-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
-\r
-import org.exolab.castor.xml.*;\r
-\r
-/**\r
- * Class JSeq.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class JSeq\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _colour\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- /**\r
- * Field _start\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * Field _id\r
- */\r
- private int _id;\r
-\r
- /**\r
- * keeps track of state for field: _id\r
- */\r
- private boolean _has_id;\r
-\r
- /**\r
- * Field _hidden\r
- */\r
- private boolean _hidden;\r
-\r
- /**\r
- * keeps track of state for field: _hidden\r
- */\r
- private boolean _has_hidden;\r
-\r
- /**\r
- * Field _featuresList\r
- */\r
- private java.util.Vector _featuresList;\r
-\r
- /**\r
- * Field _pdbidsList\r
- */\r
- private java.util.Vector _pdbidsList;\r
-\r
- /**\r
- * Field _hiddenSequencesList\r
- */\r
- private java.util.Vector _hiddenSequencesList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JSeq()\r
- {\r
- super();\r
- _featuresList = new Vector();\r
- _pdbidsList = new Vector();\r
- _hiddenSequencesList = new Vector();\r
- } //-- jalview.schemabinding.version2.JSeq()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addFeatures\r
- *\r
- *\r
- *\r
- * @param vFeatures\r
- */\r
- public void addFeatures(jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.addElement(vFeatures);\r
- } //-- void addFeatures(jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Method addFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vFeatures\r
- */\r
- public void addFeatures(int index,\r
- jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.insertElementAt(vFeatures, index);\r
- } //-- void addFeatures(int, jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Method addHiddenSequences\r
- *\r
- *\r
- *\r
- * @param vHiddenSequences\r
- */\r
- public void addHiddenSequences(int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
- } //-- void addHiddenSequences(int)\r
-\r
- /**\r
- * Method addHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vHiddenSequences\r
- */\r
- public void addHiddenSequences(int index, int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences),\r
- index);\r
- } //-- void addHiddenSequences(int, int)\r
-\r
- /**\r
- * Method addPdbids\r
- *\r
- *\r
- *\r
- * @param vPdbids\r
- */\r
- public void addPdbids(jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.addElement(vPdbids);\r
- } //-- void addPdbids(jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Method addPdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vPdbids\r
- */\r
- public void addPdbids(int index,\r
- jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.insertElementAt(vPdbids, index);\r
- } //-- void addPdbids(int, jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Method deleteColour\r
- *\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- } //-- void deleteColour()\r
-\r
- /**\r
- * Method deleteEnd\r
- *\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- } //-- void deleteEnd()\r
-\r
- /**\r
- * Method deleteHidden\r
- *\r
- */\r
- public void deleteHidden()\r
- {\r
- this._has_hidden = false;\r
- } //-- void deleteHidden()\r
-\r
- /**\r
- * Method deleteId\r
- *\r
- */\r
- public void deleteId()\r
- {\r
- this._has_id = false;\r
- } //-- void deleteId()\r
-\r
- /**\r
- * Method deleteStart\r
- *\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- } //-- void deleteStart()\r
-\r
- /**\r
- * Method enumerateFeatures\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateFeatures()\r
- {\r
- return _featuresList.elements();\r
- } //-- java.util.Enumeration enumerateFeatures()\r
-\r
- /**\r
- * Method enumerateHiddenSequences\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateHiddenSequences()\r
- {\r
- return _hiddenSequencesList.elements();\r
- } //-- java.util.Enumeration enumerateHiddenSequences()\r
-\r
- /**\r
- * Method enumeratePdbids\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumeratePdbids()\r
- {\r
- return _pdbidsList.elements();\r
- } //-- java.util.Enumeration enumeratePdbids()\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- *\r
- * @return int\r
- * @return the value of field 'colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- } //-- int getColour()\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- *\r
- * @return int\r
- * @return the value of field 'end'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- } //-- int getEnd()\r
-\r
- /**\r
- * Method getFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features getFeatures(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _featuresList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.Features) _featuresList.elementAt(\r
- index);\r
- } //-- jalview.schemabinding.version2.Features getFeatures(int)\r
-\r
- /**\r
- * Method getFeatures\r
- *\r
- *\r
- *\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features[] getFeatures()\r
- {\r
- int size = _featuresList.size();\r
- jalview.schemabinding.version2.Features[] mArray = new jalview.\r
- schemabinding.version2.Features[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.Features) _featuresList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Features[] getFeatures()\r
-\r
- /**\r
- * Method getFeaturesCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getFeaturesCount()\r
- {\r
- return _featuresList.size();\r
- } //-- int getFeaturesCount()\r
-\r
- /**\r
- * Returns the value of field 'hidden'.\r
- *\r
- * @return boolean\r
- * @return the value of field 'hidden'.\r
- */\r
- public boolean getHidden()\r
- {\r
- return this._hidden;\r
- } //-- boolean getHidden()\r
-\r
- /**\r
- * Method getHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return int\r
- */\r
- public int getHiddenSequences(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _hiddenSequencesList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return ( (java.lang.Integer) _hiddenSequencesList.elementAt(index)).\r
- intValue();\r
- } //-- int getHiddenSequences(int)\r
-\r
- /**\r
- * Method getHiddenSequences\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int[] getHiddenSequences()\r
- {\r
- int size = _hiddenSequencesList.size();\r
- int[] mArray = new int[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = ( (java.lang.Integer) _hiddenSequencesList.elementAt(\r
- index)).intValue();\r
- }\r
- return mArray;\r
- } //-- int[] getHiddenSequences()\r
-\r
- /**\r
- * Method getHiddenSequencesCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getHiddenSequencesCount()\r
- {\r
- return _hiddenSequencesList.size();\r
- } //-- int getHiddenSequencesCount()\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- *\r
- * @return int\r
- * @return the value of field 'id'.\r
- */\r
- public int getId()\r
- {\r
- return this._id;\r
- } //-- int getId()\r
-\r
- /**\r
- * Method getPdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids getPdbids(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _pdbidsList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.Pdbids) _pdbidsList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Pdbids getPdbids(int)\r
-\r
- /**\r
- * Method getPdbids\r
- *\r
- *\r
- *\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids[] getPdbids()\r
- {\r
- int size = _pdbidsList.size();\r
- jalview.schemabinding.version2.Pdbids[] mArray = new jalview.schemabinding.\r
- version2.Pdbids[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.Pdbids) _pdbidsList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Pdbids[] getPdbids()\r
-\r
- /**\r
- * Method getPdbidsCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getPdbidsCount()\r
- {\r
- return _pdbidsList.size();\r
- } //-- int getPdbidsCount()\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- *\r
- * @return int\r
- * @return the value of field 'start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- } //-- int getStart()\r
-\r
- /**\r
- * Method hasColour\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- } //-- boolean hasColour()\r
-\r
- /**\r
- * Method hasEnd\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- } //-- boolean hasEnd()\r
-\r
- /**\r
- * Method hasHidden\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasHidden()\r
- {\r
- return this._has_hidden;\r
- } //-- boolean hasHidden()\r
-\r
- /**\r
- * Method hasId\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasId()\r
- {\r
- return this._has_id;\r
- } //-- boolean hasId()\r
-\r
- /**\r
- * Method hasStart\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid()\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
- /**\r
- * Method removeAllFeatures\r
- *\r
- */\r
- public void removeAllFeatures()\r
- {\r
- _featuresList.removeAllElements();\r
- } //-- void removeAllFeatures()\r
-\r
- /**\r
- * Method removeAllHiddenSequences\r
- *\r
- */\r
- public void removeAllHiddenSequences()\r
- {\r
- _hiddenSequencesList.removeAllElements();\r
- } //-- void removeAllHiddenSequences()\r
-\r
- /**\r
- * Method removeAllPdbids\r
- *\r
- */\r
- public void removeAllPdbids()\r
- {\r
- _pdbidsList.removeAllElements();\r
- } //-- void removeAllPdbids()\r
-\r
- /**\r
- * Method removeFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Features\r
- */\r
- public jalview.schemabinding.version2.Features removeFeatures(int index)\r
- {\r
- java.lang.Object obj = _featuresList.elementAt(index);\r
- _featuresList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Features) obj;\r
- } //-- jalview.schemabinding.version2.Features removeFeatures(int)\r
-\r
- /**\r
- * Method removeHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return int\r
- */\r
- public int removeHiddenSequences(int index)\r
- {\r
- java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
- _hiddenSequencesList.removeElementAt(index);\r
- return ( (java.lang.Integer) obj).intValue();\r
- } //-- int removeHiddenSequences(int)\r
-\r
- /**\r
- * Method removePdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Pdbids\r
- */\r
- public jalview.schemabinding.version2.Pdbids removePdbids(int index)\r
- {\r
- java.lang.Object obj = _pdbidsList.elementAt(index);\r
- _pdbidsList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Pdbids) obj;\r
- } //-- jalview.schemabinding.version2.Pdbids removePdbids(int)\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- *\r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- } //-- void setColour(int)\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- *\r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- } //-- void setEnd(int)\r
-\r
- /**\r
- * Method setFeatures\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vFeatures\r
- */\r
- public void setFeatures(int index,\r
- jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _featuresList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _featuresList.setElementAt(vFeatures, index);\r
- } //-- void setFeatures(int, jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Method setFeatures\r
- *\r
- *\r
- *\r
- * @param featuresArray\r
- */\r
- public void setFeatures(jalview.schemabinding.version2.Features[]\r
- featuresArray)\r
- {\r
- //-- copy array\r
- _featuresList.removeAllElements();\r
- for (int i = 0; i < featuresArray.length; i++)\r
- {\r
- _featuresList.addElement(featuresArray[i]);\r
- }\r
- } //-- void setFeatures(jalview.schemabinding.version2.Features)\r
-\r
- /**\r
- * Sets the value of field 'hidden'.\r
- *\r
- * @param hidden the value of field 'hidden'.\r
- */\r
- public void setHidden(boolean hidden)\r
- {\r
- this._hidden = hidden;\r
- this._has_hidden = true;\r
- } //-- void setHidden(boolean)\r
-\r
- /**\r
- * Method setHiddenSequences\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vHiddenSequences\r
- */\r
- public void setHiddenSequences(int index, int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _hiddenSequencesList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences),\r
- index);\r
- } //-- void setHiddenSequences(int, int)\r
-\r
- /**\r
- * Method setHiddenSequences\r
- *\r
- *\r
- *\r
- * @param hiddenSequencesArray\r
- */\r
- public void setHiddenSequences(int[] hiddenSequencesArray)\r
- {\r
- //-- copy array\r
- _hiddenSequencesList.removeAllElements();\r
- for (int i = 0; i < hiddenSequencesArray.length; i++)\r
- {\r
- _hiddenSequencesList.addElement(new java.lang.Integer(\r
- hiddenSequencesArray[i]));\r
- }\r
- } //-- void setHiddenSequences(int)\r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- *\r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(int id)\r
- {\r
- this._id = id;\r
- this._has_id = true;\r
- } //-- void setId(int)\r
-\r
- /**\r
- * Method setPdbids\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vPdbids\r
- */\r
- public void setPdbids(int index,\r
- jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _pdbidsList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _pdbidsList.setElementAt(vPdbids, index);\r
- } //-- void setPdbids(int, jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Method setPdbids\r
- *\r
- *\r
- *\r
- * @param pdbidsArray\r
- */\r
- public void setPdbids(jalview.schemabinding.version2.Pdbids[] pdbidsArray)\r
- {\r
- //-- copy array\r
- _pdbidsList.removeAllElements();\r
- for (int i = 0; i < pdbidsArray.length; i++)\r
- {\r
- _pdbidsList.addElement(pdbidsArray[i]);\r
- }\r
- } //-- void setPdbids(jalview.schemabinding.version2.Pdbids)\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- *\r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- } //-- void setStart(int)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.\r
- schemabinding.version2.JSeq.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
- validator.validate(this);\r
- } //-- void validate()\r
-\r
-}\r
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, 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 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 java.lang.String _id;
+
+ /**
+ * Field _hidden.
+ */
+ private boolean _hidden;
+
+ /**
+ * keeps track of state for field: _hidden
+ */
+ private boolean _has_hidden;
+
+ /**
+ * Field _featuresList.
+ */
+ private java.util.Vector _featuresList;
+
+ /**
+ * Field _pdbidsList.
+ */
+ private java.util.Vector _pdbidsList;
+
+ /**
+ * Field _hiddenSequencesList.
+ */
+ private java.util.Vector _hiddenSequencesList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JSeq() {
+ super();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ this._hiddenSequencesList = 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.schemabinding.version2.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.schemabinding.version2.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenSequences
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addHiddenSequences(
+ final int vHiddenSequences)
+ throws java.lang.IndexOutOfBoundsException {
+ this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenSequences
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addHiddenSequences(
+ final int index,
+ final int vHiddenSequences)
+ throws java.lang.IndexOutOfBoundsException {
+ this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final jalview.schemabinding.version2.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.schemabinding.version2.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 deleteHidden(
+ ) {
+ this._has_hidden= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.Features elements
+ */
+ public java.util.Enumeration enumerateFeatures(
+ ) {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumerateHiddenSequences.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateHiddenSequences(
+ ) {
+ return this._hiddenSequencesList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.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.schemabinding.version2.Features at the given index
+ */
+ public jalview.schemabinding.version2.Features getFeatures(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Features) _featuresList.get(index);
+ }
+
+ /**
+ * Method getFeatures.Returns the contents of the collection in
+ * an Array. <p>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 <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Features[] getFeatures(
+ ) {
+ jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+ return (jalview.schemabinding.version2.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 'hidden'.
+ *
+ * @return the value of field 'Hidden'.
+ */
+ public boolean getHidden(
+ ) {
+ return this._hidden;
+ }
+
+ /**
+ * Method getHiddenSequences.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getHiddenSequences(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {
+ throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+ }
+
+ /**
+ * Method getHiddenSequences.Returns the contents of the
+ * collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getHiddenSequences(
+ ) {
+ int size = this._hiddenSequencesList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _hiddenSequencesList.iterator();
+ for (int index = 0; index < size; index++) {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getHiddenSequencesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getHiddenSequencesCount(
+ ) {
+ return this._hiddenSequencesList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String 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.schemabinding.version2.Pdbids at the given index
+ */
+ public jalview.schemabinding.version2.Pdbids getPdbids(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+ }
+
+ /**
+ * Method getPdbids.Returns the contents of the collection in
+ * an Array. <p>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 <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.Pdbids[] getPdbids(
+ ) {
+ jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+ return (jalview.schemabinding.version2.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 hasHidden.
+ *
+ * @return true if at least one Hidden has been added
+ */
+ public boolean hasHidden(
+ ) {
+ return this._has_hidden;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'hidden'.
+ *
+ * @return the value of field 'Hidden'.
+ */
+ public boolean isHidden(
+ ) {
+ return this._hidden;
+ }
+
+ /**
+ * 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 removeAllHiddenSequences(
+ ) {
+ this._hiddenSequencesList.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.schemabinding.version2.Features vFeatures) {
+ boolean removed = _featuresList.remove(vFeatures);
+ return removed;
+ }
+
+ /**
+ * Method removeFeaturesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Features removeFeaturesAt(
+ final int index) {
+ java.lang.Object obj = this._featuresList.remove(index);
+ return (jalview.schemabinding.version2.Features) obj;
+ }
+
+ /**
+ * Method removeHiddenSequences.
+ *
+ * @param vHiddenSequences
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeHiddenSequences(
+ final int vHiddenSequences) {
+ boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));
+ return removed;
+ }
+
+ /**
+ * Method removeHiddenSequencesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeHiddenSequencesAt(
+ final int index) {
+ java.lang.Object obj = this._hiddenSequencesList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Method removePdbids.
+ *
+ * @param vPdbids
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbids(
+ final jalview.schemabinding.version2.Pdbids vPdbids) {
+ boolean removed = _pdbidsList.remove(vPdbids);
+ return removed;
+ }
+
+ /**
+ * Method removePdbidsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+ final int index) {
+ java.lang.Object obj = this._pdbidsList.remove(index);
+ return (jalview.schemabinding.version2.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.schemabinding.version2.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ this._featuresList.set(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vFeaturesArray
+ */
+ public void setFeatures(
+ final jalview.schemabinding.version2.Features[] vFeaturesArray) {
+ //-- copy array
+ _featuresList.clear();
+
+ for (int i = 0; i < vFeaturesArray.length; i++) {
+ this._featuresList.add(vFeaturesArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'hidden'.
+ *
+ * @param hidden the value of field 'hidden'.
+ */
+ public void setHidden(
+ final boolean hidden) {
+ this._hidden = hidden;
+ this._has_hidden = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vHiddenSequences
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setHiddenSequences(
+ final int index,
+ final int vHiddenSequences)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._hiddenSequencesList.size()) {
+ throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
+ }
+
+ this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));
+ }
+
+ /**
+ *
+ *
+ * @param vHiddenSequencesArray
+ */
+ public void setHiddenSequences(
+ final int[] vHiddenSequencesArray) {
+ //-- copy array
+ _hiddenSequencesList.clear();
+
+ for (int i = 0; i < vHiddenSequencesArray.length; i++) {
+ this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @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.schemabinding.version2.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ this._pdbidsList.set(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbidsArray
+ */
+ public void setPdbids(
+ final jalview.schemabinding.version2.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.schemabinding.version2.JSeq
+ */
+ public static jalview.schemabinding.version2.JSeq unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff