X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJSeq.java;h=ecf1eb0433ae4fd6eb08baca645da57427171d4c;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=751409f0b161223878e176c9ab5f6389894670bc;hpb=ffe9b478a182cab3c8217b5c2bf002c7c1b6d7ec;p=jalview.git
diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java
old mode 100755
new mode 100644
index 751409f..ecf1eb0
--- a/src/jalview/binding/JSeq.java
+++ b/src/jalview/binding/JSeq.java
@@ -1,333 +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 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;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JSeq() {
- super();
- } //-- jalview.binding.JSeq()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * 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()
-
- /**
- * 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()
-
- /**
- * Returns the value of field 'id'.
- *
- * @return int
- * @return the value of field 'id'.
- */
- public int getId()
- {
- return this._id;
- } //-- int getId()
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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 2.8.2b1)
+ * 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.
+ */
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.util.MessageManager;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * 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();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFeatures(final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._featuresList.addElement(vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addFeatures(final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbids(final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pdbidsList.addElement(vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addPdbids(final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._pdbidsList.add(index, vPdbids);
+ }
+
+ /**
+ */
+ public void deleteColour()
+ {
+ this._has_colour = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteId()
+ {
+ this._has_id = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all jalview.binding.Features elements
+ */
+ public java.util.Enumeration enumerateFeatures()
+ {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all jalview.binding.Pdbids elements
+ */
+ public java.util.Enumeration enumeratePdbids()
+ {
+ return this._pdbidsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Method getFeatures.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Features at the given index
+ */
+ public jalview.binding.Features getFeatures(final int index)
+ 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[]{
+ "getFeatures",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._featuresList.size() - 1)).toString()
+ }));
+ }
+
+ return (jalview.binding.Features) _featuresList.get(index);
+ }
+
+ /**
+ * Method getFeatures.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.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);
+ }
+
+}