AlignmentAnnotations require id

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

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 0d8dc08..19e2e6d 100755 (executable)
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -76,6 +76,16 @@ public class JSeq implements java.io.Serializable {
     private boolean _has_id;\r
 \r
     /**\r
+     * Field _hidden\r
+     */\r
+    private boolean _hidden;\r
+\r
+    /**\r
+     * keeps track of state for field: _hidden\r
+     */\r
+    private boolean _has_hidden;\r
+\r
+    /**\r
      * Field _featuresList\r
      */\r
     private java.util.Vector _featuresList;\r
@@ -85,6 +95,11 @@ public class JSeq implements java.io.Serializable {
      */\r
     private java.util.Vector _pdbidsList;\r
 \r
+    /**\r
+     * Field _hiddenSequencesList\r
+     */\r
+    private java.util.Vector _hiddenSequencesList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -94,6 +109,7 @@ public class JSeq implements java.io.Serializable {
         super();\r
         _featuresList = new Vector();\r
         _pdbidsList = new Vector();\r
+        _hiddenSequencesList = new Vector();\r
     } //-- jalview.schemabinding.version2.JSeq()\r
 \r
 \r
@@ -129,6 +145,33 @@ public class JSeq implements java.io.Serializable {
     } //-- void addFeatures(int, jalview.schemabinding.version2.Features) \r
 \r
     /**\r
+     * Method addHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param vHiddenSequences\r
+     */\r
+    public void addHiddenSequences(int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+    } //-- void addHiddenSequences(int) \r
+\r
+    /**\r
+     * Method addHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenSequences\r
+     */\r
+    public void addHiddenSequences(int index, int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+    } //-- void addHiddenSequences(int, int) \r
+\r
+    /**\r
      * Method addPdbids\r
      * \r
      * \r
@@ -174,6 +217,15 @@ public class JSeq implements java.io.Serializable {
     } //-- void deleteEnd() \r
 \r
     /**\r
+     * Method deleteHidden\r
+     * \r
+     */\r
+    public void deleteHidden()\r
+    {\r
+        this._has_hidden= false;\r
+    } //-- void deleteHidden() \r
+\r
+    /**\r
      * Method deleteId\r
      * \r
      */\r
@@ -204,6 +256,18 @@ public class JSeq implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateFeatures() \r
 \r
     /**\r
+     * Method enumerateHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateHiddenSequences()\r
+    {\r
+        return _hiddenSequencesList.elements();\r
+    } //-- java.util.Enumeration enumerateHiddenSequences() \r
+\r
+    /**\r
      * Method enumeratePdbids\r
      * \r
      * \r
@@ -286,6 +350,65 @@ public class JSeq implements java.io.Serializable {
     } //-- int getFeaturesCount() \r
 \r
     /**\r
+     * Returns the value of field 'hidden'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'hidden'.\r
+     */\r
+    public boolean getHidden()\r
+    {\r
+        return this._hidden;\r
+    } //-- boolean getHidden() \r
+\r
+    /**\r
+     * Method getHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int getHiddenSequences(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+    } //-- int getHiddenSequences(int) \r
+\r
+    /**\r
+     * Method getHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int[] getHiddenSequences()\r
+    {\r
+        int size = _hiddenSequencesList.size();\r
+        int[] mArray = new int[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+        }\r
+        return mArray;\r
+    } //-- int[] getHiddenSequences() \r
+\r
+    /**\r
+     * Method getHiddenSequencesCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getHiddenSequencesCount()\r
+    {\r
+        return _hiddenSequencesList.size();\r
+    } //-- int getHiddenSequencesCount() \r
+\r
+    /**\r
      * Returns the value of field 'id'.\r
      * \r
      * @return int\r
@@ -380,6 +503,18 @@ public class JSeq implements java.io.Serializable {
     } //-- boolean hasEnd() \r
 \r
     /**\r
+     * Method hasHidden\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasHidden()\r
+    {\r
+        return this._has_hidden;\r
+    } //-- boolean hasHidden() \r
+\r
+    /**\r
      * Method hasId\r
      * \r
      * \r
@@ -459,6 +594,15 @@ public class JSeq implements java.io.Serializable {
     } //-- void removeAllFeatures() \r
 \r
     /**\r
+     * Method removeAllHiddenSequences\r
+     * \r
+     */\r
+    public void removeAllHiddenSequences()\r
+    {\r
+        _hiddenSequencesList.removeAllElements();\r
+    } //-- void removeAllHiddenSequences() \r
+\r
+    /**\r
      * Method removeAllPdbids\r
      * \r
      */\r
@@ -483,6 +627,21 @@ public class JSeq implements java.io.Serializable {
     } //-- jalview.schemabinding.version2.Features removeFeatures(int) \r
 \r
     /**\r
+     * Method removeHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int removeHiddenSequences(int index)\r
+    {\r
+        java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
+        _hiddenSequencesList.removeElementAt(index);\r
+        return ((java.lang.Integer)obj).intValue();\r
+    } //-- int removeHiddenSequences(int) \r
+\r
+    /**\r
      * Method removePdbids\r
      * \r
      * \r
@@ -554,6 +713,51 @@ public class JSeq implements java.io.Serializable {
     } //-- void setFeatures(jalview.schemabinding.version2.Features) \r
 \r
     /**\r
+     * Sets the value of field 'hidden'.\r
+     * \r
+     * @param hidden the value of field 'hidden'.\r
+     */\r
+    public void setHidden(boolean hidden)\r
+    {\r
+        this._hidden = hidden;\r
+        this._has_hidden = true;\r
+    } //-- void setHidden(boolean) \r
+\r
+    /**\r
+     * Method setHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenSequences\r
+     */\r
+    public void setHiddenSequences(int index, int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+    } //-- void setHiddenSequences(int, int) \r
+\r
+    /**\r
+     * Method setHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param hiddenSequencesArray\r
+     */\r
+    public void setHiddenSequences(int[] hiddenSequencesArray)\r
+    {\r
+        //-- copy array\r
+        _hiddenSequencesList.removeAllElements();\r
+        for (int i = 0; i < hiddenSequencesArray.length; i++) {\r
+            _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));\r
+        }\r
+    } //-- void setHiddenSequences(int) \r
+\r
+    /**\r
      * Sets the value of field 'id'.\r
      * \r
      * @param id the value of field 'id'.\r