X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=05da739d85593741e5a61f298d69b5565faf3354;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=e348f9a5d5b485d0ddbcc5c4a9d3013d691a076b;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java old mode 100755 new mode 100644 index e348f9a..05da739 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,26 +1,30 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.binding; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import jalview.util.MessageManager; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -82,7 +86,7 @@ public class SequenceSet implements java.io.Serializable * * @param vAnnotation * @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 addAnnotation(final jalview.binding.Annotation vAnnotation) throws java.lang.IndexOutOfBoundsException @@ -96,7 +100,7 @@ public class SequenceSet implements java.io.Serializable * @param index * @param vAnnotation * @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 addAnnotation(final int index, final jalview.binding.Annotation vAnnotation) @@ -110,7 +114,7 @@ public class SequenceSet implements java.io.Serializable * * @param vSequence * @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 addSequence(final jalview.binding.Sequence vSequence) throws java.lang.IndexOutOfBoundsException @@ -124,7 +128,7 @@ public class SequenceSet implements java.io.Serializable * @param index * @param vSequence * @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 addSequence(final int index, final jalview.binding.Sequence vSequence) @@ -134,7 +138,7 @@ public class SequenceSet implements java.io.Serializable } /** - */ + */ public void deleteAligned() { this._has_aligned = false; @@ -175,7 +179,7 @@ public class SequenceSet 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.Annotation at the given index */ public jalview.binding.Annotation getAnnotation(final int index) @@ -184,9 +188,11 @@ 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getAnnotation", + Integer.valueOf(index).toString(), + Integer.valueOf((this._annotationList.size() - 1)).toString() + })); } return (jalview.binding.Annotation) _annotationList.get(index); @@ -233,7 +239,7 @@ public class SequenceSet 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.Sequence at the given index */ public jalview.binding.Sequence getSequence(final int index) @@ -242,9 +248,11 @@ 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getSequence", + Integer.valueOf(index).toString(), + Integer.valueOf((this._sequenceList.size() - 1)).toString() + })); } return (jalview.binding.Sequence) _sequenceList.get(index); @@ -317,11 +325,10 @@ public class SequenceSet 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, @@ -335,13 +342,12 @@ public class SequenceSet 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, @@ -352,14 +358,14 @@ public class SequenceSet implements java.io.Serializable } /** - */ + */ public void removeAllAnnotation() { this._annotationList.clear(); } /** - */ + */ public void removeAllSequence() { this._sequenceList.clear(); @@ -418,7 +424,7 @@ public class SequenceSet implements java.io.Serializable * Sets the value of field 'aligned'. * * @param aligned - * the value of field 'aligned'. + * the value of field 'aligned'. */ public void setAligned(final boolean aligned) { @@ -432,7 +438,7 @@ public class SequenceSet implements java.io.Serializable * @param index * @param vAnnotation * @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 setAnnotation(final int index, final jalview.binding.Annotation vAnnotation) @@ -441,9 +447,11 @@ 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setAnnotation", + Integer.valueOf(index).toString(), + Integer.valueOf((this._annotationList.size() - 1)).toString() + })); } this._annotationList.set(index, vAnnotation); @@ -470,7 +478,7 @@ public class SequenceSet implements java.io.Serializable * Sets the value of field 'gapChar'. * * @param gapChar - * the value of field 'gapChar'. + * the value of field 'gapChar'. */ public void setGapChar(final java.lang.String gapChar) { @@ -483,7 +491,7 @@ public class SequenceSet implements java.io.Serializable * @param index * @param vSequence * @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 setSequence(final int index, final jalview.binding.Sequence vSequence) @@ -492,9 +500,11 @@ 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setSequence", + Integer.valueOf(index).toString(), + Integer.valueOf((this._sequenceList.size() - 1)).toString() + })); } this._sequenceList.set(index, vSequence); @@ -521,11 +531,10 @@ public class SequenceSet 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.SequenceSet */ public static jalview.binding.SequenceSet unmarshal( @@ -541,8 +550,7 @@ public class SequenceSet 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 {