jalview 2.5 release banner

[jalview.git] / src / jalview / binding / JalviewModelSequence.java

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 2a247c0..f8207eb 100755 (executable)
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -1,26 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 <http://www.gnu.org/licenses/>.
  */
 package jalview.binding;
 
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -90,7 +89,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param vJGroup
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addJGroup(final jalview.binding.JGroup vJGroup)
           throws java.lang.IndexOutOfBoundsException
@@ -104,7 +103,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vJGroup
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addJGroup(final int index,
           final jalview.binding.JGroup vJGroup)
@@ -118,7 +117,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param vJSeq
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addJSeq(final jalview.binding.JSeq vJSeq)
           throws java.lang.IndexOutOfBoundsException
@@ -132,7 +131,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vJSeq
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addJSeq(final int index, final jalview.binding.JSeq vJSeq)
           throws java.lang.IndexOutOfBoundsException
@@ -145,7 +144,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param vTree
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addTree(final jalview.binding.Tree vTree)
           throws java.lang.IndexOutOfBoundsException
@@ -159,7 +158,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vTree
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addTree(final int index, final jalview.binding.Tree vTree)
           throws java.lang.IndexOutOfBoundsException
@@ -172,7 +171,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param vUserColours
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addUserColours(final jalview.binding.UserColours vUserColours)
           throws java.lang.IndexOutOfBoundsException
@@ -186,7 +185,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vUserColours
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addUserColours(final int index,
           final jalview.binding.UserColours vUserColours)
@@ -200,7 +199,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param vViewport
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addViewport(final jalview.binding.Viewport vViewport)
           throws java.lang.IndexOutOfBoundsException
@@ -214,7 +213,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vViewport
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void addViewport(final int index,
           final jalview.binding.Viewport vViewport)
@@ -288,7 +287,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param index
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    * @return the value of the jalview.binding.JGroup at the given index
    */
   public jalview.binding.JGroup getJGroup(final int index)
@@ -335,7 +334,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param index
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    * @return the value of the jalview.binding.JSeq at the given index
    */
   public jalview.binding.JSeq getJSeq(final int index)
@@ -381,7 +380,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param index
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    * @return the value of the jalview.binding.Tree at the given index
    */
   public jalview.binding.Tree getTree(final int index)
@@ -427,7 +426,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param index
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    * @return the value of the jalview.binding.UserColours at the given index
    */
   public jalview.binding.UserColours getUserColours(final int index)
@@ -475,7 +474,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param index
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    * @return the value of the jalview.binding.Viewport at the given index
    */
   public jalview.binding.Viewport getViewport(final int index)
@@ -539,11 +538,10 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param out
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           if this object is an invalid instance according to the schema
    */
   public void marshal(final java.io.Writer out)
           throws org.exolab.castor.xml.MarshalException,
@@ -557,13 +555,12 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param handler
    * @throws java.io.IOException
-   *                 if an IOException occurs during marshaling
+   *           if an IOException occurs during marshaling
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           if this object is an invalid instance according to the schema
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
    */
   public void marshal(final org.xml.sax.ContentHandler handler)
           throws java.io.IOException,
@@ -574,35 +571,35 @@ public class JalviewModelSequence implements java.io.Serializable
   }
 
   /**
-   */
+     */
   public void removeAllJGroup()
   {
     this._JGroupList.clear();
   }
 
   /**
-   */
+     */
   public void removeAllJSeq()
   {
     this._JSeqList.clear();
   }
 
   /**
-   */
+     */
   public void removeAllTree()
   {
     this._treeList.clear();
   }
 
   /**
-   */
+     */
   public void removeAllUserColours()
   {
     this._userColoursList.clear();
   }
 
   /**
-   */
+     */
   public void removeAllViewport()
   {
     this._viewportList.clear();
@@ -733,7 +730,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * Sets the value of field 'featureSettings'.
    * 
    * @param featureSettings
-   *                the value of field 'featureSettings'.
+   *          the value of field 'featureSettings'.
    */
   public void setFeatureSettings(
           final jalview.binding.FeatureSettings featureSettings)
@@ -747,7 +744,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vJGroup
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void setJGroup(final int index,
           final jalview.binding.JGroup vJGroup)
@@ -786,7 +783,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vJSeq
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void setJSeq(final int index, final jalview.binding.JSeq vJSeq)
           throws java.lang.IndexOutOfBoundsException
@@ -823,7 +820,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vTree
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void setTree(final int index, final jalview.binding.Tree vTree)
           throws java.lang.IndexOutOfBoundsException
@@ -860,7 +857,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vUserColours
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void setUserColours(final int index,
           final jalview.binding.UserColours vUserColours)
@@ -900,7 +897,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * @param index
    * @param vViewport
    * @throws java.lang.IndexOutOfBoundsException
-   *                 if the index given is outside the bounds of the collection
+   *           if the index given is outside the bounds of the collection
    */
   public void setViewport(final int index,
           final jalview.binding.Viewport vViewport)
@@ -938,11 +935,10 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * @param reader
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           if this object is an invalid instance according to the schema
    * @return the unmarshaled jalview.binding.JalviewModelSequence
    */
   public static jalview.binding.JalviewModelSequence unmarshal(
@@ -958,8 +954,7 @@ public class JalviewModelSequence implements java.io.Serializable
    * 
    * 
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           if this object is an invalid instance according to the schema
    */
   public void validate() throws org.exolab.castor.xml.ValidationException
   {