X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJSeq.java;h=193b00598a6972fafb1db74ba35740516a23abeb;hb=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;hp=65b11244729d61b90da58d7e04a9de5f77325cd8;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 65b1124..193b005 100644
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -1,20 +1,3 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see
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 know + * 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'. @@ -569,6 +648,13 @@ public class JSeq implements java.io.Serializable { } /** + */ + public void removeAllRnaViewer( + ) { + this._rnaViewerList.clear(); + } + + /** * Method removeFeatures. * * @param vFeatures @@ -641,6 +727,30 @@ 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 the value of field 'colour'. @@ -789,6 +899,41 @@ 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 the value of field 'start'.