X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewModelSequence.java;h=6b056d3e46d3c9cf383b1ae4bbdcdf3ec7aa69f5;hb=077fea81a02a33eefed6895bfa7cff993609dab8;hp=2a247c0c1da259ad0a1e61a8492bda33108d7196;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index 2a247c0..6b056d3 100755 --- 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 2.6) + * 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 . */ 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 {