X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=97d68de7b0fcdd74e1b010851f3acc23a4ba2472;hb=c66902a9536b10a5477b58aaf7c2d75772890a5d;hp=2a247c0c1da259ad0a1e61a8492bda33108d7196;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java old mode 100755 new mode 100644 index 2a247c0..97d68de --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.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 2.8.2) + * Copyright (C) 2014 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; @@ -90,7 +94,7 @@ 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 +108,7 @@ 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 +122,7 @@ 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 +136,7 @@ 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 +149,7 @@ 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 +163,7 @@ 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 +176,7 @@ 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 +190,7 @@ 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 +204,7 @@ 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 +218,7 @@ 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 +292,7 @@ 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) @@ -297,9 +301,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JGroupList.size()) { - throw new IndexOutOfBoundsException("getJGroup: Index value '" - + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getJGroup", + Integer.valueOf(index).toString(), + Integer.valueOf((this._JGroupList.size() - 1)).toString() + })); } return (jalview.binding.JGroup) _JGroupList.get(index); @@ -335,7 +341,7 @@ 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) @@ -344,8 +350,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JSeqList.size()) { - throw new IndexOutOfBoundsException("getJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getJSeq", + Integer.valueOf(index).toString(), + Integer.valueOf((this._JSeqList.size() - 1)).toString() + })); } return (jalview.binding.JSeq) _JSeqList.get(index); @@ -381,7 +390,7 @@ 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) @@ -390,8 +399,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getJgetTreeSeq", + Integer.valueOf(index).toString(), + Integer.valueOf((this._treeList.size() - 1)).toString() + })); } return (jalview.binding.Tree) _treeList.get(index); @@ -427,7 +439,7 @@ 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) @@ -436,9 +448,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._userColoursList.size()) { - throw new IndexOutOfBoundsException("getUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getUserColours", + Integer.valueOf(index).toString(), + Integer.valueOf((this._userColoursList.size() - 1)).toString() + })); } return (jalview.binding.UserColours) _userColoursList.get(index); @@ -475,7 +489,7 @@ 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) @@ -484,9 +498,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._viewportList.size()) { - throw new IndexOutOfBoundsException("getViewport: Index value '" - + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getViewport", + Integer.valueOf(index).toString(), + Integer.valueOf((this._viewportList.size() - 1)).toString() + })); } return (jalview.binding.Viewport) _viewportList.get(index); @@ -539,11 +555,10 @@ 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 +572,12 @@ 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 +588,35 @@ 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 +747,7 @@ 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 +761,7 @@ 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) @@ -756,9 +770,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JGroupList.size()) { - throw new IndexOutOfBoundsException("setJGroup: Index value '" - + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setJGroup", + Integer.valueOf(index).toString(), + Integer.valueOf((this._JGroupList.size() - 1)).toString() + })); } this._JGroupList.set(index, vJGroup); @@ -786,7 +802,7 @@ 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 @@ -794,8 +810,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._JSeqList.size()) { - throw new IndexOutOfBoundsException("setJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setJSeq", + Integer.valueOf(index).toString(), + Integer.valueOf((this._JSeqList.size() - 1)).toString() + })); } this._JSeqList.set(index, vJSeq); @@ -823,7 +842,7 @@ 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 @@ -831,8 +850,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._treeList.size()) { - throw new IndexOutOfBoundsException("setTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setTree", + Integer.valueOf(index).toString(), + Integer.valueOf((this._treeList.size() - 1)).toString() + })); } this._treeList.set(index, vTree); @@ -860,7 +882,7 @@ 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) @@ -869,9 +891,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._userColoursList.size()) { - throw new IndexOutOfBoundsException("setUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setUserColours", + Integer.valueOf(index).toString(), + Integer.valueOf((this._userColoursList.size() - 1)).toString() + })); } this._userColoursList.set(index, vUserColours); @@ -900,7 +924,7 @@ 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) @@ -909,9 +933,11 @@ public class JalviewModelSequence implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._viewportList.size()) { - throw new IndexOutOfBoundsException("setViewport: Index value '" - + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setViewport", + Integer.valueOf(index).toString(), + Integer.valueOf((this._viewportList.size() - 1)).toString() + })); } this._viewportList.set(index, vViewport); @@ -938,11 +964,10 @@ 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 +983,7 @@ 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 {