X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=0000000000000000000000000000000000000000;hb=74393b51f368cb9f58589472d432a433d9c4386d;hp=962569f74872dc1b568295e6d744a2c3680ca361;hpb=7a0d503181fe41452120a8a02ca63476392aa08c;p=jalview.git diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java deleted file mode 100644 index 962569f..0000000 --- a/src/jalview/schemabinding/version2/JGroup.java +++ /dev/null @@ -1,1260 +0,0 @@ -/* - * 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); - } - -}