X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequenceSet.java;h=481c37fcaf8d5cf340b1212d86bd5dd6e0a21659;hb=22d4d2237b099daf76bd1a2ed324763972ed91aa;hp=67c34ad4e6650cfda050ea407f85043dafc9ebad;hpb=09ee1649c4427f534331aa2017a890529f0932f5;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 67c34ad..481c37f 100755
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -32,6 +32,13 @@ public class SequenceSet implements java.io.Serializable {
     private java.lang.String _gapChar;
 
     /**
+     * reference to set where jalview will gather the dataset
+     * sequences for all sequences in the set. 
+     *  
+     */
+    private java.lang.String _datasetId;
+
+    /**
      * Field _sequenceList.
      */
     private java.util.Vector _sequenceList;
@@ -46,6 +53,11 @@ public class SequenceSet implements java.io.Serializable {
      */
     private java.util.Vector _sequenceSetPropertiesList;
 
+    /**
+     * Field _alcodonFrameList.
+     */
+    private java.util.Vector _alcodonFrameList;
+
 
       //----------------/
      //- Constructors -/
@@ -56,6 +68,7 @@ public class SequenceSet implements java.io.Serializable {
         this._sequenceList = new java.util.Vector();
         this._annotationList = new java.util.Vector();
         this._sequenceSetPropertiesList = new java.util.Vector();
+        this._alcodonFrameList = new java.util.Vector();
     }
 
 
@@ -66,6 +79,34 @@ public class SequenceSet implements java.io.Serializable {
     /**
      * 
      * 
+     * @param vAlcodonFrame
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addAlcodonFrame(
+            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+    throws java.lang.IndexOutOfBoundsException {
+        this._alcodonFrameList.addElement(vAlcodonFrame);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vAlcodonFrame
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addAlcodonFrame(
+            final int index,
+            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+    throws java.lang.IndexOutOfBoundsException {
+        this._alcodonFrameList.add(index, vAlcodonFrame);
+    }
+
+    /**
+     * 
+     * 
      * @param vAnnotation
      * @throws java.lang.IndexOutOfBoundsException if the index
      * given is outside the bounds of the collection
@@ -148,6 +189,17 @@ public class SequenceSet implements java.io.Serializable {
     }
 
     /**
+     * Method enumerateAlcodonFrame.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.AlcodonFrame elements
+     */
+    public java.util.Enumeration enumerateAlcodonFrame(
+    ) {
+        return this._alcodonFrameList.elements();
+    }
+
+    /**
      * Method enumerateAnnotation.
      * 
      * @return an Enumeration over all
@@ -181,6 +233,52 @@ public class SequenceSet implements java.io.Serializable {
     }
 
     /**
+     * Method getAlcodonFrame.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.AlcodonFrame at the given inde
+     */
+    public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._alcodonFrameList.size()) {
+            throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
+        }
+        
+        return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);
+    }
+
+    /**
+     * Method getAlcodonFrame.Returns the contents of the
+     * collection in an Array.  <p>Note:  Just in case the
+     * collection contents are changing in another thread, we pass
+     * a 0-length Array of the correct type into the API call. 
+     * This way we <i>know</i> that the Array returned is of
+     * exactly the correct length.
+     * 
+     * @return this collection as an Array
+     */
+    public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(
+    ) {
+        jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
+        return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);
+    }
+
+    /**
+     * Method getAlcodonFrameCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getAlcodonFrameCount(
+    ) {
+        return this._alcodonFrameList.size();
+    }
+
+    /**
      * Method getAnnotation.
      * 
      * @param index
@@ -226,6 +324,20 @@ public class SequenceSet implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'datasetId'. The field
+     * 'datasetId' has the following description: reference to set
+     * where jalview will gather the dataset sequences for all
+     * sequences in the set. 
+     *  
+     * 
+     * @return the value of field 'DatasetId'.
+     */
+    public java.lang.String getDatasetId(
+    ) {
+        return this._datasetId;
+    }
+
+    /**
      * Returns the value of field 'gapChar'.
      * 
      * @return the value of field 'GapChar'.
@@ -375,6 +487,37 @@ public class SequenceSet implements java.io.Serializable {
     }
 
     /**
+     * Method removeAlcodonFrame.
+     * 
+     * @param vAlcodonFrame
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeAlcodonFrame(
+            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {
+        boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
+        return removed;
+    }
+
+    /**
+     * Method removeAlcodonFrameAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
+            final int index) {
+        java.lang.Object obj = this._alcodonFrameList.remove(index);
+        return (jalview.schemabinding.version2.AlcodonFrame) obj;
+    }
+
+    /**
+     */
+    public void removeAllAlcodonFrame(
+    ) {
+        this._alcodonFrameList.clear();
+    }
+
+    /**
      */
     public void removeAllAnnotation(
     ) {
@@ -471,6 +614,41 @@ public class SequenceSet implements java.io.Serializable {
      * 
      * 
      * @param index
+     * @param vAlcodonFrame
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setAlcodonFrame(
+            final int index,
+            final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._alcodonFrameList.size()) {
+            throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
+        }
+        
+        this._alcodonFrameList.set(index, vAlcodonFrame);
+    }
+
+    /**
+     * 
+     * 
+     * @param vAlcodonFrameArray
+     */
+    public void setAlcodonFrame(
+            final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {
+        //-- copy array
+        _alcodonFrameList.clear();
+        
+        for (int i = 0; i < vAlcodonFrameArray.length; i++) {
+                this._alcodonFrameList.add(vAlcodonFrameArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
      * @param vAnnotation
      * @throws java.lang.IndexOutOfBoundsException if the index
      * given is outside the bounds of the collection
@@ -503,6 +681,20 @@ public class SequenceSet implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'datasetId'. The field 'datasetId'
+     * has the following description: reference to set where
+     * jalview will gather the dataset sequences for all sequences
+     * in the set. 
+     *  
+     * 
+     * @param datasetId the value of field 'datasetId'.
+     */
+    public void setDatasetId(
+            final java.lang.String datasetId) {
+        this._datasetId = datasetId;
+    }
+
+    /**
      * Sets the value of field 'gapChar'.
      * 
      * @param gapChar the value of field 'gapChar'.