'scaleProteinAsCdna'.
+     * 
+     * @return the value of field 'ScaleProteinAsCdna'.
+     */
+    public boolean getScaleProteinAsCdna(
+    ) {
+        return this._scaleProteinAsCdna;
+    }
+
+    /**
      * Returns the value of field 'sequenceSetId'.
      * 
      * @return the value of field 'SequenceSetId'.
@@ -1409,6 +1486,17 @@ 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
@@ -1449,6 +1537,16 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Method hasScaleProteinAsCdna.
+     * 
+     * @return true if at least one ScaleProteinAsCdna has been adde
+     */
+    public boolean hasScaleProteinAsCdna(
+    ) {
+        return this._has_scaleProteinAsCdna;
+    }
+
+    /**
      * Method hasShowAnnotation.
      * 
      * @return true if at least one ShowAnnotation has been added
@@ -1733,6 +1831,16 @@ 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'.
@@ -1763,6 +1871,16 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'scaleProteinAsCdna'.
+     * 
+     * @return the value of field 'ScaleProteinAsCdna'.
+     */
+    public boolean isScaleProteinAsCdna(
+    ) {
+        return this._scaleProteinAsCdna;
+    }
+
+    /**
      * Returns the value of field 'showAnnotation'.
      * 
      * @return the value of field 'ShowAnnotation'.
@@ -2080,6 +2198,20 @@ 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 +2348,8 @@ 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 +2373,18 @@ 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'.
@@ -2284,6 +2429,18 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'scaleProteinAsCdna'.
+     * 
+     * @param scaleProteinAsCdna the value of field
+     * 'scaleProteinAsCdna'.
+     */
+    public void setScaleProteinAsCdna(
+            final boolean scaleProteinAsCdna) {
+        this._scaleProteinAsCdna = scaleProteinAsCdna;
+        this._has_scaleProteinAsCdna = true;
+    }
+
+    /**
      * Sets the value of field 'sequenceSetId'.
      * 
      * @param sequenceSetId the value of field 'sequenceSetId'.