-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\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 JGroup.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JGroup implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\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 _name.\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _colour.\r
- */\r
- private java.lang.String _colour;\r
-\r
- /**\r
- * Field _consThreshold.\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold.\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _outlineColour.\r
- */\r
- private int _outlineColour;\r
-\r
- /**\r
- * keeps track of state for field: _outlineColour\r
- */\r
- private boolean _has_outlineColour;\r
-\r
- /**\r
- * Field _displayBoxes.\r
- */\r
- private boolean _displayBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _displayBoxes\r
- */\r
- private boolean _has_displayBoxes;\r
-\r
- /**\r
- * Field _displayText.\r
- */\r
- private boolean _displayText;\r
-\r
- /**\r
- * keeps track of state for field: _displayText\r
- */\r
- private boolean _has_displayText;\r
-\r
- /**\r
- * Field _colourText.\r
- */\r
- private boolean _colourText;\r
-\r
- /**\r
- * keeps track of state for field: _colourText\r
- */\r
- private boolean _has_colourText;\r
-\r
- /**\r
- * Field _textCol1.\r
- */\r
- private int _textCol1;\r
-\r
- /**\r
- * keeps track of state for field: _textCol1\r
- */\r
- private boolean _has_textCol1;\r
-\r
- /**\r
- * Field _textCol2.\r
- */\r
- private int _textCol2;\r
-\r
- /**\r
- * keeps track of state for field: _textCol2\r
- */\r
- private boolean _has_textCol2;\r
-\r
- /**\r
- * Field _textColThreshold.\r
- */\r
- private int _textColThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _textColThreshold\r
- */\r
- private boolean _has_textColThreshold;\r
-\r
- /**\r
- * Field _showUnconserved.\r
- */\r
- private boolean _showUnconserved;\r
-\r
- /**\r
- * keeps track of state for field: _showUnconserved\r
- */\r
- private boolean _has_showUnconserved;\r
-\r
- /**\r
- * Field _ignoreGapsinConsensus.\r
- */\r
- private boolean _ignoreGapsinConsensus = true;\r
-\r
- /**\r
- * keeps track of state for field: _ignoreGapsinConsensus\r
- */\r
- private boolean _has_ignoreGapsinConsensus;\r
-\r
- /**\r
- * Field _showConsensusHistogram.\r
- */\r
- private boolean _showConsensusHistogram = true;\r
-\r
- /**\r
- * keeps track of state for field: _showConsensusHistogram\r
- */\r
- private boolean _has_showConsensusHistogram;\r
-\r
- /**\r
- * Field _showSequenceLogo.\r
- */\r
- private boolean _showSequenceLogo = false;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceLogo\r
- */\r
- private boolean _has_showSequenceLogo;\r
-\r
- /**\r
- * Optional sequence group ID (only needs to be unique for this alignment)\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _seqList.\r
- */\r
- private java.util.Vector _seqList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JGroup()\r
- {\r
- super();\r
- this._seqList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSeq(final java.lang.String vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._seqList.addElement(vSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSeq(final int index, final java.lang.String vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._seqList.add(index, vSeq);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteColourText()\r
- {\r
- this._has_colourText = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplayBoxes()\r
- {\r
- this._has_displayBoxes = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteDisplayText()\r
- {\r
- this._has_displayText = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteIgnoreGapsinConsensus()\r
- {\r
- this._has_ignoreGapsinConsensus = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteOutlineColour()\r
- {\r
- this._has_outlineColour = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowConsensusHistogram()\r
- {\r
- this._has_showConsensusHistogram = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowSequenceLogo()\r
- {\r
- this._has_showSequenceLogo = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteShowUnconserved()\r
- {\r
- this._has_showUnconserved = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol1()\r
- {\r
- this._has_textCol1 = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextCol2()\r
- {\r
- this._has_textCol2 = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteTextColThreshold()\r
- {\r
- this._has_textColThreshold = false;\r
- }\r
-\r
- /**\r
- * Method enumerateSeq.\r
- * \r
- * @return an Enumeration over all java.lang.String elements\r
- */\r
- public java.util.Enumeration enumerateSeq()\r
- {\r
- return this._seqList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return the value of field 'Colour'.\r
- */\r
- public java.lang.String getColour()\r
- {\r
- return this._colour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourText'.\r
- * \r
- * @return the value of field 'ColourText'.\r
- */\r
- public boolean getColourText()\r
- {\r
- return this._colourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return the value of field 'ConsThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayBoxes'.\r
- * \r
- * @return the value of field 'DisplayBoxes'.\r
- */\r
- public boolean getDisplayBoxes()\r
- {\r
- return this._displayBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayText'.\r
- * \r
- * @return the value of field 'DisplayText'.\r
- */\r
- public boolean getDisplayText()\r
- {\r
- return this._displayText;\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
- * Returns the value of field 'id'. The field 'id' has the following\r
- * description: Optional sequence group ID (only needs to be unique for this\r
- * alignment)\r
- * \r
- * \r
- * @return the value of field 'Id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ignoreGapsinConsensus'.\r
- * \r
- * @return the value of field 'IgnoreGapsinConsensus'.\r
- */\r
- public boolean getIgnoreGapsinConsensus()\r
- {\r
- return this._ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return the value of field 'Name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'outlineColour'.\r
- * \r
- * @return the value of field 'OutlineColour'.\r
- */\r
- public int getOutlineColour()\r
- {\r
- return this._outlineColour;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return the value of field 'PidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- }\r
-\r
- /**\r
- * Method getSeq.\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 java.lang.String at the given index\r
- */\r
- public java.lang.String getSeq(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index\r
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
- }\r
-\r
- return (java.lang.String) _seqList.get(index);\r
- }\r
-\r
- /**\r
- * Method getSeq.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 java.lang.String[] getSeq()\r
- {\r
- java.lang.String[] array = new java.lang.String[0];\r
- return (java.lang.String[]) this._seqList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSeqCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSeqCount()\r
- {\r
- return this._seqList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showConsensusHistogram'.\r
- * \r
- * @return the value of field 'ShowConsensusHistogram'.\r
- */\r
- public boolean getShowConsensusHistogram()\r
- {\r
- return this._showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceLogo'.\r
- * \r
- * @return the value of field 'ShowSequenceLogo'.\r
- */\r
- public boolean getShowSequenceLogo()\r
- {\r
- return this._showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean getShowUnconserved()\r
- {\r
- return this._showUnconserved;\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
- * Returns the value of field 'textCol1'.\r
- * \r
- * @return the value of field 'TextCol1'.\r
- */\r
- public int getTextCol1()\r
- {\r
- return this._textCol1;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textCol2'.\r
- * \r
- * @return the value of field 'TextCol2'.\r
- */\r
- public int getTextCol2()\r
- {\r
- return this._textCol2;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'textColThreshold'.\r
- * \r
- * @return the value of field 'TextColThreshold'.\r
- */\r
- public int getTextColThreshold()\r
- {\r
- return this._textColThreshold;\r
- }\r
-\r
- /**\r
- * Method hasColourText.\r
- * \r
- * @return true if at least one ColourText has been added\r
- */\r
- public boolean hasColourText()\r
- {\r
- return this._has_colourText;\r
- }\r
-\r
- /**\r
- * Method hasConsThreshold.\r
- * \r
- * @return true if at least one ConsThreshold has been added\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- }\r
-\r
- /**\r
- * Method hasDisplayBoxes.\r
- * \r
- * @return true if at least one DisplayBoxes has been added\r
- */\r
- public boolean hasDisplayBoxes()\r
- {\r
- return this._has_displayBoxes;\r
- }\r
-\r
- /**\r
- * Method hasDisplayText.\r
- * \r
- * @return true if at least one DisplayText has been added\r
- */\r
- public boolean hasDisplayText()\r
- {\r
- return this._has_displayText;\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 hasIgnoreGapsinConsensus.\r
- * \r
- * @return true if at least one IgnoreGapsinConsensus has been added\r
- */\r
- public boolean hasIgnoreGapsinConsensus()\r
- {\r
- return this._has_ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Method hasOutlineColour.\r
- * \r
- * @return true if at least one OutlineColour has been added\r
- */\r
- public boolean hasOutlineColour()\r
- {\r
- return this._has_outlineColour;\r
- }\r
-\r
- /**\r
- * Method hasPidThreshold.\r
- * \r
- * @return true if at least one PidThreshold has been added\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- }\r
-\r
- /**\r
- * Method hasShowConsensusHistogram.\r
- * \r
- * @return true if at least one ShowConsensusHistogram has been added\r
- */\r
- public boolean hasShowConsensusHistogram()\r
- {\r
- return this._has_showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Method hasShowSequenceLogo.\r
- * \r
- * @return true if at least one ShowSequenceLogo has been added\r
- */\r
- public boolean hasShowSequenceLogo()\r
- {\r
- return this._has_showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Method hasShowUnconserved.\r
- * \r
- * @return true if at least one ShowUnconserved has been added\r
- */\r
- public boolean hasShowUnconserved()\r
- {\r
- return this._has_showUnconserved;\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
- * Method hasTextCol1.\r
- * \r
- * @return true if at least one TextCol1 has been added\r
- */\r
- public boolean hasTextCol1()\r
- {\r
- return this._has_textCol1;\r
- }\r
-\r
- /**\r
- * Method hasTextCol2.\r
- * \r
- * @return true if at least one TextCol2 has been added\r
- */\r
- public boolean hasTextCol2()\r
- {\r
- return this._has_textCol2;\r
- }\r
-\r
- /**\r
- * Method hasTextColThreshold.\r
- * \r
- * @return true if at least one TextColThreshold has been added\r
- */\r
- public boolean hasTextColThreshold()\r
- {\r
- return this._has_textColThreshold;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'colourText'.\r
- * \r
- * @return the value of field 'ColourText'.\r
- */\r
- public boolean isColourText()\r
- {\r
- return this._colourText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayBoxes'.\r
- * \r
- * @return the value of field 'DisplayBoxes'.\r
- */\r
- public boolean isDisplayBoxes()\r
- {\r
- return this._displayBoxes;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'displayText'.\r
- * \r
- * @return the value of field 'DisplayText'.\r
- */\r
- public boolean isDisplayText()\r
- {\r
- return this._displayText;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'ignoreGapsinConsensus'.\r
- * \r
- * @return the value of field 'IgnoreGapsinConsensus'.\r
- */\r
- public boolean isIgnoreGapsinConsensus()\r
- {\r
- return this._ignoreGapsinConsensus;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showConsensusHistogram'.\r
- * \r
- * @return the value of field 'ShowConsensusHistogram'.\r
- */\r
- public boolean isShowConsensusHistogram()\r
- {\r
- return this._showConsensusHistogram;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showSequenceLogo'.\r
- * \r
- * @return the value of field 'ShowSequenceLogo'.\r
- */\r
- public boolean isShowSequenceLogo()\r
- {\r
- return this._showSequenceLogo;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'showUnconserved'.\r
- * \r
- * @return the value of field 'ShowUnconserved'.\r
- */\r
- public boolean isShowUnconserved()\r
- {\r
- return this._showUnconserved;\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 removeAllSeq()\r
- {\r
- this._seqList.clear();\r
- }\r
-\r
- /**\r
- * Method removeSeq.\r
- * \r
- * @param vSeq\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSeq(final java.lang.String vSeq)\r
- {\r
- boolean removed = _seqList.remove(vSeq);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSeqAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public java.lang.String removeSeqAt(final int index)\r
- {\r
- java.lang.Object obj = this._seqList.remove(index);\r
- return (java.lang.String) 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 java.lang.String colour)\r
- {\r
- this._colour = colour;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'colourText'.\r
- * \r
- * @param colourText\r
- * the value of field 'colourText'.\r
- */\r
- public void setColourText(final boolean colourText)\r
- {\r
- this._colourText = colourText;\r
- this._has_colourText = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold\r
- * the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(final int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayBoxes'.\r
- * \r
- * @param displayBoxes\r
- * the value of field 'displayBoxes'.\r
- */\r
- public void setDisplayBoxes(final boolean displayBoxes)\r
- {\r
- this._displayBoxes = displayBoxes;\r
- this._has_displayBoxes = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'displayText'.\r
- * \r
- * @param displayText\r
- * the value of field 'displayText'.\r
- */\r
- public void setDisplayText(final boolean displayText)\r
- {\r
- this._displayText = displayText;\r
- this._has_displayText = 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
- * Sets the value of field 'id'. The field 'id' has the following description:\r
- * Optional sequence group ID (only needs to be unique for this alignment)\r
- * \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
- * Sets the value of field 'ignoreGapsinConsensus'.\r
- * \r
- * @param ignoreGapsinConsensus\r
- * the value of field 'ignoreGapsinConsensus'.\r
- */\r
- public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)\r
- {\r
- this._ignoreGapsinConsensus = ignoreGapsinConsensus;\r
- this._has_ignoreGapsinConsensus = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name\r
- * the value of field 'name'.\r
- */\r
- public void setName(final java.lang.String name)\r
- {\r
- this._name = name;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'outlineColour'.\r
- * \r
- * @param outlineColour\r
- * the value of field 'outlineColour'.\r
- */\r
- public void setOutlineColour(final int outlineColour)\r
- {\r
- this._outlineColour = outlineColour;\r
- this._has_outlineColour = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold\r
- * the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(final int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSeq(final int index, final java.lang.String vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._seqList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index\r
- + "' not in range [0.." + (this._seqList.size() - 1) + "]");\r
- }\r
-\r
- this._seqList.set(index, vSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSeqArray\r
- */\r
- public void setSeq(final java.lang.String[] vSeqArray)\r
- {\r
- // -- copy array\r
- _seqList.clear();\r
-\r
- for (int i = 0; i < vSeqArray.length; i++)\r
- {\r
- this._seqList.add(vSeqArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showConsensusHistogram'.\r
- * \r
- * @param showConsensusHistogram\r
- * the value of field 'showConsensusHistogram'.\r
- */\r
- public void setShowConsensusHistogram(final boolean showConsensusHistogram)\r
- {\r
- this._showConsensusHistogram = showConsensusHistogram;\r
- this._has_showConsensusHistogram = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showSequenceLogo'.\r
- * \r
- * @param showSequenceLogo\r
- * the value of field 'showSequenceLogo'\r
- */\r
- public void setShowSequenceLogo(final boolean showSequenceLogo)\r
- {\r
- this._showSequenceLogo = showSequenceLogo;\r
- this._has_showSequenceLogo = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'showUnconserved'.\r
- * \r
- * @param showUnconserved\r
- * the value of field 'showUnconserved'.\r
- */\r
- public void setShowUnconserved(final boolean showUnconserved)\r
- {\r
- this._showUnconserved = showUnconserved;\r
- this._has_showUnconserved = true;\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
- * Sets the value of field 'textCol1'.\r
- * \r
- * @param textCol1\r
- * the value of field 'textCol1'.\r
- */\r
- public void setTextCol1(final int textCol1)\r
- {\r
- this._textCol1 = textCol1;\r
- this._has_textCol1 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textCol2'.\r
- * \r
- * @param textCol2\r
- * the value of field 'textCol2'.\r
- */\r
- public void setTextCol2(final int textCol2)\r
- {\r
- this._textCol2 = textCol2;\r
- this._has_textCol2 = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'textColThreshold'.\r
- * \r
- * @param textColThreshold\r
- * the value of field 'textColThreshold'\r
- */\r
- public void setTextColThreshold(final int textColThreshold)\r
- {\r
- this._textColThreshold = textColThreshold;\r
- this._has_textColThreshold = 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.JGroup\r
- */\r
- public static jalview.schemabinding.version2.JGroup 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.JGroup) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.JGroup.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 2.8.2b1)
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.util.MessageManager;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JGroup.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JGroup implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * 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 _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _textCol1.
+ */
+ private int _textCol1;
+
+ /**
+ * keeps track of state for field: _textCol1
+ */
+ private boolean _has_textCol1;
+
+ /**
+ * Field _textCol2.
+ */
+ private int _textCol2;
+
+ /**
+ * keeps track of state for field: _textCol2
+ */
+ private boolean _has_textCol2;
+
+ /**
+ * Field _textColThreshold.
+ */
+ private int _textColThreshold;
+
+ /**
+ * keeps track of state for field: _textColThreshold
+ */
+ private boolean _has_textColThreshold;
+
+ /**
+ * Field _showUnconserved.
+ */
+ private boolean _showUnconserved;
+
+ /**
+ * keeps track of state for field: _showUnconserved
+ */
+ private boolean _has_showUnconserved;
+
+ /**
+ * Field _ignoreGapsinConsensus.
+ */
+ private boolean _ignoreGapsinConsensus = true;
+
+ /**
+ * keeps track of state for field: _ignoreGapsinConsensus
+ */
+ private boolean _has_ignoreGapsinConsensus;
+
+ /**
+ * Field _showConsensusHistogram.
+ */
+ private boolean _showConsensusHistogram = true;
+
+ /**
+ * keeps track of state for field: _showConsensusHistogram
+ */
+ private boolean _has_showConsensusHistogram;
+
+ /**
+ * Field _showSequenceLogo.
+ */
+ private boolean _showSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _showSequenceLogo
+ */
+ private boolean _has_showSequenceLogo;
+
+ /**
+ * Field _normaliseSequenceLogo.
+ */
+ private boolean _normaliseSequenceLogo = false;
+
+ /**
+ * keeps track of state for field: _normaliseSequenceLogo
+ */
+ private boolean _has_normaliseSequenceLogo;
+
+ /**
+ * Optional sequence group ID (only needs to be unique for this alignment)
+ *
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+ /**
+ * Field _annotationColours.
+ */
+ private jalview.schemabinding.version2.AnnotationColours _annotationColours;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JGroup()
+ {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final java.lang.String vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.addElement(vSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int index, final java.lang.String vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.add(index, vSeq);
+ }
+
+ /**
+ */
+ public void deleteColourText()
+ {
+ this._has_colourText = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes()
+ {
+ this._has_displayBoxes = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText()
+ {
+ this._has_displayText = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteIgnoreGapsinConsensus()
+ {
+ this._has_ignoreGapsinConsensus = false;
+ }
+
+ /**
+ */
+ public void deleteNormaliseSequenceLogo()
+ {
+ this._has_normaliseSequenceLogo = false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour()
+ {
+ this._has_outlineColour = false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteShowConsensusHistogram()
+ {
+ this._has_showConsensusHistogram = false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceLogo()
+ {
+ this._has_showSequenceLogo = false;
+ }
+
+ /**
+ */
+ public void deleteShowUnconserved()
+ {
+ this._has_showUnconserved = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol1()
+ {
+ this._has_textCol1 = false;
+ }
+
+ /**
+ */
+ public void deleteTextCol2()
+ {
+ this._has_textCol2 = false;
+ }
+
+ /**
+ */
+ public void deleteTextColThreshold()
+ {
+ this._has_textColThreshold = false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateSeq()
+ {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'annotationColours'.
+ *
+ * @return the value of field 'AnnotationColours'.
+ */
+ public jalview.schemabinding.version2.AnnotationColours getAnnotationColours()
+ {
+ return this._annotationColours;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Optional sequence group ID (only needs to be unique for this
+ * alignment)
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean getIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean getNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour()
+ {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
+ }
+
+ return (java.lang.String) _seqList.get(index);
+ }
+
+ /**
+ * Method getSeq.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 java.lang.String[] getSeq()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._seqList.toArray(array);
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount()
+ {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean getShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean getShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean getShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Returns the value of field 'textCol1'.
+ *
+ * @return the value of field 'TextCol1'.
+ */
+ public int getTextCol1()
+ {
+ return this._textCol1;
+ }
+
+ /**
+ * Returns the value of field 'textCol2'.
+ *
+ * @return the value of field 'TextCol2'.
+ */
+ public int getTextCol2()
+ {
+ return this._textCol2;
+ }
+
+ /**
+ * Returns the value of field 'textColThreshold'.
+ *
+ * @return the value of field 'TextColThreshold'.
+ */
+ public int getTextColThreshold()
+ {
+ return this._textColThreshold;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText()
+ {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes()
+ {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText()
+ {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasIgnoreGapsinConsensus.
+ *
+ * @return true if at least one IgnoreGapsinConsensus has been added
+ */
+ public boolean hasIgnoreGapsinConsensus()
+ {
+ return this._has_ignoreGapsinConsensus;
+ }
+
+ /**
+ * Method hasNormaliseSequenceLogo.
+ *
+ * @return true if at least one NormaliseSequenceLogo has been added
+ */
+ public boolean hasNormaliseSequenceLogo()
+ {
+ return this._has_normaliseSequenceLogo;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour()
+ {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasShowConsensusHistogram.
+ *
+ * @return true if at least one ShowConsensusHistogram has been added
+ */
+ public boolean hasShowConsensusHistogram()
+ {
+ return this._has_showConsensusHistogram;
+ }
+
+ /**
+ * Method hasShowSequenceLogo.
+ *
+ * @return true if at least one ShowSequenceLogo has been added
+ */
+ public boolean hasShowSequenceLogo()
+ {
+ return this._has_showSequenceLogo;
+ }
+
+ /**
+ * Method hasShowUnconserved.
+ *
+ * @return true if at least one ShowUnconserved has been added
+ */
+ public boolean hasShowUnconserved()
+ {
+ return this._has_showUnconserved;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Method hasTextCol1.
+ *
+ * @return true if at least one TextCol1 has been added
+ */
+ public boolean hasTextCol1()
+ {
+ return this._has_textCol1;
+ }
+
+ /**
+ * Method hasTextCol2.
+ *
+ * @return true if at least one TextCol2 has been added
+ */
+ public boolean hasTextCol2()
+ {
+ return this._has_textCol2;
+ }
+
+ /**
+ * Method hasTextColThreshold.
+ *
+ * @return true if at least one TextColThreshold has been added
+ */
+ public boolean hasTextColThreshold()
+ {
+ return this._has_textColThreshold;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'ignoreGapsinConsensus'.
+ *
+ * @return the value of field 'IgnoreGapsinConsensus'.
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ return this._ignoreGapsinConsensus;
+ }
+
+ /**
+ * Returns the value of field 'normaliseSequenceLogo'.
+ *
+ * @return the value of field 'NormaliseSequenceLogo'.
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ return this._normaliseSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showConsensusHistogram'.
+ *
+ * @return the value of field 'ShowConsensusHistogram'.
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this._showConsensusHistogram;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceLogo'.
+ *
+ * @return the value of field 'ShowSequenceLogo'.
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return this._showSequenceLogo;
+ }
+
+ /**
+ * Returns the value of field 'showUnconserved'.
+ *
+ * @return the value of field 'ShowUnconserved'.
+ */
+ public boolean isShowUnconserved()
+ {
+ return this._showUnconserved;
+ }
+
+ /**
+ * 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 removeAllSeq()
+ {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(final java.lang.String vSeq)
+ {
+ boolean removed = _seqList.remove(vSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeSeqAt(final int index)
+ {
+ java.lang.Object obj = this._seqList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ * Sets the value of field 'annotationColours'.
+ *
+ * @param annotationColours
+ * the value of field 'annotationColours'.
+ */
+ public void setAnnotationColours(
+ final jalview.schemabinding.version2.AnnotationColours annotationColours)
+ {
+ this._annotationColours = annotationColours;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final java.lang.String colour)
+ {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText
+ * the value of field 'colourText'.
+ */
+ public void setColourText(final boolean colourText)
+ {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes
+ * the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(final boolean displayBoxes)
+ {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText
+ * the value of field 'displayText'.
+ */
+ public void setDisplayText(final boolean displayText)
+ {
+ this._displayText = displayText;
+ this._has_displayText = 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;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Optional sequence group ID (only needs to be unique for this alignment)
+ *
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id)
+ {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'ignoreGapsinConsensus'.
+ *
+ * @param ignoreGapsinConsensus
+ * the value of field 'ignoreGapsinConsensus'.
+ */
+ public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus)
+ {
+ this._ignoreGapsinConsensus = ignoreGapsinConsensus;
+ this._has_ignoreGapsinConsensus = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'normaliseSequenceLogo'.
+ *
+ * @param normaliseSequenceLogo
+ * the value of field 'normaliseSequenceLogo'.
+ */
+ public void setNormaliseSequenceLogo(final boolean normaliseSequenceLogo)
+ {
+ this._normaliseSequenceLogo = normaliseSequenceLogo;
+ this._has_normaliseSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour
+ * the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(final int outlineColour)
+ {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSeq(final int index, final java.lang.String vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
+ }
+
+ this._seqList.set(index, vSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(final java.lang.String[] vSeqArray)
+ {
+ // -- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++)
+ {
+ this._seqList.add(vSeqArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'showConsensusHistogram'.
+ *
+ * @param showConsensusHistogram
+ * the value of field 'showConsensusHistogram'.
+ */
+ public void setShowConsensusHistogram(final boolean showConsensusHistogram)
+ {
+ this._showConsensusHistogram = showConsensusHistogram;
+ this._has_showConsensusHistogram = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceLogo'.
+ *
+ * @param showSequenceLogo
+ * the value of field 'showSequenceLogo'
+ */
+ public void setShowSequenceLogo(final boolean showSequenceLogo)
+ {
+ this._showSequenceLogo = showSequenceLogo;
+ this._has_showSequenceLogo = true;
+ }
+
+ /**
+ * Sets the value of field 'showUnconserved'.
+ *
+ * @param showUnconserved
+ * the value of field 'showUnconserved'.
+ */
+ public void setShowUnconserved(final boolean showUnconserved)
+ {
+ this._showUnconserved = showUnconserved;
+ this._has_showUnconserved = true;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Sets the value of field 'textCol1'.
+ *
+ * @param textCol1
+ * the value of field 'textCol1'.
+ */
+ public void setTextCol1(final int textCol1)
+ {
+ this._textCol1 = textCol1;
+ this._has_textCol1 = true;
+ }
+
+ /**
+ * Sets the value of field 'textCol2'.
+ *
+ * @param textCol2
+ * the value of field 'textCol2'.
+ */
+ public void setTextCol2(final int textCol2)
+ {
+ this._textCol2 = textCol2;
+ this._has_textCol2 = true;
+ }
+
+ /**
+ * Sets the value of field 'textColThreshold'.
+ *
+ * @param textColThreshold
+ * the value of field 'textColThreshold'
+ */
+ public void setTextColThreshold(final int textColThreshold)
+ {
+ this._textColThreshold = textColThreshold;
+ this._has_textColThreshold = 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.JGroup
+ */
+ public static jalview.schemabinding.version2.JGroup unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(
+ jalview.schemabinding.version2.JGroup.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