-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.schemabinding.version2;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class JSeq.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JSeq 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 java.lang.String _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
- this._featuresList = new java.util.Vector();\r
- this._pdbidsList = new java.util.Vector();\r
- this._hiddenSequencesList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vFeatures\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addFeatures(\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._featuresList.addElement(vFeatures);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vFeatures\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addFeatures(final int index,\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._featuresList.add(index, vFeatures);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenSequences\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addHiddenSequences(final int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._hiddenSequencesList.addElement(new java.lang.Integer(\r
- vHiddenSequences));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenSequences\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addHiddenSequences(final int index, final int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._hiddenSequencesList.add(index, new java.lang.Integer(\r
- vHiddenSequences));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbids\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._pdbidsList.addElement(vPdbids);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vPdbids\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbids(final int index,\r
- final jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._pdbidsList.add(index, vPdbids);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteHidden()\r
- {\r
- this._has_hidden = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- * Method enumerateFeatures.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Features\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateFeatures()\r
- {\r
- return this._featuresList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateHiddenSequences.\r
- * \r
- * @return an Enumeration over all int elements\r
- */\r
- public java.util.Enumeration enumerateHiddenSequences()\r
- {\r
- return this._hiddenSequencesList.elements();\r
- }\r
-\r
- /**\r
- * Method enumeratePdbids.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Pdbids\r
- * elements\r
- */\r
- public java.util.Enumeration enumeratePdbids()\r
- {\r
- return this._pdbidsList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Method getFeatures.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.Features at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Features getFeatures(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._featuresList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getFeatures: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._featuresList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Features) _featuresList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getFeatures.Returns the contents of the collection in an Array.\r
- * <p>\r
- * Note: Just in case the collection contents are changing in another thread,\r
- * we pass a 0-length Array of the correct type into the API call. This way we\r
- * <i>know</i> that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.Features[] getFeatures()\r
- {\r
- jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];\r
- return (jalview.schemabinding.version2.Features[]) this._featuresList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getFeaturesCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getFeaturesCount()\r
- {\r
- return this._featuresList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'hidden'.\r
- * \r
- * @return the value of field 'Hidden'.\r
- */\r
- public boolean getHidden()\r
- {\r
- return this._hidden;\r
- }\r
-\r
- /**\r
- * Method getHiddenSequences.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- * @return the value of the int at the given index\r
- */\r
- public int getHiddenSequences(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenSequencesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "getHiddenSequences: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._hiddenSequencesList.size() - 1) + "]");\r
- }\r
-\r
- return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();\r
- }\r
-\r
- /**\r
- * Method getHiddenSequences.Returns the contents of the collection in an\r
- * Array.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public int[] getHiddenSequences()\r
- {\r
- int size = this._hiddenSequencesList.size();\r
- int[] array = new int[size];\r
- java.util.Iterator iter = _hiddenSequencesList.iterator();\r
- for (int index = 0; index < size; index++)\r
- {\r
- array[index] = ((java.lang.Integer) iter.next()).intValue();\r
- }\r
- return array;\r
- }\r
-\r
- /**\r
- * Method getHiddenSequencesCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getHiddenSequencesCount()\r
- {\r
- return this._hiddenSequencesList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return the value of field 'Id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- }\r
-\r
- /**\r
- * Method getPdbids.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.Pdbids at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.Pdbids getPdbids(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._pdbidsList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getPdbids: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._pdbidsList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);\r
- }\r
-\r
- /**\r
- * Method getPdbids.Returns the contents of the collection in an Array.\r
- * <p>\r
- * Note: Just in case the collection contents are changing in another thread,\r
- * we pass a 0-length Array of the correct type into the API call. This way we\r
- * <i>know</i> that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.Pdbids[] getPdbids()\r
- {\r
- jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];\r
- return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getPdbidsCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getPdbidsCount()\r
- {\r
- return this._pdbidsList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return the value of field 'Start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- }\r
-\r
- /**\r
- * Method hasColour.\r
- * \r
- * @return true if at least one Colour has been added\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasHidden.\r
- * \r
- * @return true if at least one Hidden has been added\r
- */\r
- public boolean hasHidden()\r
- {\r
- return this._has_hidden;\r
- }\r
-\r
- /**\r
- * Method hasStart.\r
- * \r
- * @return true if at least one Start has been added\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'hidden'.\r
- * \r
- * @return the value of field 'Hidden'.\r
- */\r
- public boolean isHidden()\r
- {\r
- return this._hidden;\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- */\r
- public void marshal(final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException\r
- * if an IOException occurs during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- */\r
- public void marshal(final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException,\r
- org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllFeatures()\r
- {\r
- this._featuresList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllHiddenSequences()\r
- {\r
- this._hiddenSequencesList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllPdbids()\r
- {\r
- this._pdbidsList.clear();\r
- }\r
-\r
- /**\r
- * Method removeFeatures.\r
- * \r
- * @param vFeatures\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeFeatures(\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- {\r
- boolean removed = _featuresList.remove(vFeatures);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeFeaturesAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Features removeFeaturesAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._featuresList.remove(index);\r
- return (jalview.schemabinding.version2.Features) obj;\r
- }\r
-\r
- /**\r
- * Method removeHiddenSequences.\r
- * \r
- * @param vHiddenSequences\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeHiddenSequences(final int vHiddenSequences)\r
- {\r
- boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(\r
- vHiddenSequences));\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeHiddenSequencesAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public int removeHiddenSequencesAt(final int index)\r
- {\r
- java.lang.Object obj = this._hiddenSequencesList.remove(index);\r
- return ((java.lang.Integer) obj).intValue();\r
- }\r
-\r
- /**\r
- * Method removePdbids.\r
- * \r
- * @param vPdbids\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removePdbids(\r
- final jalview.schemabinding.version2.Pdbids vPdbids)\r
- {\r
- boolean removed = _pdbidsList.remove(vPdbids);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removePdbidsAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Pdbids removePdbidsAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._pdbidsList.remove(index);\r
- return (jalview.schemabinding.version2.Pdbids) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour\r
- * the value of field 'colour'.\r
- */\r
- public void setColour(final int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vFeatures\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setFeatures(final int index,\r
- final jalview.schemabinding.version2.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._featuresList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setFeatures: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._featuresList.size() - 1) + "]");\r
- }\r
-\r
- this._featuresList.set(index, vFeatures);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vFeaturesArray\r
- */\r
- public void setFeatures(\r
- final jalview.schemabinding.version2.Features[] vFeaturesArray)\r
- {\r
- // -- copy array\r
- _featuresList.clear();\r
-\r
- for (int i = 0; i < vFeaturesArray.length; i++)\r
- {\r
- this._featuresList.add(vFeaturesArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'hidden'.\r
- * \r
- * @param hidden\r
- * the value of field 'hidden'.\r
- */\r
- public void setHidden(final boolean hidden)\r
- {\r
- this._hidden = hidden;\r
- this._has_hidden = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vHiddenSequences\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setHiddenSequences(final int index, final int vHiddenSequences)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._hiddenSequencesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "setHiddenSequences: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._hiddenSequencesList.size() - 1) + "]");\r
- }\r
-\r
- this._hiddenSequencesList.set(index, new java.lang.Integer(\r
- vHiddenSequences));\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vHiddenSequencesArray\r
- */\r
- public void setHiddenSequences(final int[] vHiddenSequencesArray)\r
- {\r
- // -- copy array\r
- _hiddenSequencesList.clear();\r
-\r
- for (int i = 0; i < vHiddenSequencesArray.length; i++)\r
- {\r
- this._hiddenSequencesList.add(new java.lang.Integer(\r
- vHiddenSequencesArray[i]));\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id\r
- * the value of field 'id'.\r
- */\r
- public void setId(final java.lang.String id)\r
- {\r
- this._id = id;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vPdbids\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setPdbids(final int index,\r
- final jalview.schemabinding.version2.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._pdbidsList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setPdbids: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._pdbidsList.size() - 1) + "]");\r
- }\r
-\r
- this._pdbidsList.set(index, vPdbids);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbidsArray\r
- */\r
- public void setPdbids(\r
- final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)\r
- {\r
- // -- copy array\r
- _pdbidsList.clear();\r
-\r
- for (int i = 0; i < vPdbidsArray.length; i++)\r
- {\r
- this._pdbidsList.add(vPdbidsArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start\r
- * the value of field 'start'.\r
- */\r
- public void setStart(final int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- * @return the unmarshaled jalview.schemabinding.version2.JSeq\r
- */\r
- public static jalview.schemabinding.version2.JSeq unmarshal(\r
- final 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(\r
- jalview.schemabinding.version2.JSeq.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- */\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
-}\r
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview.
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * 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