X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=ee559455cd465b7c4dbb275e78380841a7f9c497;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=9e02e6008c9183217837086591caa688f53ac03f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index 9e02e60..ee55945 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,29 +1,10 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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.binding; //---------------------------------/ @@ -34,6 +15,8 @@ import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; +import java.util.Enumeration; +import java.util.Vector; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -42,7 +25,7 @@ import org.xml.sax.ContentHandler; /** * Class JSeq. - * + * * @version $Revision$ $Date$ */ public class JSeq implements java.io.Serializable { @@ -92,6 +75,16 @@ public class JSeq implements java.io.Serializable { */ private boolean _has_id; + /** + * Field _featuresList + */ + private java.util.Vector _featuresList; + + /** + * Field _pdbidsList + */ + private java.util.Vector _pdbidsList; + //----------------/ //- Constructors -/ @@ -99,6 +92,8 @@ public class JSeq implements java.io.Serializable { public JSeq() { super(); + _featuresList = new Vector(); + _pdbidsList = new Vector(); } //-- jalview.binding.JSeq() @@ -107,138 +102,312 @@ public class JSeq implements java.io.Serializable { //-----------/ /** + * Method addFeatures + * + * + * + * @param vFeatures + */ + public void addFeatures(jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException + { + _featuresList.addElement(vFeatures); + } //-- void addFeatures(jalview.binding.Features) + + /** + * Method addFeatures + * + * + * + * @param index + * @param vFeatures + */ + public void addFeatures(int index, jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException + { + _featuresList.insertElementAt(vFeatures, index); + } //-- void addFeatures(int, jalview.binding.Features) + + /** + * Method addPdbids + * + * + * + * @param vPdbids + */ + public void addPdbids(jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException + { + _pdbidsList.addElement(vPdbids); + } //-- void addPdbids(jalview.binding.Pdbids) + + /** + * Method addPdbids + * + * + * + * @param index + * @param vPdbids + */ + public void addPdbids(int index, jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException + { + _pdbidsList.insertElementAt(vPdbids, index); + } //-- void addPdbids(int, jalview.binding.Pdbids) + + /** * Method deleteColour - * + * */ public void deleteColour() { this._has_colour= false; - } //-- void deleteColour() + } //-- void deleteColour() /** * Method deleteEnd - * + * */ public void deleteEnd() { this._has_end= false; - } //-- void deleteEnd() + } //-- void deleteEnd() /** * Method deleteId - * + * */ public void deleteId() { this._has_id= false; - } //-- void deleteId() + } //-- void deleteId() /** * Method deleteStart - * + * */ public void deleteStart() { this._has_start= false; - } //-- void deleteStart() + } //-- void deleteStart() + + /** + * Method enumerateFeatures + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateFeatures() + { + return _featuresList.elements(); + } //-- java.util.Enumeration enumerateFeatures() + + /** + * Method enumeratePdbids + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumeratePdbids() + { + return _pdbidsList.elements(); + } //-- java.util.Enumeration enumeratePdbids() /** * Returns the value of field 'colour'. - * + * * @return int * @return the value of field 'colour'. */ public int getColour() { return this._colour; - } //-- int getColour() + } //-- int getColour() /** * Returns the value of field 'end'. - * + * * @return int * @return the value of field 'end'. */ public int getEnd() { return this._end; - } //-- int getEnd() + } //-- int getEnd() + + /** + * Method getFeatures + * + * + * + * @param index + * @return Features + */ + public jalview.binding.Features getFeatures(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _featuresList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Features) _featuresList.elementAt(index); + } //-- jalview.binding.Features getFeatures(int) + + /** + * Method getFeatures + * + * + * + * @return Features + */ + public jalview.binding.Features[] getFeatures() + { + int size = _featuresList.size(); + jalview.binding.Features[] mArray = new jalview.binding.Features[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Features[] getFeatures() + + /** + * Method getFeaturesCount + * + * + * + * @return int + */ + public int getFeaturesCount() + { + return _featuresList.size(); + } //-- int getFeaturesCount() /** * Returns the value of field 'id'. - * + * * @return int * @return the value of field 'id'. */ public int getId() { return this._id; - } //-- int getId() + } //-- int getId() + + /** + * Method getPdbids + * + * + * + * @param index + * @return Pdbids + */ + public jalview.binding.Pdbids getPdbids(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _pdbidsList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Pdbids) _pdbidsList.elementAt(index); + } //-- jalview.binding.Pdbids getPdbids(int) + + /** + * Method getPdbids + * + * + * + * @return Pdbids + */ + public jalview.binding.Pdbids[] getPdbids() + { + int size = _pdbidsList.size(); + jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Pdbids[] getPdbids() + + /** + * Method getPdbidsCount + * + * + * + * @return int + */ + public int getPdbidsCount() + { + return _pdbidsList.size(); + } //-- int getPdbidsCount() /** * Returns the value of field 'start'. - * + * * @return int * @return the value of field 'start'. */ public int getStart() { return this._start; - } //-- int getStart() + } //-- int getStart() /** * Method hasColour - * - * - * + * + * + * * @return boolean */ public boolean hasColour() { return this._has_colour; - } //-- boolean hasColour() + } //-- boolean hasColour() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ public boolean hasEnd() { return this._has_end; - } //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasId - * - * - * + * + * + * * @return boolean */ public boolean hasId() { return this._has_id; - } //-- boolean hasId() + } //-- boolean hasId() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ public boolean hasStart() { return this._has_start; - } //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -250,85 +419,201 @@ public class JSeq implements java.io.Serializable { return false; } return true; - } //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } //-- void marshal(java.io.Writer) /** * Method marshal - * - * - * + * + * + * * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) + + /** + * Method removeAllFeatures + * + */ + public void removeAllFeatures() + { + _featuresList.removeAllElements(); + } //-- void removeAllFeatures() + + /** + * Method removeAllPdbids + * + */ + public void removeAllPdbids() + { + _pdbidsList.removeAllElements(); + } //-- void removeAllPdbids() + + /** + * Method removeFeatures + * + * + * + * @param index + * @return Features + */ + public jalview.binding.Features removeFeatures(int index) + { + java.lang.Object obj = _featuresList.elementAt(index); + _featuresList.removeElementAt(index); + return (jalview.binding.Features) obj; + } //-- jalview.binding.Features removeFeatures(int) + + /** + * Method removePdbids + * + * + * + * @param index + * @return Pdbids + */ + public jalview.binding.Pdbids removePdbids(int index) + { + java.lang.Object obj = _pdbidsList.elementAt(index); + _pdbidsList.removeElementAt(index); + return (jalview.binding.Pdbids) obj; + } //-- jalview.binding.Pdbids removePdbids(int) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ public void setColour(int colour) { this._colour = colour; this._has_colour = true; - } //-- void setColour(int) + } //-- void setColour(int) /** * Sets the value of field 'end'. - * + * * @param end the value of field 'end'. */ public void setEnd(int end) { this._end = end; this._has_end = true; - } //-- void setEnd(int) + } //-- void setEnd(int) + + /** + * Method setFeatures + * + * + * + * @param index + * @param vFeatures + */ + public void setFeatures(int index, jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _featuresList.size())) { + throw new IndexOutOfBoundsException(); + } + _featuresList.setElementAt(vFeatures, index); + } //-- void setFeatures(int, jalview.binding.Features) + + /** + * Method setFeatures + * + * + * + * @param featuresArray + */ + public void setFeatures(jalview.binding.Features[] featuresArray) + { + //-- copy array + _featuresList.removeAllElements(); + for (int i = 0; i < featuresArray.length; i++) { + _featuresList.addElement(featuresArray[i]); + } + } //-- void setFeatures(jalview.binding.Features) /** * Sets the value of field 'id'. - * + * * @param id the value of field 'id'. */ public void setId(int id) { this._id = id; this._has_id = true; - } //-- void setId(int) + } //-- void setId(int) + + /** + * Method setPdbids + * + * + * + * @param index + * @param vPdbids + */ + public void setPdbids(int index, jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _pdbidsList.size())) { + throw new IndexOutOfBoundsException(); + } + _pdbidsList.setElementAt(vPdbids, index); + } //-- void setPdbids(int, jalview.binding.Pdbids) + + /** + * Method setPdbids + * + * + * + * @param pdbidsArray + */ + public void setPdbids(jalview.binding.Pdbids[] pdbidsArray) + { + //-- copy array + _pdbidsList.removeAllElements(); + for (int i = 0; i < pdbidsArray.length; i++) { + _pdbidsList.addElement(pdbidsArray[i]); + } + } //-- void setPdbids(jalview.binding.Pdbids) /** * Sets the value of field 'start'. - * + * * @param start the value of field 'start'. */ public void setStart(int start) { this._start = start; this._has_start = true; - } //-- void setStart(int) + } //-- void setStart(int) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ @@ -336,17 +621,17 @@ public class JSeq implements java.io.Serializable { throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() + } //-- void validate() }