/*******************************************************************************
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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); } }