X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=68d545f12822a6db896309bdd245e2d7c9221e7e;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=19ef2aeb8e699a0855c77237057855f37bf8fd03;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java old mode 100755 new mode 100644 index 19ef2ae..68d545f --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.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; @@ -107,7 +111,7 @@ public class JSeq implements java.io.Serializable * * @param vFeatures * @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 addFeatures(final jalview.binding.Features vFeatures) throws java.lang.IndexOutOfBoundsException @@ -121,7 +125,7 @@ public class JSeq implements java.io.Serializable * @param index * @param vFeatures * @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 addFeatures(final int index, final jalview.binding.Features vFeatures) @@ -135,7 +139,7 @@ public class JSeq implements java.io.Serializable * * @param vPdbids * @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 addPdbids(final jalview.binding.Pdbids vPdbids) throws java.lang.IndexOutOfBoundsException @@ -149,7 +153,7 @@ public class JSeq implements java.io.Serializable * @param index * @param vPdbids * @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 addPdbids(final int index, final jalview.binding.Pdbids vPdbids) @@ -159,28 +163,28 @@ public class JSeq implements java.io.Serializable } /** - */ + */ public void deleteColour() { this._has_colour = false; } /** - */ + */ public void deleteEnd() { this._has_end = false; } /** - */ + */ public void deleteId() { this._has_id = false; } /** - */ + */ public void deleteStart() { this._has_start = false; @@ -231,7 +235,7 @@ public class JSeq 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.Features at the given index */ public jalview.binding.Features getFeatures(final int index) @@ -240,9 +244,11 @@ public class JSeq implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._featuresList.size()) { - throw new IndexOutOfBoundsException("getFeatures: Index value '" - + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getFeatures", + Integer.valueOf(index).toString(), + Integer.valueOf((this._featuresList.size() - 1)).toString() + })); } return (jalview.binding.Features) _featuresList.get(index); @@ -288,7 +294,7 @@ public class JSeq 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.Pdbids at the given index */ public jalview.binding.Pdbids getPdbids(final int index) @@ -297,9 +303,11 @@ public class JSeq implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._pdbidsList.size()) { - throw new IndexOutOfBoundsException("getPdbids: Index value '" - + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getPdbids", + Integer.valueOf(index).toString(), + Integer.valueOf((this._pdbidsList.size() - 1)).toString() + })); } return (jalview.binding.Pdbids) _pdbidsList.get(index); @@ -402,11 +410,10 @@ public class JSeq 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, @@ -420,13 +427,12 @@ public class JSeq 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, @@ -437,14 +443,14 @@ public class JSeq implements java.io.Serializable } /** - */ + */ public void removeAllFeatures() { this._featuresList.clear(); } /** - */ + */ public void removeAllPdbids() { this._pdbidsList.clear(); @@ -502,7 +508,7 @@ public class JSeq implements java.io.Serializable * Sets the value of field 'colour'. * * @param colour - * the value of field 'colour'. + * the value of field 'colour'. */ public void setColour(final int colour) { @@ -514,7 +520,7 @@ public class JSeq implements java.io.Serializable * Sets the value of field 'end'. * * @param end - * the value of field 'end'. + * the value of field 'end'. */ public void setEnd(final int end) { @@ -528,7 +534,7 @@ public class JSeq implements java.io.Serializable * @param index * @param vFeatures * @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 setFeatures(final int index, final jalview.binding.Features vFeatures) @@ -537,9 +543,11 @@ public class JSeq implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._featuresList.size()) { - throw new IndexOutOfBoundsException("setFeatures: Index value '" - + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setFeatures", + Integer.valueOf(index).toString(), + Integer.valueOf((this._featuresList.size() - 1)).toString() + })); } this._featuresList.set(index, vFeatures); @@ -565,7 +573,7 @@ public class JSeq implements java.io.Serializable * Sets the value of field 'id'. * * @param id - * the value of field 'id'. + * the value of field 'id'. */ public void setId(final int id) { @@ -579,7 +587,7 @@ public class JSeq implements java.io.Serializable * @param index * @param vPdbids * @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 setPdbids(final int index, final jalview.binding.Pdbids vPdbids) @@ -588,9 +596,11 @@ public class JSeq implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._pdbidsList.size()) { - throw new IndexOutOfBoundsException("setPdbids: Index value '" - + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setPdbids", + Integer.valueOf(index).toString(), + Integer.valueOf((this._pdbidsList.size() - 1)).toString() + })); } this._pdbidsList.set(index, vPdbids); @@ -616,7 +626,7 @@ public class JSeq implements java.io.Serializable * Sets the value of field 'start'. * * @param start - * the value of field 'start'. + * the value of field 'start'. */ public void setStart(final int start) { @@ -629,11 +639,10 @@ public class JSeq 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.JSeq */ public static jalview.binding.JSeq unmarshal(final java.io.Reader reader) @@ -648,8 +657,7 @@ public class JSeq 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 {