X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=7e2b7b15f463a1b13fba97500c2532ae8e06cafb;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=ee559455cd465b7c4dbb275e78380841a7f9c497;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
old mode 100755
new mode 100644
index ee55945..7e2b7b1
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,637 +1,668 @@
-/*
- * 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 JSeq.
- *
- * @version $Revision$ $Date$
- */
-public class JSeq implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _colour
- */
- private int _colour;
-
- /**
- * keeps track of state for field: _colour
- */
- private boolean _has_colour;
-
- /**
- * Field _start
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _id
- */
- private int _id;
-
- /**
- * keeps track of state for field: _id
- */
- private boolean _has_id;
-
- /**
- * Field _featuresList
- */
- private java.util.Vector _featuresList;
-
- /**
- * Field _pdbidsList
- */
- private java.util.Vector _pdbidsList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JSeq() {
- super();
- _featuresList = new Vector();
- _pdbidsList = new Vector();
- } //-- jalview.binding.JSeq()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * 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()
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * Method deleteId
- *
- */
- public void deleteId()
- {
- this._has_id= false;
- } //-- void deleteId()
-
- /**
- * Method deleteStart
- *
- */
- public void deleteStart()
- {
- this._has_start= false;
- } //-- 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()
-
- /**
- * Returns the value of field 'end'.
- *
- * @return int
- * @return the value of field 'end'.
- */
- public int getEnd()
- {
- return this._end;
- } //-- 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()
-
- /**
- * 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()
-
- /**
- * Method hasColour
- *
- *
- *
- * @return boolean
- */
- public boolean hasColour()
- {
- return this._has_colour;
- } //-- boolean hasColour()
-
- /**
- * Method hasEnd
- *
- *
- *
- * @return boolean
- */
- public boolean hasEnd()
- {
- return this._has_end;
- } //-- boolean hasEnd()
-
- /**
- * Method hasId
- *
- *
- *
- * @return boolean
- */
- public boolean hasId()
- {
- return this._has_id;
- } //-- boolean hasId()
-
- /**
- * Method hasStart
- *
- *
- *
- * @return boolean
- */
- public boolean hasStart()
- {
- return this._has_start;
- } //-- boolean hasStart()
-
- /**
- * 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 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)
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.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 2.8.2)
+ * 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
+ * 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.Features[] getFeatures() + { + jalview.binding.Features[] array = new jalview.binding.Features[0]; + return (jalview.binding.Features[]) this._featuresList.toArray(array); + } + + /** + * Method getFeaturesCount. + * + * @return the size of this collection + */ + public int getFeaturesCount() + { + return this._featuresList.size(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public int getId() + { + return this._id; + } + + /** + * Method getPdbids. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the jalview.binding.Pdbids at the given index + */ + public jalview.binding.Pdbids getPdbids(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) + { + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "getPdbids", + Integer.valueOf(index).toString(), + Integer.valueOf((this._pdbidsList.size() - 1)).toString() + })); + } + + return (jalview.binding.Pdbids) _pdbidsList.get(index); + } + + /** + * Method getPdbids.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.Pdbids[] getPdbids() + { + jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; + return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); + } + + /** + * Method getPdbidsCount. + * + * @return the size of this collection + */ + public int getPdbidsCount() + { + return this._pdbidsList.size(); + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart() + { + return this._start; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour() + { + return this._has_colour; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd() + { + return this._has_end; + } + + /** + * Method hasId. + * + * @return true if at least one Id has been added + */ + public boolean hasId() + { + return this._has_id; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart() + { + return this._has_start; + } + + /** + * 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 removeAllFeatures() + { + this._featuresList.clear(); + } + + /** + */ + public void removeAllPdbids() + { + this._pdbidsList.clear(); + } + + /** + * Method removeFeatures. + * + * @param vFeatures + * @return true if the object was removed from the collection. + */ + public boolean removeFeatures(final jalview.binding.Features vFeatures) + { + boolean removed = _featuresList.remove(vFeatures); + return removed; + } + + /** + * Method removeFeaturesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Features removeFeaturesAt(final int index) + { + java.lang.Object obj = this._featuresList.remove(index); + return (jalview.binding.Features) obj; + } + + /** + * Method removePdbids. + * + * @param vPdbids + * @return true if the object was removed from the collection. + */ + public boolean removePdbids(final jalview.binding.Pdbids vPdbids) + { + boolean removed = _pdbidsList.remove(vPdbids); + return removed; + } + + /** + * Method removePdbidsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Pdbids removePdbidsAt(final int index) + { + java.lang.Object obj = this._pdbidsList.remove(index); + return (jalview.binding.Pdbids) obj; + } + + /** + * Sets the value of field 'colour'. + * + * @param colour + * the value of field 'colour'. + */ + public void setColour(final int colour) + { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'end'. + * + * @param end + * the value of field 'end'. + */ + public void setEnd(final int end) + { + this._end = end; + this._has_end = true; + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setFeatures(final int index, + final jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) + { + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setFeatures", + Integer.valueOf(index).toString(), + Integer.valueOf((this._featuresList.size() - 1)).toString() + })); + } + + this._featuresList.set(index, vFeatures); + } + + /** + * + * + * @param vFeaturesArray + */ + public void setFeatures(final jalview.binding.Features[] vFeaturesArray) + { + // -- copy array + _featuresList.clear(); + + for (int i = 0; i < vFeaturesArray.length; i++) + { + this._featuresList.add(vFeaturesArray[i]); + } + } + + /** + * Sets the value of field 'id'. + * + * @param id + * the value of field 'id'. + */ + public void setId(final int id) + { + this._id = id; + this._has_id = true; + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setPdbids(final int index, + final jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) + { + throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setPdbids", + Integer.valueOf(index).toString(), + Integer.valueOf((this._pdbidsList.size() - 1)).toString() + })); + } + + this._pdbidsList.set(index, vPdbids); + } + + /** + * + * + * @param vPdbidsArray + */ + public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray) + { + // -- copy array + _pdbidsList.clear(); + + for (int i = 0; i < vPdbidsArray.length; i++) + { + this._pdbidsList.add(vPdbidsArray[i]); + } + } + + /** + * Sets the value of field 'start'. + * + * @param start + * the value of field 'start'. + */ + public void setStart(final int start) + { + this._start = start; + this._has_start = true; + } + + /** + * 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.JSeq + */ + public static jalview.binding.JSeq unmarshal(final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.JSeq) Unmarshaller.unmarshal( + jalview.binding.JSeq.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); + } + +}