- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public 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 '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 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 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; - } - - /** - * 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 '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 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * 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("setSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - 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 '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); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, 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 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("getSeq: Index value '" + index + + "' not in range [0.." + (this._seqList.size() - 1) + "]"); + } + + return (java.lang.String) _seqList.get(index); + } + + /** + * Method getSeq.Returns the contents of the collection in an Array. + *
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public 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("setSeq: Index value '" + index + + "' not in range [0.." + (this._seqList.size() - 1) + "]"); + } + + 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); + } + +}