X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=9ca6708cfaf1b424ecba1684a9164a679942c375;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=1a116076b773469b3459060a10c4051dd12a3909;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 1a11607..9ca6708 100644
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -86,6 +86,15 @@ public class JSeq implements java.io.Serializable
    */
   private java.util.Vector _hiddenSequencesList;
 
+  /**
+   * Reference to a viewer showing RNA structure for this sequence. Schema
+   * supports one viewer showing multiple annotations for multiple sequences,
+   * though currently only one annotation for one sequence (gapped or trimmed)
+   * is used
+   * 
+   */
+  private java.util.Vector _rnaViewerList;
+
   // ----------------/
   // - Constructors -/
   // ----------------/
@@ -96,6 +105,7 @@ public class JSeq implements java.io.Serializable
     this._featuresList = new java.util.Vector();
     this._pdbidsList = new java.util.Vector();
     this._hiddenSequencesList = new java.util.Vector();
+    this._rnaViewerList = new java.util.Vector();
   }
 
   // -----------/
@@ -189,6 +199,35 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * 
+   * 
+   * @param vRnaViewer
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addRnaViewer(
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._rnaViewerList.addElement(vRnaViewer);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vRnaViewer
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addRnaViewer(final int index,
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._rnaViewerList.add(index, vRnaViewer);
+  }
+
+  /**
      */
   public void deleteColour()
   {
@@ -249,6 +288,17 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Method enumerateRnaViewer.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
+   *         elements
+   */
+  public java.util.Enumeration enumerateRnaViewer()
+  {
+    return this._rnaViewerList.elements();
+  }
+
+  /**
    * Returns the value of field 'colour'.
    * 
    * @return the value of field 'Colour'.
@@ -439,6 +489,56 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Method getRnaViewer.
+   * 
+   * @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.RnaViewer at the
+   *         given index
+   */
+  public jalview.schemabinding.version2.RnaViewer getRnaViewer(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._rnaViewerList.size())
+    {
+      throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
+              + index + "' not in range [0.."
+              + (this._rnaViewerList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
+            .get(index);
+  }
+
+  /**
+   * Method getRnaViewer.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.RnaViewer[] getRnaViewer()
+  {
+    jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
+    return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
+            .toArray(array);
+  }
+
+  /**
+   * Method getRnaViewerCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getRnaViewerCount()
+  {
+    return this._rnaViewerList.size();
+  }
+
+  /**
    * Returns the value of field 'start'.
    * 
    * @return the value of field 'Start'.
@@ -574,6 +674,13 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+     */
+  public void removeAllRnaViewer()
+  {
+    this._rnaViewerList.clear();
+  }
+
+  /**
    * Method removeFeatures.
    * 
    * @param vFeatures
@@ -651,6 +758,32 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Method removeRnaViewer.
+   * 
+   * @param vRnaViewer
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeRnaViewer(
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+  {
+    boolean removed = _rnaViewerList.remove(vRnaViewer);
+    return removed;
+  }
+
+  /**
+   * Method removeRnaViewerAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
+          final int index)
+  {
+    java.lang.Object obj = this._rnaViewerList.remove(index);
+    return (jalview.schemabinding.version2.RnaViewer) obj;
+  }
+
+  /**
    * Sets the value of field 'colour'.
    * 
    * @param colour
@@ -819,6 +952,46 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * 
+   * 
+   * @param index
+   * @param vRnaViewer
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setRnaViewer(final int index,
+          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._rnaViewerList.size())
+    {
+      throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
+              + index + "' not in range [0.."
+              + (this._rnaViewerList.size() - 1) + "]");
+    }
+
+    this._rnaViewerList.set(index, vRnaViewer);
+  }
+
+  /**
+   * 
+   * 
+   * @param vRnaViewerArray
+   */
+  public void setRnaViewer(
+          final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
+  {
+    // -- copy array
+    _rnaViewerList.clear();
+
+    for (int i = 0; i < vRnaViewerArray.length; i++)
+    {
+      this._rnaViewerList.add(vRnaViewerArray[i]);
+    }
+  }
+
+  /**
    * Sets the value of field 'start'.
    * 
    * @param start