X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequence.java;h=fa2c1d4353d1601e1dda24719fbc1b5ff5a45ff1;hb=3b4eda86f1f240a932cc778658dc1fbe56e9630d;hp=46058a643593f8acfbe049da199eac24de8ada03;hpb=65540422b57569f5bb9766742eccacc75f1368f0;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java old mode 100755 new mode 100644 index 46058a6..fa2c1d4 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,322 +1,338 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, 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 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. - * - * 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 - */ -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends jalview.schemabinding.version2.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * dataset sequence id for this sequence. Will be created as - * union of sequences. - * - */ - private java.lang.String _dsseqid; - - /** - * Field _DBRefList. - */ - private java.util.Vector _DBRefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() { - super(); - this._DBRefList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addDBRef( - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException { - this._DBRefList.addElement(vDBRef); - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addDBRef( - final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException { - this._DBRefList.add(index, vDBRef); - } - - /** - * Method enumerateDBRef. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.DBRef elements - */ - public java.util.Enumeration enumerateDBRef( - ) { - return this._DBRefList.elements(); - } - - /** - * Method getDBRef. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.DBRef at the given index - */ - public jalview.schemabinding.version2.DBRef getDBRef( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) { - throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); - } - - /** - * Method getDBRef.Returns the contents of the collection in an - * Array.
Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we know
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.DBRef[] getDBRef(
- ) {
- jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
- return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array);
- }
-
- /**
- * Method getDBRefCount.
- *
- * @return the size of this collection
- */
- public int getDBRefCount(
- ) {
- return this._DBRefList.size();
- }
-
- /**
- * Returns the value of field 'dsseqid'. The field 'dsseqid'
- * has the following description: dataset sequence id for this
- * sequence. Will be created as union of sequences.
- *
- *
- * @return the value of field 'Dsseqid'.
- */
- public java.lang.String getDsseqid(
- ) {
- return this._dsseqid;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException 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
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException 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
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- */
- public void removeAllDBRef(
- ) {
- this._DBRefList.clear();
- }
-
- /**
- * Method removeDBRef.
- *
- * @param vDBRef
- * @return true if the object was removed from the collection.
- */
- public boolean removeDBRef(
- final jalview.schemabinding.version2.DBRef vDBRef) {
- boolean removed = _DBRefList.remove(vDBRef);
- return removed;
- }
-
- /**
- * Method removeDBRefAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.DBRef removeDBRefAt(
- final int index) {
- java.lang.Object obj = this._DBRefList.remove(index);
- return (jalview.schemabinding.version2.DBRef) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vDBRef
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setDBRef(
- final int index,
- final jalview.schemabinding.version2.DBRef vDBRef)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._DBRefList.size()) {
- throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
- }
-
- this._DBRefList.set(index, vDBRef);
- }
-
- /**
- *
- *
- * @param vDBRefArray
- */
- public void setDBRef(
- final jalview.schemabinding.version2.DBRef[] vDBRefArray) {
- //-- copy array
- _DBRefList.clear();
-
- for (int i = 0; i < vDBRefArray.length; i++) {
- this._DBRefList.add(vDBRefArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'dsseqid'. The field 'dsseqid' has
- * the following description: dataset sequence id for this
- * sequence. Will be created as union of sequences.
- *
- *
- * @param dsseqid the value of field 'dsseqid'.
- */
- public void setDsseqid(
- final java.lang.String dsseqid) {
- this._dsseqid = dsseqid;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException 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
- * @return the unmarshaled
- * jalview.schemabinding.version2.SequenceType
- */
- public static jalview.schemabinding.version2.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.DBRef[] getDBRef() + { + jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; + return (jalview.schemabinding.version2.DBRef[]) this._DBRefList + .toArray(array); + } + + /** + * Method getDBRefCount. + * + * @return the size of this collection + */ + public int getDBRefCount() + { + return this._DBRefList.size(); + } + + /** + * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following + * description: dataset sequence id for this sequence. Will be created as + * union of sequences. + * + * + * @return the value of field 'Dsseqid'. + */ + public java.lang.String getDsseqid() + { + return this._dsseqid; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid() + { + try + { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) + { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException + * 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 + */ + public void marshal(final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException + * if an IOException occurs during marshaling + * @throws org.exolab.castor.xml.ValidationException + * 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 + */ + public void marshal(final org.xml.sax.ContentHandler handler) + throws java.io.IOException, + org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllDBRef() + { + this._DBRefList.clear(); + } + + /** + * Method removeDBRef. + * + * @param vDBRef + * @return true if the object was removed from the collection. + */ + public boolean removeDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) + { + boolean removed = _DBRefList.remove(vDBRef); + return removed; + } + + /** + * Method removeDBRefAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index) + { + java.lang.Object obj = this._DBRefList.remove(index); + return (jalview.schemabinding.version2.DBRef) obj; + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setDBRef(final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._DBRefList.size()) + { + throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + } + + this._DBRefList.set(index, vDBRef); + } + + /** + * + * + * @param vDBRefArray + */ + public void setDBRef( + final jalview.schemabinding.version2.DBRef[] vDBRefArray) + { + // -- copy array + _DBRefList.clear(); + + for (int i = 0; i < vDBRefArray.length; i++) + { + this._DBRefList.add(vDBRefArray[i]); + } + } + + /** + * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following + * description: dataset sequence id for this sequence. Will be created as + * union of sequences. + * + * + * @param dsseqid + * the value of field 'dsseqid'. + */ + public void setDsseqid(final java.lang.String dsseqid) + { + this._dsseqid = dsseqid; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException + * 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 + * @return the unmarshaled jalview.schemabinding.version2.SequenceType + */ + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller + .unmarshal(jalview.schemabinding.version2.Sequence.class, + reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException + * if this object is an invalid instance according to the schema + */ + public void validate() throws org.exolab.castor.xml.ValidationException + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +}