X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=19e2e6dbf94148a3b0af4277f2d6faab7fadcb0c;hb=77dd1ea813b06b331614520a8b3d561435f27880;hp=0d8dc087db944741f15ec6861df01a5bae3e6700;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

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