X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeature.java;h=a5a4944d418aaf5005d56b5f178f8781648173a8;hb=46ca91c8b2a49f1d2f80b6823ade9f1c29c4121c;hp=90aba344eb7359cbcf52c1261b2f42db38c32945;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java index 90aba34..a5a4944 100755 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.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 2.5) + * 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.schemabinding.version2; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -111,7 +110,7 @@ public class Feature implements java.io.Serializable * * @param vOtherData * @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 addOtherData( final jalview.schemabinding.version2.OtherData vOtherData) @@ -126,7 +125,7 @@ public class Feature implements java.io.Serializable * @param index * @param vOtherData * @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 addOtherData(final int index, final jalview.schemabinding.version2.OtherData vOtherData) @@ -136,21 +135,21 @@ public class Feature implements java.io.Serializable } /** - */ + */ public void deleteBegin() { this._has_begin = false; } /** - */ + */ public void deleteEnd() { this._has_end = false; } /** - */ + */ public void deleteScore() { this._has_score = false; @@ -212,7 +211,7 @@ public class Feature 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.schemabinding.version2.OtherData at the * given index */ @@ -339,11 +338,10 @@ public class Feature 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, @@ -357,13 +355,12 @@ public class Feature 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, @@ -374,7 +371,7 @@ public class Feature implements java.io.Serializable } /** - */ + */ public void removeAllOtherData() { this._otherDataList.clear(); @@ -410,7 +407,7 @@ public class Feature implements java.io.Serializable * Sets the value of field 'begin'. * * @param begin - * the value of field 'begin'. + * the value of field 'begin'. */ public void setBegin(final int begin) { @@ -422,7 +419,7 @@ public class Feature implements java.io.Serializable * Sets the value of field 'description'. * * @param description - * the value of field 'description'. + * the value of field 'description'. */ public void setDescription(final java.lang.String description) { @@ -433,7 +430,7 @@ public class Feature 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) { @@ -445,7 +442,7 @@ public class Feature implements java.io.Serializable * Sets the value of field 'featureGroup'. * * @param featureGroup - * the value of field 'featureGroup'. + * the value of field 'featureGroup'. */ public void setFeatureGroup(final java.lang.String featureGroup) { @@ -458,7 +455,7 @@ public class Feature implements java.io.Serializable * @param index * @param vOtherData * @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 setOtherData(final int index, final jalview.schemabinding.version2.OtherData vOtherData) @@ -496,7 +493,7 @@ public class Feature implements java.io.Serializable * Sets the value of field 'score'. * * @param score - * the value of field 'score'. + * the value of field 'score'. */ public void setScore(final float score) { @@ -508,7 +505,7 @@ public class Feature implements java.io.Serializable * Sets the value of field 'status'. * * @param status - * the value of field 'status'. + * the value of field 'status'. */ public void setStatus(final java.lang.String status) { @@ -519,7 +516,7 @@ public class Feature implements java.io.Serializable * Sets the value of field 'type'. * * @param type - * the value of field 'type'. + * the value of field 'type'. */ public void setType(final java.lang.String type) { @@ -531,11 +528,10 @@ public class Feature 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.schemabinding.version2.Featur */ public static jalview.schemabinding.version2.Feature unmarshal( @@ -551,8 +547,7 @@ public class Feature 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 {