X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequenceSet.java;h=568df1f43e1544c1bdd7ae0fcc24814a9b78c74c;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=91b00577d5bddcbb712889706edbfe27c33ede1b;hpb=682c69b6a050a742d20f643459d8d8fbfecf40e1;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
old mode 100755
new mode 100644
index 91b0057..568df1f
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,602 +1,891 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
- //---------------------------------/
- //- 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;
-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;
-
-/**
- * Class SequenceSet.
- *
- * @version $Revision$ $Date$
- */
-public class SequenceSet implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _gapChar
- */
- private java.lang.String _gapChar;
-
- /**
- * Field _sequenceList
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _annotationList
- */
- private java.util.Vector _annotationList;
-
- /**
- * Field _sequenceSetPropertiesList
- */
- private java.util.Vector _sequenceSetPropertiesList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceSet() {
- super();
- _sequenceList = new Vector();
- _annotationList = new Vector();
- _sequenceSetPropertiesList = new Vector();
- } //-- jalview.schemabinding.version2.SequenceSet()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAnnotation
- *
- *
- *
- * @param vAnnotation
- */
- public void addAnnotation(jalview.schemabinding.version2.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationList.addElement(vAnnotation);
- } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)
-
- /**
- * Method addAnnotation
- *
- *
- *
- * @param index
- * @param vAnnotation
- */
- public void addAnnotation(int index, jalview.schemabinding.version2.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _annotationList.insertElementAt(vAnnotation, index);
- } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param vSequence
- */
- public void addSequence(jalview.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.addElement(vSequence);
- } //-- void addSequence(jalview.schemabinding.version2.Sequence)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void addSequence(int index, jalview.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.insertElementAt(vSequence, index);
- } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)
-
- /**
- * Method addSequenceSetProperties
- *
- *
- *
- * @param vSequenceSetProperties
- */
- public void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetPropertiesList.addElement(vSequenceSetProperties);
- } //-- void addSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties)
-
- /**
- * Method addSequenceSetProperties
- *
- *
- *
- * @param index
- * @param vSequenceSetProperties
- */
- public void addSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetPropertiesList.insertElementAt(vSequenceSetProperties, index);
- } //-- void addSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties)
-
- /**
- * 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()
-
- /**
- * Method enumerateSequenceSetProperties
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequenceSetProperties()
- {
- return _sequenceSetPropertiesList.elements();
- } //-- java.util.Enumeration enumerateSequenceSetProperties()
-
- /**
- * Method getAnnotation
- *
- *
- *
- * @param index
- * @return Annotation
- */
- public jalview.schemabinding.version2.Annotation getAnnotation(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _annotationList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
- } //-- jalview.schemabinding.version2.Annotation getAnnotation(int)
-
- /**
- * Method getAnnotation
- *
- *
- *
- * @return Annotation
- */
- public jalview.schemabinding.version2.Annotation[] getAnnotation()
- {
- int size = _annotationList.size();
- jalview.schemabinding.version2.Annotation[] mArray = new jalview.schemabinding.version2.Annotation[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.schemabinding.version2.Annotation) _annotationList.elementAt(index);
- }
- return mArray;
- } //-- jalview.schemabinding.version2.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.schemabinding.version2.Sequence getSequence(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
- } //-- jalview.schemabinding.version2.Sequence getSequence(int)
-
- /**
- * Method getSequence
- *
- *
- *
- * @return Sequence
- */
- public jalview.schemabinding.version2.Sequence[] getSequence()
- {
- int size = _sequenceList.size();
- jalview.schemabinding.version2.Sequence[] mArray = new jalview.schemabinding.version2.Sequence[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(index);
- }
- return mArray;
- } //-- jalview.schemabinding.version2.Sequence[] getSequence()
-
- /**
- * Method getSequenceCount
- *
- *
- *
- * @return int
- */
- public int getSequenceCount()
- {
- return _sequenceList.size();
- } //-- int getSequenceCount()
-
- /**
- * Method getSequenceSetProperties
- *
- *
- *
- * @param index
- * @return SequenceSetProperties
- */
- public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);
- } //-- jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(int)
-
- /**
- * Method getSequenceSetProperties
- *
- *
- *
- * @return SequenceSetProperties
- */
- public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
- {
- int size = _sequenceSetPropertiesList.size();
- jalview.schemabinding.version2.SequenceSetProperties[] mArray = new jalview.schemabinding.version2.SequenceSetProperties[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.elementAt(index);
- }
- return mArray;
- } //-- jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()
-
- /**
- * Method getSequenceSetPropertiesCount
- *
- *
- *
- * @return int
- */
- public int getSequenceSetPropertiesCount()
- {
- return _sequenceSetPropertiesList.size();
- } //-- int getSequenceSetPropertiesCount()
-
- /**
- * 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 removeAllSequenceSetProperties
- *
- */
- public void removeAllSequenceSetProperties()
- {
- _sequenceSetPropertiesList.removeAllElements();
- } //-- void removeAllSequenceSetProperties()
-
- /**
- * Method removeAnnotation
- *
- *
- *
- * @param index
- * @return Annotation
- */
- public jalview.schemabinding.version2.Annotation removeAnnotation(int index)
- {
- java.lang.Object obj = _annotationList.elementAt(index);
- _annotationList.removeElementAt(index);
- return (jalview.schemabinding.version2.Annotation) obj;
- } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int)
-
- /**
- * Method removeSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public jalview.schemabinding.version2.Sequence removeSequence(int index)
- {
- java.lang.Object obj = _sequenceList.elementAt(index);
- _sequenceList.removeElementAt(index);
- return (jalview.schemabinding.version2.Sequence) obj;
- } //-- jalview.schemabinding.version2.Sequence removeSequence(int)
-
- /**
- * Method removeSequenceSetProperties
- *
- *
- *
- * @param index
- * @return SequenceSetProperties
- */
- public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int index)
- {
- java.lang.Object obj = _sequenceSetPropertiesList.elementAt(index);
- _sequenceSetPropertiesList.removeElementAt(index);
- return (jalview.schemabinding.version2.SequenceSetProperties) obj;
- } //-- jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetProperties(int)
-
- /**
- * Method setAnnotation
- *
- *
- *
- * @param index
- * @param vAnnotation
- */
- public void setAnnotation(int index, jalview.schemabinding.version2.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.schemabinding.version2.Annotation)
-
- /**
- * Method setAnnotation
- *
- *
- *
- * @param annotationArray
- */
- public void setAnnotation(jalview.schemabinding.version2.Annotation[] annotationArray)
- {
- //-- copy array
- _annotationList.removeAllElements();
- for (int i = 0; i < annotationArray.length; i++) {
- _annotationList.addElement(annotationArray[i]);
- }
- } //-- void setAnnotation(jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param sequenceArray
- */
- public void setSequence(jalview.schemabinding.version2.Sequence[] sequenceArray)
- {
- //-- copy array
- _sequenceList.removeAllElements();
- for (int i = 0; i < sequenceArray.length; i++) {
- _sequenceList.addElement(sequenceArray[i]);
- }
- } //-- void setSequence(jalview.schemabinding.version2.Sequence)
-
- /**
- * Method setSequenceSetProperties
- *
- *
- *
- * @param index
- * @param vSequenceSetProperties
- */
- public void setSequenceSetProperties(int index, jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetPropertiesList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _sequenceSetPropertiesList.setElementAt(vSequenceSetProperties, index);
- } //-- void setSequenceSetProperties(int, jalview.schemabinding.version2.SequenceSetProperties)
-
- /**
- * Method setSequenceSetProperties
- *
- *
- *
- * @param sequenceSetPropertiesArray
- */
- public void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties[] sequenceSetPropertiesArray)
- {
- //-- copy array
- _sequenceSetPropertiesList.removeAllElements();
- for (int i = 0; i < sequenceSetPropertiesArray.length; i++) {
- _sequenceSetPropertiesList.addElement(sequenceSetPropertiesArray[i]);
- }
- } //-- void setSequenceSetProperties(jalview.schemabinding.version2.SequenceSetProperties)
-
- /**
- * 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.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * Castor 1.1, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SequenceSet.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequenceSet implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _gapChar.
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * reference to set where jalview will gather the dataset sequences for all
+ * sequences in the set.
+ *
+ */
+ private java.lang.String _datasetId;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+ /**
+ * Field _sequenceSetPropertiesList.
+ */
+ private java.util.Vector _sequenceSetPropertiesList;
+
+ /**
+ * Field _alcodonFrameList.
+ */
+ private java.util.Vector _alcodonFrameList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceSet()
+ {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ this._sequenceSetPropertiesList = new java.util.Vector();
+ this._alcodonFrameList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodonFrameList.addElement(vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlcodonFrame(final int index,
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._alcodonFrameList.add(index, vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationList.addElement(vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAnnotation(final int index,
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._annotationList.add(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final jalview.schemabinding.version2.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceList.addElement(vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequence(final int index,
+ final jalview.schemabinding.version2.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSequenceSetProperties(
+ final int index,
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);
+ }
+
+ /**
+ * Method enumerateAlcodonFrame.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame
+ * elements
+ */
+ public java.util.Enumeration enumerateAlcodonFrame()
+ {
+ return this._alcodonFrameList.elements();
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Annotation
+ * elements
+ */
+ public java.util.Enumeration enumerateAnnotation()
+ {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Sequence
+ * elements
+ */
+ public java.util.Enumeration enumerateSequence()
+ {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSetProperties.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SequenceSetProperties elements
+ */
+ public java.util.Enumeration enumerateSequenceSetProperties()
+ {
+ return this._sequenceSetPropertiesList.elements();
+ }
+
+ /**
+ * Method getAlcodonFrame.
+ *
+ * @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.AlcodonFrame at the
+ * given inde
+ */
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonFrameList.size())
+ {
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodonFrameList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
+ .get(index);
+ }
+
+ /**
+ * Method getAlcodonFrame.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.AlcodonFrame[] getAlcodonFrame()
+ {
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlcodonFrameCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodonFrameCount()
+ {
+ return this._alcodonFrameList.size();
+ }
+
+ /**
+ * Method getAnnotation.
+ *
+ * @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.Annotation at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Annotation getAnnotation(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size())
+ {
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+ + index + "' not in range [0.."
+ + (this._annotationList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Annotation) _annotationList
+ .get(index);
+ }
+
+ /**
+ * Method getAnnotation.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.Annotation[] getAnnotation()
+ {
+ jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];
+ return (jalview.schemabinding.version2.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 'datasetId'. The field 'datasetId' has the
+ * following description: reference to set where jalview will gather the
+ * dataset sequences for all sequences in the set.
+ *
+ *
+ * @return the value of field 'DatasetId'.
+ */
+ public java.lang.String getDatasetId()
+ {
+ return this._datasetId;
+ }
+
+ /**
+ * 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.schemabinding.version2.Sequence at the
+ * given index
+ */
+ public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence[] getSequence()
+ {
+ jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];
+ return (jalview.schemabinding.version2.Sequence[]) this._sequenceList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount()
+ {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method getSequenceSetProperties.
+ *
+ * @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.SequenceSetProperties at the given
+ * index
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(
+ final int index) throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "getSequenceSetProperties: Index value '" + index
+ + "' not in range [0.."
+ + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
+ .get(index);
+ }
+
+ /**
+ * Method getSequenceSetProperties.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.SequenceSetProperties[] getSequenceSetProperties()
+ {
+ jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
+ return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetPropertiesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetPropertiesCount()
+ {
+ return this._sequenceSetPropertiesList.size();
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Method removeAlcodonFrame.
+ *
+ * @param vAlcodonFrame
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ {
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodonFrameAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
+ final int index)
+ {
+ java.lang.Object obj = this._alcodonFrameList.remove(index);
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlcodonFrame()
+ {
+ this._alcodonFrameList.clear();
+ }
+
+ /**
+ */
+ public void removeAllAnnotation()
+ {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence()
+ {
+ this._sequenceList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSetProperties()
+ {
+ this._sequenceSetPropertiesList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.schemabinding.version2.Annotation vAnnotation)
+ {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Annotation removeAnnotationAt(
+ final int index)
+ {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.schemabinding.version2.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final jalview.schemabinding.version2.Sequence vSequence)
+ {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Sequence removeSequenceAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.schemabinding.version2.Sequence) obj;
+ }
+
+ /**
+ * Method removeSequenceSetProperties.
+ *
+ * @param vSequenceSetProperties
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ {
+ boolean removed = _sequenceSetPropertiesList
+ .remove(vSequenceSetProperties);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetPropertiesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
+ final int index)
+ {
+ java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
+ return (jalview.schemabinding.version2.SequenceSetProperties) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodonFrame
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlcodonFrame(final int index,
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonFrameList.size())
+ {
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
+ + index + "' not in range [0.."
+ + (this._alcodonFrameList.size() - 1) + "]");
+ }
+
+ this._alcodonFrameList.set(index, vAlcodonFrame);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodonFrameArray
+ */
+ public void setAlcodonFrame(
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)
+ {
+ // -- copy array
+ _alcodonFrameList.clear();
+
+ for (int i = 0; i < vAlcodonFrameArray.length; i++)
+ {
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @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.schemabinding.version2.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.schemabinding.version2.Annotation[] vAnnotationArray)
+ {
+ // -- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++)
+ {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'datasetId'. The field 'datasetId' has the
+ * following description: reference to set where jalview will gather the
+ * dataset sequences for all sequences in the set.
+ *
+ *
+ * @param datasetId
+ * the value of field 'datasetId'.
+ */
+ public void setDatasetId(final java.lang.String datasetId)
+ {
+ this._datasetId = datasetId;
+ }
+
+ /**
+ * 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.schemabinding.version2.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.schemabinding.version2.Sequence[] vSequenceArray)
+ {
+ // -- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++)
+ {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSetProperties
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSequenceSetProperties(
+ final int index,
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size())
+ {
+ throw new IndexOutOfBoundsException(
+ "setSequenceSetProperties: Index value '" + index
+ + "' not in range [0.."
+ + (this._sequenceSetPropertiesList.size() - 1) + "]");
+ }
+
+ this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetPropertiesArray
+ */
+ public void setSequenceSetProperties(
+ final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)
+ {
+ // -- copy array
+ _sequenceSetPropertiesList.clear();
+
+ for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)
+ {
+ this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[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.schemabinding.version2.SequenceSet
+ */
+ public static jalview.schemabinding.version2.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceSet) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.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);
+ }
+
+}