X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJGroup.java;h=8b807509268208db69b2b74fad802c69ec974d3b;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=8c113756873a8077db9d7f70232ce81cc703a465;hpb=d423f22792e47dbc800ae220a58677f988971d06;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 8c11375..8b80750
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -1,1184 +1,1244 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 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 '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 '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 '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);
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 '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); + } + +}