X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=3d81baeaf1d8a297d9323a37d95bef95fc2b3eab;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=1bf6c3df1f19938ee105e487622ae20b4ed6c311;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
old mode 100755
new mode 100644
index 1bf6c3d..3d81bae
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,20 +1,10 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
+ * This class was automatically generated with
+ * Castor 1.1, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
//---------------------------------/
@@ -183,9 +173,9 @@ public class SequenceSet implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getAnnotation: Index value '" + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
}
return (jalview.binding.Annotation) _annotationList.get(index);
@@ -241,9 +231,9 @@ public class SequenceSet implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("getSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "getSequence: Index value '" + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
}
return (jalview.binding.Sequence) _sequenceList.get(index);
@@ -438,9 +428,9 @@ public class SequenceSet implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._annotationList.size())
{
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"
- + index + "' not in range [0.."
- + (this._annotationList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setAnnotation: Index value '" + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
}
this._annotationList.set(index, vAnnotation);
@@ -489,9 +479,9 @@ public class SequenceSet implements java.io.Serializable
// check bounds for index
if (index < 0 || index >= this._sequenceList.size())
{
- throw new IndexOutOfBoundsException("setSequence: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceList.size() - 1) + "]");
+ throw new IndexOutOfBoundsException(
+ "setSequence: Index value '" + index + "' not in range [0.."
+ + (this._sequenceList.size() - 1) + "]");
}
this._sequenceList.set(index, vSequence);
@@ -529,8 +519,8 @@ public class SequenceSet implements java.io.Serializable
throws org.exolab.castor.xml.MarshalException,
org.exolab.castor.xml.ValidationException
{
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(
- jalview.binding.SequenceSet.class, reader);
+ return (jalview.binding.SequenceSet) Unmarshaller
+ .unmarshal(jalview.binding.SequenceSet.class, reader);
}
/**