X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=7856de9dc3c83ac5c5ccc6161676b083d53971c5;hb=5964cc48187a5dbf0544f3058c09d553c845afa0;hp=b4237b85bf82880a9d5374673c94f37bae3243d0;hpb=124589ea0c58cbb7b3788bbf13b687a0ece3c9e0;p=jalview.git
diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
old mode 100755
new mode 100644
index b4237b8..7856de9
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,576 +1,612 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
- //---------------------------------/
- //- 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 VAMSAS.
- *
- * @version $Revision$ $Date$
- */
-public class VAMSAS implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _alignmentList
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _sequenceSetList
- */
- private java.util.Vector _sequenceSetList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public VAMSAS() {
- super();
- _alignmentList = new Vector();
- _treeList = new Vector();
- _sequenceSetList = new Vector();
- } //-- jalview.binding.VAMSAS()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param vAlignment
- */
- public void addAlignment(jalview.binding.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.addElement(vAlignment);
- } //-- void addAlignment(jalview.binding.Alignment)
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void addAlignment(int index, jalview.binding.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.insertElementAt(vAlignment, index);
- } //-- void addAlignment(int, jalview.binding.Alignment)
-
- /**
- * Method addSequenceSet
- *
- *
- *
- * @param vSequenceSet
- */
- public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetList.addElement(vSequenceSet);
- } //-- void addSequenceSet(jalview.binding.SequenceSet)
-
- /**
- * Method addSequenceSet
- *
- *
- *
- * @param index
- * @param vSequenceSet
- */
- public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceSetList.insertElementAt(vSequenceSet, index);
- } //-- void addSequenceSet(int, jalview.binding.SequenceSet)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(java.lang.String)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, java.lang.String)
-
- /**
- * Method enumerateAlignment
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignment()
- {
- return _alignmentList.elements();
- } //-- java.util.Enumeration enumerateAlignment()
-
- /**
- * Method enumerateSequenceSet
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequenceSet()
- {
- return _sequenceSetList.elements();
- } //-- java.util.Enumeration enumerateSequenceSet()
-
- /**
- * Method enumerateTree
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateTree()
- {
- return _treeList.elements();
- } //-- java.util.Enumeration enumerateTree()
-
- /**
- * Method getAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public jalview.binding.Alignment getAlignment(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.binding.Alignment) _alignmentList.elementAt(index);
- } //-- jalview.binding.Alignment getAlignment(int)
-
- /**
- * Method getAlignment
- *
- *
- *
- * @return Alignment
- */
- public jalview.binding.Alignment[] getAlignment()
- {
- int size = _alignmentList.size();
- jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);
- }
- return mArray;
- } //-- jalview.binding.Alignment[] getAlignment()
-
- /**
- * Method getAlignmentCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentCount()
- {
- return _alignmentList.size();
- } //-- int getAlignmentCount()
-
- /**
- * Method getSequenceSet
- *
- *
- *
- * @param index
- * @return SequenceSet
- */
- public jalview.binding.SequenceSet getSequenceSet(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
- } //-- jalview.binding.SequenceSet getSequenceSet(int)
-
- /**
- * Method getSequenceSet
- *
- *
- *
- * @return SequenceSet
- */
- public jalview.binding.SequenceSet[] getSequenceSet()
- {
- int size = _sequenceSetList.size();
- jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);
- }
- return mArray;
- } //-- jalview.binding.SequenceSet[] getSequenceSet()
-
- /**
- * Method getSequenceSetCount
- *
- *
- *
- * @return int
- */
- public int getSequenceSetCount()
- {
- return _sequenceSetList.size();
- } //-- int getSequenceSetCount()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return String
- */
- public java.lang.String getTree(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (String)_treeList.elementAt(index);
- } //-- java.lang.String getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return String
- */
- public java.lang.String[] getTree()
- {
- int size = _treeList.size();
- java.lang.String[] mArray = new java.lang.String[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (String)_treeList.elementAt(index);
- }
- return mArray;
- } //-- java.lang.String[] getTree()
-
- /**
- * Method getTreeCount
- *
- *
- *
- * @return int
- */
- public int getTreeCount()
- {
- return _treeList.size();
- } //-- int getTreeCount()
-
- /**
- * 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 removeAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public jalview.binding.Alignment removeAlignment(int index)
- {
- java.lang.Object obj = _alignmentList.elementAt(index);
- _alignmentList.removeElementAt(index);
- return (jalview.binding.Alignment) obj;
- } //-- jalview.binding.Alignment removeAlignment(int)
-
- /**
- * Method removeAllAlignment
- *
- */
- public void removeAllAlignment()
- {
- _alignmentList.removeAllElements();
- } //-- void removeAllAlignment()
-
- /**
- * Method removeAllSequenceSet
- *
- */
- public void removeAllSequenceSet()
- {
- _sequenceSetList.removeAllElements();
- } //-- void removeAllSequenceSet()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeSequenceSet
- *
- *
- *
- * @param index
- * @return SequenceSet
- */
- public jalview.binding.SequenceSet removeSequenceSet(int index)
- {
- java.lang.Object obj = _sequenceSetList.elementAt(index);
- _sequenceSetList.removeElementAt(index);
- return (jalview.binding.SequenceSet) obj;
- } //-- jalview.binding.SequenceSet removeSequenceSet(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return String
- */
- public java.lang.String removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (String)obj;
- } //-- java.lang.String removeTree(int)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void setAlignment(int index, jalview.binding.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _alignmentList.setElementAt(vAlignment, index);
- } //-- void setAlignment(int, jalview.binding.Alignment)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param alignmentArray
- */
- public void setAlignment(jalview.binding.Alignment[] alignmentArray)
- {
- //-- copy array
- _alignmentList.removeAllElements();
- for (int i = 0; i < alignmentArray.length; i++) {
- _alignmentList.addElement(alignmentArray[i]);
- }
- } //-- void setAlignment(jalview.binding.Alignment)
-
- /**
- * Method setSequenceSet
- *
- *
- *
- * @param index
- * @param vSequenceSet
- */
- public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceSetList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _sequenceSetList.setElementAt(vSequenceSet, index);
- } //-- void setSequenceSet(int, jalview.binding.SequenceSet)
-
- /**
- * Method setSequenceSet
- *
- *
- *
- * @param sequenceSetArray
- */
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)
- {
- //-- copy array
- _sequenceSetList.removeAllElements();
- for (int i = 0; i < sequenceSetArray.length; i++) {
- _sequenceSetList.addElement(sequenceSetArray[i]);
- }
- } //-- void setSequenceSet(jalview.binding.SequenceSet)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _treeList.setElementAt(vTree, index);
- } //-- void setTree(int, java.lang.String)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(java.lang.String[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(java.lang.String)
-
- /**
- * 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.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.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)
+ * 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 Alignment[] getAlignment() + { + Alignment[] array = new Alignment[0]; + return (Alignment[]) this._alignmentList.toArray(array); + } + + /** + * Method getAlignmentCount. + * + * @return the size of this collection + */ + public int getAlignmentCount() + { + return this._alignmentList.size(); + } + + /** + * Method getSequenceSet. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the SequenceSet at the given index + */ + public SequenceSet getSequenceSet(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) + { + throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + + index + "' not in range [0.." + + (this._sequenceSetList.size() - 1) + "]"); + } + + return (SequenceSet) _sequenceSetList.get(index); + } + + /** + * Method getSequenceSet.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 SequenceSet[] getSequenceSet() + { + SequenceSet[] array = new SequenceSet[0]; + return (SequenceSet[]) this._sequenceSetList.toArray(array); + } + + /** + * Method getSequenceSetCount. + * + * @return the size of this collection + */ + public int getSequenceSetCount() + { + return this._sequenceSetList.size(); + } + + /** + * Method getTree. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the java.lang.String at the given index + */ + public java.lang.String getTree(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) + { + throw new IndexOutOfBoundsException("getTree: Index value '" + index + + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + return (java.lang.String) _treeList.get(index); + } + + /** + * Method getTree.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 java.lang.String[] getTree() + { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._treeList.toArray(array); + } + + /** + * Method getTreeCount. + * + * @return the size of this collection + */ + public int getTreeCount() + { + return this._treeList.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 removeAlignment. + * + * @param vAlignment + * @return true if the object was removed from the collection. + */ + public boolean removeAlignment(final Alignment vAlignment) + { + boolean removed = _alignmentList.remove(vAlignment); + return removed; + } + + /** + * Method removeAlignmentAt. + * + * @param index + * @return the element removed from the collection + */ + public Alignment removeAlignmentAt(final int index) + { + java.lang.Object obj = this._alignmentList.remove(index); + return (Alignment) obj; + } + + /** + */ + public void removeAllAlignment() + { + this._alignmentList.clear(); + } + + /** + */ + public void removeAllSequenceSet() + { + this._sequenceSetList.clear(); + } + + /** + */ + public void removeAllTree() + { + this._treeList.clear(); + } + + /** + * Method removeSequenceSet. + * + * @param vSequenceSet + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSet(final SequenceSet vSequenceSet) + { + boolean removed = _sequenceSetList.remove(vSequenceSet); + return removed; + } + + /** + * Method removeSequenceSetAt. + * + * @param index + * @return the element removed from the collection + */ + public SequenceSet removeSequenceSetAt(final int index) + { + java.lang.Object obj = this._sequenceSetList.remove(index); + return (SequenceSet) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree(final java.lang.String vTree) + { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeTreeAt(final int index) + { + java.lang.Object obj = this._treeList.remove(index); + return (java.lang.String) obj; + } + + /** + * + * + * @param index + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setAlignment(final int index, final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alignmentList.size()) + { + throw new IndexOutOfBoundsException("setAlignment: Index value '" + + index + "' not in range [0.." + + (this._alignmentList.size() - 1) + "]"); + } + + this._alignmentList.set(index, vAlignment); + } + + /** + * + * + * @param vAlignmentArray + */ + public void setAlignment(final Alignment[] vAlignmentArray) + { + // -- copy array + _alignmentList.clear(); + + for (int i = 0; i < vAlignmentArray.length; i++) + { + this._alignmentList.add(vAlignmentArray[i]); + } + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setSequenceSet(final int index, final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) + { + throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + + index + "' not in range [0.." + + (this._sequenceSetList.size() - 1) + "]"); + } + + this._sequenceSetList.set(index, vSequenceSet); + } + + /** + * + * + * @param vSequenceSetArray + */ + public void setSequenceSet(final SequenceSet[] vSequenceSetArray) + { + // -- copy array + _sequenceSetList.clear(); + + for (int i = 0; i < vSequenceSetArray.length; i++) + { + this._sequenceSetList.add(vSequenceSetArray[i]); + } + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setTree(final int index, final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) + { + throw new IndexOutOfBoundsException("setTree: Index value '" + index + + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + this._treeList.set(index, vTree); + } + + /** + * + * + * @param vTreeArray + */ + public void setTree(final java.lang.String[] vTreeArray) + { + // -- copy array + _treeList.clear(); + + for (int i = 0; i < vTreeArray.length; i++) + { + this._treeList.add(vTreeArray[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.VAMSAS + */ + public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.VAMSAS) Unmarshaller.unmarshal( + jalview.binding.VAMSAS.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); + } + +}