src/jalview/xml/binding/jalview/JalviewModel.java

   1 //
   2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
   3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
   4 // Any modifications to this file will be lost upon recompilation of the source schema.
   5 // Generated on: 2020.12.10 at 10:15:41 AM GMT
   6 //
   7
   8
   9 package jalview.xml.binding.jalview;
  10
  11 import java.util.ArrayList;
  12 import java.util.List;
  13 import javax.xml.bind.annotation.XmlAccessType;
  14 import javax.xml.bind.annotation.XmlAccessorType;
  15 import javax.xml.bind.annotation.XmlAttribute;
  16 import javax.xml.bind.annotation.XmlElement;
  17 import javax.xml.bind.annotation.XmlID;
  18 import javax.xml.bind.annotation.XmlSchemaType;
  19 import javax.xml.bind.annotation.XmlType;
  20 import javax.xml.bind.annotation.XmlValue;
  21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
  22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  23 import javax.xml.datatype.XMLGregorianCalendar;
  24
  25
  26 /**
  27  * <p>Java class for JalviewModel complex type.
  28  *
  29  * <p>The following schema fragment specifies the expected content contained within this class.
  30  *
  31  * <pre>
  32  * &lt;complexType name="JalviewModel">
  33  *   &lt;complexContent>
  34  *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  35  *       &lt;sequence>
  36  *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
  37  *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
  38  *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
  39  *         &lt;sequence>
  40  *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  41  *             &lt;complexType>
  42  *               &lt;complexContent>
  43  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  44  *                   &lt;sequence>
  45  *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
  46  *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
  47  *                       &lt;complexType>
  48  *                         &lt;complexContent>
  49  *                           &lt;extension base="{www.jalview.org}pdbentry">
  50  *                             &lt;sequence>
  51  *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
  52  *                                 &lt;complexType>
  53  *                                   &lt;simpleContent>
  54  *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
  55  *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  56  *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  57  *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  58  *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  59  *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  60  *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  61  *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
  62  *                                     &lt;/extension>
  63  *                                   &lt;/simpleContent>
  64  *                                 &lt;/complexType>
  65  *                               &lt;/element>
  66  *                             &lt;/sequence>
  67  *                           &lt;/extension>
  68  *                         &lt;/complexContent>
  69  *                       &lt;/complexType>
  70  *                     &lt;/element>
  71  *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
  72  *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
  73  *                       &lt;complexType>
  74  *                         &lt;complexContent>
  75  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  76  *                             &lt;sequence>
  77  *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
  78  *                                 &lt;complexType>
  79  *                                   &lt;complexContent>
  80  *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  81  *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  82  *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  83  *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  84  *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
  85  *                                     &lt;/restriction>
  86  *                                   &lt;/complexContent>
  87  *                                 &lt;/complexType>
  88  *                               &lt;/element>
  89  *                             &lt;/sequence>
  90  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  91  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  92  *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  93  *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
  94  *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
  95  *                           &lt;/restriction>
  96  *                         &lt;/complexContent>
  97  *                       &lt;/complexType>
  98  *                     &lt;/element>
  99  *                   &lt;/sequence>
 100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                 &lt;/restriction>
 107  *               &lt;/complexContent>
 108  *             &lt;/complexType>
 109  *           &lt;/element>
 110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 111  *             &lt;complexType>
 112  *               &lt;complexContent>
 113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 114  *                   &lt;sequence>
 115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 117  *                   &lt;/sequence>
 118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 137  *                 &lt;/restriction>
 138  *               &lt;/complexContent>
 139  *             &lt;/complexType>
 140  *           &lt;/element>
 141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 142  *             &lt;complexType>
 143  *               &lt;complexContent>
 144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 145  *                   &lt;sequence>
 146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 148  *                       &lt;complexType>
 149  *                         &lt;complexContent>
 150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                           &lt;/restriction>
 154  *                         &lt;/complexContent>
 155  *                       &lt;/complexType>
 156  *                     &lt;/element>
 157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 158  *                       &lt;complexType>
 159  *                         &lt;complexContent>
 160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 164  *                           &lt;/extension>
 165  *                         &lt;/complexContent>
 166  *                       &lt;/complexType>
 167  *                     &lt;/element>
 168  *                     &lt;element name="overview" minOccurs="0">
 169  *                       &lt;complexType>
 170  *                         &lt;complexContent>
 171  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 172  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 173  *                             &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 174  *                             &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 175  *                             &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 176  *                             &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 177  *                           &lt;/restriction>
 178  *                         &lt;/complexContent>
 179  *                       &lt;/complexType>
 180  *                     &lt;/element>
 181  *                   &lt;/sequence>
 182  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 183  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 184  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 185  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 186  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 187  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 188  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 189  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 190  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 191  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 192  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 193  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 194  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 195  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 196  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 197  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 198  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 199  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 200  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 201  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 202  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 203  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 204  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 205  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 206  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 207  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 208  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 209  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 210  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 211  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 212  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 213  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 214  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 215  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 216  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 217  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 218  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 219  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 220  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 221  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 222  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 223  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 224  *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 225  *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 226  *                 &lt;/restriction>
 227  *               &lt;/complexContent>
 228  *             &lt;/complexType>
 229  *           &lt;/element>
 230  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 231  *             &lt;complexType>
 232  *               &lt;complexContent>
 233  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 234  *                   &lt;sequence>
 235  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 236  *                   &lt;/sequence>
 237  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 238  *                 &lt;/restriction>
 239  *               &lt;/complexContent>
 240  *             &lt;/complexType>
 241  *           &lt;/element>
 242  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 243  *             &lt;complexType>
 244  *               &lt;complexContent>
 245  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 246  *                   &lt;sequence minOccurs="0">
 247  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 248  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 249  *                   &lt;/sequence>
 250  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 251  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 252  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 253  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 254  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 255  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 256  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 257  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 258  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 259  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 260  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 261  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 262  *                 &lt;/restriction>
 263  *               &lt;/complexContent>
 264  *             &lt;/complexType>
 265  *           &lt;/element>
 266  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 267  *             &lt;complexType>
 268  *               &lt;complexContent>
 269  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 270  *                   &lt;sequence>
 271  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 272  *                       &lt;complexType>
 273  *                         &lt;complexContent>
 274  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 275  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 276  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 277  *                           &lt;/restriction>
 278  *                         &lt;/complexContent>
 279  *                       &lt;/complexType>
 280  *                     &lt;/element>
 281  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 282  *                       &lt;complexType>
 283  *                         &lt;complexContent>
 284  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 285  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 286  *                           &lt;/restriction>
 287  *                         &lt;/complexContent>
 288  *                       &lt;/complexType>
 289  *                     &lt;/element>
 290  *                     &lt;element name="seqPointMin">
 291  *                       &lt;complexType>
 292  *                         &lt;complexContent>
 293  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 294  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 295  *                           &lt;/restriction>
 296  *                         &lt;/complexContent>
 297  *                       &lt;/complexType>
 298  *                     &lt;/element>
 299  *                     &lt;element name="seqPointMax">
 300  *                       &lt;complexType>
 301  *                         &lt;complexContent>
 302  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 303  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 304  *                           &lt;/restriction>
 305  *                         &lt;/complexContent>
 306  *                       &lt;/complexType>
 307  *                     &lt;/element>
 308  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 309  *                   &lt;/sequence>
 310  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 311  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 312  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 313  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 314  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 315  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 316  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 317  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 318  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 319  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 320  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 321  *                 &lt;/restriction>
 322  *               &lt;/complexContent>
 323  *             &lt;/complexType>
 324  *           &lt;/element>
 325  *           &lt;element name="FeatureSettings" minOccurs="0">
 326  *             &lt;complexType>
 327  *               &lt;complexContent>
 328  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 329  *                   &lt;sequence>
 330  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 331  *                       &lt;complexType>
 332  *                         &lt;complexContent>
 333  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 334  *                             &lt;sequence>
 335  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 336  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 337  *                             &lt;/sequence>
 338  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 339  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 340  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 341  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 342  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 343  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 344  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 345  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 346  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 347  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 348  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 349  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 350  *                           &lt;/restriction>
 351  *                         &lt;/complexContent>
 352  *                       &lt;/complexType>
 353  *                     &lt;/element>
 354  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 355  *                       &lt;complexType>
 356  *                         &lt;complexContent>
 357  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 358  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 359  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 360  *                           &lt;/restriction>
 361  *                         &lt;/complexContent>
 362  *                       &lt;/complexType>
 363  *                     &lt;/element>
 364  *                   &lt;/sequence>
 365  *                 &lt;/restriction>
 366  *               &lt;/complexContent>
 367  *             &lt;/complexType>
 368  *           &lt;/element>
 369  *         &lt;/sequence>
 370  *       &lt;/sequence>
 371  *     &lt;/restriction>
 372  *   &lt;/complexContent>
 373  * &lt;/complexType>
 374  * </pre>
 375  *
 376  *
 377  */
 378 @XmlAccessorType(XmlAccessType.FIELD)
 379 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 380     "creationDate",
 381     "version",
 382     "vamsasModel",
 383     "jSeq",
 384     "jGroup",
 385     "viewport",
 386     "userColours",
 387     "tree",
 388     "pcaViewer",
 389     "featureSettings"
 390 })
 391 public class JalviewModel {
 392
 393     @XmlElement(required = true)
 394     @XmlSchemaType(name = "dateTime")
 395     protected XMLGregorianCalendar creationDate;
 396     @XmlElement(required = true)
 397     protected String version;
 398     @XmlElement(required = true)
 399     protected VAMSAS vamsasModel;
 400     @XmlElement(name = "JSeq")
 401     protected List<JalviewModel.JSeq> jSeq;
 402     @XmlElement(name = "JGroup")
 403     protected List<JalviewModel.JGroup> jGroup;
 404     @XmlElement(name = "Viewport")
 405     protected List<JalviewModel.Viewport> viewport;
 406     @XmlElement(name = "UserColours")
 407     protected List<JalviewModel.UserColours> userColours;
 408     protected List<JalviewModel.Tree> tree;
 409     @XmlElement(name = "PcaViewer")
 410     protected List<JalviewModel.PcaViewer> pcaViewer;
 411     @XmlElement(name = "FeatureSettings")
 412     protected JalviewModel.FeatureSettings featureSettings;
 413
 414     /**
 415      * Gets the value of the creationDate property.
 416      *
 417      * @return
 418      *     possible object is
 419      *     {@link XMLGregorianCalendar }
 420      *
 421      */
 422     public XMLGregorianCalendar getCreationDate() {
 423         return creationDate;
 424     }
 425
 426     /**
 427      * Sets the value of the creationDate property.
 428      *
 429      * @param value
 430      *     allowed object is
 431      *     {@link XMLGregorianCalendar }
 432      *
 433      */
 434     public void setCreationDate(XMLGregorianCalendar value) {
 435         this.creationDate = value;
 436     }
 437
 438     /**
 439      * Gets the value of the version property.
 440      *
 441      * @return
 442      *     possible object is
 443      *     {@link String }
 444      *
 445      */
 446     public String getVersion() {
 447         return version;
 448     }
 449
 450     /**
 451      * Sets the value of the version property.
 452      *
 453      * @param value
 454      *     allowed object is
 455      *     {@link String }
 456      *
 457      */
 458     public void setVersion(String value) {
 459         this.version = value;
 460     }
 461
 462     /**
 463      * Gets the value of the vamsasModel property.
 464      *
 465      * @return
 466      *     possible object is
 467      *     {@link VAMSAS }
 468      *
 469      */
 470     public VAMSAS getVamsasModel() {
 471         return vamsasModel;
 472     }
 473
 474     /**
 475      * Sets the value of the vamsasModel property.
 476      *
 477      * @param value
 478      *     allowed object is
 479      *     {@link VAMSAS }
 480      *
 481      */
 482     public void setVamsasModel(VAMSAS value) {
 483         this.vamsasModel = value;
 484     }
 485
 486     /**
 487      * Gets the value of the jSeq property.
 488      *
 489      * <p>
 490      * This accessor method returns a reference to the live list,
 491      * not a snapshot. Therefore any modification you make to the
 492      * returned list will be present inside the JAXB object.
 493      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 494      *
 495      * <p>
 496      * For example, to add a new item, do as follows:
 497      * <pre>
 498      *    getJSeq().add(newItem);
 499      * </pre>
 500      *
 501      *
 502      * <p>
 503      * Objects of the following type(s) are allowed in the list
 504      * {@link JalviewModel.JSeq }
 505      *
 506      *
 507      */
 508     public List<JalviewModel.JSeq> getJSeq() {
 509         if (jSeq == null) {
 510             jSeq = new ArrayList<JalviewModel.JSeq>();
 511         }
 512         return this.jSeq;
 513     }
 514
 515     /**
 516      * Gets the value of the jGroup property.
 517      *
 518      * <p>
 519      * This accessor method returns a reference to the live list,
 520      * not a snapshot. Therefore any modification you make to the
 521      * returned list will be present inside the JAXB object.
 522      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 523      *
 524      * <p>
 525      * For example, to add a new item, do as follows:
 526      * <pre>
 527      *    getJGroup().add(newItem);
 528      * </pre>
 529      *
 530      *
 531      * <p>
 532      * Objects of the following type(s) are allowed in the list
 533      * {@link JalviewModel.JGroup }
 534      *
 535      *
 536      */
 537     public List<JalviewModel.JGroup> getJGroup() {
 538         if (jGroup == null) {
 539             jGroup = new ArrayList<JalviewModel.JGroup>();
 540         }
 541         return this.jGroup;
 542     }
 543
 544     /**
 545      * Gets the value of the viewport property.
 546      *
 547      * <p>
 548      * This accessor method returns a reference to the live list,
 549      * not a snapshot. Therefore any modification you make to the
 550      * returned list will be present inside the JAXB object.
 551      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 552      *
 553      * <p>
 554      * For example, to add a new item, do as follows:
 555      * <pre>
 556      *    getViewport().add(newItem);
 557      * </pre>
 558      *
 559      *
 560      * <p>
 561      * Objects of the following type(s) are allowed in the list
 562      * {@link JalviewModel.Viewport }
 563      *
 564      *
 565      */
 566     public List<JalviewModel.Viewport> getViewport() {
 567         if (viewport == null) {
 568             viewport = new ArrayList<JalviewModel.Viewport>();
 569         }
 570         return this.viewport;
 571     }
 572
 573     /**
 574      * Gets the value of the userColours property.
 575      *
 576      * <p>
 577      * This accessor method returns a reference to the live list,
 578      * not a snapshot. Therefore any modification you make to the
 579      * returned list will be present inside the JAXB object.
 580      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 581      *
 582      * <p>
 583      * For example, to add a new item, do as follows:
 584      * <pre>
 585      *    getUserColours().add(newItem);
 586      * </pre>
 587      *
 588      *
 589      * <p>
 590      * Objects of the following type(s) are allowed in the list
 591      * {@link JalviewModel.UserColours }
 592      *
 593      *
 594      */
 595     public List<JalviewModel.UserColours> getUserColours() {
 596         if (userColours == null) {
 597             userColours = new ArrayList<JalviewModel.UserColours>();
 598         }
 599         return this.userColours;
 600     }
 601
 602     /**
 603      * Gets the value of the tree property.
 604      *
 605      * <p>
 606      * This accessor method returns a reference to the live list,
 607      * not a snapshot. Therefore any modification you make to the
 608      * returned list will be present inside the JAXB object.
 609      * This is why there is not a <CODE>set</CODE> method for the tree property.
 610      *
 611      * <p>
 612      * For example, to add a new item, do as follows:
 613      * <pre>
 614      *    getTree().add(newItem);
 615      * </pre>
 616      *
 617      *
 618      * <p>
 619      * Objects of the following type(s) are allowed in the list
 620      * {@link JalviewModel.Tree }
 621      *
 622      *
 623      */
 624     public List<JalviewModel.Tree> getTree() {
 625         if (tree == null) {
 626             tree = new ArrayList<JalviewModel.Tree>();
 627         }
 628         return this.tree;
 629     }
 630
 631     /**
 632      * Gets the value of the pcaViewer property.
 633      *
 634      * <p>
 635      * This accessor method returns a reference to the live list,
 636      * not a snapshot. Therefore any modification you make to the
 637      * returned list will be present inside the JAXB object.
 638      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 639      *
 640      * <p>
 641      * For example, to add a new item, do as follows:
 642      * <pre>
 643      *    getPcaViewer().add(newItem);
 644      * </pre>
 645      *
 646      *
 647      * <p>
 648      * Objects of the following type(s) are allowed in the list
 649      * {@link JalviewModel.PcaViewer }
 650      *
 651      *
 652      */
 653     public List<JalviewModel.PcaViewer> getPcaViewer() {
 654         if (pcaViewer == null) {
 655             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 656         }
 657         return this.pcaViewer;
 658     }
 659
 660     /**
 661      * Gets the value of the featureSettings property.
 662      *
 663      * @return
 664      *     possible object is
 665      *     {@link JalviewModel.FeatureSettings }
 666      *
 667      */
 668     public JalviewModel.FeatureSettings getFeatureSettings() {
 669         return featureSettings;
 670     }
 671
 672     /**
 673      * Sets the value of the featureSettings property.
 674      *
 675      * @param value
 676      *     allowed object is
 677      *     {@link JalviewModel.FeatureSettings }
 678      *
 679      */
 680     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 681         this.featureSettings = value;
 682     }
 683
 684
 685     /**
 686      * <p>Java class for anonymous complex type.
 687      *
 688      * <p>The following schema fragment specifies the expected content contained within this class.
 689      *
 690      * <pre>
 691      * &lt;complexType>
 692      *   &lt;complexContent>
 693      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 694      *       &lt;sequence>
 695      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 696      *           &lt;complexType>
 697      *             &lt;complexContent>
 698      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 699      *                 &lt;sequence>
 700      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 701      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 702      *                 &lt;/sequence>
 703      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 704      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 705      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 706      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 707      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 708      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 709      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 710      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 711      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 712      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 713      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 714      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 715      *               &lt;/restriction>
 716      *             &lt;/complexContent>
 717      *           &lt;/complexType>
 718      *         &lt;/element>
 719      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 720      *           &lt;complexType>
 721      *             &lt;complexContent>
 722      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 723      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 724      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 725      *               &lt;/restriction>
 726      *             &lt;/complexContent>
 727      *           &lt;/complexType>
 728      *         &lt;/element>
 729      *       &lt;/sequence>
 730      *     &lt;/restriction>
 731      *   &lt;/complexContent>
 732      * &lt;/complexType>
 733      * </pre>
 734      *
 735      *
 736      */
 737     @XmlAccessorType(XmlAccessType.FIELD)
 738     @XmlType(name = "", propOrder = {
 739         "setting",
 740         "group"
 741     })
 742     public static class FeatureSettings {
 743
 744         @XmlElement(namespace = "www.jalview.org")
 745         protected List<JalviewModel.FeatureSettings.Setting> setting;
 746         @XmlElement(namespace = "www.jalview.org")
 747         protected List<JalviewModel.FeatureSettings.Group> group;
 748
 749         /**
 750          * Gets the value of the setting property.
 751          *
 752          * <p>
 753          * This accessor method returns a reference to the live list,
 754          * not a snapshot. Therefore any modification you make to the
 755          * returned list will be present inside the JAXB object.
 756          * This is why there is not a <CODE>set</CODE> method for the setting property.
 757          *
 758          * <p>
 759          * For example, to add a new item, do as follows:
 760          * <pre>
 761          *    getSetting().add(newItem);
 762          * </pre>
 763          *
 764          *
 765          * <p>
 766          * Objects of the following type(s) are allowed in the list
 767          * {@link JalviewModel.FeatureSettings.Setting }
 768          *
 769          *
 770          */
 771         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 772             if (setting == null) {
 773                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 774             }
 775             return this.setting;
 776         }
 777
 778         /**
 779          * Gets the value of the group property.
 780          *
 781          * <p>
 782          * This accessor method returns a reference to the live list,
 783          * not a snapshot. Therefore any modification you make to the
 784          * returned list will be present inside the JAXB object.
 785          * This is why there is not a <CODE>set</CODE> method for the group property.
 786          *
 787          * <p>
 788          * For example, to add a new item, do as follows:
 789          * <pre>
 790          *    getGroup().add(newItem);
 791          * </pre>
 792          *
 793          *
 794          * <p>
 795          * Objects of the following type(s) are allowed in the list
 796          * {@link JalviewModel.FeatureSettings.Group }
 797          *
 798          *
 799          */
 800         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 801             if (group == null) {
 802                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 803             }
 804             return this.group;
 805         }
 806
 807
 808         /**
 809          * <p>Java class for anonymous complex type.
 810          *
 811          * <p>The following schema fragment specifies the expected content contained within this class.
 812          *
 813          * <pre>
 814          * &lt;complexType>
 815          *   &lt;complexContent>
 816          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 817          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 818          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 819          *     &lt;/restriction>
 820          *   &lt;/complexContent>
 821          * &lt;/complexType>
 822          * </pre>
 823          *
 824          *
 825          */
 826         @XmlAccessorType(XmlAccessType.FIELD)
 827         @XmlType(name = "")
 828         public static class Group {
 829
 830             @XmlAttribute(name = "name", required = true)
 831             protected String name;
 832             @XmlAttribute(name = "display", required = true)
 833             protected boolean display;
 834
 835             /**
 836              * Gets the value of the name property.
 837              *
 838              * @return
 839              *     possible object is
 840              *     {@link String }
 841              *
 842              */
 843             public String getName() {
 844                 return name;
 845             }
 846
 847             /**
 848              * Sets the value of the name property.
 849              *
 850              * @param value
 851              *     allowed object is
 852              *     {@link String }
 853              *
 854              */
 855             public void setName(String value) {
 856                 this.name = value;
 857             }
 858
 859             /**
 860              * Gets the value of the display property.
 861              *
 862              */
 863             public boolean isDisplay() {
 864                 return display;
 865             }
 866
 867             /**
 868              * Sets the value of the display property.
 869              *
 870              */
 871             public void setDisplay(boolean value) {
 872                 this.display = value;
 873             }
 874
 875         }
 876
 877
 878         /**
 879          * <p>Java class for anonymous complex type.
 880          *
 881          * <p>The following schema fragment specifies the expected content contained within this class.
 882          *
 883          * <pre>
 884          * &lt;complexType>
 885          *   &lt;complexContent>
 886          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 887          *       &lt;sequence>
 888          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 889          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 890          *       &lt;/sequence>
 891          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 892          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 893          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 894          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 895          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 896          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 897          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 898          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 899          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 900          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 901          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 902          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 903          *     &lt;/restriction>
 904          *   &lt;/complexContent>
 905          * &lt;/complexType>
 906          * </pre>
 907          *
 908          *
 909          */
 910         @XmlAccessorType(XmlAccessType.FIELD)
 911         @XmlType(name = "", propOrder = {
 912             "attributeName",
 913             "matcherSet"
 914         })
 915         public static class Setting {
 916
 917             @XmlElement(namespace = "www.jalview.org")
 918             protected List<String> attributeName;
 919             @XmlElement(namespace = "www.jalview.org")
 920             protected FeatureMatcherSet matcherSet;
 921             @XmlAttribute(name = "type", required = true)
 922             protected String type;
 923             @XmlAttribute(name = "colour", required = true)
 924             protected int colour;
 925             @XmlAttribute(name = "display", required = true)
 926             protected boolean display;
 927             @XmlAttribute(name = "order")
 928             protected Float order;
 929             @XmlAttribute(name = "mincolour")
 930             protected Integer mincolour;
 931             @XmlAttribute(name = "noValueColour")
 932             protected NoValueColour noValueColour;
 933             @XmlAttribute(name = "threshold")
 934             protected Float threshold;
 935             @XmlAttribute(name = "threshstate")
 936             protected Integer threshstate;
 937             @XmlAttribute(name = "max")
 938             protected Float max;
 939             @XmlAttribute(name = "min")
 940             protected Float min;
 941             @XmlAttribute(name = "colourByLabel")
 942             protected Boolean colourByLabel;
 943             @XmlAttribute(name = "autoScale")
 944             protected Boolean autoScale;
 945
 946             /**
 947              * Gets the value of the attributeName property.
 948              *
 949              * <p>
 950              * This accessor method returns a reference to the live list,
 951              * not a snapshot. Therefore any modification you make to the
 952              * returned list will be present inside the JAXB object.
 953              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 954              *
 955              * <p>
 956              * For example, to add a new item, do as follows:
 957              * <pre>
 958              *    getAttributeName().add(newItem);
 959              * </pre>
 960              *
 961              *
 962              * <p>
 963              * Objects of the following type(s) are allowed in the list
 964              * {@link String }
 965              *
 966              *
 967              */
 968             public List<String> getAttributeName() {
 969                 if (attributeName == null) {
 970                     attributeName = new ArrayList<String>();
 971                 }
 972                 return this.attributeName;
 973             }
 974
 975             /**
 976              * Gets the value of the matcherSet property.
 977              *
 978              * @return
 979              *     possible object is
 980              *     {@link FeatureMatcherSet }
 981              *
 982              */
 983             public FeatureMatcherSet getMatcherSet() {
 984                 return matcherSet;
 985             }
 986
 987             /**
 988              * Sets the value of the matcherSet property.
 989              *
 990              * @param value
 991              *     allowed object is
 992              *     {@link FeatureMatcherSet }
 993              *
 994              */
 995             public void setMatcherSet(FeatureMatcherSet value) {
 996                 this.matcherSet = value;
 997             }
 998
 999             /**
1000              * Gets the value of the type property.
1001              *
1002              * @return
1003              *     possible object is
1004              *     {@link String }
1005              *
1006              */
1007             public String getType() {
1008                 return type;
1009             }
1010
1011             /**
1012              * Sets the value of the type property.
1013              *
1014              * @param value
1015              *     allowed object is
1016              *     {@link String }
1017              *
1018              */
1019             public void setType(String value) {
1020                 this.type = value;
1021             }
1022
1023             /**
1024              * Gets the value of the colour property.
1025              *
1026              */
1027             public int getColour() {
1028                 return colour;
1029             }
1030
1031             /**
1032              * Sets the value of the colour property.
1033              *
1034              */
1035             public void setColour(int value) {
1036                 this.colour = value;
1037             }
1038
1039             /**
1040              * Gets the value of the display property.
1041              *
1042              */
1043             public boolean isDisplay() {
1044                 return display;
1045             }
1046
1047             /**
1048              * Sets the value of the display property.
1049              *
1050              */
1051             public void setDisplay(boolean value) {
1052                 this.display = value;
1053             }
1054
1055             /**
1056              * Gets the value of the order property.
1057              *
1058              * @return
1059              *     possible object is
1060              *     {@link Float }
1061              *
1062              */
1063             public Float getOrder() {
1064                 return order;
1065             }
1066
1067             /**
1068              * Sets the value of the order property.
1069              *
1070              * @param value
1071              *     allowed object is
1072              *     {@link Float }
1073              *
1074              */
1075             public void setOrder(Float value) {
1076                 this.order = value;
1077             }
1078
1079             /**
1080              * Gets the value of the mincolour property.
1081              *
1082              * @return
1083              *     possible object is
1084              *     {@link Integer }
1085              *
1086              */
1087             public Integer getMincolour() {
1088                 return mincolour;
1089             }
1090
1091             /**
1092              * Sets the value of the mincolour property.
1093              *
1094              * @param value
1095              *     allowed object is
1096              *     {@link Integer }
1097              *
1098              */
1099             public void setMincolour(Integer value) {
1100                 this.mincolour = value;
1101             }
1102
1103             /**
1104              * Gets the value of the noValueColour property.
1105              *
1106              * @return
1107              *     possible object is
1108              *     {@link NoValueColour }
1109              *
1110              */
1111             public NoValueColour getNoValueColour() {
1112                 if (noValueColour == null) {
1113                     return NoValueColour.MIN;
1114                 } else {
1115                     return noValueColour;
1116                 }
1117             }
1118
1119             /**
1120              * Sets the value of the noValueColour property.
1121              *
1122              * @param value
1123              *     allowed object is
1124              *     {@link NoValueColour }
1125              *
1126              */
1127             public void setNoValueColour(NoValueColour value) {
1128                 this.noValueColour = value;
1129             }
1130
1131             /**
1132              * Gets the value of the threshold property.
1133              *
1134              * @return
1135              *     possible object is
1136              *     {@link Float }
1137              *
1138              */
1139             public Float getThreshold() {
1140                 return threshold;
1141             }
1142
1143             /**
1144              * Sets the value of the threshold property.
1145              *
1146              * @param value
1147              *     allowed object is
1148              *     {@link Float }
1149              *
1150              */
1151             public void setThreshold(Float value) {
1152                 this.threshold = value;
1153             }
1154
1155             /**
1156              * Gets the value of the threshstate property.
1157              *
1158              * @return
1159              *     possible object is
1160              *     {@link Integer }
1161              *
1162              */
1163             public Integer getThreshstate() {
1164                 return threshstate;
1165             }
1166
1167             /**
1168              * Sets the value of the threshstate property.
1169              *
1170              * @param value
1171              *     allowed object is
1172              *     {@link Integer }
1173              *
1174              */
1175             public void setThreshstate(Integer value) {
1176                 this.threshstate = value;
1177             }
1178
1179             /**
1180              * Gets the value of the max property.
1181              *
1182              * @return
1183              *     possible object is
1184              *     {@link Float }
1185              *
1186              */
1187             public Float getMax() {
1188                 return max;
1189             }
1190
1191             /**
1192              * Sets the value of the max property.
1193              *
1194              * @param value
1195              *     allowed object is
1196              *     {@link Float }
1197              *
1198              */
1199             public void setMax(Float value) {
1200                 this.max = value;
1201             }
1202
1203             /**
1204              * Gets the value of the min property.
1205              *
1206              * @return
1207              *     possible object is
1208              *     {@link Float }
1209              *
1210              */
1211             public Float getMin() {
1212                 return min;
1213             }
1214
1215             /**
1216              * Sets the value of the min property.
1217              *
1218              * @param value
1219              *     allowed object is
1220              *     {@link Float }
1221              *
1222              */
1223             public void setMin(Float value) {
1224                 this.min = value;
1225             }
1226
1227             /**
1228              * Gets the value of the colourByLabel property.
1229              *
1230              * @return
1231              *     possible object is
1232              *     {@link Boolean }
1233              *
1234              */
1235             public Boolean isColourByLabel() {
1236                 return colourByLabel;
1237             }
1238
1239             /**
1240              * Sets the value of the colourByLabel property.
1241              *
1242              * @param value
1243              *     allowed object is
1244              *     {@link Boolean }
1245              *
1246              */
1247             public void setColourByLabel(Boolean value) {
1248                 this.colourByLabel = value;
1249             }
1250
1251             /**
1252              * Gets the value of the autoScale property.
1253              *
1254              * @return
1255              *     possible object is
1256              *     {@link Boolean }
1257              *
1258              */
1259             public Boolean isAutoScale() {
1260                 return autoScale;
1261             }
1262
1263             /**
1264              * Sets the value of the autoScale property.
1265              *
1266              * @param value
1267              *     allowed object is
1268              *     {@link Boolean }
1269              *
1270              */
1271             public void setAutoScale(Boolean value) {
1272                 this.autoScale = value;
1273             }
1274
1275         }
1276
1277     }
1278
1279
1280     /**
1281      * <p>Java class for anonymous complex type.
1282      *
1283      * <p>The following schema fragment specifies the expected content contained within this class.
1284      *
1285      * <pre>
1286      * &lt;complexType>
1287      *   &lt;complexContent>
1288      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1289      *       &lt;sequence>
1290      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1291      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1292      *       &lt;/sequence>
1293      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1294      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1295      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1296      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1297      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1298      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1299      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1300      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1301      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1302      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1303      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1304      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1305      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1306      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1307      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1308      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1309      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1310      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1311      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1312      *     &lt;/restriction>
1313      *   &lt;/complexContent>
1314      * &lt;/complexType>
1315      * </pre>
1316      *
1317      *
1318      */
1319     @XmlAccessorType(XmlAccessType.FIELD)
1320     @XmlType(name = "", propOrder = {
1321         "seq",
1322         "annotationColours"
1323     })
1324     public static class JGroup {
1325
1326         @XmlElement(namespace = "www.jalview.org", required = true)
1327         protected List<String> seq;
1328         @XmlElement(namespace = "www.jalview.org")
1329         protected AnnotationColourScheme annotationColours;
1330         @XmlAttribute(name = "start")
1331         protected Integer start;
1332         @XmlAttribute(name = "end")
1333         protected Integer end;
1334         @XmlAttribute(name = "name")
1335         protected String name;
1336         @XmlAttribute(name = "colour")
1337         protected String colour;
1338         @XmlAttribute(name = "consThreshold")
1339         protected Integer consThreshold;
1340         @XmlAttribute(name = "pidThreshold")
1341         protected Integer pidThreshold;
1342         @XmlAttribute(name = "outlineColour")
1343         protected Integer outlineColour;
1344         @XmlAttribute(name = "displayBoxes")
1345         protected Boolean displayBoxes;
1346         @XmlAttribute(name = "displayText")
1347         protected Boolean displayText;
1348         @XmlAttribute(name = "colourText")
1349         protected Boolean colourText;
1350         @XmlAttribute(name = "textCol1")
1351         protected Integer textCol1;
1352         @XmlAttribute(name = "textCol2")
1353         protected Integer textCol2;
1354         @XmlAttribute(name = "textColThreshold")
1355         protected Integer textColThreshold;
1356         @XmlAttribute(name = "showUnconserved")
1357         protected Boolean showUnconserved;
1358         @XmlAttribute(name = "ignoreGapsinConsensus")
1359         protected Boolean ignoreGapsinConsensus;
1360         @XmlAttribute(name = "showConsensusHistogram")
1361         protected Boolean showConsensusHistogram;
1362         @XmlAttribute(name = "showSequenceLogo")
1363         protected Boolean showSequenceLogo;
1364         @XmlAttribute(name = "normaliseSequenceLogo")
1365         protected Boolean normaliseSequenceLogo;
1366         @XmlAttribute(name = "id")
1367         protected String id;
1368
1369         /**
1370          * Gets the value of the seq property.
1371          *
1372          * <p>
1373          * This accessor method returns a reference to the live list,
1374          * not a snapshot. Therefore any modification you make to the
1375          * returned list will be present inside the JAXB object.
1376          * This is why there is not a <CODE>set</CODE> method for the seq property.
1377          *
1378          * <p>
1379          * For example, to add a new item, do as follows:
1380          * <pre>
1381          *    getSeq().add(newItem);
1382          * </pre>
1383          *
1384          *
1385          * <p>
1386          * Objects of the following type(s) are allowed in the list
1387          * {@link String }
1388          *
1389          *
1390          */
1391         public List<String> getSeq() {
1392             if (seq == null) {
1393                 seq = new ArrayList<String>();
1394             }
1395             return this.seq;
1396         }
1397
1398         /**
1399          * Gets the value of the annotationColours property.
1400          *
1401          * @return
1402          *     possible object is
1403          *     {@link AnnotationColourScheme }
1404          *
1405          */
1406         public AnnotationColourScheme getAnnotationColours() {
1407             return annotationColours;
1408         }
1409
1410         /**
1411          * Sets the value of the annotationColours property.
1412          *
1413          * @param value
1414          *     allowed object is
1415          *     {@link AnnotationColourScheme }
1416          *
1417          */
1418         public void setAnnotationColours(AnnotationColourScheme value) {
1419             this.annotationColours = value;
1420         }
1421
1422         /**
1423          * Gets the value of the start property.
1424          *
1425          * @return
1426          *     possible object is
1427          *     {@link Integer }
1428          *
1429          */
1430         public Integer getStart() {
1431             return start;
1432         }
1433
1434         /**
1435          * Sets the value of the start property.
1436          *
1437          * @param value
1438          *     allowed object is
1439          *     {@link Integer }
1440          *
1441          */
1442         public void setStart(Integer value) {
1443             this.start = value;
1444         }
1445
1446         /**
1447          * Gets the value of the end property.
1448          *
1449          * @return
1450          *     possible object is
1451          *     {@link Integer }
1452          *
1453          */
1454         public Integer getEnd() {
1455             return end;
1456         }
1457
1458         /**
1459          * Sets the value of the end property.
1460          *
1461          * @param value
1462          *     allowed object is
1463          *     {@link Integer }
1464          *
1465          */
1466         public void setEnd(Integer value) {
1467             this.end = value;
1468         }
1469
1470         /**
1471          * Gets the value of the name property.
1472          *
1473          * @return
1474          *     possible object is
1475          *     {@link String }
1476          *
1477          */
1478         public String getName() {
1479             return name;
1480         }
1481
1482         /**
1483          * Sets the value of the name property.
1484          *
1485          * @param value
1486          *     allowed object is
1487          *     {@link String }
1488          *
1489          */
1490         public void setName(String value) {
1491             this.name = value;
1492         }
1493
1494         /**
1495          * Gets the value of the colour property.
1496          *
1497          * @return
1498          *     possible object is
1499          *     {@link String }
1500          *
1501          */
1502         public String getColour() {
1503             return colour;
1504         }
1505
1506         /**
1507          * Sets the value of the colour property.
1508          *
1509          * @param value
1510          *     allowed object is
1511          *     {@link String }
1512          *
1513          */
1514         public void setColour(String value) {
1515             this.colour = value;
1516         }
1517
1518         /**
1519          * Gets the value of the consThreshold property.
1520          *
1521          * @return
1522          *     possible object is
1523          *     {@link Integer }
1524          *
1525          */
1526         public Integer getConsThreshold() {
1527             return consThreshold;
1528         }
1529
1530         /**
1531          * Sets the value of the consThreshold property.
1532          *
1533          * @param value
1534          *     allowed object is
1535          *     {@link Integer }
1536          *
1537          */
1538         public void setConsThreshold(Integer value) {
1539             this.consThreshold = value;
1540         }
1541
1542         /**
1543          * Gets the value of the pidThreshold property.
1544          *
1545          * @return
1546          *     possible object is
1547          *     {@link Integer }
1548          *
1549          */
1550         public Integer getPidThreshold() {
1551             return pidThreshold;
1552         }
1553
1554         /**
1555          * Sets the value of the pidThreshold property.
1556          *
1557          * @param value
1558          *     allowed object is
1559          *     {@link Integer }
1560          *
1561          */
1562         public void setPidThreshold(Integer value) {
1563             this.pidThreshold = value;
1564         }
1565
1566         /**
1567          * Gets the value of the outlineColour property.
1568          *
1569          * @return
1570          *     possible object is
1571          *     {@link Integer }
1572          *
1573          */
1574         public Integer getOutlineColour() {
1575             return outlineColour;
1576         }
1577
1578         /**
1579          * Sets the value of the outlineColour property.
1580          *
1581          * @param value
1582          *     allowed object is
1583          *     {@link Integer }
1584          *
1585          */
1586         public void setOutlineColour(Integer value) {
1587             this.outlineColour = value;
1588         }
1589
1590         /**
1591          * Gets the value of the displayBoxes property.
1592          *
1593          * @return
1594          *     possible object is
1595          *     {@link Boolean }
1596          *
1597          */
1598         public Boolean isDisplayBoxes() {
1599             return displayBoxes;
1600         }
1601
1602         /**
1603          * Sets the value of the displayBoxes property.
1604          *
1605          * @param value
1606          *     allowed object is
1607          *     {@link Boolean }
1608          *
1609          */
1610         public void setDisplayBoxes(Boolean value) {
1611             this.displayBoxes = value;
1612         }
1613
1614         /**
1615          * Gets the value of the displayText property.
1616          *
1617          * @return
1618          *     possible object is
1619          *     {@link Boolean }
1620          *
1621          */
1622         public Boolean isDisplayText() {
1623             return displayText;
1624         }
1625
1626         /**
1627          * Sets the value of the displayText property.
1628          *
1629          * @param value
1630          *     allowed object is
1631          *     {@link Boolean }
1632          *
1633          */
1634         public void setDisplayText(Boolean value) {
1635             this.displayText = value;
1636         }
1637
1638         /**
1639          * Gets the value of the colourText property.
1640          *
1641          * @return
1642          *     possible object is
1643          *     {@link Boolean }
1644          *
1645          */
1646         public Boolean isColourText() {
1647             return colourText;
1648         }
1649
1650         /**
1651          * Sets the value of the colourText property.
1652          *
1653          * @param value
1654          *     allowed object is
1655          *     {@link Boolean }
1656          *
1657          */
1658         public void setColourText(Boolean value) {
1659             this.colourText = value;
1660         }
1661
1662         /**
1663          * Gets the value of the textCol1 property.
1664          *
1665          * @return
1666          *     possible object is
1667          *     {@link Integer }
1668          *
1669          */
1670         public Integer getTextCol1() {
1671             return textCol1;
1672         }
1673
1674         /**
1675          * Sets the value of the textCol1 property.
1676          *
1677          * @param value
1678          *     allowed object is
1679          *     {@link Integer }
1680          *
1681          */
1682         public void setTextCol1(Integer value) {
1683             this.textCol1 = value;
1684         }
1685
1686         /**
1687          * Gets the value of the textCol2 property.
1688          *
1689          * @return
1690          *     possible object is
1691          *     {@link Integer }
1692          *
1693          */
1694         public Integer getTextCol2() {
1695             return textCol2;
1696         }
1697
1698         /**
1699          * Sets the value of the textCol2 property.
1700          *
1701          * @param value
1702          *     allowed object is
1703          *     {@link Integer }
1704          *
1705          */
1706         public void setTextCol2(Integer value) {
1707             this.textCol2 = value;
1708         }
1709
1710         /**
1711          * Gets the value of the textColThreshold property.
1712          *
1713          * @return
1714          *     possible object is
1715          *     {@link Integer }
1716          *
1717          */
1718         public Integer getTextColThreshold() {
1719             return textColThreshold;
1720         }
1721
1722         /**
1723          * Sets the value of the textColThreshold property.
1724          *
1725          * @param value
1726          *     allowed object is
1727          *     {@link Integer }
1728          *
1729          */
1730         public void setTextColThreshold(Integer value) {
1731             this.textColThreshold = value;
1732         }
1733
1734         /**
1735          * Gets the value of the showUnconserved property.
1736          *
1737          * @return
1738          *     possible object is
1739          *     {@link Boolean }
1740          *
1741          */
1742         public Boolean isShowUnconserved() {
1743             return showUnconserved;
1744         }
1745
1746         /**
1747          * Sets the value of the showUnconserved property.
1748          *
1749          * @param value
1750          *     allowed object is
1751          *     {@link Boolean }
1752          *
1753          */
1754         public void setShowUnconserved(Boolean value) {
1755             this.showUnconserved = value;
1756         }
1757
1758         /**
1759          * Gets the value of the ignoreGapsinConsensus property.
1760          *
1761          * @return
1762          *     possible object is
1763          *     {@link Boolean }
1764          *
1765          */
1766         public boolean isIgnoreGapsinConsensus() {
1767             if (ignoreGapsinConsensus == null) {
1768                 return true;
1769             } else {
1770                 return ignoreGapsinConsensus;
1771             }
1772         }
1773
1774         /**
1775          * Sets the value of the ignoreGapsinConsensus property.
1776          *
1777          * @param value
1778          *     allowed object is
1779          *     {@link Boolean }
1780          *
1781          */
1782         public void setIgnoreGapsinConsensus(Boolean value) {
1783             this.ignoreGapsinConsensus = value;
1784         }
1785
1786         /**
1787          * Gets the value of the showConsensusHistogram property.
1788          *
1789          * @return
1790          *     possible object is
1791          *     {@link Boolean }
1792          *
1793          */
1794         public boolean isShowConsensusHistogram() {
1795             if (showConsensusHistogram == null) {
1796                 return true;
1797             } else {
1798                 return showConsensusHistogram;
1799             }
1800         }
1801
1802         /**
1803          * Sets the value of the showConsensusHistogram property.
1804          *
1805          * @param value
1806          *     allowed object is
1807          *     {@link Boolean }
1808          *
1809          */
1810         public void setShowConsensusHistogram(Boolean value) {
1811             this.showConsensusHistogram = value;
1812         }
1813
1814         /**
1815          * Gets the value of the showSequenceLogo property.
1816          *
1817          * @return
1818          *     possible object is
1819          *     {@link Boolean }
1820          *
1821          */
1822         public boolean isShowSequenceLogo() {
1823             if (showSequenceLogo == null) {
1824                 return false;
1825             } else {
1826                 return showSequenceLogo;
1827             }
1828         }
1829
1830         /**
1831          * Sets the value of the showSequenceLogo property.
1832          *
1833          * @param value
1834          *     allowed object is
1835          *     {@link Boolean }
1836          *
1837          */
1838         public void setShowSequenceLogo(Boolean value) {
1839             this.showSequenceLogo = value;
1840         }
1841
1842         /**
1843          * Gets the value of the normaliseSequenceLogo property.
1844          *
1845          * @return
1846          *     possible object is
1847          *     {@link Boolean }
1848          *
1849          */
1850         public boolean isNormaliseSequenceLogo() {
1851             if (normaliseSequenceLogo == null) {
1852                 return false;
1853             } else {
1854                 return normaliseSequenceLogo;
1855             }
1856         }
1857
1858         /**
1859          * Sets the value of the normaliseSequenceLogo property.
1860          *
1861          * @param value
1862          *     allowed object is
1863          *     {@link Boolean }
1864          *
1865          */
1866         public void setNormaliseSequenceLogo(Boolean value) {
1867             this.normaliseSequenceLogo = value;
1868         }
1869
1870         /**
1871          * Gets the value of the id property.
1872          *
1873          * @return
1874          *     possible object is
1875          *     {@link String }
1876          *
1877          */
1878         public String getId() {
1879             return id;
1880         }
1881
1882         /**
1883          * Sets the value of the id property.
1884          *
1885          * @param value
1886          *     allowed object is
1887          *     {@link String }
1888          *
1889          */
1890         public void setId(String value) {
1891             this.id = value;
1892         }
1893
1894     }
1895
1896
1897     /**
1898      * <p>Java class for anonymous complex type.
1899      *
1900      * <p>The following schema fragment specifies the expected content contained within this class.
1901      *
1902      * <pre>
1903      * &lt;complexType>
1904      *   &lt;complexContent>
1905      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1906      *       &lt;sequence>
1907      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1908      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1909      *           &lt;complexType>
1910      *             &lt;complexContent>
1911      *               &lt;extension base="{www.jalview.org}pdbentry">
1912      *                 &lt;sequence>
1913      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1914      *                     &lt;complexType>
1915      *                       &lt;simpleContent>
1916      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1917      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1918      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1919      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1920      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1921      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1922      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1923      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1924      *                         &lt;/extension>
1925      *                       &lt;/simpleContent>
1926      *                     &lt;/complexType>
1927      *                   &lt;/element>
1928      *                 &lt;/sequence>
1929      *               &lt;/extension>
1930      *             &lt;/complexContent>
1931      *           &lt;/complexType>
1932      *         &lt;/element>
1933      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1934      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1935      *           &lt;complexType>
1936      *             &lt;complexContent>
1937      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1938      *                 &lt;sequence>
1939      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1940      *                     &lt;complexType>
1941      *                       &lt;complexContent>
1942      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1943      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1944      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1945      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1946      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1947      *                         &lt;/restriction>
1948      *                       &lt;/complexContent>
1949      *                     &lt;/complexType>
1950      *                   &lt;/element>
1951      *                 &lt;/sequence>
1952      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1953      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1954      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1955      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1956      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1957      *               &lt;/restriction>
1958      *             &lt;/complexContent>
1959      *           &lt;/complexType>
1960      *         &lt;/element>
1961      *       &lt;/sequence>
1962      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1963      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1964      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1965      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1966      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1967      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1968      *     &lt;/restriction>
1969      *   &lt;/complexContent>
1970      * &lt;/complexType>
1971      * </pre>
1972      *
1973      *
1974      */
1975     @XmlAccessorType(XmlAccessType.FIELD)
1976     @XmlType(name = "", propOrder = {
1977         "features",
1978         "pdbids",
1979         "hiddenSequences",
1980         "rnaViewer"
1981     })
1982     public static class JSeq {
1983
1984         @XmlElement(namespace = "www.jalview.org")
1985         protected List<Feature> features;
1986         @XmlElement(namespace = "www.jalview.org")
1987         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1988         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1989         protected List<Integer> hiddenSequences;
1990         @XmlElement(namespace = "www.jalview.org")
1991         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1992         @XmlAttribute(name = "colour")
1993         protected Integer colour;
1994         @XmlAttribute(name = "start", required = true)
1995         protected int start;
1996         @XmlAttribute(name = "end", required = true)
1997         protected int end;
1998         @XmlAttribute(name = "id", required = true)
1999         protected String id;
2000         @XmlAttribute(name = "hidden")
2001         protected Boolean hidden;
2002         @XmlAttribute(name = "viewreference")
2003         protected Boolean viewreference;
2004
2005         /**
2006          * Gets the value of the features property.
2007          *
2008          * <p>
2009          * This accessor method returns a reference to the live list,
2010          * not a snapshot. Therefore any modification you make to the
2011          * returned list will be present inside the JAXB object.
2012          * This is why there is not a <CODE>set</CODE> method for the features property.
2013          *
2014          * <p>
2015          * For example, to add a new item, do as follows:
2016          * <pre>
2017          *    getFeatures().add(newItem);
2018          * </pre>
2019          *
2020          *
2021          * <p>
2022          * Objects of the following type(s) are allowed in the list
2023          * {@link Feature }
2024          *
2025          *
2026          */
2027         public List<Feature> getFeatures() {
2028             if (features == null) {
2029                 features = new ArrayList<Feature>();
2030             }
2031             return this.features;
2032         }
2033
2034         /**
2035          * Gets the value of the pdbids property.
2036          *
2037          * <p>
2038          * This accessor method returns a reference to the live list,
2039          * not a snapshot. Therefore any modification you make to the
2040          * returned list will be present inside the JAXB object.
2041          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2042          *
2043          * <p>
2044          * For example, to add a new item, do as follows:
2045          * <pre>
2046          *    getPdbids().add(newItem);
2047          * </pre>
2048          *
2049          *
2050          * <p>
2051          * Objects of the following type(s) are allowed in the list
2052          * {@link JalviewModel.JSeq.Pdbids }
2053          *
2054          *
2055          */
2056         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2057             if (pdbids == null) {
2058                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2059             }
2060             return this.pdbids;
2061         }
2062
2063         /**
2064          * Gets the value of the hiddenSequences property.
2065          *
2066          * <p>
2067          * This accessor method returns a reference to the live list,
2068          * not a snapshot. Therefore any modification you make to the
2069          * returned list will be present inside the JAXB object.
2070          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2071          *
2072          * <p>
2073          * For example, to add a new item, do as follows:
2074          * <pre>
2075          *    getHiddenSequences().add(newItem);
2076          * </pre>
2077          *
2078          *
2079          * <p>
2080          * Objects of the following type(s) are allowed in the list
2081          * {@link Integer }
2082          *
2083          *
2084          */
2085         public List<Integer> getHiddenSequences() {
2086             if (hiddenSequences == null) {
2087                 hiddenSequences = new ArrayList<Integer>();
2088             }
2089             return this.hiddenSequences;
2090         }
2091
2092         /**
2093          * Gets the value of the rnaViewer property.
2094          *
2095          * <p>
2096          * This accessor method returns a reference to the live list,
2097          * not a snapshot. Therefore any modification you make to the
2098          * returned list will be present inside the JAXB object.
2099          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2100          *
2101          * <p>
2102          * For example, to add a new item, do as follows:
2103          * <pre>
2104          *    getRnaViewer().add(newItem);
2105          * </pre>
2106          *
2107          *
2108          * <p>
2109          * Objects of the following type(s) are allowed in the list
2110          * {@link JalviewModel.JSeq.RnaViewer }
2111          *
2112          *
2113          */
2114         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2115             if (rnaViewer == null) {
2116                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2117             }
2118             return this.rnaViewer;
2119         }
2120
2121         /**
2122          * Gets the value of the colour property.
2123          *
2124          * @return
2125          *     possible object is
2126          *     {@link Integer }
2127          *
2128          */
2129         public Integer getColour() {
2130             return colour;
2131         }
2132
2133         /**
2134          * Sets the value of the colour property.
2135          *
2136          * @param value
2137          *     allowed object is
2138          *     {@link Integer }
2139          *
2140          */
2141         public void setColour(Integer value) {
2142             this.colour = value;
2143         }
2144
2145         /**
2146          * Gets the value of the start property.
2147          *
2148          */
2149         public int getStart() {
2150             return start;
2151         }
2152
2153         /**
2154          * Sets the value of the start property.
2155          *
2156          */
2157         public void setStart(int value) {
2158             this.start = value;
2159         }
2160
2161         /**
2162          * Gets the value of the end property.
2163          *
2164          */
2165         public int getEnd() {
2166             return end;
2167         }
2168
2169         /**
2170          * Sets the value of the end property.
2171          *
2172          */
2173         public void setEnd(int value) {
2174             this.end = value;
2175         }
2176
2177         /**
2178          * Gets the value of the id property.
2179          *
2180          * @return
2181          *     possible object is
2182          *     {@link String }
2183          *
2184          */
2185         public String getId() {
2186             return id;
2187         }
2188
2189         /**
2190          * Sets the value of the id property.
2191          *
2192          * @param value
2193          *     allowed object is
2194          *     {@link String }
2195          *
2196          */
2197         public void setId(String value) {
2198             this.id = value;
2199         }
2200
2201         /**
2202          * Gets the value of the hidden property.
2203          *
2204          * @return
2205          *     possible object is
2206          *     {@link Boolean }
2207          *
2208          */
2209         public Boolean isHidden() {
2210             return hidden;
2211         }
2212
2213         /**
2214          * Sets the value of the hidden property.
2215          *
2216          * @param value
2217          *     allowed object is
2218          *     {@link Boolean }
2219          *
2220          */
2221         public void setHidden(Boolean value) {
2222             this.hidden = value;
2223         }
2224
2225         /**
2226          * Gets the value of the viewreference property.
2227          *
2228          * @return
2229          *     possible object is
2230          *     {@link Boolean }
2231          *
2232          */
2233         public Boolean isViewreference() {
2234             return viewreference;
2235         }
2236
2237         /**
2238          * Sets the value of the viewreference property.
2239          *
2240          * @param value
2241          *     allowed object is
2242          *     {@link Boolean }
2243          *
2244          */
2245         public void setViewreference(Boolean value) {
2246             this.viewreference = value;
2247         }
2248
2249
2250         /**
2251          * <p>Java class for anonymous complex type.
2252          *
2253          * <p>The following schema fragment specifies the expected content contained within this class.
2254          *
2255          * <pre>
2256          * &lt;complexType>
2257          *   &lt;complexContent>
2258          *     &lt;extension base="{www.jalview.org}pdbentry">
2259          *       &lt;sequence>
2260          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2261          *           &lt;complexType>
2262          *             &lt;simpleContent>
2263          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2264          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2265          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2266          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2267          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2268          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2269          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2270          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2271          *               &lt;/extension>
2272          *             &lt;/simpleContent>
2273          *           &lt;/complexType>
2274          *         &lt;/element>
2275          *       &lt;/sequence>
2276          *     &lt;/extension>
2277          *   &lt;/complexContent>
2278          * &lt;/complexType>
2279          * </pre>
2280          *
2281          *
2282          */
2283         @XmlAccessorType(XmlAccessType.FIELD)
2284         @XmlType(name = "", propOrder = {
2285             "structureState"
2286         })
2287         public static class Pdbids
2288             extends Pdbentry
2289         {
2290
2291             @XmlElement(namespace = "www.jalview.org")
2292             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2293
2294             /**
2295              * Gets the value of the structureState property.
2296              *
2297              * <p>
2298              * This accessor method returns a reference to the live list,
2299              * not a snapshot. Therefore any modification you make to the
2300              * returned list will be present inside the JAXB object.
2301              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2302              *
2303              * <p>
2304              * For example, to add a new item, do as follows:
2305              * <pre>
2306              *    getStructureState().add(newItem);
2307              * </pre>
2308              *
2309              *
2310              * <p>
2311              * Objects of the following type(s) are allowed in the list
2312              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2313              *
2314              *
2315              */
2316             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2317                 if (structureState == null) {
2318                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2319                 }
2320                 return this.structureState;
2321             }
2322
2323
2324             /**
2325              * <p>Java class for anonymous complex type.
2326              *
2327              * <p>The following schema fragment specifies the expected content contained within this class.
2328              *
2329              * <pre>
2330              * &lt;complexType>
2331              *   &lt;simpleContent>
2332              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2333              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2334              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2335              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2336              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2337              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2338              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2339              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2340              *     &lt;/extension>
2341              *   &lt;/simpleContent>
2342              * &lt;/complexType>
2343              * </pre>
2344              *
2345              *
2346              */
2347             @XmlAccessorType(XmlAccessType.FIELD)
2348             @XmlType(name = "", propOrder = {
2349                 "value"
2350             })
2351             public static class StructureState {
2352
2353                 @XmlValue
2354                 protected String value;
2355                 @XmlAttribute(name = "visible")
2356                 protected Boolean visible;
2357                 @XmlAttribute(name = "viewId")
2358                 protected String viewId;
2359                 @XmlAttribute(name = "alignwithAlignPanel")
2360                 protected Boolean alignwithAlignPanel;
2361                 @XmlAttribute(name = "colourwithAlignPanel")
2362                 protected Boolean colourwithAlignPanel;
2363                 @XmlAttribute(name = "colourByJmol")
2364                 protected Boolean colourByJmol;
2365                 @XmlAttribute(name = "type")
2366                 protected String type;
2367                 @XmlAttribute(name = "width")
2368                 protected Integer width;
2369                 @XmlAttribute(name = "height")
2370                 protected Integer height;
2371                 @XmlAttribute(name = "xpos")
2372                 protected Integer xpos;
2373                 @XmlAttribute(name = "ypos")
2374                 protected Integer ypos;
2375
2376                 /**
2377                  * Gets the value of the value property.
2378                  *
2379                  * @return
2380                  *     possible object is
2381                  *     {@link String }
2382                  *
2383                  */
2384                 public String getValue() {
2385                     return value;
2386                 }
2387
2388                 /**
2389                  * Sets the value of the value property.
2390                  *
2391                  * @param value
2392                  *     allowed object is
2393                  *     {@link String }
2394                  *
2395                  */
2396                 public void setValue(String value) {
2397                     this.value = value;
2398                 }
2399
2400                 /**
2401                  * Gets the value of the visible property.
2402                  *
2403                  * @return
2404                  *     possible object is
2405                  *     {@link Boolean }
2406                  *
2407                  */
2408                 public Boolean isVisible() {
2409                     return visible;
2410                 }
2411
2412                 /**
2413                  * Sets the value of the visible property.
2414                  *
2415                  * @param value
2416                  *     allowed object is
2417                  *     {@link Boolean }
2418                  *
2419                  */
2420                 public void setVisible(Boolean value) {
2421                     this.visible = value;
2422                 }
2423
2424                 /**
2425                  * Gets the value of the viewId property.
2426                  *
2427                  * @return
2428                  *     possible object is
2429                  *     {@link String }
2430                  *
2431                  */
2432                 public String getViewId() {
2433                     return viewId;
2434                 }
2435
2436                 /**
2437                  * Sets the value of the viewId property.
2438                  *
2439                  * @param value
2440                  *     allowed object is
2441                  *     {@link String }
2442                  *
2443                  */
2444                 public void setViewId(String value) {
2445                     this.viewId = value;
2446                 }
2447
2448                 /**
2449                  * Gets the value of the alignwithAlignPanel property.
2450                  *
2451                  * @return
2452                  *     possible object is
2453                  *     {@link Boolean }
2454                  *
2455                  */
2456                 public boolean isAlignwithAlignPanel() {
2457                     if (alignwithAlignPanel == null) {
2458                         return true;
2459                     } else {
2460                         return alignwithAlignPanel;
2461                     }
2462                 }
2463
2464                 /**
2465                  * Sets the value of the alignwithAlignPanel property.
2466                  *
2467                  * @param value
2468                  *     allowed object is
2469                  *     {@link Boolean }
2470                  *
2471                  */
2472                 public void setAlignwithAlignPanel(Boolean value) {
2473                     this.alignwithAlignPanel = value;
2474                 }
2475
2476                 /**
2477                  * Gets the value of the colourwithAlignPanel property.
2478                  *
2479                  * @return
2480                  *     possible object is
2481                  *     {@link Boolean }
2482                  *
2483                  */
2484                 public boolean isColourwithAlignPanel() {
2485                     if (colourwithAlignPanel == null) {
2486                         return false;
2487                     } else {
2488                         return colourwithAlignPanel;
2489                     }
2490                 }
2491
2492                 /**
2493                  * Sets the value of the colourwithAlignPanel property.
2494                  *
2495                  * @param value
2496                  *     allowed object is
2497                  *     {@link Boolean }
2498                  *
2499                  */
2500                 public void setColourwithAlignPanel(Boolean value) {
2501                     this.colourwithAlignPanel = value;
2502                 }
2503
2504                 /**
2505                  * Gets the value of the colourByJmol property.
2506                  *
2507                  * @return
2508                  *     possible object is
2509                  *     {@link Boolean }
2510                  *
2511                  */
2512                 public boolean isColourByJmol() {
2513                     if (colourByJmol == null) {
2514                         return true;
2515                     } else {
2516                         return colourByJmol;
2517                     }
2518                 }
2519
2520                 /**
2521                  * Sets the value of the colourByJmol property.
2522                  *
2523                  * @param value
2524                  *     allowed object is
2525                  *     {@link Boolean }
2526                  *
2527                  */
2528                 public void setColourByJmol(Boolean value) {
2529                     this.colourByJmol = value;
2530                 }
2531
2532                 /**
2533                  * Gets the value of the type property.
2534                  *
2535                  * @return
2536                  *     possible object is
2537                  *     {@link String }
2538                  *
2539                  */
2540                 public String getType() {
2541                     return type;
2542                 }
2543
2544                 /**
2545                  * Sets the value of the type property.
2546                  *
2547                  * @param value
2548                  *     allowed object is
2549                  *     {@link String }
2550                  *
2551                  */
2552                 public void setType(String value) {
2553                     this.type = value;
2554                 }
2555
2556                 /**
2557                  * Gets the value of the width property.
2558                  *
2559                  * @return
2560                  *     possible object is
2561                  *     {@link Integer }
2562                  *
2563                  */
2564                 public Integer getWidth() {
2565                     return width;
2566                 }
2567
2568                 /**
2569                  * Sets the value of the width property.
2570                  *
2571                  * @param value
2572                  *     allowed object is
2573                  *     {@link Integer }
2574                  *
2575                  */
2576                 public void setWidth(Integer value) {
2577                     this.width = value;
2578                 }
2579
2580                 /**
2581                  * Gets the value of the height property.
2582                  *
2583                  * @return
2584                  *     possible object is
2585                  *     {@link Integer }
2586                  *
2587                  */
2588                 public Integer getHeight() {
2589                     return height;
2590                 }
2591
2592                 /**
2593                  * Sets the value of the height property.
2594                  *
2595                  * @param value
2596                  *     allowed object is
2597                  *     {@link Integer }
2598                  *
2599                  */
2600                 public void setHeight(Integer value) {
2601                     this.height = value;
2602                 }
2603
2604                 /**
2605                  * Gets the value of the xpos property.
2606                  *
2607                  * @return
2608                  *     possible object is
2609                  *     {@link Integer }
2610                  *
2611                  */
2612                 public Integer getXpos() {
2613                     return xpos;
2614                 }
2615
2616                 /**
2617                  * Sets the value of the xpos property.
2618                  *
2619                  * @param value
2620                  *     allowed object is
2621                  *     {@link Integer }
2622                  *
2623                  */
2624                 public void setXpos(Integer value) {
2625                     this.xpos = value;
2626                 }
2627
2628                 /**
2629                  * Gets the value of the ypos property.
2630                  *
2631                  * @return
2632                  *     possible object is
2633                  *     {@link Integer }
2634                  *
2635                  */
2636                 public Integer getYpos() {
2637                     return ypos;
2638                 }
2639
2640                 /**
2641                  * Sets the value of the ypos property.
2642                  *
2643                  * @param value
2644                  *     allowed object is
2645                  *     {@link Integer }
2646                  *
2647                  */
2648                 public void setYpos(Integer value) {
2649                     this.ypos = value;
2650                 }
2651
2652             }
2653
2654         }
2655
2656
2657         /**
2658          * <p>Java class for anonymous complex type.
2659          *
2660          * <p>The following schema fragment specifies the expected content contained within this class.
2661          *
2662          * <pre>
2663          * &lt;complexType>
2664          *   &lt;complexContent>
2665          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2666          *       &lt;sequence>
2667          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2668          *           &lt;complexType>
2669          *             &lt;complexContent>
2670          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2671          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2672          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2673          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2674          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2675          *               &lt;/restriction>
2676          *             &lt;/complexContent>
2677          *           &lt;/complexType>
2678          *         &lt;/element>
2679          *       &lt;/sequence>
2680          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2681          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2682          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2683          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2684          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2685          *     &lt;/restriction>
2686          *   &lt;/complexContent>
2687          * &lt;/complexType>
2688          * </pre>
2689          *
2690          *
2691          */
2692         @XmlAccessorType(XmlAccessType.FIELD)
2693         @XmlType(name = "", propOrder = {
2694             "secondaryStructure"
2695         })
2696         public static class RnaViewer {
2697
2698             @XmlElement(namespace = "www.jalview.org", required = true)
2699             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2700             @XmlAttribute(name = "title")
2701             protected String title;
2702             @XmlAttribute(name = "viewId")
2703             protected String viewId;
2704             @XmlAttribute(name = "dividerLocation")
2705             protected Integer dividerLocation;
2706             @XmlAttribute(name = "selectedRna")
2707             protected Integer selectedRna;
2708             @XmlAttribute(name = "width")
2709             protected Integer width;
2710             @XmlAttribute(name = "height")
2711             protected Integer height;
2712             @XmlAttribute(name = "xpos")
2713             protected Integer xpos;
2714             @XmlAttribute(name = "ypos")
2715             protected Integer ypos;
2716
2717             /**
2718              * Gets the value of the secondaryStructure property.
2719              *
2720              * <p>
2721              * This accessor method returns a reference to the live list,
2722              * not a snapshot. Therefore any modification you make to the
2723              * returned list will be present inside the JAXB object.
2724              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2725              *
2726              * <p>
2727              * For example, to add a new item, do as follows:
2728              * <pre>
2729              *    getSecondaryStructure().add(newItem);
2730              * </pre>
2731              *
2732              *
2733              * <p>
2734              * Objects of the following type(s) are allowed in the list
2735              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2736              *
2737              *
2738              */
2739             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2740                 if (secondaryStructure == null) {
2741                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2742                 }
2743                 return this.secondaryStructure;
2744             }
2745
2746             /**
2747              * Gets the value of the title property.
2748              *
2749              * @return
2750              *     possible object is
2751              *     {@link String }
2752              *
2753              */
2754             public String getTitle() {
2755                 return title;
2756             }
2757
2758             /**
2759              * Sets the value of the title property.
2760              *
2761              * @param value
2762              *     allowed object is
2763              *     {@link String }
2764              *
2765              */
2766             public void setTitle(String value) {
2767                 this.title = value;
2768             }
2769
2770             /**
2771              * Gets the value of the viewId property.
2772              *
2773              * @return
2774              *     possible object is
2775              *     {@link String }
2776              *
2777              */
2778             public String getViewId() {
2779                 return viewId;
2780             }
2781
2782             /**
2783              * Sets the value of the viewId property.
2784              *
2785              * @param value
2786              *     allowed object is
2787              *     {@link String }
2788              *
2789              */
2790             public void setViewId(String value) {
2791                 this.viewId = value;
2792             }
2793
2794             /**
2795              * Gets the value of the dividerLocation property.
2796              *
2797              * @return
2798              *     possible object is
2799              *     {@link Integer }
2800              *
2801              */
2802             public Integer getDividerLocation() {
2803                 return dividerLocation;
2804             }
2805
2806             /**
2807              * Sets the value of the dividerLocation property.
2808              *
2809              * @param value
2810              *     allowed object is
2811              *     {@link Integer }
2812              *
2813              */
2814             public void setDividerLocation(Integer value) {
2815                 this.dividerLocation = value;
2816             }
2817
2818             /**
2819              * Gets the value of the selectedRna property.
2820              *
2821              * @return
2822              *     possible object is
2823              *     {@link Integer }
2824              *
2825              */
2826             public Integer getSelectedRna() {
2827                 return selectedRna;
2828             }
2829
2830             /**
2831              * Sets the value of the selectedRna property.
2832              *
2833              * @param value
2834              *     allowed object is
2835              *     {@link Integer }
2836              *
2837              */
2838             public void setSelectedRna(Integer value) {
2839                 this.selectedRna = value;
2840             }
2841
2842             /**
2843              * Gets the value of the width property.
2844              *
2845              * @return
2846              *     possible object is
2847              *     {@link Integer }
2848              *
2849              */
2850             public Integer getWidth() {
2851                 return width;
2852             }
2853
2854             /**
2855              * Sets the value of the width property.
2856              *
2857              * @param value
2858              *     allowed object is
2859              *     {@link Integer }
2860              *
2861              */
2862             public void setWidth(Integer value) {
2863                 this.width = value;
2864             }
2865
2866             /**
2867              * Gets the value of the height property.
2868              *
2869              * @return
2870              *     possible object is
2871              *     {@link Integer }
2872              *
2873              */
2874             public Integer getHeight() {
2875                 return height;
2876             }
2877
2878             /**
2879              * Sets the value of the height property.
2880              *
2881              * @param value
2882              *     allowed object is
2883              *     {@link Integer }
2884              *
2885              */
2886             public void setHeight(Integer value) {
2887                 this.height = value;
2888             }
2889
2890             /**
2891              * Gets the value of the xpos property.
2892              *
2893              * @return
2894              *     possible object is
2895              *     {@link Integer }
2896              *
2897              */
2898             public Integer getXpos() {
2899                 return xpos;
2900             }
2901
2902             /**
2903              * Sets the value of the xpos property.
2904              *
2905              * @param value
2906              *     allowed object is
2907              *     {@link Integer }
2908              *
2909              */
2910             public void setXpos(Integer value) {
2911                 this.xpos = value;
2912             }
2913
2914             /**
2915              * Gets the value of the ypos property.
2916              *
2917              * @return
2918              *     possible object is
2919              *     {@link Integer }
2920              *
2921              */
2922             public Integer getYpos() {
2923                 return ypos;
2924             }
2925
2926             /**
2927              * Sets the value of the ypos property.
2928              *
2929              * @param value
2930              *     allowed object is
2931              *     {@link Integer }
2932              *
2933              */
2934             public void setYpos(Integer value) {
2935                 this.ypos = value;
2936             }
2937
2938
2939             /**
2940              * <p>Java class for anonymous complex type.
2941              *
2942              * <p>The following schema fragment specifies the expected content contained within this class.
2943              *
2944              * <pre>
2945              * &lt;complexType>
2946              *   &lt;complexContent>
2947              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2948              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2949              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2950              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2951              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2952              *     &lt;/restriction>
2953              *   &lt;/complexContent>
2954              * &lt;/complexType>
2955              * </pre>
2956              *
2957              *
2958              */
2959             @XmlAccessorType(XmlAccessType.FIELD)
2960             @XmlType(name = "")
2961             public static class SecondaryStructure {
2962
2963                 @XmlAttribute(name = "title")
2964                 protected String title;
2965                 @XmlAttribute(name = "annotationId", required = true)
2966                 protected String annotationId;
2967                 @XmlAttribute(name = "gapped")
2968                 protected Boolean gapped;
2969                 @XmlAttribute(name = "viewerState")
2970                 protected String viewerState;
2971
2972                 /**
2973                  * Gets the value of the title property.
2974                  *
2975                  * @return
2976                  *     possible object is
2977                  *     {@link String }
2978                  *
2979                  */
2980                 public String getTitle() {
2981                     return title;
2982                 }
2983
2984                 /**
2985                  * Sets the value of the title property.
2986                  *
2987                  * @param value
2988                  *     allowed object is
2989                  *     {@link String }
2990                  *
2991                  */
2992                 public void setTitle(String value) {
2993                     this.title = value;
2994                 }
2995
2996                 /**
2997                  * Gets the value of the annotationId property.
2998                  *
2999                  * @return
3000                  *     possible object is
3001                  *     {@link String }
3002                  *
3003                  */
3004                 public String getAnnotationId() {
3005                     return annotationId;
3006                 }
3007
3008                 /**
3009                  * Sets the value of the annotationId property.
3010                  *
3011                  * @param value
3012                  *     allowed object is
3013                  *     {@link String }
3014                  *
3015                  */
3016                 public void setAnnotationId(String value) {
3017                     this.annotationId = value;
3018                 }
3019
3020                 /**
3021                  * Gets the value of the gapped property.
3022                  *
3023                  * @return
3024                  *     possible object is
3025                  *     {@link Boolean }
3026                  *
3027                  */
3028                 public Boolean isGapped() {
3029                     return gapped;
3030                 }
3031
3032                 /**
3033                  * Sets the value of the gapped property.
3034                  *
3035                  * @param value
3036                  *     allowed object is
3037                  *     {@link Boolean }
3038                  *
3039                  */
3040                 public void setGapped(Boolean value) {
3041                     this.gapped = value;
3042                 }
3043
3044                 /**
3045                  * Gets the value of the viewerState property.
3046                  *
3047                  * @return
3048                  *     possible object is
3049                  *     {@link String }
3050                  *
3051                  */
3052                 public String getViewerState() {
3053                     return viewerState;
3054                 }
3055
3056                 /**
3057                  * Sets the value of the viewerState property.
3058                  *
3059                  * @param value
3060                  *     allowed object is
3061                  *     {@link String }
3062                  *
3063                  */
3064                 public void setViewerState(String value) {
3065                     this.viewerState = value;
3066                 }
3067
3068             }
3069
3070         }
3071
3072     }
3073
3074
3075     /**
3076      * <p>Java class for anonymous complex type.
3077      *
3078      * <p>The following schema fragment specifies the expected content contained within this class.
3079      *
3080      * <pre>
3081      * &lt;complexType>
3082      *   &lt;complexContent>
3083      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3084      *       &lt;sequence>
3085      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3086      *           &lt;complexType>
3087      *             &lt;complexContent>
3088      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3089      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3090      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3091      *               &lt;/restriction>
3092      *             &lt;/complexContent>
3093      *           &lt;/complexType>
3094      *         &lt;/element>
3095      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3096      *           &lt;complexType>
3097      *             &lt;complexContent>
3098      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3099      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3100      *               &lt;/restriction>
3101      *             &lt;/complexContent>
3102      *           &lt;/complexType>
3103      *         &lt;/element>
3104      *         &lt;element name="seqPointMin">
3105      *           &lt;complexType>
3106      *             &lt;complexContent>
3107      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3108      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3109      *               &lt;/restriction>
3110      *             &lt;/complexContent>
3111      *           &lt;/complexType>
3112      *         &lt;/element>
3113      *         &lt;element name="seqPointMax">
3114      *           &lt;complexType>
3115      *             &lt;complexContent>
3116      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3117      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3118      *               &lt;/restriction>
3119      *             &lt;/complexContent>
3120      *           &lt;/complexType>
3121      *         &lt;/element>
3122      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3123      *       &lt;/sequence>
3124      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3125      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3126      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3127      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3128      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3129      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3130      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3131      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3132      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3133      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3134      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3135      *     &lt;/restriction>
3136      *   &lt;/complexContent>
3137      * &lt;/complexType>
3138      * </pre>
3139      *
3140      *
3141      */
3142     @XmlAccessorType(XmlAccessType.FIELD)
3143     @XmlType(name = "", propOrder = {
3144         "sequencePoint",
3145         "axis",
3146         "seqPointMin",
3147         "seqPointMax",
3148         "pcaData"
3149     })
3150     public static class PcaViewer {
3151
3152         @XmlElement(namespace = "www.jalview.org", required = true)
3153         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3154         @XmlElement(namespace = "www.jalview.org", required = true)
3155         protected List<JalviewModel.PcaViewer.Axis> axis;
3156         @XmlElement(namespace = "www.jalview.org", required = true)
3157         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3158         @XmlElement(namespace = "www.jalview.org", required = true)
3159         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3160         @XmlElement(namespace = "www.jalview.org", required = true)
3161         protected PcaDataType pcaData;
3162         @XmlAttribute(name = "title")
3163         protected String title;
3164         @XmlAttribute(name = "scoreModelName")
3165         protected String scoreModelName;
3166         @XmlAttribute(name = "xDim")
3167         protected Integer xDim;
3168         @XmlAttribute(name = "yDim")
3169         protected Integer yDim;
3170         @XmlAttribute(name = "zDim")
3171         protected Integer zDim;
3172         @XmlAttribute(name = "bgColour")
3173         protected Integer bgColour;
3174         @XmlAttribute(name = "scaleFactor")
3175         protected Float scaleFactor;
3176         @XmlAttribute(name = "showLabels")
3177         protected Boolean showLabels;
3178         @XmlAttribute(name = "linkToAllViews")
3179         protected Boolean linkToAllViews;
3180         @XmlAttribute(name = "width")
3181         protected Integer width;
3182         @XmlAttribute(name = "height")
3183         protected Integer height;
3184         @XmlAttribute(name = "xpos")
3185         protected Integer xpos;
3186         @XmlAttribute(name = "ypos")
3187         protected Integer ypos;
3188         @XmlAttribute(name = "includeGaps")
3189         protected Boolean includeGaps;
3190         @XmlAttribute(name = "matchGaps")
3191         protected Boolean matchGaps;
3192         @XmlAttribute(name = "includeGappedColumns")
3193         protected Boolean includeGappedColumns;
3194         @XmlAttribute(name = "denominateByShortestLength")
3195         protected Boolean denominateByShortestLength;
3196
3197         /**
3198          * Gets the value of the sequencePoint property.
3199          *
3200          * <p>
3201          * This accessor method returns a reference to the live list,
3202          * not a snapshot. Therefore any modification you make to the
3203          * returned list will be present inside the JAXB object.
3204          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3205          *
3206          * <p>
3207          * For example, to add a new item, do as follows:
3208          * <pre>
3209          *    getSequencePoint().add(newItem);
3210          * </pre>
3211          *
3212          *
3213          * <p>
3214          * Objects of the following type(s) are allowed in the list
3215          * {@link JalviewModel.PcaViewer.SequencePoint }
3216          *
3217          *
3218          */
3219         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3220             if (sequencePoint == null) {
3221                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3222             }
3223             return this.sequencePoint;
3224         }
3225
3226         /**
3227          * Gets the value of the axis property.
3228          *
3229          * <p>
3230          * This accessor method returns a reference to the live list,
3231          * not a snapshot. Therefore any modification you make to the
3232          * returned list will be present inside the JAXB object.
3233          * This is why there is not a <CODE>set</CODE> method for the axis property.
3234          *
3235          * <p>
3236          * For example, to add a new item, do as follows:
3237          * <pre>
3238          *    getAxis().add(newItem);
3239          * </pre>
3240          *
3241          *
3242          * <p>
3243          * Objects of the following type(s) are allowed in the list
3244          * {@link JalviewModel.PcaViewer.Axis }
3245          *
3246          *
3247          */
3248         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3249             if (axis == null) {
3250                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3251             }
3252             return this.axis;
3253         }
3254
3255         /**
3256          * Gets the value of the seqPointMin property.
3257          *
3258          * @return
3259          *     possible object is
3260          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3261          *
3262          */
3263         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3264             return seqPointMin;
3265         }
3266
3267         /**
3268          * Sets the value of the seqPointMin property.
3269          *
3270          * @param value
3271          *     allowed object is
3272          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3273          *
3274          */
3275         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3276             this.seqPointMin = value;
3277         }
3278
3279         /**
3280          * Gets the value of the seqPointMax property.
3281          *
3282          * @return
3283          *     possible object is
3284          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3285          *
3286          */
3287         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3288             return seqPointMax;
3289         }
3290
3291         /**
3292          * Sets the value of the seqPointMax property.
3293          *
3294          * @param value
3295          *     allowed object is
3296          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3297          *
3298          */
3299         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3300             this.seqPointMax = value;
3301         }
3302
3303         /**
3304          * Gets the value of the pcaData property.
3305          *
3306          * @return
3307          *     possible object is
3308          *     {@link PcaDataType }
3309          *
3310          */
3311         public PcaDataType getPcaData() {
3312             return pcaData;
3313         }
3314
3315         /**
3316          * Sets the value of the pcaData property.
3317          *
3318          * @param value
3319          *     allowed object is
3320          *     {@link PcaDataType }
3321          *
3322          */
3323         public void setPcaData(PcaDataType value) {
3324             this.pcaData = value;
3325         }
3326
3327         /**
3328          * Gets the value of the title property.
3329          *
3330          * @return
3331          *     possible object is
3332          *     {@link String }
3333          *
3334          */
3335         public String getTitle() {
3336             return title;
3337         }
3338
3339         /**
3340          * Sets the value of the title property.
3341          *
3342          * @param value
3343          *     allowed object is
3344          *     {@link String }
3345          *
3346          */
3347         public void setTitle(String value) {
3348             this.title = value;
3349         }
3350
3351         /**
3352          * Gets the value of the scoreModelName property.
3353          *
3354          * @return
3355          *     possible object is
3356          *     {@link String }
3357          *
3358          */
3359         public String getScoreModelName() {
3360             return scoreModelName;
3361         }
3362
3363         /**
3364          * Sets the value of the scoreModelName property.
3365          *
3366          * @param value
3367          *     allowed object is
3368          *     {@link String }
3369          *
3370          */
3371         public void setScoreModelName(String value) {
3372             this.scoreModelName = value;
3373         }
3374
3375         /**
3376          * Gets the value of the xDim property.
3377          *
3378          * @return
3379          *     possible object is
3380          *     {@link Integer }
3381          *
3382          */
3383         public Integer getXDim() {
3384             return xDim;
3385         }
3386
3387         /**
3388          * Sets the value of the xDim property.
3389          *
3390          * @param value
3391          *     allowed object is
3392          *     {@link Integer }
3393          *
3394          */
3395         public void setXDim(Integer value) {
3396             this.xDim = value;
3397         }
3398
3399         /**
3400          * Gets the value of the yDim property.
3401          *
3402          * @return
3403          *     possible object is
3404          *     {@link Integer }
3405          *
3406          */
3407         public Integer getYDim() {
3408             return yDim;
3409         }
3410
3411         /**
3412          * Sets the value of the yDim property.
3413          *
3414          * @param value
3415          *     allowed object is
3416          *     {@link Integer }
3417          *
3418          */
3419         public void setYDim(Integer value) {
3420             this.yDim = value;
3421         }
3422
3423         /**
3424          * Gets the value of the zDim property.
3425          *
3426          * @return
3427          *     possible object is
3428          *     {@link Integer }
3429          *
3430          */
3431         public Integer getZDim() {
3432             return zDim;
3433         }
3434
3435         /**
3436          * Sets the value of the zDim property.
3437          *
3438          * @param value
3439          *     allowed object is
3440          *     {@link Integer }
3441          *
3442          */
3443         public void setZDim(Integer value) {
3444             this.zDim = value;
3445         }
3446
3447         /**
3448          * Gets the value of the bgColour property.
3449          *
3450          * @return
3451          *     possible object is
3452          *     {@link Integer }
3453          *
3454          */
3455         public Integer getBgColour() {
3456             return bgColour;
3457         }
3458
3459         /**
3460          * Sets the value of the bgColour property.
3461          *
3462          * @param value
3463          *     allowed object is
3464          *     {@link Integer }
3465          *
3466          */
3467         public void setBgColour(Integer value) {
3468             this.bgColour = value;
3469         }
3470
3471         /**
3472          * Gets the value of the scaleFactor property.
3473          *
3474          * @return
3475          *     possible object is
3476          *     {@link Float }
3477          *
3478          */
3479         public Float getScaleFactor() {
3480             return scaleFactor;
3481         }
3482
3483         /**
3484          * Sets the value of the scaleFactor property.
3485          *
3486          * @param value
3487          *     allowed object is
3488          *     {@link Float }
3489          *
3490          */
3491         public void setScaleFactor(Float value) {
3492             this.scaleFactor = value;
3493         }
3494
3495         /**
3496          * Gets the value of the showLabels property.
3497          *
3498          * @return
3499          *     possible object is
3500          *     {@link Boolean }
3501          *
3502          */
3503         public Boolean isShowLabels() {
3504             return showLabels;
3505         }
3506
3507         /**
3508          * Sets the value of the showLabels property.
3509          *
3510          * @param value
3511          *     allowed object is
3512          *     {@link Boolean }
3513          *
3514          */
3515         public void setShowLabels(Boolean value) {
3516             this.showLabels = value;
3517         }
3518
3519         /**
3520          * Gets the value of the linkToAllViews property.
3521          *
3522          * @return
3523          *     possible object is
3524          *     {@link Boolean }
3525          *
3526          */
3527         public Boolean isLinkToAllViews() {
3528             return linkToAllViews;
3529         }
3530
3531         /**
3532          * Sets the value of the linkToAllViews property.
3533          *
3534          * @param value
3535          *     allowed object is
3536          *     {@link Boolean }
3537          *
3538          */
3539         public void setLinkToAllViews(Boolean value) {
3540             this.linkToAllViews = value;
3541         }
3542
3543         /**
3544          * Gets the value of the width property.
3545          *
3546          * @return
3547          *     possible object is
3548          *     {@link Integer }
3549          *
3550          */
3551         public Integer getWidth() {
3552             return width;
3553         }
3554
3555         /**
3556          * Sets the value of the width property.
3557          *
3558          * @param value
3559          *     allowed object is
3560          *     {@link Integer }
3561          *
3562          */
3563         public void setWidth(Integer value) {
3564             this.width = value;
3565         }
3566
3567         /**
3568          * Gets the value of the height property.
3569          *
3570          * @return
3571          *     possible object is
3572          *     {@link Integer }
3573          *
3574          */
3575         public Integer getHeight() {
3576             return height;
3577         }
3578
3579         /**
3580          * Sets the value of the height property.
3581          *
3582          * @param value
3583          *     allowed object is
3584          *     {@link Integer }
3585          *
3586          */
3587         public void setHeight(Integer value) {
3588             this.height = value;
3589         }
3590
3591         /**
3592          * Gets the value of the xpos property.
3593          *
3594          * @return
3595          *     possible object is
3596          *     {@link Integer }
3597          *
3598          */
3599         public Integer getXpos() {
3600             return xpos;
3601         }
3602
3603         /**
3604          * Sets the value of the xpos property.
3605          *
3606          * @param value
3607          *     allowed object is
3608          *     {@link Integer }
3609          *
3610          */
3611         public void setXpos(Integer value) {
3612             this.xpos = value;
3613         }
3614
3615         /**
3616          * Gets the value of the ypos property.
3617          *
3618          * @return
3619          *     possible object is
3620          *     {@link Integer }
3621          *
3622          */
3623         public Integer getYpos() {
3624             return ypos;
3625         }
3626
3627         /**
3628          * Sets the value of the ypos property.
3629          *
3630          * @param value
3631          *     allowed object is
3632          *     {@link Integer }
3633          *
3634          */
3635         public void setYpos(Integer value) {
3636             this.ypos = value;
3637         }
3638
3639         /**
3640          * Gets the value of the includeGaps property.
3641          *
3642          * @return
3643          *     possible object is
3644          *     {@link Boolean }
3645          *
3646          */
3647         public Boolean isIncludeGaps() {
3648             return includeGaps;
3649         }
3650
3651         /**
3652          * Sets the value of the includeGaps property.
3653          *
3654          * @param value
3655          *     allowed object is
3656          *     {@link Boolean }
3657          *
3658          */
3659         public void setIncludeGaps(Boolean value) {
3660             this.includeGaps = value;
3661         }
3662
3663         /**
3664          * Gets the value of the matchGaps property.
3665          *
3666          * @return
3667          *     possible object is
3668          *     {@link Boolean }
3669          *
3670          */
3671         public Boolean isMatchGaps() {
3672             return matchGaps;
3673         }
3674
3675         /**
3676          * Sets the value of the matchGaps property.
3677          *
3678          * @param value
3679          *     allowed object is
3680          *     {@link Boolean }
3681          *
3682          */
3683         public void setMatchGaps(Boolean value) {
3684             this.matchGaps = value;
3685         }
3686
3687         /**
3688          * Gets the value of the includeGappedColumns property.
3689          *
3690          * @return
3691          *     possible object is
3692          *     {@link Boolean }
3693          *
3694          */
3695         public Boolean isIncludeGappedColumns() {
3696             return includeGappedColumns;
3697         }
3698
3699         /**
3700          * Sets the value of the includeGappedColumns property.
3701          *
3702          * @param value
3703          *     allowed object is
3704          *     {@link Boolean }
3705          *
3706          */
3707         public void setIncludeGappedColumns(Boolean value) {
3708             this.includeGappedColumns = value;
3709         }
3710
3711         /**
3712          * Gets the value of the denominateByShortestLength property.
3713          *
3714          * @return
3715          *     possible object is
3716          *     {@link Boolean }
3717          *
3718          */
3719         public Boolean isDenominateByShortestLength() {
3720             return denominateByShortestLength;
3721         }
3722
3723         /**
3724          * Sets the value of the denominateByShortestLength property.
3725          *
3726          * @param value
3727          *     allowed object is
3728          *     {@link Boolean }
3729          *
3730          */
3731         public void setDenominateByShortestLength(Boolean value) {
3732             this.denominateByShortestLength = value;
3733         }
3734
3735
3736         /**
3737          * <p>Java class for anonymous complex type.
3738          *
3739          * <p>The following schema fragment specifies the expected content contained within this class.
3740          *
3741          * <pre>
3742          * &lt;complexType>
3743          *   &lt;complexContent>
3744          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3745          *       &lt;attGroup ref="{www.jalview.org}position"/>
3746          *     &lt;/restriction>
3747          *   &lt;/complexContent>
3748          * &lt;/complexType>
3749          * </pre>
3750          *
3751          *
3752          */
3753         @XmlAccessorType(XmlAccessType.FIELD)
3754         @XmlType(name = "")
3755         public static class Axis {
3756
3757             @XmlAttribute(name = "xPos")
3758             protected Float xPos;
3759             @XmlAttribute(name = "yPos")
3760             protected Float yPos;
3761             @XmlAttribute(name = "zPos")
3762             protected Float zPos;
3763
3764             /**
3765              * Gets the value of the xPos property.
3766              *
3767              * @return
3768              *     possible object is
3769              *     {@link Float }
3770              *
3771              */
3772             public Float getXPos() {
3773                 return xPos;
3774             }
3775
3776             /**
3777              * Sets the value of the xPos property.
3778              *
3779              * @param value
3780              *     allowed object is
3781              *     {@link Float }
3782              *
3783              */
3784             public void setXPos(Float value) {
3785                 this.xPos = value;
3786             }
3787
3788             /**
3789              * Gets the value of the yPos property.
3790              *
3791              * @return
3792              *     possible object is
3793              *     {@link Float }
3794              *
3795              */
3796             public Float getYPos() {
3797                 return yPos;
3798             }
3799
3800             /**
3801              * Sets the value of the yPos property.
3802              *
3803              * @param value
3804              *     allowed object is
3805              *     {@link Float }
3806              *
3807              */
3808             public void setYPos(Float value) {
3809                 this.yPos = value;
3810             }
3811
3812             /**
3813              * Gets the value of the zPos property.
3814              *
3815              * @return
3816              *     possible object is
3817              *     {@link Float }
3818              *
3819              */
3820             public Float getZPos() {
3821                 return zPos;
3822             }
3823
3824             /**
3825              * Sets the value of the zPos property.
3826              *
3827              * @param value
3828              *     allowed object is
3829              *     {@link Float }
3830              *
3831              */
3832             public void setZPos(Float value) {
3833                 this.zPos = value;
3834             }
3835
3836         }
3837
3838
3839         /**
3840          * <p>Java class for anonymous complex type.
3841          *
3842          * <p>The following schema fragment specifies the expected content contained within this class.
3843          *
3844          * <pre>
3845          * &lt;complexType>
3846          *   &lt;complexContent>
3847          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3848          *       &lt;attGroup ref="{www.jalview.org}position"/>
3849          *     &lt;/restriction>
3850          *   &lt;/complexContent>
3851          * &lt;/complexType>
3852          * </pre>
3853          *
3854          *
3855          */
3856         @XmlAccessorType(XmlAccessType.FIELD)
3857         @XmlType(name = "")
3858         public static class SeqPointMax {
3859
3860             @XmlAttribute(name = "xPos")
3861             protected Float xPos;
3862             @XmlAttribute(name = "yPos")
3863             protected Float yPos;
3864             @XmlAttribute(name = "zPos")
3865             protected Float zPos;
3866
3867             /**
3868              * Gets the value of the xPos property.
3869              *
3870              * @return
3871              *     possible object is
3872              *     {@link Float }
3873              *
3874              */
3875             public Float getXPos() {
3876                 return xPos;
3877             }
3878
3879             /**
3880              * Sets the value of the xPos property.
3881              *
3882              * @param value
3883              *     allowed object is
3884              *     {@link Float }
3885              *
3886              */
3887             public void setXPos(Float value) {
3888                 this.xPos = value;
3889             }
3890
3891             /**
3892              * Gets the value of the yPos property.
3893              *
3894              * @return
3895              *     possible object is
3896              *     {@link Float }
3897              *
3898              */
3899             public Float getYPos() {
3900                 return yPos;
3901             }
3902
3903             /**
3904              * Sets the value of the yPos property.
3905              *
3906              * @param value
3907              *     allowed object is
3908              *     {@link Float }
3909              *
3910              */
3911             public void setYPos(Float value) {
3912                 this.yPos = value;
3913             }
3914
3915             /**
3916              * Gets the value of the zPos property.
3917              *
3918              * @return
3919              *     possible object is
3920              *     {@link Float }
3921              *
3922              */
3923             public Float getZPos() {
3924                 return zPos;
3925             }
3926
3927             /**
3928              * Sets the value of the zPos property.
3929              *
3930              * @param value
3931              *     allowed object is
3932              *     {@link Float }
3933              *
3934              */
3935             public void setZPos(Float value) {
3936                 this.zPos = value;
3937             }
3938
3939         }
3940
3941
3942         /**
3943          * <p>Java class for anonymous complex type.
3944          *
3945          * <p>The following schema fragment specifies the expected content contained within this class.
3946          *
3947          * <pre>
3948          * &lt;complexType>
3949          *   &lt;complexContent>
3950          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3951          *       &lt;attGroup ref="{www.jalview.org}position"/>
3952          *     &lt;/restriction>
3953          *   &lt;/complexContent>
3954          * &lt;/complexType>
3955          * </pre>
3956          *
3957          *
3958          */
3959         @XmlAccessorType(XmlAccessType.FIELD)
3960         @XmlType(name = "")
3961         public static class SeqPointMin {
3962
3963             @XmlAttribute(name = "xPos")
3964             protected Float xPos;
3965             @XmlAttribute(name = "yPos")
3966             protected Float yPos;
3967             @XmlAttribute(name = "zPos")
3968             protected Float zPos;
3969
3970             /**
3971              * Gets the value of the xPos property.
3972              *
3973              * @return
3974              *     possible object is
3975              *     {@link Float }
3976              *
3977              */
3978             public Float getXPos() {
3979                 return xPos;
3980             }
3981
3982             /**
3983              * Sets the value of the xPos property.
3984              *
3985              * @param value
3986              *     allowed object is
3987              *     {@link Float }
3988              *
3989              */
3990             public void setXPos(Float value) {
3991                 this.xPos = value;
3992             }
3993
3994             /**
3995              * Gets the value of the yPos property.
3996              *
3997              * @return
3998              *     possible object is
3999              *     {@link Float }
4000              *
4001              */
4002             public Float getYPos() {
4003                 return yPos;
4004             }
4005
4006             /**
4007              * Sets the value of the yPos property.
4008              *
4009              * @param value
4010              *     allowed object is
4011              *     {@link Float }
4012              *
4013              */
4014             public void setYPos(Float value) {
4015                 this.yPos = value;
4016             }
4017
4018             /**
4019              * Gets the value of the zPos property.
4020              *
4021              * @return
4022              *     possible object is
4023              *     {@link Float }
4024              *
4025              */
4026             public Float getZPos() {
4027                 return zPos;
4028             }
4029
4030             /**
4031              * Sets the value of the zPos property.
4032              *
4033              * @param value
4034              *     allowed object is
4035              *     {@link Float }
4036              *
4037              */
4038             public void setZPos(Float value) {
4039                 this.zPos = value;
4040             }
4041
4042         }
4043
4044
4045         /**
4046          * <p>Java class for anonymous complex type.
4047          *
4048          * <p>The following schema fragment specifies the expected content contained within this class.
4049          *
4050          * <pre>
4051          * &lt;complexType>
4052          *   &lt;complexContent>
4053          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4054          *       &lt;attGroup ref="{www.jalview.org}position"/>
4055          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4056          *     &lt;/restriction>
4057          *   &lt;/complexContent>
4058          * &lt;/complexType>
4059          * </pre>
4060          *
4061          *
4062          */
4063         @XmlAccessorType(XmlAccessType.FIELD)
4064         @XmlType(name = "")
4065         public static class SequencePoint {
4066
4067             @XmlAttribute(name = "sequenceRef")
4068             protected String sequenceRef;
4069             @XmlAttribute(name = "xPos")
4070             protected Float xPos;
4071             @XmlAttribute(name = "yPos")
4072             protected Float yPos;
4073             @XmlAttribute(name = "zPos")
4074             protected Float zPos;
4075
4076             /**
4077              * Gets the value of the sequenceRef property.
4078              *
4079              * @return
4080              *     possible object is
4081              *     {@link String }
4082              *
4083              */
4084             public String getSequenceRef() {
4085                 return sequenceRef;
4086             }
4087
4088             /**
4089              * Sets the value of the sequenceRef property.
4090              *
4091              * @param value
4092              *     allowed object is
4093              *     {@link String }
4094              *
4095              */
4096             public void setSequenceRef(String value) {
4097                 this.sequenceRef = value;
4098             }
4099
4100             /**
4101              * Gets the value of the xPos property.
4102              *
4103              * @return
4104              *     possible object is
4105              *     {@link Float }
4106              *
4107              */
4108             public Float getXPos() {
4109                 return xPos;
4110             }
4111
4112             /**
4113              * Sets the value of the xPos property.
4114              *
4115              * @param value
4116              *     allowed object is
4117              *     {@link Float }
4118              *
4119              */
4120             public void setXPos(Float value) {
4121                 this.xPos = value;
4122             }
4123
4124             /**
4125              * Gets the value of the yPos property.
4126              *
4127              * @return
4128              *     possible object is
4129              *     {@link Float }
4130              *
4131              */
4132             public Float getYPos() {
4133                 return yPos;
4134             }
4135
4136             /**
4137              * Sets the value of the yPos property.
4138              *
4139              * @param value
4140              *     allowed object is
4141              *     {@link Float }
4142              *
4143              */
4144             public void setYPos(Float value) {
4145                 this.yPos = value;
4146             }
4147
4148             /**
4149              * Gets the value of the zPos property.
4150              *
4151              * @return
4152              *     possible object is
4153              *     {@link Float }
4154              *
4155              */
4156             public Float getZPos() {
4157                 return zPos;
4158             }
4159
4160             /**
4161              * Sets the value of the zPos property.
4162              *
4163              * @param value
4164              *     allowed object is
4165              *     {@link Float }
4166              *
4167              */
4168             public void setZPos(Float value) {
4169                 this.zPos = value;
4170             }
4171
4172         }
4173
4174     }
4175
4176
4177     /**
4178      * <p>Java class for anonymous complex type.
4179      *
4180      * <p>The following schema fragment specifies the expected content contained within this class.
4181      *
4182      * <pre>
4183      * &lt;complexType>
4184      *   &lt;complexContent>
4185      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4186      *       &lt;sequence minOccurs="0">
4187      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4188      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4189      *       &lt;/sequence>
4190      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4191      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4192      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4193      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4194      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4195      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4196      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4197      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4198      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4199      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4200      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4201      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4202      *     &lt;/restriction>
4203      *   &lt;/complexContent>
4204      * &lt;/complexType>
4205      * </pre>
4206      *
4207      *
4208      */
4209     @XmlAccessorType(XmlAccessType.FIELD)
4210     @XmlType(name = "", propOrder = {
4211         "title",
4212         "newick"
4213     })
4214     public static class Tree {
4215
4216         @XmlElement(namespace = "www.jalview.org")
4217         protected String title;
4218         @XmlElement(namespace = "www.jalview.org")
4219         protected String newick;
4220         @XmlAttribute(name = "fontName")
4221         protected String fontName;
4222         @XmlAttribute(name = "fontSize")
4223         protected Integer fontSize;
4224         @XmlAttribute(name = "fontStyle")
4225         protected Integer fontStyle;
4226         @XmlAttribute(name = "threshold")
4227         protected Float threshold;
4228         @XmlAttribute(name = "showBootstrap")
4229         protected Boolean showBootstrap;
4230         @XmlAttribute(name = "showDistances")
4231         protected Boolean showDistances;
4232         @XmlAttribute(name = "markUnlinked")
4233         protected Boolean markUnlinked;
4234         @XmlAttribute(name = "fitToWindow")
4235         protected Boolean fitToWindow;
4236         @XmlAttribute(name = "currentTree")
4237         protected Boolean currentTree;
4238         @XmlAttribute(name = "id")
4239         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4240         @XmlID
4241         @XmlSchemaType(name = "ID")
4242         protected String id;
4243         @XmlAttribute(name = "linkToAllViews")
4244         protected Boolean linkToAllViews;
4245         @XmlAttribute(name = "width")
4246         protected Integer width;
4247         @XmlAttribute(name = "height")
4248         protected Integer height;
4249         @XmlAttribute(name = "xpos")
4250         protected Integer xpos;
4251         @XmlAttribute(name = "ypos")
4252         protected Integer ypos;
4253
4254         /**
4255          * Gets the value of the title property.
4256          *
4257          * @return
4258          *     possible object is
4259          *     {@link String }
4260          *
4261          */
4262         public String getTitle() {
4263             return title;
4264         }
4265
4266         /**
4267          * Sets the value of the title property.
4268          *
4269          * @param value
4270          *     allowed object is
4271          *     {@link String }
4272          *
4273          */
4274         public void setTitle(String value) {
4275             this.title = value;
4276         }
4277
4278         /**
4279          * Gets the value of the newick property.
4280          *
4281          * @return
4282          *     possible object is
4283          *     {@link String }
4284          *
4285          */
4286         public String getNewick() {
4287             return newick;
4288         }
4289
4290         /**
4291          * Sets the value of the newick property.
4292          *
4293          * @param value
4294          *     allowed object is
4295          *     {@link String }
4296          *
4297          */
4298         public void setNewick(String value) {
4299             this.newick = value;
4300         }
4301
4302         /**
4303          * Gets the value of the fontName property.
4304          *
4305          * @return
4306          *     possible object is
4307          *     {@link String }
4308          *
4309          */
4310         public String getFontName() {
4311             return fontName;
4312         }
4313
4314         /**
4315          * Sets the value of the fontName property.
4316          *
4317          * @param value
4318          *     allowed object is
4319          *     {@link String }
4320          *
4321          */
4322         public void setFontName(String value) {
4323             this.fontName = value;
4324         }
4325
4326         /**
4327          * Gets the value of the fontSize property.
4328          *
4329          * @return
4330          *     possible object is
4331          *     {@link Integer }
4332          *
4333          */
4334         public Integer getFontSize() {
4335             return fontSize;
4336         }
4337
4338         /**
4339          * Sets the value of the fontSize property.
4340          *
4341          * @param value
4342          *     allowed object is
4343          *     {@link Integer }
4344          *
4345          */
4346         public void setFontSize(Integer value) {
4347             this.fontSize = value;
4348         }
4349
4350         /**
4351          * Gets the value of the fontStyle property.
4352          *
4353          * @return
4354          *     possible object is
4355          *     {@link Integer }
4356          *
4357          */
4358         public Integer getFontStyle() {
4359             return fontStyle;
4360         }
4361
4362         /**
4363          * Sets the value of the fontStyle property.
4364          *
4365          * @param value
4366          *     allowed object is
4367          *     {@link Integer }
4368          *
4369          */
4370         public void setFontStyle(Integer value) {
4371             this.fontStyle = value;
4372         }
4373
4374         /**
4375          * Gets the value of the threshold property.
4376          *
4377          * @return
4378          *     possible object is
4379          *     {@link Float }
4380          *
4381          */
4382         public Float getThreshold() {
4383             return threshold;
4384         }
4385
4386         /**
4387          * Sets the value of the threshold property.
4388          *
4389          * @param value
4390          *     allowed object is
4391          *     {@link Float }
4392          *
4393          */
4394         public void setThreshold(Float value) {
4395             this.threshold = value;
4396         }
4397
4398         /**
4399          * Gets the value of the showBootstrap property.
4400          *
4401          * @return
4402          *     possible object is
4403          *     {@link Boolean }
4404          *
4405          */
4406         public Boolean isShowBootstrap() {
4407             return showBootstrap;
4408         }
4409
4410         /**
4411          * Sets the value of the showBootstrap property.
4412          *
4413          * @param value
4414          *     allowed object is
4415          *     {@link Boolean }
4416          *
4417          */
4418         public void setShowBootstrap(Boolean value) {
4419             this.showBootstrap = value;
4420         }
4421
4422         /**
4423          * Gets the value of the showDistances property.
4424          *
4425          * @return
4426          *     possible object is
4427          *     {@link Boolean }
4428          *
4429          */
4430         public Boolean isShowDistances() {
4431             return showDistances;
4432         }
4433
4434         /**
4435          * Sets the value of the showDistances property.
4436          *
4437          * @param value
4438          *     allowed object is
4439          *     {@link Boolean }
4440          *
4441          */
4442         public void setShowDistances(Boolean value) {
4443             this.showDistances = value;
4444         }
4445
4446         /**
4447          * Gets the value of the markUnlinked property.
4448          *
4449          * @return
4450          *     possible object is
4451          *     {@link Boolean }
4452          *
4453          */
4454         public Boolean isMarkUnlinked() {
4455             return markUnlinked;
4456         }
4457
4458         /**
4459          * Sets the value of the markUnlinked property.
4460          *
4461          * @param value
4462          *     allowed object is
4463          *     {@link Boolean }
4464          *
4465          */
4466         public void setMarkUnlinked(Boolean value) {
4467             this.markUnlinked = value;
4468         }
4469
4470         /**
4471          * Gets the value of the fitToWindow property.
4472          *
4473          * @return
4474          *     possible object is
4475          *     {@link Boolean }
4476          *
4477          */
4478         public Boolean isFitToWindow() {
4479             return fitToWindow;
4480         }
4481
4482         /**
4483          * Sets the value of the fitToWindow property.
4484          *
4485          * @param value
4486          *     allowed object is
4487          *     {@link Boolean }
4488          *
4489          */
4490         public void setFitToWindow(Boolean value) {
4491             this.fitToWindow = value;
4492         }
4493
4494         /**
4495          * Gets the value of the currentTree property.
4496          *
4497          * @return
4498          *     possible object is
4499          *     {@link Boolean }
4500          *
4501          */
4502         public Boolean isCurrentTree() {
4503             return currentTree;
4504         }
4505
4506         /**
4507          * Sets the value of the currentTree property.
4508          *
4509          * @param value
4510          *     allowed object is
4511          *     {@link Boolean }
4512          *
4513          */
4514         public void setCurrentTree(Boolean value) {
4515             this.currentTree = value;
4516         }
4517
4518         /**
4519          * Gets the value of the id property.
4520          *
4521          * @return
4522          *     possible object is
4523          *     {@link String }
4524          *
4525          */
4526         public String getId() {
4527             return id;
4528         }
4529
4530         /**
4531          * Sets the value of the id property.
4532          *
4533          * @param value
4534          *     allowed object is
4535          *     {@link String }
4536          *
4537          */
4538         public void setId(String value) {
4539             this.id = value;
4540         }
4541
4542         /**
4543          * Gets the value of the linkToAllViews property.
4544          *
4545          * @return
4546          *     possible object is
4547          *     {@link Boolean }
4548          *
4549          */
4550         public boolean isLinkToAllViews() {
4551             if (linkToAllViews == null) {
4552                 return false;
4553             } else {
4554                 return linkToAllViews;
4555             }
4556         }
4557
4558         /**
4559          * Sets the value of the linkToAllViews property.
4560          *
4561          * @param value
4562          *     allowed object is
4563          *     {@link Boolean }
4564          *
4565          */
4566         public void setLinkToAllViews(Boolean value) {
4567             this.linkToAllViews = value;
4568         }
4569
4570         /**
4571          * Gets the value of the width property.
4572          *
4573          * @return
4574          *     possible object is
4575          *     {@link Integer }
4576          *
4577          */
4578         public Integer getWidth() {
4579             return width;
4580         }
4581
4582         /**
4583          * Sets the value of the width property.
4584          *
4585          * @param value
4586          *     allowed object is
4587          *     {@link Integer }
4588          *
4589          */
4590         public void setWidth(Integer value) {
4591             this.width = value;
4592         }
4593
4594         /**
4595          * Gets the value of the height property.
4596          *
4597          * @return
4598          *     possible object is
4599          *     {@link Integer }
4600          *
4601          */
4602         public Integer getHeight() {
4603             return height;
4604         }
4605
4606         /**
4607          * Sets the value of the height property.
4608          *
4609          * @param value
4610          *     allowed object is
4611          *     {@link Integer }
4612          *
4613          */
4614         public void setHeight(Integer value) {
4615             this.height = value;
4616         }
4617
4618         /**
4619          * Gets the value of the xpos property.
4620          *
4621          * @return
4622          *     possible object is
4623          *     {@link Integer }
4624          *
4625          */
4626         public Integer getXpos() {
4627             return xpos;
4628         }
4629
4630         /**
4631          * Sets the value of the xpos property.
4632          *
4633          * @param value
4634          *     allowed object is
4635          *     {@link Integer }
4636          *
4637          */
4638         public void setXpos(Integer value) {
4639             this.xpos = value;
4640         }
4641
4642         /**
4643          * Gets the value of the ypos property.
4644          *
4645          * @return
4646          *     possible object is
4647          *     {@link Integer }
4648          *
4649          */
4650         public Integer getYpos() {
4651             return ypos;
4652         }
4653
4654         /**
4655          * Sets the value of the ypos property.
4656          *
4657          * @param value
4658          *     allowed object is
4659          *     {@link Integer }
4660          *
4661          */
4662         public void setYpos(Integer value) {
4663             this.ypos = value;
4664         }
4665
4666     }
4667
4668
4669     /**
4670      * <p>Java class for anonymous complex type.
4671      *
4672      * <p>The following schema fragment specifies the expected content contained within this class.
4673      *
4674      * <pre>
4675      * &lt;complexType>
4676      *   &lt;complexContent>
4677      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4678      *       &lt;sequence>
4679      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4680      *       &lt;/sequence>
4681      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4682      *     &lt;/restriction>
4683      *   &lt;/complexContent>
4684      * &lt;/complexType>
4685      * </pre>
4686      *
4687      *
4688      */
4689     @XmlAccessorType(XmlAccessType.FIELD)
4690     @XmlType(name = "", propOrder = {
4691         "userColourScheme"
4692     })
4693     public static class UserColours {
4694
4695         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4696         protected JalviewUserColours userColourScheme;
4697         @XmlAttribute(name = "id")
4698         protected String id;
4699
4700         /**
4701          * Gets the value of the userColourScheme property.
4702          *
4703          * @return
4704          *     possible object is
4705          *     {@link JalviewUserColours }
4706          *
4707          */
4708         public JalviewUserColours getUserColourScheme() {
4709             return userColourScheme;
4710         }
4711
4712         /**
4713          * Sets the value of the userColourScheme property.
4714          *
4715          * @param value
4716          *     allowed object is
4717          *     {@link JalviewUserColours }
4718          *
4719          */
4720         public void setUserColourScheme(JalviewUserColours value) {
4721             this.userColourScheme = value;
4722         }
4723
4724         /**
4725          * Gets the value of the id property.
4726          *
4727          * @return
4728          *     possible object is
4729          *     {@link String }
4730          *
4731          */
4732         public String getId() {
4733             return id;
4734         }
4735
4736         /**
4737          * Sets the value of the id property.
4738          *
4739          * @param value
4740          *     allowed object is
4741          *     {@link String }
4742          *
4743          */
4744         public void setId(String value) {
4745             this.id = value;
4746         }
4747
4748     }
4749
4750
4751     /**
4752      * <p>Java class for anonymous complex type.
4753      *
4754      * <p>The following schema fragment specifies the expected content contained within this class.
4755      *
4756      * <pre>
4757      * &lt;complexType>
4758      *   &lt;complexContent>
4759      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4760      *       &lt;sequence>
4761      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4762      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4763      *           &lt;complexType>
4764      *             &lt;complexContent>
4765      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4766      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4767      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4768      *               &lt;/restriction>
4769      *             &lt;/complexContent>
4770      *           &lt;/complexType>
4771      *         &lt;/element>
4772      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4773      *           &lt;complexType>
4774      *             &lt;complexContent>
4775      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4776      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4777      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4778      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4779      *               &lt;/extension>
4780      *             &lt;/complexContent>
4781      *           &lt;/complexType>
4782      *         &lt;/element>
4783      *         &lt;element name="overview" minOccurs="0">
4784      *           &lt;complexType>
4785      *             &lt;complexContent>
4786      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4787      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4788      *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4789      *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4790      *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4791      *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4792      *               &lt;/restriction>
4793      *             &lt;/complexContent>
4794      *           &lt;/complexType>
4795      *         &lt;/element>
4796      *       &lt;/sequence>
4797      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4798      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4799      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4800      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4801      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4802      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4803      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4804      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4805      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4806      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4807      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4809      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4816      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4817      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4818      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4819      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4820      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4821      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4822      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4825      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4826      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4827      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4828      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4829      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4830      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4831      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4832      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4833      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4834      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4835      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4836      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4837      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4838      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4839      *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4840      *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4841      *     &lt;/restriction>
4842      *   &lt;/complexContent>
4843      * &lt;/complexType>
4844      * </pre>
4845      *
4846      *
4847      */
4848     @XmlAccessorType(XmlAccessType.FIELD)
4849     @XmlType(name = "", propOrder = {
4850         "annotationColours",
4851         "hiddenColumns",
4852         "calcIdParam",
4853         "overview"
4854     })
4855     public static class Viewport {
4856
4857         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4858         protected AnnotationColourScheme annotationColours;
4859         @XmlElement(namespace = "www.jalview.org")
4860         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4861         @XmlElement(namespace = "www.jalview.org")
4862         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4863         @XmlElement(namespace = "www.jalview.org")
4864         protected JalviewModel.Viewport.Overview overview;
4865         @XmlAttribute(name = "conservationSelected")
4866         protected Boolean conservationSelected;
4867         @XmlAttribute(name = "pidSelected")
4868         protected Boolean pidSelected;
4869         @XmlAttribute(name = "bgColour")
4870         protected String bgColour;
4871         @XmlAttribute(name = "consThreshold")
4872         protected Integer consThreshold;
4873         @XmlAttribute(name = "pidThreshold")
4874         protected Integer pidThreshold;
4875         @XmlAttribute(name = "title")
4876         protected String title;
4877         @XmlAttribute(name = "showFullId")
4878         protected Boolean showFullId;
4879         @XmlAttribute(name = "rightAlignIds")
4880         protected Boolean rightAlignIds;
4881         @XmlAttribute(name = "showText")
4882         protected Boolean showText;
4883         @XmlAttribute(name = "showColourText")
4884         protected Boolean showColourText;
4885         @XmlAttribute(name = "showUnconserved")
4886         protected Boolean showUnconserved;
4887         @XmlAttribute(name = "showBoxes")
4888         protected Boolean showBoxes;
4889         @XmlAttribute(name = "wrapAlignment")
4890         protected Boolean wrapAlignment;
4891         @XmlAttribute(name = "renderGaps")
4892         protected Boolean renderGaps;
4893         @XmlAttribute(name = "showSequenceFeatures")
4894         protected Boolean showSequenceFeatures;
4895         @XmlAttribute(name = "showNPfeatureTooltip")
4896         protected Boolean showNPfeatureTooltip;
4897         @XmlAttribute(name = "showDbRefTooltip")
4898         protected Boolean showDbRefTooltip;
4899         @XmlAttribute(name = "followHighlight")
4900         protected Boolean followHighlight;
4901         @XmlAttribute(name = "followSelection")
4902         protected Boolean followSelection;
4903         @XmlAttribute(name = "showAnnotation")
4904         protected Boolean showAnnotation;
4905         @XmlAttribute(name = "centreColumnLabels")
4906         protected Boolean centreColumnLabels;
4907         @XmlAttribute(name = "showGroupConservation")
4908         protected Boolean showGroupConservation;
4909         @XmlAttribute(name = "showGroupConsensus")
4910         protected Boolean showGroupConsensus;
4911         @XmlAttribute(name = "showConsensusHistogram")
4912         protected Boolean showConsensusHistogram;
4913         @XmlAttribute(name = "showSequenceLogo")
4914         protected Boolean showSequenceLogo;
4915         @XmlAttribute(name = "normaliseSequenceLogo")
4916         protected Boolean normaliseSequenceLogo;
4917         @XmlAttribute(name = "ignoreGapsinConsensus")
4918         protected Boolean ignoreGapsinConsensus;
4919         @XmlAttribute(name = "startRes")
4920         protected Integer startRes;
4921         @XmlAttribute(name = "startSeq")
4922         protected Integer startSeq;
4923         @XmlAttribute(name = "fontName")
4924         protected String fontName;
4925         @XmlAttribute(name = "fontSize")
4926         protected Integer fontSize;
4927         @XmlAttribute(name = "fontStyle")
4928         protected Integer fontStyle;
4929         @XmlAttribute(name = "scaleProteinAsCdna")
4930         protected Boolean scaleProteinAsCdna;
4931         @XmlAttribute(name = "viewName")
4932         protected String viewName;
4933         @XmlAttribute(name = "sequenceSetId")
4934         protected String sequenceSetId;
4935         @XmlAttribute(name = "gatheredViews")
4936         protected Boolean gatheredViews;
4937         @XmlAttribute(name = "textCol1")
4938         protected Integer textCol1;
4939         @XmlAttribute(name = "textCol2")
4940         protected Integer textCol2;
4941         @XmlAttribute(name = "textColThreshold")
4942         protected Integer textColThreshold;
4943         @XmlAttribute(name = "id")
4944         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4945         @XmlID
4946         @XmlSchemaType(name = "ID")
4947         protected String id;
4948         @XmlAttribute(name = "complementId")
4949         protected String complementId;
4950         @XmlAttribute(name = "showComplementFeatures")
4951         protected Boolean showComplementFeatures;
4952         @XmlAttribute(name = "showComplementFeaturesOnTop")
4953         protected Boolean showComplementFeaturesOnTop;
4954         @XmlAttribute(name = "width")
4955         protected Integer width;
4956         @XmlAttribute(name = "height")
4957         protected Integer height;
4958         @XmlAttribute(name = "xpos")
4959         protected Integer xpos;
4960         @XmlAttribute(name = "ypos")
4961         protected Integer ypos;
4962
4963         /**
4964          * Gets the value of the annotationColours property.
4965          *
4966          * @return
4967          *     possible object is
4968          *     {@link AnnotationColourScheme }
4969          *
4970          */
4971         public AnnotationColourScheme getAnnotationColours() {
4972             return annotationColours;
4973         }
4974
4975         /**
4976          * Sets the value of the annotationColours property.
4977          *
4978          * @param value
4979          *     allowed object is
4980          *     {@link AnnotationColourScheme }
4981          *
4982          */
4983         public void setAnnotationColours(AnnotationColourScheme value) {
4984             this.annotationColours = value;
4985         }
4986
4987         /**
4988          * Gets the value of the hiddenColumns property.
4989          *
4990          * <p>
4991          * This accessor method returns a reference to the live list,
4992          * not a snapshot. Therefore any modification you make to the
4993          * returned list will be present inside the JAXB object.
4994          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4995          *
4996          * <p>
4997          * For example, to add a new item, do as follows:
4998          * <pre>
4999          *    getHiddenColumns().add(newItem);
5000          * </pre>
5001          *
5002          *
5003          * <p>
5004          * Objects of the following type(s) are allowed in the list
5005          * {@link JalviewModel.Viewport.HiddenColumns }
5006          *
5007          *
5008          */
5009         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5010             if (hiddenColumns == null) {
5011                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5012             }
5013             return this.hiddenColumns;
5014         }
5015
5016         /**
5017          * Gets the value of the calcIdParam property.
5018          *
5019          * <p>
5020          * This accessor method returns a reference to the live list,
5021          * not a snapshot. Therefore any modification you make to the
5022          * returned list will be present inside the JAXB object.
5023          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5024          *
5025          * <p>
5026          * For example, to add a new item, do as follows:
5027          * <pre>
5028          *    getCalcIdParam().add(newItem);
5029          * </pre>
5030          *
5031          *
5032          * <p>
5033          * Objects of the following type(s) are allowed in the list
5034          * {@link JalviewModel.Viewport.CalcIdParam }
5035          *
5036          *
5037          */
5038         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5039             if (calcIdParam == null) {
5040                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5041             }
5042             return this.calcIdParam;
5043         }
5044
5045         /**
5046          * Gets the value of the overview property.
5047          *
5048          * @return
5049          *     possible object is
5050          *     {@link JalviewModel.Viewport.Overview }
5051          *
5052          */
5053         public JalviewModel.Viewport.Overview getOverview() {
5054             return overview;
5055         }
5056
5057         /**
5058          * Sets the value of the overview property.
5059          *
5060          * @param value
5061          *     allowed object is
5062          *     {@link JalviewModel.Viewport.Overview }
5063          *
5064          */
5065         public void setOverview(JalviewModel.Viewport.Overview value) {
5066             this.overview = value;
5067         }
5068
5069         /**
5070          * Gets the value of the conservationSelected property.
5071          *
5072          * @return
5073          *     possible object is
5074          *     {@link Boolean }
5075          *
5076          */
5077         public Boolean isConservationSelected() {
5078             return conservationSelected;
5079         }
5080
5081         /**
5082          * Sets the value of the conservationSelected property.
5083          *
5084          * @param value
5085          *     allowed object is
5086          *     {@link Boolean }
5087          *
5088          */
5089         public void setConservationSelected(Boolean value) {
5090             this.conservationSelected = value;
5091         }
5092
5093         /**
5094          * Gets the value of the pidSelected property.
5095          *
5096          * @return
5097          *     possible object is
5098          *     {@link Boolean }
5099          *
5100          */
5101         public Boolean isPidSelected() {
5102             return pidSelected;
5103         }
5104
5105         /**
5106          * Sets the value of the pidSelected property.
5107          *
5108          * @param value
5109          *     allowed object is
5110          *     {@link Boolean }
5111          *
5112          */
5113         public void setPidSelected(Boolean value) {
5114             this.pidSelected = value;
5115         }
5116
5117         /**
5118          * Gets the value of the bgColour property.
5119          *
5120          * @return
5121          *     possible object is
5122          *     {@link String }
5123          *
5124          */
5125         public String getBgColour() {
5126             return bgColour;
5127         }
5128
5129         /**
5130          * Sets the value of the bgColour property.
5131          *
5132          * @param value
5133          *     allowed object is
5134          *     {@link String }
5135          *
5136          */
5137         public void setBgColour(String value) {
5138             this.bgColour = value;
5139         }
5140
5141         /**
5142          * Gets the value of the consThreshold property.
5143          *
5144          * @return
5145          *     possible object is
5146          *     {@link Integer }
5147          *
5148          */
5149         public Integer getConsThreshold() {
5150             return consThreshold;
5151         }
5152
5153         /**
5154          * Sets the value of the consThreshold property.
5155          *
5156          * @param value
5157          *     allowed object is
5158          *     {@link Integer }
5159          *
5160          */
5161         public void setConsThreshold(Integer value) {
5162             this.consThreshold = value;
5163         }
5164
5165         /**
5166          * Gets the value of the pidThreshold property.
5167          *
5168          * @return
5169          *     possible object is
5170          *     {@link Integer }
5171          *
5172          */
5173         public Integer getPidThreshold() {
5174             return pidThreshold;
5175         }
5176
5177         /**
5178          * Sets the value of the pidThreshold property.
5179          *
5180          * @param value
5181          *     allowed object is
5182          *     {@link Integer }
5183          *
5184          */
5185         public void setPidThreshold(Integer value) {
5186             this.pidThreshold = value;
5187         }
5188
5189         /**
5190          * Gets the value of the title property.
5191          *
5192          * @return
5193          *     possible object is
5194          *     {@link String }
5195          *
5196          */
5197         public String getTitle() {
5198             return title;
5199         }
5200
5201         /**
5202          * Sets the value of the title property.
5203          *
5204          * @param value
5205          *     allowed object is
5206          *     {@link String }
5207          *
5208          */
5209         public void setTitle(String value) {
5210             this.title = value;
5211         }
5212
5213         /**
5214          * Gets the value of the showFullId property.
5215          *
5216          * @return
5217          *     possible object is
5218          *     {@link Boolean }
5219          *
5220          */
5221         public Boolean isShowFullId() {
5222             return showFullId;
5223         }
5224
5225         /**
5226          * Sets the value of the showFullId property.
5227          *
5228          * @param value
5229          *     allowed object is
5230          *     {@link Boolean }
5231          *
5232          */
5233         public void setShowFullId(Boolean value) {
5234             this.showFullId = value;
5235         }
5236
5237         /**
5238          * Gets the value of the rightAlignIds property.
5239          *
5240          * @return
5241          *     possible object is
5242          *     {@link Boolean }
5243          *
5244          */
5245         public Boolean isRightAlignIds() {
5246             return rightAlignIds;
5247         }
5248
5249         /**
5250          * Sets the value of the rightAlignIds property.
5251          *
5252          * @param value
5253          *     allowed object is
5254          *     {@link Boolean }
5255          *
5256          */
5257         public void setRightAlignIds(Boolean value) {
5258             this.rightAlignIds = value;
5259         }
5260
5261         /**
5262          * Gets the value of the showText property.
5263          *
5264          * @return
5265          *     possible object is
5266          *     {@link Boolean }
5267          *
5268          */
5269         public Boolean isShowText() {
5270             return showText;
5271         }
5272
5273         /**
5274          * Sets the value of the showText property.
5275          *
5276          * @param value
5277          *     allowed object is
5278          *     {@link Boolean }
5279          *
5280          */
5281         public void setShowText(Boolean value) {
5282             this.showText = value;
5283         }
5284
5285         /**
5286          * Gets the value of the showColourText property.
5287          *
5288          * @return
5289          *     possible object is
5290          *     {@link Boolean }
5291          *
5292          */
5293         public Boolean isShowColourText() {
5294             return showColourText;
5295         }
5296
5297         /**
5298          * Sets the value of the showColourText property.
5299          *
5300          * @param value
5301          *     allowed object is
5302          *     {@link Boolean }
5303          *
5304          */
5305         public void setShowColourText(Boolean value) {
5306             this.showColourText = value;
5307         }
5308
5309         /**
5310          * Gets the value of the showUnconserved property.
5311          *
5312          * @return
5313          *     possible object is
5314          *     {@link Boolean }
5315          *
5316          */
5317         public boolean isShowUnconserved() {
5318             if (showUnconserved == null) {
5319                 return false;
5320             } else {
5321                 return showUnconserved;
5322             }
5323         }
5324
5325         /**
5326          * Sets the value of the showUnconserved property.
5327          *
5328          * @param value
5329          *     allowed object is
5330          *     {@link Boolean }
5331          *
5332          */
5333         public void setShowUnconserved(Boolean value) {
5334             this.showUnconserved = value;
5335         }
5336
5337         /**
5338          * Gets the value of the showBoxes property.
5339          *
5340          * @return
5341          *     possible object is
5342          *     {@link Boolean }
5343          *
5344          */
5345         public Boolean isShowBoxes() {
5346             return showBoxes;
5347         }
5348
5349         /**
5350          * Sets the value of the showBoxes property.
5351          *
5352          * @param value
5353          *     allowed object is
5354          *     {@link Boolean }
5355          *
5356          */
5357         public void setShowBoxes(Boolean value) {
5358             this.showBoxes = value;
5359         }
5360
5361         /**
5362          * Gets the value of the wrapAlignment property.
5363          *
5364          * @return
5365          *     possible object is
5366          *     {@link Boolean }
5367          *
5368          */
5369         public Boolean isWrapAlignment() {
5370             return wrapAlignment;
5371         }
5372
5373         /**
5374          * Sets the value of the wrapAlignment property.
5375          *
5376          * @param value
5377          *     allowed object is
5378          *     {@link Boolean }
5379          *
5380          */
5381         public void setWrapAlignment(Boolean value) {
5382             this.wrapAlignment = value;
5383         }
5384
5385         /**
5386          * Gets the value of the renderGaps property.
5387          *
5388          * @return
5389          *     possible object is
5390          *     {@link Boolean }
5391          *
5392          */
5393         public Boolean isRenderGaps() {
5394             return renderGaps;
5395         }
5396
5397         /**
5398          * Sets the value of the renderGaps property.
5399          *
5400          * @param value
5401          *     allowed object is
5402          *     {@link Boolean }
5403          *
5404          */
5405         public void setRenderGaps(Boolean value) {
5406             this.renderGaps = value;
5407         }
5408
5409         /**
5410          * Gets the value of the showSequenceFeatures property.
5411          *
5412          * @return
5413          *     possible object is
5414          *     {@link Boolean }
5415          *
5416          */
5417         public Boolean isShowSequenceFeatures() {
5418             return showSequenceFeatures;
5419         }
5420
5421         /**
5422          * Sets the value of the showSequenceFeatures property.
5423          *
5424          * @param value
5425          *     allowed object is
5426          *     {@link Boolean }
5427          *
5428          */
5429         public void setShowSequenceFeatures(Boolean value) {
5430             this.showSequenceFeatures = value;
5431         }
5432
5433         /**
5434          * Gets the value of the showNPfeatureTooltip property.
5435          *
5436          * @return
5437          *     possible object is
5438          *     {@link Boolean }
5439          *
5440          */
5441         public Boolean isShowNPfeatureTooltip() {
5442             return showNPfeatureTooltip;
5443         }
5444
5445         /**
5446          * Sets the value of the showNPfeatureTooltip property.
5447          *
5448          * @param value
5449          *     allowed object is
5450          *     {@link Boolean }
5451          *
5452          */
5453         public void setShowNPfeatureTooltip(Boolean value) {
5454             this.showNPfeatureTooltip = value;
5455         }
5456
5457         /**
5458          * Gets the value of the showDbRefTooltip property.
5459          *
5460          * @return
5461          *     possible object is
5462          *     {@link Boolean }
5463          *
5464          */
5465         public Boolean isShowDbRefTooltip() {
5466             return showDbRefTooltip;
5467         }
5468
5469         /**
5470          * Sets the value of the showDbRefTooltip property.
5471          *
5472          * @param value
5473          *     allowed object is
5474          *     {@link Boolean }
5475          *
5476          */
5477         public void setShowDbRefTooltip(Boolean value) {
5478             this.showDbRefTooltip = value;
5479         }
5480
5481         /**
5482          * Gets the value of the followHighlight property.
5483          *
5484          * @return
5485          *     possible object is
5486          *     {@link Boolean }
5487          *
5488          */
5489         public boolean isFollowHighlight() {
5490             if (followHighlight == null) {
5491                 return true;
5492             } else {
5493                 return followHighlight;
5494             }
5495         }
5496
5497         /**
5498          * Sets the value of the followHighlight property.
5499          *
5500          * @param value
5501          *     allowed object is
5502          *     {@link Boolean }
5503          *
5504          */
5505         public void setFollowHighlight(Boolean value) {
5506             this.followHighlight = value;
5507         }
5508
5509         /**
5510          * Gets the value of the followSelection property.
5511          *
5512          * @return
5513          *     possible object is
5514          *     {@link Boolean }
5515          *
5516          */
5517         public boolean isFollowSelection() {
5518             if (followSelection == null) {
5519                 return true;
5520             } else {
5521                 return followSelection;
5522             }
5523         }
5524
5525         /**
5526          * Sets the value of the followSelection property.
5527          *
5528          * @param value
5529          *     allowed object is
5530          *     {@link Boolean }
5531          *
5532          */
5533         public void setFollowSelection(Boolean value) {
5534             this.followSelection = value;
5535         }
5536
5537         /**
5538          * Gets the value of the showAnnotation property.
5539          *
5540          * @return
5541          *     possible object is
5542          *     {@link Boolean }
5543          *
5544          */
5545         public Boolean isShowAnnotation() {
5546             return showAnnotation;
5547         }
5548
5549         /**
5550          * Sets the value of the showAnnotation property.
5551          *
5552          * @param value
5553          *     allowed object is
5554          *     {@link Boolean }
5555          *
5556          */
5557         public void setShowAnnotation(Boolean value) {
5558             this.showAnnotation = value;
5559         }
5560
5561         /**
5562          * Gets the value of the centreColumnLabels property.
5563          *
5564          * @return
5565          *     possible object is
5566          *     {@link Boolean }
5567          *
5568          */
5569         public boolean isCentreColumnLabels() {
5570             if (centreColumnLabels == null) {
5571                 return false;
5572             } else {
5573                 return centreColumnLabels;
5574             }
5575         }
5576
5577         /**
5578          * Sets the value of the centreColumnLabels property.
5579          *
5580          * @param value
5581          *     allowed object is
5582          *     {@link Boolean }
5583          *
5584          */
5585         public void setCentreColumnLabels(Boolean value) {
5586             this.centreColumnLabels = value;
5587         }
5588
5589         /**
5590          * Gets the value of the showGroupConservation property.
5591          *
5592          * @return
5593          *     possible object is
5594          *     {@link Boolean }
5595          *
5596          */
5597         public boolean isShowGroupConservation() {
5598             if (showGroupConservation == null) {
5599                 return false;
5600             } else {
5601                 return showGroupConservation;
5602             }
5603         }
5604
5605         /**
5606          * Sets the value of the showGroupConservation property.
5607          *
5608          * @param value
5609          *     allowed object is
5610          *     {@link Boolean }
5611          *
5612          */
5613         public void setShowGroupConservation(Boolean value) {
5614             this.showGroupConservation = value;
5615         }
5616
5617         /**
5618          * Gets the value of the showGroupConsensus property.
5619          *
5620          * @return
5621          *     possible object is
5622          *     {@link Boolean }
5623          *
5624          */
5625         public boolean isShowGroupConsensus() {
5626             if (showGroupConsensus == null) {
5627                 return false;
5628             } else {
5629                 return showGroupConsensus;
5630             }
5631         }
5632
5633         /**
5634          * Sets the value of the showGroupConsensus property.
5635          *
5636          * @param value
5637          *     allowed object is
5638          *     {@link Boolean }
5639          *
5640          */
5641         public void setShowGroupConsensus(Boolean value) {
5642             this.showGroupConsensus = value;
5643         }
5644
5645         /**
5646          * Gets the value of the showConsensusHistogram property.
5647          *
5648          * @return
5649          *     possible object is
5650          *     {@link Boolean }
5651          *
5652          */
5653         public boolean isShowConsensusHistogram() {
5654             if (showConsensusHistogram == null) {
5655                 return true;
5656             } else {
5657                 return showConsensusHistogram;
5658             }
5659         }
5660
5661         /**
5662          * Sets the value of the showConsensusHistogram property.
5663          *
5664          * @param value
5665          *     allowed object is
5666          *     {@link Boolean }
5667          *
5668          */
5669         public void setShowConsensusHistogram(Boolean value) {
5670             this.showConsensusHistogram = value;
5671         }
5672
5673         /**
5674          * Gets the value of the showSequenceLogo property.
5675          *
5676          * @return
5677          *     possible object is
5678          *     {@link Boolean }
5679          *
5680          */
5681         public boolean isShowSequenceLogo() {
5682             if (showSequenceLogo == null) {
5683                 return false;
5684             } else {
5685                 return showSequenceLogo;
5686             }
5687         }
5688
5689         /**
5690          * Sets the value of the showSequenceLogo property.
5691          *
5692          * @param value
5693          *     allowed object is
5694          *     {@link Boolean }
5695          *
5696          */
5697         public void setShowSequenceLogo(Boolean value) {
5698             this.showSequenceLogo = value;
5699         }
5700
5701         /**
5702          * Gets the value of the normaliseSequenceLogo property.
5703          *
5704          * @return
5705          *     possible object is
5706          *     {@link Boolean }
5707          *
5708          */
5709         public boolean isNormaliseSequenceLogo() {
5710             if (normaliseSequenceLogo == null) {
5711                 return false;
5712             } else {
5713                 return normaliseSequenceLogo;
5714             }
5715         }
5716
5717         /**
5718          * Sets the value of the normaliseSequenceLogo property.
5719          *
5720          * @param value
5721          *     allowed object is
5722          *     {@link Boolean }
5723          *
5724          */
5725         public void setNormaliseSequenceLogo(Boolean value) {
5726             this.normaliseSequenceLogo = value;
5727         }
5728
5729         /**
5730          * Gets the value of the ignoreGapsinConsensus property.
5731          *
5732          * @return
5733          *     possible object is
5734          *     {@link Boolean }
5735          *
5736          */
5737         public boolean isIgnoreGapsinConsensus() {
5738             if (ignoreGapsinConsensus == null) {
5739                 return true;
5740             } else {
5741                 return ignoreGapsinConsensus;
5742             }
5743         }
5744
5745         /**
5746          * Sets the value of the ignoreGapsinConsensus property.
5747          *
5748          * @param value
5749          *     allowed object is
5750          *     {@link Boolean }
5751          *
5752          */
5753         public void setIgnoreGapsinConsensus(Boolean value) {
5754             this.ignoreGapsinConsensus = value;
5755         }
5756
5757         /**
5758          * Gets the value of the startRes property.
5759          *
5760          * @return
5761          *     possible object is
5762          *     {@link Integer }
5763          *
5764          */
5765         public Integer getStartRes() {
5766             return startRes;
5767         }
5768
5769         /**
5770          * Sets the value of the startRes property.
5771          *
5772          * @param value
5773          *     allowed object is
5774          *     {@link Integer }
5775          *
5776          */
5777         public void setStartRes(Integer value) {
5778             this.startRes = value;
5779         }
5780
5781         /**
5782          * Gets the value of the startSeq property.
5783          *
5784          * @return
5785          *     possible object is
5786          *     {@link Integer }
5787          *
5788          */
5789         public Integer getStartSeq() {
5790             return startSeq;
5791         }
5792
5793         /**
5794          * Sets the value of the startSeq property.
5795          *
5796          * @param value
5797          *     allowed object is
5798          *     {@link Integer }
5799          *
5800          */
5801         public void setStartSeq(Integer value) {
5802             this.startSeq = value;
5803         }
5804
5805         /**
5806          * Gets the value of the fontName property.
5807          *
5808          * @return
5809          *     possible object is
5810          *     {@link String }
5811          *
5812          */
5813         public String getFontName() {
5814             return fontName;
5815         }
5816
5817         /**
5818          * Sets the value of the fontName property.
5819          *
5820          * @param value
5821          *     allowed object is
5822          *     {@link String }
5823          *
5824          */
5825         public void setFontName(String value) {
5826             this.fontName = value;
5827         }
5828
5829         /**
5830          * Gets the value of the fontSize property.
5831          *
5832          * @return
5833          *     possible object is
5834          *     {@link Integer }
5835          *
5836          */
5837         public Integer getFontSize() {
5838             return fontSize;
5839         }
5840
5841         /**
5842          * Sets the value of the fontSize property.
5843          *
5844          * @param value
5845          *     allowed object is
5846          *     {@link Integer }
5847          *
5848          */
5849         public void setFontSize(Integer value) {
5850             this.fontSize = value;
5851         }
5852
5853         /**
5854          * Gets the value of the fontStyle property.
5855          *
5856          * @return
5857          *     possible object is
5858          *     {@link Integer }
5859          *
5860          */
5861         public Integer getFontStyle() {
5862             return fontStyle;
5863         }
5864
5865         /**
5866          * Sets the value of the fontStyle property.
5867          *
5868          * @param value
5869          *     allowed object is
5870          *     {@link Integer }
5871          *
5872          */
5873         public void setFontStyle(Integer value) {
5874             this.fontStyle = value;
5875         }
5876
5877         /**
5878          * Gets the value of the scaleProteinAsCdna property.
5879          *
5880          * @return
5881          *     possible object is
5882          *     {@link Boolean }
5883          *
5884          */
5885         public boolean isScaleProteinAsCdna() {
5886             if (scaleProteinAsCdna == null) {
5887                 return true;
5888             } else {
5889                 return scaleProteinAsCdna;
5890             }
5891         }
5892
5893         /**
5894          * Sets the value of the scaleProteinAsCdna property.
5895          *
5896          * @param value
5897          *     allowed object is
5898          *     {@link Boolean }
5899          *
5900          */
5901         public void setScaleProteinAsCdna(Boolean value) {
5902             this.scaleProteinAsCdna = value;
5903         }
5904
5905         /**
5906          * Gets the value of the viewName property.
5907          *
5908          * @return
5909          *     possible object is
5910          *     {@link String }
5911          *
5912          */
5913         public String getViewName() {
5914             return viewName;
5915         }
5916
5917         /**
5918          * Sets the value of the viewName property.
5919          *
5920          * @param value
5921          *     allowed object is
5922          *     {@link String }
5923          *
5924          */
5925         public void setViewName(String value) {
5926             this.viewName = value;
5927         }
5928
5929         /**
5930          * Gets the value of the sequenceSetId property.
5931          *
5932          * @return
5933          *     possible object is
5934          *     {@link String }
5935          *
5936          */
5937         public String getSequenceSetId() {
5938             return sequenceSetId;
5939         }
5940
5941         /**
5942          * Sets the value of the sequenceSetId property.
5943          *
5944          * @param value
5945          *     allowed object is
5946          *     {@link String }
5947          *
5948          */
5949         public void setSequenceSetId(String value) {
5950             this.sequenceSetId = value;
5951         }
5952
5953         /**
5954          * Gets the value of the gatheredViews property.
5955          *
5956          * @return
5957          *     possible object is
5958          *     {@link Boolean }
5959          *
5960          */
5961         public Boolean isGatheredViews() {
5962             return gatheredViews;
5963         }
5964
5965         /**
5966          * Sets the value of the gatheredViews property.
5967          *
5968          * @param value
5969          *     allowed object is
5970          *     {@link Boolean }
5971          *
5972          */
5973         public void setGatheredViews(Boolean value) {
5974             this.gatheredViews = value;
5975         }
5976
5977         /**
5978          * Gets the value of the textCol1 property.
5979          *
5980          * @return
5981          *     possible object is
5982          *     {@link Integer }
5983          *
5984          */
5985         public Integer getTextCol1() {
5986             return textCol1;
5987         }
5988
5989         /**
5990          * Sets the value of the textCol1 property.
5991          *
5992          * @param value
5993          *     allowed object is
5994          *     {@link Integer }
5995          *
5996          */
5997         public void setTextCol1(Integer value) {
5998             this.textCol1 = value;
5999         }
6000
6001         /**
6002          * Gets the value of the textCol2 property.
6003          *
6004          * @return
6005          *     possible object is
6006          *     {@link Integer }
6007          *
6008          */
6009         public Integer getTextCol2() {
6010             return textCol2;
6011         }
6012
6013         /**
6014          * Sets the value of the textCol2 property.
6015          *
6016          * @param value
6017          *     allowed object is
6018          *     {@link Integer }
6019          *
6020          */
6021         public void setTextCol2(Integer value) {
6022             this.textCol2 = value;
6023         }
6024
6025         /**
6026          * Gets the value of the textColThreshold property.
6027          *
6028          * @return
6029          *     possible object is
6030          *     {@link Integer }
6031          *
6032          */
6033         public Integer getTextColThreshold() {
6034             return textColThreshold;
6035         }
6036
6037         /**
6038          * Sets the value of the textColThreshold property.
6039          *
6040          * @param value
6041          *     allowed object is
6042          *     {@link Integer }
6043          *
6044          */
6045         public void setTextColThreshold(Integer value) {
6046             this.textColThreshold = value;
6047         }
6048
6049         /**
6050          * Gets the value of the id property.
6051          *
6052          * @return
6053          *     possible object is
6054          *     {@link String }
6055          *
6056          */
6057         public String getId() {
6058             return id;
6059         }
6060
6061         /**
6062          * Sets the value of the id property.
6063          *
6064          * @param value
6065          *     allowed object is
6066          *     {@link String }
6067          *
6068          */
6069         public void setId(String value) {
6070             this.id = value;
6071         }
6072
6073         /**
6074          * Gets the value of the complementId property.
6075          *
6076          * @return
6077          *     possible object is
6078          *     {@link String }
6079          *
6080          */
6081         public String getComplementId() {
6082             return complementId;
6083         }
6084
6085         /**
6086          * Sets the value of the complementId property.
6087          *
6088          * @param value
6089          *     allowed object is
6090          *     {@link String }
6091          *
6092          */
6093         public void setComplementId(String value) {
6094             this.complementId = value;
6095         }
6096
6097         /**
6098          * Gets the value of the showComplementFeatures property.
6099          *
6100          * @return
6101          *     possible object is
6102          *     {@link Boolean }
6103          *
6104          */
6105         public boolean isShowComplementFeatures() {
6106             if (showComplementFeatures == null) {
6107                 return false;
6108             } else {
6109                 return showComplementFeatures;
6110             }
6111         }
6112
6113         /**
6114          * Sets the value of the showComplementFeatures property.
6115          *
6116          * @param value
6117          *     allowed object is
6118          *     {@link Boolean }
6119          *
6120          */
6121         public void setShowComplementFeatures(Boolean value) {
6122             this.showComplementFeatures = value;
6123         }
6124
6125         /**
6126          * Gets the value of the showComplementFeaturesOnTop property.
6127          *
6128          * @return
6129          *     possible object is
6130          *     {@link Boolean }
6131          *
6132          */
6133         public boolean isShowComplementFeaturesOnTop() {
6134             if (showComplementFeaturesOnTop == null) {
6135                 return false;
6136             } else {
6137                 return showComplementFeaturesOnTop;
6138             }
6139         }
6140
6141         /**
6142          * Sets the value of the showComplementFeaturesOnTop property.
6143          *
6144          * @param value
6145          *     allowed object is
6146          *     {@link Boolean }
6147          *
6148          */
6149         public void setShowComplementFeaturesOnTop(Boolean value) {
6150             this.showComplementFeaturesOnTop = value;
6151         }
6152
6153         /**
6154          * Gets the value of the width property.
6155          *
6156          * @return
6157          *     possible object is
6158          *     {@link Integer }
6159          *
6160          */
6161         public Integer getWidth() {
6162             return width;
6163         }
6164
6165         /**
6166          * Sets the value of the width property.
6167          *
6168          * @param value
6169          *     allowed object is
6170          *     {@link Integer }
6171          *
6172          */
6173         public void setWidth(Integer value) {
6174             this.width = value;
6175         }
6176
6177         /**
6178          * Gets the value of the height property.
6179          *
6180          * @return
6181          *     possible object is
6182          *     {@link Integer }
6183          *
6184          */
6185         public Integer getHeight() {
6186             return height;
6187         }
6188
6189         /**
6190          * Sets the value of the height property.
6191          *
6192          * @param value
6193          *     allowed object is
6194          *     {@link Integer }
6195          *
6196          */
6197         public void setHeight(Integer value) {
6198             this.height = value;
6199         }
6200
6201         /**
6202          * Gets the value of the xpos property.
6203          *
6204          * @return
6205          *     possible object is
6206          *     {@link Integer }
6207          *
6208          */
6209         public Integer getXpos() {
6210             return xpos;
6211         }
6212
6213         /**
6214          * Sets the value of the xpos property.
6215          *
6216          * @param value
6217          *     allowed object is
6218          *     {@link Integer }
6219          *
6220          */
6221         public void setXpos(Integer value) {
6222             this.xpos = value;
6223         }
6224
6225         /**
6226          * Gets the value of the ypos property.
6227          *
6228          * @return
6229          *     possible object is
6230          *     {@link Integer }
6231          *
6232          */
6233         public Integer getYpos() {
6234             return ypos;
6235         }
6236
6237         /**
6238          * Sets the value of the ypos property.
6239          *
6240          * @param value
6241          *     allowed object is
6242          *     {@link Integer }
6243          *
6244          */
6245         public void setYpos(Integer value) {
6246             this.ypos = value;
6247         }
6248
6249
6250         /**
6251          * <p>Java class for anonymous complex type.
6252          *
6253          * <p>The following schema fragment specifies the expected content contained within this class.
6254          *
6255          * <pre>
6256          * &lt;complexType>
6257          *   &lt;complexContent>
6258          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6259          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6260          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6261          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6262          *     &lt;/extension>
6263          *   &lt;/complexContent>
6264          * &lt;/complexType>
6265          * </pre>
6266          *
6267          *
6268          */
6269         @XmlAccessorType(XmlAccessType.FIELD)
6270         @XmlType(name = "")
6271         public static class CalcIdParam
6272             extends WebServiceParameterSet
6273         {
6274
6275             @XmlAttribute(name = "calcId", required = true)
6276             protected String calcId;
6277             @XmlAttribute(name = "needsUpdate")
6278             protected Boolean needsUpdate;
6279             @XmlAttribute(name = "autoUpdate", required = true)
6280             protected boolean autoUpdate;
6281
6282             /**
6283              * Gets the value of the calcId property.
6284              *
6285              * @return
6286              *     possible object is
6287              *     {@link String }
6288              *
6289              */
6290             public String getCalcId() {
6291                 return calcId;
6292             }
6293
6294             /**
6295              * Sets the value of the calcId property.
6296              *
6297              * @param value
6298              *     allowed object is
6299              *     {@link String }
6300              *
6301              */
6302             public void setCalcId(String value) {
6303                 this.calcId = value;
6304             }
6305
6306             /**
6307              * Gets the value of the needsUpdate property.
6308              *
6309              * @return
6310              *     possible object is
6311              *     {@link Boolean }
6312              *
6313              */
6314             public boolean isNeedsUpdate() {
6315                 if (needsUpdate == null) {
6316                     return false;
6317                 } else {
6318                     return needsUpdate;
6319                 }
6320             }
6321
6322             /**
6323              * Sets the value of the needsUpdate property.
6324              *
6325              * @param value
6326              *     allowed object is
6327              *     {@link Boolean }
6328              *
6329              */
6330             public void setNeedsUpdate(Boolean value) {
6331                 this.needsUpdate = value;
6332             }
6333
6334             /**
6335              * Gets the value of the autoUpdate property.
6336              *
6337              */
6338             public boolean isAutoUpdate() {
6339                 return autoUpdate;
6340             }
6341
6342             /**
6343              * Sets the value of the autoUpdate property.
6344              *
6345              */
6346             public void setAutoUpdate(boolean value) {
6347                 this.autoUpdate = value;
6348             }
6349
6350         }
6351
6352
6353         /**
6354          * <p>Java class for anonymous complex type.
6355          *
6356          * <p>The following schema fragment specifies the expected content contained within this class.
6357          *
6358          * <pre>
6359          * &lt;complexType>
6360          *   &lt;complexContent>
6361          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6362          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6363          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6364          *     &lt;/restriction>
6365          *   &lt;/complexContent>
6366          * &lt;/complexType>
6367          * </pre>
6368          *
6369          *
6370          */
6371         @XmlAccessorType(XmlAccessType.FIELD)
6372         @XmlType(name = "")
6373         public static class HiddenColumns {
6374
6375             @XmlAttribute(name = "start")
6376             protected Integer start;
6377             @XmlAttribute(name = "end")
6378             protected Integer end;
6379
6380             /**
6381              * Gets the value of the start property.
6382              *
6383              * @return
6384              *     possible object is
6385              *     {@link Integer }
6386              *
6387              */
6388             public Integer getStart() {
6389                 return start;
6390             }
6391
6392             /**
6393              * Sets the value of the start property.
6394              *
6395              * @param value
6396              *     allowed object is
6397              *     {@link Integer }
6398              *
6399              */
6400             public void setStart(Integer value) {
6401                 this.start = value;
6402             }
6403
6404             /**
6405              * Gets the value of the end property.
6406              *
6407              * @return
6408              *     possible object is
6409              *     {@link Integer }
6410              *
6411              */
6412             public Integer getEnd() {
6413                 return end;
6414             }
6415
6416             /**
6417              * Sets the value of the end property.
6418              *
6419              * @param value
6420              *     allowed object is
6421              *     {@link Integer }
6422              *
6423              */
6424             public void setEnd(Integer value) {
6425                 this.end = value;
6426             }
6427
6428         }
6429
6430
6431         /**
6432          * <p>Java class for anonymous complex type.
6433          *
6434          * <p>The following schema fragment specifies the expected content contained within this class.
6435          *
6436          * <pre>
6437          * &lt;complexType>
6438          *   &lt;complexContent>
6439          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6440          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
6441          *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6442          *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6443          *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6444          *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6445          *     &lt;/restriction>
6446          *   &lt;/complexContent>
6447          * &lt;/complexType>
6448          * </pre>
6449          *
6450          *
6451          */
6452         @XmlAccessorType(XmlAccessType.FIELD)
6453         @XmlType(name = "")
6454         public static class Overview {
6455
6456             @XmlAttribute(name = "showHidden")
6457             protected Boolean showHidden;
6458             @XmlAttribute(name = "residueColour")
6459             protected Integer residueColour;
6460             @XmlAttribute(name = "gapColour")
6461             protected Integer gapColour;
6462             @XmlAttribute(name = "hiddenColour")
6463             protected Integer hiddenColour;
6464             @XmlAttribute(name = "width")
6465             protected Integer width;
6466             @XmlAttribute(name = "height")
6467             protected Integer height;
6468             @XmlAttribute(name = "xpos")
6469             protected Integer xpos;
6470             @XmlAttribute(name = "ypos")
6471             protected Integer ypos;
6472
6473             /**
6474              * Gets the value of the showHidden property.
6475              *
6476              * @return
6477              *     possible object is
6478              *     {@link Boolean }
6479              *
6480              */
6481             public Boolean isShowHidden() {
6482                 return showHidden;
6483             }
6484
6485             /**
6486              * Sets the value of the showHidden property.
6487              *
6488              * @param value
6489              *     allowed object is
6490              *     {@link Boolean }
6491              *
6492              */
6493             public void setShowHidden(Boolean value) {
6494                 this.showHidden = value;
6495             }
6496
6497             /**
6498              * Gets the value of the residueColour property.
6499              *
6500              * @return
6501              *     possible object is
6502              *     {@link Integer }
6503              *
6504              */
6505             public Integer getResidueColour() {
6506                 return residueColour;
6507             }
6508
6509             /**
6510              * Sets the value of the residueColour property.
6511              *
6512              * @param value
6513              *     allowed object is
6514              *     {@link Integer }
6515              *
6516              */
6517             public void setResidueColour(Integer value) {
6518                 this.residueColour = value;
6519             }
6520
6521             /**
6522              * Gets the value of the gapColour property.
6523              *
6524              * @return
6525              *     possible object is
6526              *     {@link Integer }
6527              *
6528              */
6529             public Integer getGapColour() {
6530                 return gapColour;
6531             }
6532
6533             /**
6534              * Sets the value of the gapColour property.
6535              *
6536              * @param value
6537              *     allowed object is
6538              *     {@link Integer }
6539              *
6540              */
6541             public void setGapColour(Integer value) {
6542                 this.gapColour = value;
6543             }
6544
6545             /**
6546              * Gets the value of the hiddenColour property.
6547              *
6548              * @return
6549              *     possible object is
6550              *     {@link Integer }
6551              *
6552              */
6553             public Integer getHiddenColour() {
6554                 return hiddenColour;
6555             }
6556
6557             /**
6558              * Sets the value of the hiddenColour property.
6559              *
6560              * @param value
6561              *     allowed object is
6562              *     {@link Integer }
6563              *
6564              */
6565             public void setHiddenColour(Integer value) {
6566                 this.hiddenColour = value;
6567             }
6568
6569             /**
6570              * Gets the value of the width property.
6571              *
6572              * @return
6573              *     possible object is
6574              *     {@link Integer }
6575              *
6576              */
6577             public Integer getWidth() {
6578                 return width;
6579             }
6580
6581             /**
6582              * Sets the value of the width property.
6583              *
6584              * @param value
6585              *     allowed object is
6586              *     {@link Integer }
6587              *
6588              */
6589             public void setWidth(Integer value) {
6590                 this.width = value;
6591             }
6592
6593             /**
6594              * Gets the value of the height property.
6595              *
6596              * @return
6597              *     possible object is
6598              *     {@link Integer }
6599              *
6600              */
6601             public Integer getHeight() {
6602                 return height;
6603             }
6604
6605             /**
6606              * Sets the value of the height property.
6607              *
6608              * @param value
6609              *     allowed object is
6610              *     {@link Integer }
6611              *
6612              */
6613             public void setHeight(Integer value) {
6614                 this.height = value;
6615             }
6616
6617             /**
6618              * Gets the value of the xpos property.
6619              *
6620              * @return
6621              *     possible object is
6622              *     {@link Integer }
6623              *
6624              */
6625             public Integer getXpos() {
6626                 return xpos;
6627             }
6628
6629             /**
6630              * Sets the value of the xpos property.
6631              *
6632              * @param value
6633              *     allowed object is
6634              *     {@link Integer }
6635              *
6636              */
6637             public void setXpos(Integer value) {
6638                 this.xpos = value;
6639             }
6640
6641             /**
6642              * Gets the value of the ypos property.
6643              *
6644              * @return
6645              *     possible object is
6646              *     {@link Integer }
6647              *
6648              */
6649             public Integer getYpos() {
6650                 return ypos;
6651             }
6652
6653             /**
6654              * Sets the value of the ypos property.
6655              *
6656              * @param value
6657              *     allowed object is
6658              *     {@link Integer }
6659              *
6660              */
6661             public void setYpos(Integer value) {
6662                 this.ypos = value;
6663             }
6664
6665         }
6666
6667     }
6668
6669 }