X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=b0dda8921c23a5ca40df729ff20d8771cbaa85e6;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;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..b0dda89 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,26 +1,26 @@ /* - * 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 + * You should have received a copy of the GNU General Public License 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 org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -107,7 +107,7 @@ 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 +121,7 @@ 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 +135,7 @@ 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 +149,7 @@ 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 +159,28 @@ 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 +231,7 @@ 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) @@ -288,7 +288,7 @@ 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) @@ -402,11 +402,10 @@ 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 +419,12 @@ 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 +435,14 @@ public class JSeq implements java.io.Serializable } /** - */ + */ public void removeAllFeatures() { this._featuresList.clear(); } /** - */ + */ public void removeAllPdbids() { this._pdbidsList.clear(); @@ -502,7 +500,7 @@ 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 +512,7 @@ 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 +526,7 @@ 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) @@ -565,7 +563,7 @@ 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 +577,7 @@ 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) @@ -616,7 +614,7 @@ 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 +627,10 @@ 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 +645,7 @@ 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 {