fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view...

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

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index ca77ed2..309e704 100755 (executable)
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -147,6 +147,53 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_textColThreshold;\r
 \r
     /**\r
+     * Field _showUnconserved.\r
+     */\r
+    private boolean _showUnconserved;\r
+\r
+    /**\r
+     * keeps track of state for field: _showUnconserved\r
+     */\r
+    private boolean _has_showUnconserved;\r
+\r
+    /**\r
+     * Field _ignoreGapsinConsensus.\r
+     */\r
+    private boolean _ignoreGapsinConsensus = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _ignoreGapsinConsensus\r
+     */\r
+    private boolean _has_ignoreGapsinConsensus;\r
+\r
+    /**\r
+     * Field _showConsensusHistogram.\r
+     */\r
+    private boolean _showConsensusHistogram = true;\r
+\r
+    /**\r
+     * keeps track of state for field: _showConsensusHistogram\r
+     */\r
+    private boolean _has_showConsensusHistogram;\r
+\r
+    /**\r
+     * Field _showSequenceLogo.\r
+     */\r
+    private boolean _showSequenceLogo = false;\r
+\r
+    /**\r
+     * keeps track of state for field: _showSequenceLogo\r
+     */\r
+    private boolean _has_showSequenceLogo;\r
+\r
+    /**\r
+     * Optional sequence group ID (only needs to be unique for this\r
+     * alignment)\r
+     *  \r
+     */\r
+    private java.lang.String _id;\r
+\r
+    /**\r
      * Field _seqList.\r
      */\r
     private java.util.Vector _seqList;\r
@@ -231,6 +278,13 @@ public class JGroup implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteIgnoreGapsinConsensus(\r
+    ) {\r
+        this._has_ignoreGapsinConsensus= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteOutlineColour(\r
     ) {\r
         this._has_outlineColour= false;\r
@@ -245,6 +299,27 @@ public class JGroup implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowConsensusHistogram(\r
+    ) {\r
+        this._has_showConsensusHistogram= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowSequenceLogo(\r
+    ) {\r
+        this._has_showSequenceLogo= false;\r
+    }\r
+\r
+    /**\r
+     */\r
+    public void deleteShowUnconserved(\r
+    ) {\r
+        this._has_showUnconserved= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteStart(\r
     ) {\r
         this._has_start= false;\r
@@ -342,6 +417,29 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'id'. The field 'id' has the\r
+     * following description: Optional sequence group ID (only\r
+     * needs to be unique for this alignment)\r
+     *  \r
+     * \r
+     * @return the value of field 'Id'.\r
+     */\r
+    public java.lang.String getId(\r
+    ) {\r
+        return this._id;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @return the value of field 'IgnoreGapsinConsensus'.\r
+     */\r
+    public boolean getIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'name'.\r
      * \r
      * @return the value of field 'Name'.\r
@@ -416,6 +514,36 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @return the value of field 'ShowConsensusHistogram'.\r
+     */\r
+    public boolean getShowConsensusHistogram(\r
+    ) {\r
+        return this._showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showSequenceLogo'.\r
+     * \r
+     * @return the value of field 'ShowSequenceLogo'.\r
+     */\r
+    public boolean getShowSequenceLogo(\r
+    ) {\r
+        return this._showSequenceLogo;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean getShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'start'.\r
      * \r
      * @return the value of field 'Start'.\r
@@ -506,6 +634,17 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasIgnoreGapsinConsensus.\r
+     * \r
+     * @return true if at least one IgnoreGapsinConsensus has been\r
+     * added\r
+     */\r
+    public boolean hasIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._has_ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
      * Method hasOutlineColour.\r
      * \r
      * @return true if at least one OutlineColour has been added\r
@@ -526,6 +665,37 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowConsensusHistogram.\r
+     * \r
+     * @return true if at least one ShowConsensusHistogram has been\r
+     * added\r
+     */\r
+    public boolean hasShowConsensusHistogram(\r
+    ) {\r
+        return this._has_showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowSequenceLogo.\r
+     * \r
+     * @return true if at least one ShowSequenceLogo has been added\r
+     */\r
+    public boolean hasShowSequenceLogo(\r
+    ) {\r
+        return this._has_showSequenceLogo;\r
+    }\r
+\r
+    /**\r
+     * Method hasShowUnconserved.\r
+     * \r
+     * @return true if at least one ShowUnconserved has been added\r
+     */\r
+    public boolean hasShowUnconserved(\r
+    ) {\r
+        return this._has_showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method hasStart.\r
      * \r
      * @return true if at least one Start has been added\r
@@ -596,6 +766,46 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @return the value of field 'IgnoreGapsinConsensus'.\r
+     */\r
+    public boolean isIgnoreGapsinConsensus(\r
+    ) {\r
+        return this._ignoreGapsinConsensus;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @return the value of field 'ShowConsensusHistogram'.\r
+     */\r
+    public boolean isShowConsensusHistogram(\r
+    ) {\r
+        return this._showConsensusHistogram;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showSequenceLogo'.\r
+     * \r
+     * @return the value of field 'ShowSequenceLogo'.\r
+     */\r
+    public boolean isShowSequenceLogo(\r
+    ) {\r
+        return this._showSequenceLogo;\r
+    }\r
+\r
+    /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean isShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method isValid.\r
      * \r
      * @return true if this object is valid according to the schema\r
@@ -739,6 +949,31 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'id'. The field 'id' has the\r
+     * following description: Optional sequence group ID (only\r
+     * needs to be unique for this alignment)\r
+     *  \r
+     * \r
+     * @param id the value of field 'id'.\r
+     */\r
+    public void setId(\r
+            final java.lang.String id) {\r
+        this._id = id;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'ignoreGapsinConsensus'.\r
+     * \r
+     * @param ignoreGapsinConsensus the value of field\r
+     * 'ignoreGapsinConsensus'.\r
+     */\r
+    public void setIgnoreGapsinConsensus(\r
+            final boolean ignoreGapsinConsensus) {\r
+        this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
+        this._has_ignoreGapsinConsensus = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'name'.\r
      * \r
      * @param name the value of field 'name'.\r
@@ -806,6 +1041,40 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showConsensusHistogram'.\r
+     * \r
+     * @param showConsensusHistogram the value of field\r
+     * 'showConsensusHistogram'.\r
+     */\r
+    public void setShowConsensusHistogram(\r
+            final boolean showConsensusHistogram) {\r
+        this._showConsensusHistogram = showConsensusHistogram;\r
+        this._has_showConsensusHistogram = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showSequenceLogo'.\r
+     * \r
+     * @param showSequenceLogo the value of field 'showSequenceLogo'\r
+     */\r
+    public void setShowSequenceLogo(\r
+            final boolean showSequenceLogo) {\r
+        this._showSequenceLogo = showSequenceLogo;\r
+        this._has_showSequenceLogo = true;\r
+    }\r
+\r
+    /**\r
+     * Sets the value of field 'showUnconserved'.\r
+     * \r
+     * @param showUnconserved the value of field 'showUnconserved'.\r
+     */\r
+    public void setShowUnconserved(\r
+            final boolean showUnconserved) {\r
+        this._showUnconserved = showUnconserved;\r
+        this._has_showUnconserved = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'start'.\r
      * \r
      * @param start the value of field 'start'.\r