X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbinding%2FSequenceSet.java;h=a459891b3c0c77369afdfc2d8bd08e4caffc357b;hb=f9dac76937139e7b03fc25abfb4b53faa4823521;hp=4300c3951138022ebea8373e76a81051127bcae9;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java
old mode 100755
new mode 100644
index 4300c39..a459891
--- a/src/jalview/binding/SequenceSet.java
+++ b/src/jalview/binding/SequenceSet.java
@@ -1,520 +1,531 @@
-/*
- * 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;
-
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-
-import org.xml.sax.ContentHandler;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-
-import java.util.Enumeration;
-import java.util.Vector;
-
-
-/**
- * Class SequenceSet.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceSet implements java.io.Serializable {
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _gapChar
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _aligned
- */
- private boolean _aligned;
-
- /**
- * keeps track of state for field: _aligned
- */
- private boolean _has_aligned;
-
- /**
- * Field _sequenceList
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList
- */
- private java.util.Vector _annotationList;
-
- //----------------/
- //- Constructors -/
- //----------------/
- public SequenceSet() {
- super();
- _sequenceList = new Vector();
- _annotationList = new Vector();
- }
- //-- jalview.binding.SequenceSet()
- //-----------/
-
- public void addAnnotation(jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- _annotationList.addElement(vAnnotation);
- }
- //-- void addAnnotation(jalview.binding.Annotation)
-
- /**
- * Method addAnnotation
- *
- *
- *
- * @param index
- * @param vAnnotation
- */
- public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- _annotationList.insertElementAt(vAnnotation, index);
- }
- //-- void addAnnotation(int, jalview.binding.Annotation)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param vSequence
- */
- public void addSequence(jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- _sequenceList.addElement(vSequence);
- }
- //-- void addSequence(jalview.binding.Sequence)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void addSequence(int index, jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- _sequenceList.insertElementAt(vSequence, index);
- }
- //-- void addSequence(int, jalview.binding.Sequence)
-
- /**
- * Method deleteAligned
- *
- */
- public void deleteAligned() {
- this._has_aligned = false;
- }
- //-- void deleteAligned()
-
- /**
- * Method enumerateAnnotation
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAnnotation() {
- return _annotationList.elements();
- }
- //-- java.util.Enumeration enumerateAnnotation()
-
- /**
- * Method enumerateSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequence() {
- return _sequenceList.elements();
- }
- //-- java.util.Enumeration enumerateSequence()
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return boolean
- * @return the value of field 'aligned'.
- */
- public boolean getAligned() {
- return this._aligned;
- }
- //-- boolean getAligned()
-
- /**
- * Method getAnnotation
- *
- *
- *
- * @param index
- * @return Annotation
- */
- public jalview.binding.Annotation getAnnotation(int index)
- throws java.lang.IndexOutOfBoundsException {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.binding.Annotation) _annotationList.elementAt(index);
- }
- //-- jalview.binding.Annotation getAnnotation(int)
-
- /**
- * Method getAnnotation
- *
- *
- *
- * @return Annotation
- */
- public jalview.binding.Annotation[] getAnnotation() {
- int size = _annotationList.size();
- jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];
-
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);
- }
-
- return mArray;
- }
- //-- jalview.binding.Annotation[] getAnnotation()
-
- /**
- * Method getAnnotationCount
- *
- *
- *
- * @return int
- */
- public int getAnnotationCount() {
- return _annotationList.size();
- }
- //-- int getAnnotationCount()
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return String
- * @return the value of field 'gapChar'.
- */
- public java.lang.String getGapChar() {
- return this._gapChar;
- }
- //-- java.lang.String getGapChar()
-
- /**
- * Method getSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public jalview.binding.Sequence getSequence(int index)
- throws java.lang.IndexOutOfBoundsException {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.binding.Sequence) _sequenceList.elementAt(index);
- }
- //-- jalview.binding.Sequence getSequence(int)
-
- /**
- * Method getSequence
- *
- *
- *
- * @return Sequence
- */
- public jalview.binding.Sequence[] getSequence() {
- int size = _sequenceList.size();
- jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];
-
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);
- }
-
- return mArray;
- }
- //-- jalview.binding.Sequence[] getSequence()
-
- /**
- * Method getSequenceCount
- *
- *
- *
- * @return int
- */
- public int getSequenceCount() {
- return _sequenceList.size();
- }
- //-- int getSequenceCount()
-
- /**
- * Method hasAligned
- *
- *
- *
- * @return boolean
- */
- public boolean hasAligned() {
- return this._has_aligned;
- }
- //-- boolean hasAligned()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid() {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
-
- return true;
- }
- //-- 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)
-
- /**
- * 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)
-
- /**
- * Method removeAllAnnotation
- *
- */
- public void removeAllAnnotation() {
- _annotationList.removeAllElements();
- }
- //-- void removeAllAnnotation()
-
- /**
- * Method removeAllSequence
- *
- */
- public void removeAllSequence() {
- _sequenceList.removeAllElements();
- }
- //-- void removeAllSequence()
-
- /**
- * Method removeAnnotation
- *
- *
- *
- * @param index
- * @return Annotation
- */
- public jalview.binding.Annotation removeAnnotation(int index) {
- java.lang.Object obj = _annotationList.elementAt(index);
- _annotationList.removeElementAt(index);
-
- return (jalview.binding.Annotation) obj;
- }
- //-- jalview.binding.Annotation removeAnnotation(int)
-
- /**
- * Method removeSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public jalview.binding.Sequence removeSequence(int index) {
- java.lang.Object obj = _sequenceList.elementAt(index);
- _sequenceList.removeElementAt(index);
-
- return (jalview.binding.Sequence) obj;
- }
- //-- jalview.binding.Sequence removeSequence(int)
-
- /**
- * Sets the value of field 'aligned'.
- *
- * @param aligned the value of field 'aligned'.
- */
- public void setAligned(boolean aligned) {
- this._aligned = aligned;
- this._has_aligned = true;
- }
- //-- void setAligned(boolean)
-
- /**
- * Method setAnnotation
- *
- *
- *
- * @param index
- * @param vAnnotation
- */
- public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- _annotationList.setElementAt(vAnnotation, index);
- }
- //-- void setAnnotation(int, jalview.binding.Annotation)
-
- /**
- * Method setAnnotation
- *
- *
- *
- * @param annotationArray
- */
- public void setAnnotation(jalview.binding.Annotation[] annotationArray) {
- //-- copy array
- _annotationList.removeAllElements();
-
- for (int i = 0; i < annotationArray.length; i++) {
- _annotationList.addElement(annotationArray[i]);
- }
- }
- //-- void setAnnotation(jalview.binding.Annotation)
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(java.lang.String gapChar) {
- this._gapChar = gapChar;
- }
- //-- void setGapChar(java.lang.String)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void setSequence(int index, jalview.binding.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- _sequenceList.setElementAt(vSequence, index);
- }
- //-- void setSequence(int, jalview.binding.Sequence)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param sequenceArray
- */
- public void setSequence(jalview.binding.Sequence[] sequenceArray) {
- //-- copy array
- _sequenceList.removeAllElements();
-
- for (int i = 0; i < sequenceArray.length; i++) {
- _sequenceList.addElement(sequenceArray[i]);
- }
- }
- //-- void setSequence(jalview.binding.Sequence)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException {
- return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class,
- 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()
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.binding.Annotation[] getAnnotation( + ) { + jalview.binding.Annotation[] array = new jalview.binding.Annotation[0]; + return (jalview.binding.Annotation[]) this._annotationList.toArray(array); + } + + /** + * Method getAnnotationCount. + * + * @return the size of this collection + */ + public int getAnnotationCount( + ) { + return this._annotationList.size(); + } + + /** + * Returns the value of field 'gapChar'. + * + * @return the value of field 'GapChar'. + */ + public java.lang.String getGapChar( + ) { + return this._gapChar; + } + + /** + * Method getSequence. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Sequence at the + * given index + */ + public jalview.binding.Sequence getSequence( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + return (jalview.binding.Sequence) _sequenceList.get(index); + } + + /** + * Method getSequence.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.binding.Sequence[] getSequence( + ) { + jalview.binding.Sequence[] array = new jalview.binding.Sequence[0]; + return (jalview.binding.Sequence[]) this._sequenceList.toArray(array); + } + + /** + * Method getSequenceCount. + * + * @return the size of this collection + */ + public int getSequenceCount( + ) { + return this._sequenceList.size(); + } + + /** + * Method hasAligned. + * + * @return true if at least one Aligned has been added + */ + public boolean hasAligned( + ) { + return this._has_aligned; + } + + /** + * Returns the value of field 'aligned'. + * + * @return the value of field 'Aligned'. + */ + public boolean isAligned( + ) { + return this._aligned; + } + + /** + * 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 removeAllAnnotation( + ) { + this._annotationList.clear(); + } + + /** + */ + public void removeAllSequence( + ) { + this._sequenceList.clear(); + } + + /** + * Method removeAnnotation. + * + * @param vAnnotation + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotation( + final jalview.binding.Annotation vAnnotation) { + boolean removed = _annotationList.remove(vAnnotation); + return removed; + } + + /** + * Method removeAnnotationAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Annotation removeAnnotationAt( + final int index) { + java.lang.Object obj = this._annotationList.remove(index); + return (jalview.binding.Annotation) obj; + } + + /** + * Method removeSequence. + * + * @param vSequence + * @return true if the object was removed from the collection. + */ + public boolean removeSequence( + final jalview.binding.Sequence vSequence) { + boolean removed = _sequenceList.remove(vSequence); + return removed; + } + + /** + * Method removeSequenceAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Sequence removeSequenceAt( + final int index) { + java.lang.Object obj = this._sequenceList.remove(index); + return (jalview.binding.Sequence) obj; + } + + /** + * Sets the value of field 'aligned'. + * + * @param aligned the value of field 'aligned'. + */ + public void setAligned( + final boolean aligned) { + this._aligned = aligned; + this._has_aligned = true; + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotation( + final int index, + final jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + this._annotationList.set(index, vAnnotation); + } + + /** + * + * + * @param vAnnotationArray + */ + public void setAnnotation( + final jalview.binding.Annotation[] vAnnotationArray) { + //-- copy array + _annotationList.clear(); + + for (int i = 0; i < vAnnotationArray.length; i++) { + this._annotationList.add(vAnnotationArray[i]); + } + } + + /** + * Sets the value of field 'gapChar'. + * + * @param gapChar the value of field 'gapChar'. + */ + public void setGapChar( + final java.lang.String gapChar) { + this._gapChar = gapChar; + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequence( + final int index, + final jalview.binding.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + this._sequenceList.set(index, vSequence); + } + + /** + * + * + * @param vSequenceArray + */ + public void setSequence( + final jalview.binding.Sequence[] vSequenceArray) { + //-- copy array + _sequenceList.clear(); + + for (int i = 0; i < vSequenceArray.length; i++) { + this._sequenceList.add(vSequenceArray[i]); + } + } + + /** + * 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.binding.SequenceSet + */ + public static jalview.binding.SequenceSet unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.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); + } + +}