X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=523115fcf86507ff7f2b517a45e247cf388b35e4;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=06eb940abe27440ea2248f7b2814964b8ce6d099;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
old mode 100755
new mode 100644
index 06eb940..523115f
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,909 +1,1281 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * 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 _seqList
- */
- private java.util.Vector _seqList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JGroup() {
- super();
- _seqList = new Vector();
- } //-- jalview.schemabinding.version2.JGroup()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addSeq
- *
- *
- *
- * @param vSeq
- */
- public void addSeq(int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- _seqList.addElement(new java.lang.Integer(vSeq));
- } //-- void addSeq(int)
-
- /**
- * Method addSeq
- *
- *
- *
- * @param index
- * @param vSeq
- */
- public void addSeq(int index, int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- _seqList.insertElementAt(new java.lang.Integer(vSeq), index);
- } //-- void addSeq(int, int)
-
- /**
- * Method deleteColourText
- *
- */
- public void deleteColourText()
- {
- this._has_colourText= false;
- } //-- void deleteColourText()
-
- /**
- * Method deleteConsThreshold
- *
- */
- public void deleteConsThreshold()
- {
- this._has_consThreshold= false;
- } //-- void deleteConsThreshold()
-
- /**
- * Method deleteDisplayBoxes
- *
- */
- public void deleteDisplayBoxes()
- {
- this._has_displayBoxes= false;
- } //-- void deleteDisplayBoxes()
-
- /**
- * Method deleteDisplayText
- *
- */
- public void deleteDisplayText()
- {
- this._has_displayText= false;
- } //-- void deleteDisplayText()
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * Method deleteOutlineColour
- *
- */
- public void deleteOutlineColour()
- {
- this._has_outlineColour= false;
- } //-- void deleteOutlineColour()
-
- /**
- * Method deletePidThreshold
- *
- */
- public void deletePidThreshold()
- {
- this._has_pidThreshold= false;
- } //-- void deletePidThreshold()
-
- /**
- * Method deleteStart
- *
- */
- public void deleteStart()
- {
- this._has_start= false;
- } //-- void deleteStart()
-
- /**
- * Method deleteTextCol1
- *
- */
- public void deleteTextCol1()
- {
- this._has_textCol1= false;
- } //-- void deleteTextCol1()
-
- /**
- * Method deleteTextCol2
- *
- */
- public void deleteTextCol2()
- {
- this._has_textCol2= false;
- } //-- void deleteTextCol2()
-
- /**
- * Method deleteTextColThreshold
- *
- */
- public void deleteTextColThreshold()
- {
- this._has_textColThreshold= false;
- } //-- void deleteTextColThreshold()
-
- /**
- * Method enumerateSeq
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSeq()
- {
- return _seqList.elements();
- } //-- java.util.Enumeration enumerateSeq()
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return String
- * @return the value of field 'colour'.
- */
- public java.lang.String getColour()
- {
- return this._colour;
- } //-- java.lang.String getColour()
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return boolean
- * @return the value of field 'colourText'.
- */
- public boolean getColourText()
- {
- return this._colourText;
- } //-- boolean getColourText()
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return int
- * @return the value of field 'consThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- } //-- int getConsThreshold()
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return boolean
- * @return the value of field 'displayBoxes'.
- */
- public boolean getDisplayBoxes()
- {
- return this._displayBoxes;
- } //-- boolean getDisplayBoxes()
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return boolean
- * @return the value of field 'displayText'.
- */
- public boolean getDisplayText()
- {
- return this._displayText;
- } //-- boolean getDisplayText()
-
- /**
- * Returns the value of field 'end'.
- *
- * @return int
- * @return the value of field 'end'.
- */
- public int getEnd()
- {
- return this._end;
- } //-- int getEnd()
-
- /**
- * Returns the value of field 'name'.
- *
- * @return String
- * @return the value of field 'name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- } //-- java.lang.String getName()
-
- /**
- * Returns the value of field 'outlineColour'.
- *
- * @return int
- * @return the value of field 'outlineColour'.
- */
- public int getOutlineColour()
- {
- return this._outlineColour;
- } //-- int getOutlineColour()
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return int
- * @return the value of field 'pidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- } //-- int getPidThreshold()
-
- /**
- * Method getSeq
- *
- *
- *
- * @param index
- * @return int
- */
- public int getSeq(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _seqList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return ((java.lang.Integer)_seqList.elementAt(index)).intValue();
- } //-- int getSeq(int)
-
- /**
- * Method getSeq
- *
- *
- *
- * @return int
- */
- public int[] getSeq()
- {
- int size = _seqList.size();
- int[] mArray = new int[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();
- }
- return mArray;
- } //-- int[] getSeq()
-
- /**
- * Method getSeqCount
- *
- *
- *
- * @return int
- */
- public int getSeqCount()
- {
- return _seqList.size();
- } //-- int getSeqCount()
-
- /**
- * Returns the value of field 'start'.
- *
- * @return int
- * @return the value of field 'start'.
- */
- public int getStart()
- {
- return this._start;
- } //-- int getStart()
-
- /**
- * Returns the value of field 'textCol1'.
- *
- * @return int
- * @return the value of field 'textCol1'.
- */
- public int getTextCol1()
- {
- return this._textCol1;
- } //-- int getTextCol1()
-
- /**
- * Returns the value of field 'textCol2'.
- *
- * @return int
- * @return the value of field 'textCol2'.
- */
- public int getTextCol2()
- {
- return this._textCol2;
- } //-- int getTextCol2()
-
- /**
- * Returns the value of field 'textColThreshold'.
- *
- * @return int
- * @return the value of field 'textColThreshold'.
- */
- public int getTextColThreshold()
- {
- return this._textColThreshold;
- } //-- int getTextColThreshold()
-
- /**
- * Method hasColourText
- *
- *
- *
- * @return boolean
- */
- public boolean hasColourText()
- {
- return this._has_colourText;
- } //-- boolean hasColourText()
-
- /**
- * Method hasConsThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- } //-- boolean hasConsThreshold()
-
- /**
- * Method hasDisplayBoxes
- *
- *
- *
- * @return boolean
- */
- public boolean hasDisplayBoxes()
- {
- return this._has_displayBoxes;
- } //-- boolean hasDisplayBoxes()
-
- /**
- * Method hasDisplayText
- *
- *
- *
- * @return boolean
- */
- public boolean hasDisplayText()
- {
- return this._has_displayText;
- } //-- boolean hasDisplayText()
-
- /**
- * Method hasEnd
- *
- *
- *
- * @return boolean
- */
- public boolean hasEnd()
- {
- return this._has_end;
- } //-- boolean hasEnd()
-
- /**
- * Method hasOutlineColour
- *
- *
- *
- * @return boolean
- */
- public boolean hasOutlineColour()
- {
- return this._has_outlineColour;
- } //-- boolean hasOutlineColour()
-
- /**
- * Method hasPidThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- } //-- boolean hasPidThreshold()
-
- /**
- * Method hasStart
- *
- *
- *
- * @return boolean
- */
- public boolean hasStart()
- {
- return this._has_start;
- } //-- boolean hasStart()
-
- /**
- * Method hasTextCol1
- *
- *
- *
- * @return boolean
- */
- public boolean hasTextCol1()
- {
- return this._has_textCol1;
- } //-- boolean hasTextCol1()
-
- /**
- * Method hasTextCol2
- *
- *
- *
- * @return boolean
- */
- public boolean hasTextCol2()
- {
- return this._has_textCol2;
- } //-- boolean hasTextCol2()
-
- /**
- * Method hasTextColThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasTextColThreshold()
- {
- return this._has_textColThreshold;
- } //-- boolean hasTextColThreshold()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllSeq
- *
- */
- public void removeAllSeq()
- {
- _seqList.removeAllElements();
- } //-- void removeAllSeq()
-
- /**
- * Method removeSeq
- *
- *
- *
- * @param index
- * @return int
- */
- public int removeSeq(int index)
- {
- java.lang.Object obj = _seqList.elementAt(index);
- _seqList.removeElementAt(index);
- return ((java.lang.Integer)obj).intValue();
- } //-- int removeSeq(int)
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(java.lang.String colour)
- {
- this._colour = colour;
- } //-- void setColour(java.lang.String)
-
- /**
- * Sets the value of field 'colourText'.
- *
- * @param colourText the value of field 'colourText'.
- */
- public void setColourText(boolean colourText)
- {
- this._colourText = colourText;
- this._has_colourText = true;
- } //-- void setColourText(boolean)
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- } //-- void setConsThreshold(int)
-
- /**
- * Sets the value of field 'displayBoxes'.
- *
- * @param displayBoxes the value of field 'displayBoxes'.
- */
- public void setDisplayBoxes(boolean displayBoxes)
- {
- this._displayBoxes = displayBoxes;
- this._has_displayBoxes = true;
- } //-- void setDisplayBoxes(boolean)
-
- /**
- * Sets the value of field 'displayText'.
- *
- * @param displayText the value of field 'displayText'.
- */
- public void setDisplayText(boolean displayText)
- {
- this._displayText = displayText;
- this._has_displayText = true;
- } //-- void setDisplayText(boolean)
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(int end)
- {
- this._end = end;
- this._has_end = true;
- } //-- void setEnd(int)
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(java.lang.String name)
- {
- this._name = name;
- } //-- void setName(java.lang.String)
-
- /**
- * Sets the value of field 'outlineColour'.
- *
- * @param outlineColour the value of field 'outlineColour'.
- */
- public void setOutlineColour(int outlineColour)
- {
- this._outlineColour = outlineColour;
- this._has_outlineColour = true;
- } //-- void setOutlineColour(int)
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- } //-- void setPidThreshold(int)
-
- /**
- * Method setSeq
- *
- *
- *
- * @param index
- * @param vSeq
- */
- public void setSeq(int index, int vSeq)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _seqList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _seqList.setElementAt(new java.lang.Integer(vSeq), index);
- } //-- void setSeq(int, int)
-
- /**
- * Method setSeq
- *
- *
- *
- * @param seqArray
- */
- public void setSeq(int[] seqArray)
- {
- //-- copy array
- _seqList.removeAllElements();
- for (int i = 0; i < seqArray.length; i++) {
- _seqList.addElement(new java.lang.Integer(seqArray[i]));
- }
- } //-- void setSeq(int)
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(int start)
- {
- this._start = start;
- this._has_start = true;
- } //-- void setStart(int)
-
- /**
- * Sets the value of field 'textCol1'.
- *
- * @param textCol1 the value of field 'textCol1'.
- */
- public void setTextCol1(int textCol1)
- {
- this._textCol1 = textCol1;
- this._has_textCol1 = true;
- } //-- void setTextCol1(int)
-
- /**
- * Sets the value of field 'textCol2'.
- *
- * @param textCol2 the value of field 'textCol2'.
- */
- public void setTextCol2(int textCol2)
- {
- this._textCol2 = textCol2;
- this._has_textCol2 = true;
- } //-- void setTextCol2(int)
-
- /**
- * Sets the value of field 'textColThreshold'.
- *
- * @param textColThreshold the value of field 'textColThreshold'
- */
- public void setTextColThreshold(int textColThreshold)
- {
- this._textColThreshold = textColThreshold;
- this._has_textColThreshold = true;
- } //-- void setTextColThreshold(int)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*
+ * 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
+ * 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(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); + } + +}