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: 2019.07.10 at 12:10:00 PM BST
   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;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
 100  *                   &lt;/sequence>
 101  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 104  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 105  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 107  *                 &lt;/restriction>
 108  *               &lt;/complexContent>
 109  *             &lt;/complexType>
 110  *           &lt;/element>
 111  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 112  *             &lt;complexType>
 113  *               &lt;complexContent>
 114  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 115  *                   &lt;sequence>
 116  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 117  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 118  *                   &lt;/sequence>
 119  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 121  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 123  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 126  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 129  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 132  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 133  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 135  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 137  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 138  *                 &lt;/restriction>
 139  *               &lt;/complexContent>
 140  *             &lt;/complexType>
 141  *           &lt;/element>
 142  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 143  *             &lt;complexType>
 144  *               &lt;complexContent>
 145  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 146  *                   &lt;sequence>
 147  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 148  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 149  *                       &lt;complexType>
 150  *                         &lt;complexContent>
 151  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 152  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 154  *                           &lt;/restriction>
 155  *                         &lt;/complexContent>
 156  *                       &lt;/complexType>
 157  *                     &lt;/element>
 158  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 159  *                       &lt;complexType>
 160  *                         &lt;complexContent>
 161  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 162  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 163  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 164  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 165  *                           &lt;/extension>
 166  *                         &lt;/complexContent>
 167  *                       &lt;/complexType>
 168  *                     &lt;/element>
 169  *                   &lt;/sequence>
 170  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 171  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 172  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 173  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 174  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 175  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 176  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 177  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 178  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 179  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 180  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 181  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 182  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 183  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 184  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 185  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 186  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 187  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 188  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 189  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 190  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 191  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 192  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 193  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 194  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 195  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 196  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 197  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 198  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 199  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 200  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 201  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 202  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 203  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 204  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 205  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 206  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 207  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 208  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 209  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 210  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 211  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 212  *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 213  *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 214  *                 &lt;/restriction>
 215  *               &lt;/complexContent>
 216  *             &lt;/complexType>
 217  *           &lt;/element>
 218  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 219  *             &lt;complexType>
 220  *               &lt;complexContent>
 221  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 222  *                   &lt;sequence>
 223  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 224  *                   &lt;/sequence>
 225  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 226  *                 &lt;/restriction>
 227  *               &lt;/complexContent>
 228  *             &lt;/complexType>
 229  *           &lt;/element>
 230  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 231  *             &lt;complexType>
 232  *               &lt;complexContent>
 233  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 234  *                   &lt;sequence minOccurs="0">
 235  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 236  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 237  *                   &lt;/sequence>
 238  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 239  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 240  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 241  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 242  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 243  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 244  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 245  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 246  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 247  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 248  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 249  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 250  *                 &lt;/restriction>
 251  *               &lt;/complexContent>
 252  *             &lt;/complexType>
 253  *           &lt;/element>
 254  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 255  *             &lt;complexType>
 256  *               &lt;complexContent>
 257  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 258  *                   &lt;sequence>
 259  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 260  *                       &lt;complexType>
 261  *                         &lt;complexContent>
 262  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 263  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 264  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 265  *                           &lt;/restriction>
 266  *                         &lt;/complexContent>
 267  *                       &lt;/complexType>
 268  *                     &lt;/element>
 269  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 270  *                       &lt;complexType>
 271  *                         &lt;complexContent>
 272  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 273  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 274  *                           &lt;/restriction>
 275  *                         &lt;/complexContent>
 276  *                       &lt;/complexType>
 277  *                     &lt;/element>
 278  *                     &lt;element name="seqPointMin">
 279  *                       &lt;complexType>
 280  *                         &lt;complexContent>
 281  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 282  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 283  *                           &lt;/restriction>
 284  *                         &lt;/complexContent>
 285  *                       &lt;/complexType>
 286  *                     &lt;/element>
 287  *                     &lt;element name="seqPointMax">
 288  *                       &lt;complexType>
 289  *                         &lt;complexContent>
 290  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 291  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 292  *                           &lt;/restriction>
 293  *                         &lt;/complexContent>
 294  *                       &lt;/complexType>
 295  *                     &lt;/element>
 296  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 297  *                   &lt;/sequence>
 298  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 299  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 300  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 301  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 302  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 303  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 304  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 305  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 306  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 307  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 308  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 309  *                 &lt;/restriction>
 310  *               &lt;/complexContent>
 311  *             &lt;/complexType>
 312  *           &lt;/element>
 313  *           &lt;element name="FeatureSettings" minOccurs="0">
 314  *             &lt;complexType>
 315  *               &lt;complexContent>
 316  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 317  *                   &lt;sequence>
 318  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 319  *                       &lt;complexType>
 320  *                         &lt;complexContent>
 321  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 322  *                             &lt;sequence>
 323  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 324  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 325  *                             &lt;/sequence>
 326  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 327  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 328  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 329  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 330  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 331  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 332  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 333  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 334  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 335  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 336  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 337  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 338  *                           &lt;/restriction>
 339  *                         &lt;/complexContent>
 340  *                       &lt;/complexType>
 341  *                     &lt;/element>
 342  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 343  *                       &lt;complexType>
 344  *                         &lt;complexContent>
 345  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 346  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 347  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 348  *                           &lt;/restriction>
 349  *                         &lt;/complexContent>
 350  *                       &lt;/complexType>
 351  *                     &lt;/element>
 352  *                   &lt;/sequence>
 353  *                 &lt;/restriction>
 354  *               &lt;/complexContent>
 355  *             &lt;/complexType>
 356  *           &lt;/element>
 357  *         &lt;/sequence>
 358  *       &lt;/sequence>
 359  *     &lt;/restriction>
 360  *   &lt;/complexContent>
 361  * &lt;/complexType>
 362  * </pre>
 363  *
 364  *
 365  */
 366 @XmlAccessorType(XmlAccessType.FIELD)
 367 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 368     "creationDate",
 369     "version",
 370     "vamsasModel",
 371     "jSeq",
 372     "jGroup",
 373     "viewport",
 374     "userColours",
 375     "tree",
 376     "pcaViewer",
 377     "featureSettings"
 378 })
 379 public class JalviewModel {
 380
 381     @XmlElement(required = true)
 382     @XmlSchemaType(name = "dateTime")
 383     protected XMLGregorianCalendar creationDate;
 384     @XmlElement(required = true)
 385     protected String version;
 386     @XmlElement(required = true)
 387     protected VAMSAS vamsasModel;
 388     @XmlElement(name = "JSeq")
 389     protected List<JalviewModel.JSeq> jSeq;
 390     @XmlElement(name = "JGroup")
 391     protected List<JalviewModel.JGroup> jGroup;
 392     @XmlElement(name = "Viewport")
 393     protected List<JalviewModel.Viewport> viewport;
 394     @XmlElement(name = "UserColours")
 395     protected List<JalviewModel.UserColours> userColours;
 396     protected List<JalviewModel.Tree> tree;
 397     @XmlElement(name = "PcaViewer")
 398     protected List<JalviewModel.PcaViewer> pcaViewer;
 399     @XmlElement(name = "FeatureSettings")
 400     protected JalviewModel.FeatureSettings featureSettings;
 401
 402     /**
 403      * Gets the value of the creationDate property.
 404      *
 405      * @return
 406      *     possible object is
 407      *     {@link XMLGregorianCalendar }
 408      *
 409      */
 410     public XMLGregorianCalendar getCreationDate() {
 411         return creationDate;
 412     }
 413
 414     /**
 415      * Sets the value of the creationDate property.
 416      *
 417      * @param value
 418      *     allowed object is
 419      *     {@link XMLGregorianCalendar }
 420      *
 421      */
 422     public void setCreationDate(XMLGregorianCalendar value) {
 423         this.creationDate = value;
 424     }
 425
 426     /**
 427      * Gets the value of the version property.
 428      *
 429      * @return
 430      *     possible object is
 431      *     {@link String }
 432      *
 433      */
 434     public String getVersion() {
 435         return version;
 436     }
 437
 438     /**
 439      * Sets the value of the version property.
 440      *
 441      * @param value
 442      *     allowed object is
 443      *     {@link String }
 444      *
 445      */
 446     public void setVersion(String value) {
 447         this.version = value;
 448     }
 449
 450     /**
 451      * Gets the value of the vamsasModel property.
 452      *
 453      * @return
 454      *     possible object is
 455      *     {@link VAMSAS }
 456      *
 457      */
 458     public VAMSAS getVamsasModel() {
 459         return vamsasModel;
 460     }
 461
 462     /**
 463      * Sets the value of the vamsasModel property.
 464      *
 465      * @param value
 466      *     allowed object is
 467      *     {@link VAMSAS }
 468      *
 469      */
 470     public void setVamsasModel(VAMSAS value) {
 471         this.vamsasModel = value;
 472     }
 473
 474     /**
 475      * Gets the value of the jSeq property.
 476      *
 477      * <p>
 478      * This accessor method returns a reference to the live list,
 479      * not a snapshot. Therefore any modification you make to the
 480      * returned list will be present inside the JAXB object.
 481      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 482      *
 483      * <p>
 484      * For example, to add a new item, do as follows:
 485      * <pre>
 486      *    getJSeq().add(newItem);
 487      * </pre>
 488      *
 489      *
 490      * <p>
 491      * Objects of the following type(s) are allowed in the list
 492      * {@link JalviewModel.JSeq }
 493      *
 494      *
 495      */
 496     public List<JalviewModel.JSeq> getJSeq() {
 497         if (jSeq == null) {
 498             jSeq = new ArrayList<JalviewModel.JSeq>();
 499         }
 500         return this.jSeq;
 501     }
 502
 503     /**
 504      * Gets the value of the jGroup property.
 505      *
 506      * <p>
 507      * This accessor method returns a reference to the live list,
 508      * not a snapshot. Therefore any modification you make to the
 509      * returned list will be present inside the JAXB object.
 510      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 511      *
 512      * <p>
 513      * For example, to add a new item, do as follows:
 514      * <pre>
 515      *    getJGroup().add(newItem);
 516      * </pre>
 517      *
 518      *
 519      * <p>
 520      * Objects of the following type(s) are allowed in the list
 521      * {@link JalviewModel.JGroup }
 522      *
 523      *
 524      */
 525     public List<JalviewModel.JGroup> getJGroup() {
 526         if (jGroup == null) {
 527             jGroup = new ArrayList<JalviewModel.JGroup>();
 528         }
 529         return this.jGroup;
 530     }
 531
 532     /**
 533      * Gets the value of the viewport property.
 534      *
 535      * <p>
 536      * This accessor method returns a reference to the live list,
 537      * not a snapshot. Therefore any modification you make to the
 538      * returned list will be present inside the JAXB object.
 539      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 540      *
 541      * <p>
 542      * For example, to add a new item, do as follows:
 543      * <pre>
 544      *    getViewport().add(newItem);
 545      * </pre>
 546      *
 547      *
 548      * <p>
 549      * Objects of the following type(s) are allowed in the list
 550      * {@link JalviewModel.Viewport }
 551      *
 552      *
 553      */
 554     public List<JalviewModel.Viewport> getViewport() {
 555         if (viewport == null) {
 556             viewport = new ArrayList<JalviewModel.Viewport>();
 557         }
 558         return this.viewport;
 559     }
 560
 561     /**
 562      * Gets the value of the userColours property.
 563      *
 564      * <p>
 565      * This accessor method returns a reference to the live list,
 566      * not a snapshot. Therefore any modification you make to the
 567      * returned list will be present inside the JAXB object.
 568      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 569      *
 570      * <p>
 571      * For example, to add a new item, do as follows:
 572      * <pre>
 573      *    getUserColours().add(newItem);
 574      * </pre>
 575      *
 576      *
 577      * <p>
 578      * Objects of the following type(s) are allowed in the list
 579      * {@link JalviewModel.UserColours }
 580      *
 581      *
 582      */
 583     public List<JalviewModel.UserColours> getUserColours() {
 584         if (userColours == null) {
 585             userColours = new ArrayList<JalviewModel.UserColours>();
 586         }
 587         return this.userColours;
 588     }
 589
 590     /**
 591      * Gets the value of the tree property.
 592      *
 593      * <p>
 594      * This accessor method returns a reference to the live list,
 595      * not a snapshot. Therefore any modification you make to the
 596      * returned list will be present inside the JAXB object.
 597      * This is why there is not a <CODE>set</CODE> method for the tree property.
 598      *
 599      * <p>
 600      * For example, to add a new item, do as follows:
 601      * <pre>
 602      *    getTree().add(newItem);
 603      * </pre>
 604      *
 605      *
 606      * <p>
 607      * Objects of the following type(s) are allowed in the list
 608      * {@link JalviewModel.Tree }
 609      *
 610      *
 611      */
 612     public List<JalviewModel.Tree> getTree() {
 613         if (tree == null) {
 614             tree = new ArrayList<JalviewModel.Tree>();
 615         }
 616         return this.tree;
 617     }
 618
 619     /**
 620      * Gets the value of the pcaViewer property.
 621      *
 622      * <p>
 623      * This accessor method returns a reference to the live list,
 624      * not a snapshot. Therefore any modification you make to the
 625      * returned list will be present inside the JAXB object.
 626      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 627      *
 628      * <p>
 629      * For example, to add a new item, do as follows:
 630      * <pre>
 631      *    getPcaViewer().add(newItem);
 632      * </pre>
 633      *
 634      *
 635      * <p>
 636      * Objects of the following type(s) are allowed in the list
 637      * {@link JalviewModel.PcaViewer }
 638      *
 639      *
 640      */
 641     public List<JalviewModel.PcaViewer> getPcaViewer() {
 642         if (pcaViewer == null) {
 643             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 644         }
 645         return this.pcaViewer;
 646     }
 647
 648     /**
 649      * Gets the value of the featureSettings property.
 650      *
 651      * @return
 652      *     possible object is
 653      *     {@link JalviewModel.FeatureSettings }
 654      *
 655      */
 656     public JalviewModel.FeatureSettings getFeatureSettings() {
 657         return featureSettings;
 658     }
 659
 660     /**
 661      * Sets the value of the featureSettings property.
 662      *
 663      * @param value
 664      *     allowed object is
 665      *     {@link JalviewModel.FeatureSettings }
 666      *
 667      */
 668     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 669         this.featureSettings = value;
 670     }
 671
 672
 673     /**
 674      * <p>Java class for anonymous complex type.
 675      *
 676      * <p>The following schema fragment specifies the expected content contained within this class.
 677      *
 678      * <pre>
 679      * &lt;complexType>
 680      *   &lt;complexContent>
 681      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 682      *       &lt;sequence>
 683      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 684      *           &lt;complexType>
 685      *             &lt;complexContent>
 686      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 687      *                 &lt;sequence>
 688      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 689      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 690      *                 &lt;/sequence>
 691      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 692      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 693      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 694      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 695      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 696      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 697      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 698      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 699      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 700      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 701      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 702      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 703      *               &lt;/restriction>
 704      *             &lt;/complexContent>
 705      *           &lt;/complexType>
 706      *         &lt;/element>
 707      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 708      *           &lt;complexType>
 709      *             &lt;complexContent>
 710      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 711      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 712      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 713      *               &lt;/restriction>
 714      *             &lt;/complexContent>
 715      *           &lt;/complexType>
 716      *         &lt;/element>
 717      *       &lt;/sequence>
 718      *     &lt;/restriction>
 719      *   &lt;/complexContent>
 720      * &lt;/complexType>
 721      * </pre>
 722      *
 723      *
 724      */
 725     @XmlAccessorType(XmlAccessType.FIELD)
 726     @XmlType(name = "", propOrder = {
 727         "setting",
 728         "group"
 729     })
 730     public static class FeatureSettings {
 731
 732         @XmlElement(namespace = "www.jalview.org")
 733         protected List<JalviewModel.FeatureSettings.Setting> setting;
 734         @XmlElement(namespace = "www.jalview.org")
 735         protected List<JalviewModel.FeatureSettings.Group> group;
 736
 737         /**
 738          * Gets the value of the setting property.
 739          *
 740          * <p>
 741          * This accessor method returns a reference to the live list,
 742          * not a snapshot. Therefore any modification you make to the
 743          * returned list will be present inside the JAXB object.
 744          * This is why there is not a <CODE>set</CODE> method for the setting property.
 745          *
 746          * <p>
 747          * For example, to add a new item, do as follows:
 748          * <pre>
 749          *    getSetting().add(newItem);
 750          * </pre>
 751          *
 752          *
 753          * <p>
 754          * Objects of the following type(s) are allowed in the list
 755          * {@link JalviewModel.FeatureSettings.Setting }
 756          *
 757          *
 758          */
 759         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 760             if (setting == null) {
 761                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 762             }
 763             return this.setting;
 764         }
 765
 766         /**
 767          * Gets the value of the group property.
 768          *
 769          * <p>
 770          * This accessor method returns a reference to the live list,
 771          * not a snapshot. Therefore any modification you make to the
 772          * returned list will be present inside the JAXB object.
 773          * This is why there is not a <CODE>set</CODE> method for the group property.
 774          *
 775          * <p>
 776          * For example, to add a new item, do as follows:
 777          * <pre>
 778          *    getGroup().add(newItem);
 779          * </pre>
 780          *
 781          *
 782          * <p>
 783          * Objects of the following type(s) are allowed in the list
 784          * {@link JalviewModel.FeatureSettings.Group }
 785          *
 786          *
 787          */
 788         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 789             if (group == null) {
 790                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 791             }
 792             return this.group;
 793         }
 794
 795
 796         /**
 797          * <p>Java class for anonymous complex type.
 798          *
 799          * <p>The following schema fragment specifies the expected content contained within this class.
 800          *
 801          * <pre>
 802          * &lt;complexType>
 803          *   &lt;complexContent>
 804          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 805          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 806          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 807          *     &lt;/restriction>
 808          *   &lt;/complexContent>
 809          * &lt;/complexType>
 810          * </pre>
 811          *
 812          *
 813          */
 814         @XmlAccessorType(XmlAccessType.FIELD)
 815         @XmlType(name = "")
 816         public static class Group {
 817
 818             @XmlAttribute(name = "name", required = true)
 819             protected String name;
 820             @XmlAttribute(name = "display", required = true)
 821             protected boolean display;
 822
 823             /**
 824              * Gets the value of the name property.
 825              *
 826              * @return
 827              *     possible object is
 828              *     {@link String }
 829              *
 830              */
 831             public String getName() {
 832                 return name;
 833             }
 834
 835             /**
 836              * Sets the value of the name property.
 837              *
 838              * @param value
 839              *     allowed object is
 840              *     {@link String }
 841              *
 842              */
 843             public void setName(String value) {
 844                 this.name = value;
 845             }
 846
 847             /**
 848              * Gets the value of the display property.
 849              *
 850              */
 851             public boolean isDisplay() {
 852                 return display;
 853             }
 854
 855             /**
 856              * Sets the value of the display property.
 857              *
 858              */
 859             public void setDisplay(boolean value) {
 860                 this.display = value;
 861             }
 862
 863         }
 864
 865
 866         /**
 867          * <p>Java class for anonymous complex type.
 868          *
 869          * <p>The following schema fragment specifies the expected content contained within this class.
 870          *
 871          * <pre>
 872          * &lt;complexType>
 873          *   &lt;complexContent>
 874          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 875          *       &lt;sequence>
 876          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 877          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 878          *       &lt;/sequence>
 879          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 880          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 881          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 882          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 883          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 884          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 885          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 886          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 887          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 888          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 889          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 890          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 891          *     &lt;/restriction>
 892          *   &lt;/complexContent>
 893          * &lt;/complexType>
 894          * </pre>
 895          *
 896          *
 897          */
 898         @XmlAccessorType(XmlAccessType.FIELD)
 899         @XmlType(name = "", propOrder = {
 900             "attributeName",
 901             "matcherSet"
 902         })
 903         public static class Setting {
 904
 905             @XmlElement(namespace = "www.jalview.org")
 906             protected List<String> attributeName;
 907             @XmlElement(namespace = "www.jalview.org")
 908             protected FeatureMatcherSet matcherSet;
 909             @XmlAttribute(name = "type", required = true)
 910             protected String type;
 911             @XmlAttribute(name = "colour", required = true)
 912             protected int colour;
 913             @XmlAttribute(name = "display", required = true)
 914             protected boolean display;
 915             @XmlAttribute(name = "order")
 916             protected Float order;
 917             @XmlAttribute(name = "mincolour")
 918             protected Integer mincolour;
 919             @XmlAttribute(name = "noValueColour")
 920             protected NoValueColour noValueColour;
 921             @XmlAttribute(name = "threshold")
 922             protected Float threshold;
 923             @XmlAttribute(name = "threshstate")
 924             protected Integer threshstate;
 925             @XmlAttribute(name = "max")
 926             protected Float max;
 927             @XmlAttribute(name = "min")
 928             protected Float min;
 929             @XmlAttribute(name = "colourByLabel")
 930             protected Boolean colourByLabel;
 931             @XmlAttribute(name = "autoScale")
 932             protected Boolean autoScale;
 933
 934             /**
 935              * Gets the value of the attributeName property.
 936              *
 937              * <p>
 938              * This accessor method returns a reference to the live list,
 939              * not a snapshot. Therefore any modification you make to the
 940              * returned list will be present inside the JAXB object.
 941              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 942              *
 943              * <p>
 944              * For example, to add a new item, do as follows:
 945              * <pre>
 946              *    getAttributeName().add(newItem);
 947              * </pre>
 948              *
 949              *
 950              * <p>
 951              * Objects of the following type(s) are allowed in the list
 952              * {@link String }
 953              *
 954              *
 955              */
 956             public List<String> getAttributeName() {
 957                 if (attributeName == null) {
 958                     attributeName = new ArrayList<String>();
 959                 }
 960                 return this.attributeName;
 961             }
 962
 963             /**
 964              * Gets the value of the matcherSet property.
 965              *
 966              * @return
 967              *     possible object is
 968              *     {@link FeatureMatcherSet }
 969              *
 970              */
 971             public FeatureMatcherSet getMatcherSet() {
 972                 return matcherSet;
 973             }
 974
 975             /**
 976              * Sets the value of the matcherSet property.
 977              *
 978              * @param value
 979              *     allowed object is
 980              *     {@link FeatureMatcherSet }
 981              *
 982              */
 983             public void setMatcherSet(FeatureMatcherSet value) {
 984                 this.matcherSet = value;
 985             }
 986
 987             /**
 988              * Gets the value of the type property.
 989              *
 990              * @return
 991              *     possible object is
 992              *     {@link String }
 993              *
 994              */
 995             public String getType() {
 996                 return type;
 997             }
 998
 999             /**
1000              * Sets the value of the type property.
1001              *
1002              * @param value
1003              *     allowed object is
1004              *     {@link String }
1005              *
1006              */
1007             public void setType(String value) {
1008                 this.type = value;
1009             }
1010
1011             /**
1012              * Gets the value of the colour property.
1013              *
1014              */
1015             public int getColour() {
1016                 return colour;
1017             }
1018
1019             /**
1020              * Sets the value of the colour property.
1021              *
1022              */
1023             public void setColour(int value) {
1024                 this.colour = value;
1025             }
1026
1027             /**
1028              * Gets the value of the display property.
1029              *
1030              */
1031             public boolean isDisplay() {
1032                 return display;
1033             }
1034
1035             /**
1036              * Sets the value of the display property.
1037              *
1038              */
1039             public void setDisplay(boolean value) {
1040                 this.display = value;
1041             }
1042
1043             /**
1044              * Gets the value of the order property.
1045              *
1046              * @return
1047              *     possible object is
1048              *     {@link Float }
1049              *
1050              */
1051             public Float getOrder() {
1052                 return order;
1053             }
1054
1055             /**
1056              * Sets the value of the order property.
1057              *
1058              * @param value
1059              *     allowed object is
1060              *     {@link Float }
1061              *
1062              */
1063             public void setOrder(Float value) {
1064                 this.order = value;
1065             }
1066
1067             /**
1068              * Gets the value of the mincolour property.
1069              *
1070              * @return
1071              *     possible object is
1072              *     {@link Integer }
1073              *
1074              */
1075             public Integer getMincolour() {
1076                 return mincolour;
1077             }
1078
1079             /**
1080              * Sets the value of the mincolour property.
1081              *
1082              * @param value
1083              *     allowed object is
1084              *     {@link Integer }
1085              *
1086              */
1087             public void setMincolour(Integer value) {
1088                 this.mincolour = value;
1089             }
1090
1091             /**
1092              * Gets the value of the noValueColour property.
1093              *
1094              * @return
1095              *     possible object is
1096              *     {@link NoValueColour }
1097              *
1098              */
1099             public NoValueColour getNoValueColour() {
1100                 if (noValueColour == null) {
1101                     return NoValueColour.MIN;
1102                 } else {
1103                     return noValueColour;
1104                 }
1105             }
1106
1107             /**
1108              * Sets the value of the noValueColour property.
1109              *
1110              * @param value
1111              *     allowed object is
1112              *     {@link NoValueColour }
1113              *
1114              */
1115             public void setNoValueColour(NoValueColour value) {
1116                 this.noValueColour = value;
1117             }
1118
1119             /**
1120              * Gets the value of the threshold property.
1121              *
1122              * @return
1123              *     possible object is
1124              *     {@link Float }
1125              *
1126              */
1127             public Float getThreshold() {
1128                 return threshold;
1129             }
1130
1131             /**
1132              * Sets the value of the threshold property.
1133              *
1134              * @param value
1135              *     allowed object is
1136              *     {@link Float }
1137              *
1138              */
1139             public void setThreshold(Float value) {
1140                 this.threshold = value;
1141             }
1142
1143             /**
1144              * Gets the value of the threshstate property.
1145              *
1146              * @return
1147              *     possible object is
1148              *     {@link Integer }
1149              *
1150              */
1151             public Integer getThreshstate() {
1152                 return threshstate;
1153             }
1154
1155             /**
1156              * Sets the value of the threshstate property.
1157              *
1158              * @param value
1159              *     allowed object is
1160              *     {@link Integer }
1161              *
1162              */
1163             public void setThreshstate(Integer value) {
1164                 this.threshstate = value;
1165             }
1166
1167             /**
1168              * Gets the value of the max property.
1169              *
1170              * @return
1171              *     possible object is
1172              *     {@link Float }
1173              *
1174              */
1175             public Float getMax() {
1176                 return max;
1177             }
1178
1179             /**
1180              * Sets the value of the max property.
1181              *
1182              * @param value
1183              *     allowed object is
1184              *     {@link Float }
1185              *
1186              */
1187             public void setMax(Float value) {
1188                 this.max = value;
1189             }
1190
1191             /**
1192              * Gets the value of the min property.
1193              *
1194              * @return
1195              *     possible object is
1196              *     {@link Float }
1197              *
1198              */
1199             public Float getMin() {
1200                 return min;
1201             }
1202
1203             /**
1204              * Sets the value of the min property.
1205              *
1206              * @param value
1207              *     allowed object is
1208              *     {@link Float }
1209              *
1210              */
1211             public void setMin(Float value) {
1212                 this.min = value;
1213             }
1214
1215             /**
1216              * Gets the value of the colourByLabel property.
1217              *
1218              * @return
1219              *     possible object is
1220              *     {@link Boolean }
1221              *
1222              */
1223             public Boolean isColourByLabel() {
1224                 return colourByLabel;
1225             }
1226
1227             /**
1228              * Sets the value of the colourByLabel property.
1229              *
1230              * @param value
1231              *     allowed object is
1232              *     {@link Boolean }
1233              *
1234              */
1235             public void setColourByLabel(Boolean value) {
1236                 this.colourByLabel = value;
1237             }
1238
1239             /**
1240              * Gets the value of the autoScale property.
1241              *
1242              * @return
1243              *     possible object is
1244              *     {@link Boolean }
1245              *
1246              */
1247             public Boolean isAutoScale() {
1248                 return autoScale;
1249             }
1250
1251             /**
1252              * Sets the value of the autoScale property.
1253              *
1254              * @param value
1255              *     allowed object is
1256              *     {@link Boolean }
1257              *
1258              */
1259             public void setAutoScale(Boolean value) {
1260                 this.autoScale = value;
1261             }
1262
1263         }
1264
1265     }
1266
1267
1268     /**
1269      * <p>Java class for anonymous complex type.
1270      *
1271      * <p>The following schema fragment specifies the expected content contained within this class.
1272      *
1273      * <pre>
1274      * &lt;complexType>
1275      *   &lt;complexContent>
1276      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1277      *       &lt;sequence>
1278      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1279      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1280      *       &lt;/sequence>
1281      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1282      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1283      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1284      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1285      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1286      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1287      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1288      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1289      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1290      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1291      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1292      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1293      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1294      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1295      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1296      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1297      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1298      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1299      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1300      *     &lt;/restriction>
1301      *   &lt;/complexContent>
1302      * &lt;/complexType>
1303      * </pre>
1304      *
1305      *
1306      */
1307     @XmlAccessorType(XmlAccessType.FIELD)
1308     @XmlType(name = "", propOrder = {
1309         "seq",
1310         "annotationColours"
1311     })
1312     public static class JGroup {
1313
1314         @XmlElement(namespace = "www.jalview.org", required = true)
1315         protected List<String> seq;
1316         @XmlElement(namespace = "www.jalview.org")
1317         protected AnnotationColourScheme annotationColours;
1318         @XmlAttribute(name = "start")
1319         protected Integer start;
1320         @XmlAttribute(name = "end")
1321         protected Integer end;
1322         @XmlAttribute(name = "name")
1323         protected String name;
1324         @XmlAttribute(name = "colour")
1325         protected String colour;
1326         @XmlAttribute(name = "consThreshold")
1327         protected Integer consThreshold;
1328         @XmlAttribute(name = "pidThreshold")
1329         protected Integer pidThreshold;
1330         @XmlAttribute(name = "outlineColour")
1331         protected Integer outlineColour;
1332         @XmlAttribute(name = "displayBoxes")
1333         protected Boolean displayBoxes;
1334         @XmlAttribute(name = "displayText")
1335         protected Boolean displayText;
1336         @XmlAttribute(name = "colourText")
1337         protected Boolean colourText;
1338         @XmlAttribute(name = "textCol1")
1339         protected Integer textCol1;
1340         @XmlAttribute(name = "textCol2")
1341         protected Integer textCol2;
1342         @XmlAttribute(name = "textColThreshold")
1343         protected Integer textColThreshold;
1344         @XmlAttribute(name = "showUnconserved")
1345         protected Boolean showUnconserved;
1346         @XmlAttribute(name = "ignoreGapsinConsensus")
1347         protected Boolean ignoreGapsinConsensus;
1348         @XmlAttribute(name = "showConsensusHistogram")
1349         protected Boolean showConsensusHistogram;
1350         @XmlAttribute(name = "showSequenceLogo")
1351         protected Boolean showSequenceLogo;
1352         @XmlAttribute(name = "normaliseSequenceLogo")
1353         protected Boolean normaliseSequenceLogo;
1354         @XmlAttribute(name = "id")
1355         protected String id;
1356
1357         /**
1358          * Gets the value of the seq property.
1359          *
1360          * <p>
1361          * This accessor method returns a reference to the live list,
1362          * not a snapshot. Therefore any modification you make to the
1363          * returned list will be present inside the JAXB object.
1364          * This is why there is not a <CODE>set</CODE> method for the seq property.
1365          *
1366          * <p>
1367          * For example, to add a new item, do as follows:
1368          * <pre>
1369          *    getSeq().add(newItem);
1370          * </pre>
1371          *
1372          *
1373          * <p>
1374          * Objects of the following type(s) are allowed in the list
1375          * {@link String }
1376          *
1377          *
1378          */
1379         public List<String> getSeq() {
1380             if (seq == null) {
1381                 seq = new ArrayList<String>();
1382             }
1383             return this.seq;
1384         }
1385
1386         /**
1387          * Gets the value of the annotationColours property.
1388          *
1389          * @return
1390          *     possible object is
1391          *     {@link AnnotationColourScheme }
1392          *
1393          */
1394         public AnnotationColourScheme getAnnotationColours() {
1395             return annotationColours;
1396         }
1397
1398         /**
1399          * Sets the value of the annotationColours property.
1400          *
1401          * @param value
1402          *     allowed object is
1403          *     {@link AnnotationColourScheme }
1404          *
1405          */
1406         public void setAnnotationColours(AnnotationColourScheme value) {
1407             this.annotationColours = value;
1408         }
1409
1410         /**
1411          * Gets the value of the start property.
1412          *
1413          * @return
1414          *     possible object is
1415          *     {@link Integer }
1416          *
1417          */
1418         public Integer getStart() {
1419             return start;
1420         }
1421
1422         /**
1423          * Sets the value of the start property.
1424          *
1425          * @param value
1426          *     allowed object is
1427          *     {@link Integer }
1428          *
1429          */
1430         public void setStart(Integer value) {
1431             this.start = value;
1432         }
1433
1434         /**
1435          * Gets the value of the end property.
1436          *
1437          * @return
1438          *     possible object is
1439          *     {@link Integer }
1440          *
1441          */
1442         public Integer getEnd() {
1443             return end;
1444         }
1445
1446         /**
1447          * Sets the value of the end property.
1448          *
1449          * @param value
1450          *     allowed object is
1451          *     {@link Integer }
1452          *
1453          */
1454         public void setEnd(Integer value) {
1455             this.end = value;
1456         }
1457
1458         /**
1459          * Gets the value of the name property.
1460          *
1461          * @return
1462          *     possible object is
1463          *     {@link String }
1464          *
1465          */
1466         public String getName() {
1467             return name;
1468         }
1469
1470         /**
1471          * Sets the value of the name property.
1472          *
1473          * @param value
1474          *     allowed object is
1475          *     {@link String }
1476          *
1477          */
1478         public void setName(String value) {
1479             this.name = value;
1480         }
1481
1482         /**
1483          * Gets the value of the colour property.
1484          *
1485          * @return
1486          *     possible object is
1487          *     {@link String }
1488          *
1489          */
1490         public String getColour() {
1491             return colour;
1492         }
1493
1494         /**
1495          * Sets the value of the colour property.
1496          *
1497          * @param value
1498          *     allowed object is
1499          *     {@link String }
1500          *
1501          */
1502         public void setColour(String value) {
1503             this.colour = value;
1504         }
1505
1506         /**
1507          * Gets the value of the consThreshold property.
1508          *
1509          * @return
1510          *     possible object is
1511          *     {@link Integer }
1512          *
1513          */
1514         public Integer getConsThreshold() {
1515             return consThreshold;
1516         }
1517
1518         /**
1519          * Sets the value of the consThreshold property.
1520          *
1521          * @param value
1522          *     allowed object is
1523          *     {@link Integer }
1524          *
1525          */
1526         public void setConsThreshold(Integer value) {
1527             this.consThreshold = value;
1528         }
1529
1530         /**
1531          * Gets the value of the pidThreshold property.
1532          *
1533          * @return
1534          *     possible object is
1535          *     {@link Integer }
1536          *
1537          */
1538         public Integer getPidThreshold() {
1539             return pidThreshold;
1540         }
1541
1542         /**
1543          * Sets the value of the pidThreshold property.
1544          *
1545          * @param value
1546          *     allowed object is
1547          *     {@link Integer }
1548          *
1549          */
1550         public void setPidThreshold(Integer value) {
1551             this.pidThreshold = value;
1552         }
1553
1554         /**
1555          * Gets the value of the outlineColour property.
1556          *
1557          * @return
1558          *     possible object is
1559          *     {@link Integer }
1560          *
1561          */
1562         public Integer getOutlineColour() {
1563             return outlineColour;
1564         }
1565
1566         /**
1567          * Sets the value of the outlineColour property.
1568          *
1569          * @param value
1570          *     allowed object is
1571          *     {@link Integer }
1572          *
1573          */
1574         public void setOutlineColour(Integer value) {
1575             this.outlineColour = value;
1576         }
1577
1578         /**
1579          * Gets the value of the displayBoxes property.
1580          *
1581          * @return
1582          *     possible object is
1583          *     {@link Boolean }
1584          *
1585          */
1586         public Boolean isDisplayBoxes() {
1587             return displayBoxes;
1588         }
1589
1590         /**
1591          * Sets the value of the displayBoxes property.
1592          *
1593          * @param value
1594          *     allowed object is
1595          *     {@link Boolean }
1596          *
1597          */
1598         public void setDisplayBoxes(Boolean value) {
1599             this.displayBoxes = value;
1600         }
1601
1602         /**
1603          * Gets the value of the displayText property.
1604          *
1605          * @return
1606          *     possible object is
1607          *     {@link Boolean }
1608          *
1609          */
1610         public Boolean isDisplayText() {
1611             return displayText;
1612         }
1613
1614         /**
1615          * Sets the value of the displayText property.
1616          *
1617          * @param value
1618          *     allowed object is
1619          *     {@link Boolean }
1620          *
1621          */
1622         public void setDisplayText(Boolean value) {
1623             this.displayText = value;
1624         }
1625
1626         /**
1627          * Gets the value of the colourText property.
1628          *
1629          * @return
1630          *     possible object is
1631          *     {@link Boolean }
1632          *
1633          */
1634         public Boolean isColourText() {
1635             return colourText;
1636         }
1637
1638         /**
1639          * Sets the value of the colourText property.
1640          *
1641          * @param value
1642          *     allowed object is
1643          *     {@link Boolean }
1644          *
1645          */
1646         public void setColourText(Boolean value) {
1647             this.colourText = value;
1648         }
1649
1650         /**
1651          * Gets the value of the textCol1 property.
1652          *
1653          * @return
1654          *     possible object is
1655          *     {@link Integer }
1656          *
1657          */
1658         public Integer getTextCol1() {
1659             return textCol1;
1660         }
1661
1662         /**
1663          * Sets the value of the textCol1 property.
1664          *
1665          * @param value
1666          *     allowed object is
1667          *     {@link Integer }
1668          *
1669          */
1670         public void setTextCol1(Integer value) {
1671             this.textCol1 = value;
1672         }
1673
1674         /**
1675          * Gets the value of the textCol2 property.
1676          *
1677          * @return
1678          *     possible object is
1679          *     {@link Integer }
1680          *
1681          */
1682         public Integer getTextCol2() {
1683             return textCol2;
1684         }
1685
1686         /**
1687          * Sets the value of the textCol2 property.
1688          *
1689          * @param value
1690          *     allowed object is
1691          *     {@link Integer }
1692          *
1693          */
1694         public void setTextCol2(Integer value) {
1695             this.textCol2 = value;
1696         }
1697
1698         /**
1699          * Gets the value of the textColThreshold property.
1700          *
1701          * @return
1702          *     possible object is
1703          *     {@link Integer }
1704          *
1705          */
1706         public Integer getTextColThreshold() {
1707             return textColThreshold;
1708         }
1709
1710         /**
1711          * Sets the value of the textColThreshold property.
1712          *
1713          * @param value
1714          *     allowed object is
1715          *     {@link Integer }
1716          *
1717          */
1718         public void setTextColThreshold(Integer value) {
1719             this.textColThreshold = value;
1720         }
1721
1722         /**
1723          * Gets the value of the showUnconserved property.
1724          *
1725          * @return
1726          *     possible object is
1727          *     {@link Boolean }
1728          *
1729          */
1730         public Boolean isShowUnconserved() {
1731             return showUnconserved;
1732         }
1733
1734         /**
1735          * Sets the value of the showUnconserved property.
1736          *
1737          * @param value
1738          *     allowed object is
1739          *     {@link Boolean }
1740          *
1741          */
1742         public void setShowUnconserved(Boolean value) {
1743             this.showUnconserved = value;
1744         }
1745
1746         /**
1747          * Gets the value of the ignoreGapsinConsensus property.
1748          *
1749          * @return
1750          *     possible object is
1751          *     {@link Boolean }
1752          *
1753          */
1754         public boolean isIgnoreGapsinConsensus() {
1755             if (ignoreGapsinConsensus == null) {
1756                 return true;
1757             } else {
1758                 return ignoreGapsinConsensus;
1759             }
1760         }
1761
1762         /**
1763          * Sets the value of the ignoreGapsinConsensus property.
1764          *
1765          * @param value
1766          *     allowed object is
1767          *     {@link Boolean }
1768          *
1769          */
1770         public void setIgnoreGapsinConsensus(Boolean value) {
1771             this.ignoreGapsinConsensus = value;
1772         }
1773
1774         /**
1775          * Gets the value of the showConsensusHistogram property.
1776          *
1777          * @return
1778          *     possible object is
1779          *     {@link Boolean }
1780          *
1781          */
1782         public boolean isShowConsensusHistogram() {
1783             if (showConsensusHistogram == null) {
1784                 return true;
1785             } else {
1786                 return showConsensusHistogram;
1787             }
1788         }
1789
1790         /**
1791          * Sets the value of the showConsensusHistogram property.
1792          *
1793          * @param value
1794          *     allowed object is
1795          *     {@link Boolean }
1796          *
1797          */
1798         public void setShowConsensusHistogram(Boolean value) {
1799             this.showConsensusHistogram = value;
1800         }
1801
1802         /**
1803          * Gets the value of the showSequenceLogo property.
1804          *
1805          * @return
1806          *     possible object is
1807          *     {@link Boolean }
1808          *
1809          */
1810         public boolean isShowSequenceLogo() {
1811             if (showSequenceLogo == null) {
1812                 return false;
1813             } else {
1814                 return showSequenceLogo;
1815             }
1816         }
1817
1818         /**
1819          * Sets the value of the showSequenceLogo property.
1820          *
1821          * @param value
1822          *     allowed object is
1823          *     {@link Boolean }
1824          *
1825          */
1826         public void setShowSequenceLogo(Boolean value) {
1827             this.showSequenceLogo = value;
1828         }
1829
1830         /**
1831          * Gets the value of the normaliseSequenceLogo property.
1832          *
1833          * @return
1834          *     possible object is
1835          *     {@link Boolean }
1836          *
1837          */
1838         public boolean isNormaliseSequenceLogo() {
1839             if (normaliseSequenceLogo == null) {
1840                 return false;
1841             } else {
1842                 return normaliseSequenceLogo;
1843             }
1844         }
1845
1846         /**
1847          * Sets the value of the normaliseSequenceLogo property.
1848          *
1849          * @param value
1850          *     allowed object is
1851          *     {@link Boolean }
1852          *
1853          */
1854         public void setNormaliseSequenceLogo(Boolean value) {
1855             this.normaliseSequenceLogo = value;
1856         }
1857
1858         /**
1859          * Gets the value of the id property.
1860          *
1861          * @return
1862          *     possible object is
1863          *     {@link String }
1864          *
1865          */
1866         public String getId() {
1867             return id;
1868         }
1869
1870         /**
1871          * Sets the value of the id property.
1872          *
1873          * @param value
1874          *     allowed object is
1875          *     {@link String }
1876          *
1877          */
1878         public void setId(String value) {
1879             this.id = value;
1880         }
1881
1882     }
1883
1884
1885     /**
1886      * <p>Java class for anonymous complex type.
1887      *
1888      * <p>The following schema fragment specifies the expected content contained within this class.
1889      *
1890      * <pre>
1891      * &lt;complexType>
1892      *   &lt;complexContent>
1893      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1894      *       &lt;sequence>
1895      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1896      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1897      *           &lt;complexType>
1898      *             &lt;complexContent>
1899      *               &lt;extension base="{www.jalview.org}pdbentry">
1900      *                 &lt;sequence>
1901      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1902      *                     &lt;complexType>
1903      *                       &lt;simpleContent>
1904      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1905      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1906      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1907      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1908      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1909      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1910      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1911      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1912      *                         &lt;/extension>
1913      *                       &lt;/simpleContent>
1914      *                     &lt;/complexType>
1915      *                   &lt;/element>
1916      *                 &lt;/sequence>
1917      *               &lt;/extension>
1918      *             &lt;/complexContent>
1919      *           &lt;/complexType>
1920      *         &lt;/element>
1921      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1922      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1923      *           &lt;complexType>
1924      *             &lt;complexContent>
1925      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1926      *                 &lt;sequence>
1927      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1928      *                     &lt;complexType>
1929      *                       &lt;complexContent>
1930      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1931      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1932      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1933      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1934      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1935      *                         &lt;/restriction>
1936      *                       &lt;/complexContent>
1937      *                     &lt;/complexType>
1938      *                   &lt;/element>
1939      *                 &lt;/sequence>
1940      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1941      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1942      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1943      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1944      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1945      *               &lt;/restriction>
1946      *             &lt;/complexContent>
1947      *           &lt;/complexType>
1948      *         &lt;/element>
1949      *         &lt;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
1950      *       &lt;/sequence>
1951      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1952      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1953      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1954      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1955      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1956      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1957      *     &lt;/restriction>
1958      *   &lt;/complexContent>
1959      * &lt;/complexType>
1960      * </pre>
1961      *
1962      *
1963      */
1964     @XmlAccessorType(XmlAccessType.FIELD)
1965     @XmlType(name = "", propOrder = {
1966         "features",
1967         "pdbids",
1968         "hiddenSequences",
1969         "rnaViewer",
1970         "hmmerProfile"
1971     })
1972     public static class JSeq {
1973
1974         @XmlElement(namespace = "www.jalview.org")
1975         protected List<Feature> features;
1976         @XmlElement(namespace = "www.jalview.org")
1977         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1978         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1979         protected List<Integer> hiddenSequences;
1980         @XmlElement(namespace = "www.jalview.org")
1981         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1982         @XmlElement(namespace = "www.jalview.org")
1983         protected String hmmerProfile;
1984         @XmlAttribute(name = "colour")
1985         protected Integer colour;
1986         @XmlAttribute(name = "start", required = true)
1987         protected int start;
1988         @XmlAttribute(name = "end", required = true)
1989         protected int end;
1990         @XmlAttribute(name = "id", required = true)
1991         protected String id;
1992         @XmlAttribute(name = "hidden")
1993         protected Boolean hidden;
1994         @XmlAttribute(name = "viewreference")
1995         protected Boolean viewreference;
1996
1997         /**
1998          * Gets the value of the features property.
1999          *
2000          * <p>
2001          * This accessor method returns a reference to the live list,
2002          * not a snapshot. Therefore any modification you make to the
2003          * returned list will be present inside the JAXB object.
2004          * This is why there is not a <CODE>set</CODE> method for the features property.
2005          *
2006          * <p>
2007          * For example, to add a new item, do as follows:
2008          * <pre>
2009          *    getFeatures().add(newItem);
2010          * </pre>
2011          *
2012          *
2013          * <p>
2014          * Objects of the following type(s) are allowed in the list
2015          * {@link Feature }
2016          *
2017          *
2018          */
2019         public List<Feature> getFeatures() {
2020             if (features == null) {
2021                 features = new ArrayList<Feature>();
2022             }
2023             return this.features;
2024         }
2025
2026         /**
2027          * Gets the value of the pdbids property.
2028          *
2029          * <p>
2030          * This accessor method returns a reference to the live list,
2031          * not a snapshot. Therefore any modification you make to the
2032          * returned list will be present inside the JAXB object.
2033          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2034          *
2035          * <p>
2036          * For example, to add a new item, do as follows:
2037          * <pre>
2038          *    getPdbids().add(newItem);
2039          * </pre>
2040          *
2041          *
2042          * <p>
2043          * Objects of the following type(s) are allowed in the list
2044          * {@link JalviewModel.JSeq.Pdbids }
2045          *
2046          *
2047          */
2048         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2049             if (pdbids == null) {
2050                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2051             }
2052             return this.pdbids;
2053         }
2054
2055         /**
2056          * Gets the value of the hiddenSequences property.
2057          *
2058          * <p>
2059          * This accessor method returns a reference to the live list,
2060          * not a snapshot. Therefore any modification you make to the
2061          * returned list will be present inside the JAXB object.
2062          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2063          *
2064          * <p>
2065          * For example, to add a new item, do as follows:
2066          * <pre>
2067          *    getHiddenSequences().add(newItem);
2068          * </pre>
2069          *
2070          *
2071          * <p>
2072          * Objects of the following type(s) are allowed in the list
2073          * {@link Integer }
2074          *
2075          *
2076          */
2077         public List<Integer> getHiddenSequences() {
2078             if (hiddenSequences == null) {
2079                 hiddenSequences = new ArrayList<Integer>();
2080             }
2081             return this.hiddenSequences;
2082         }
2083
2084         /**
2085          * Gets the value of the rnaViewer property.
2086          *
2087          * <p>
2088          * This accessor method returns a reference to the live list,
2089          * not a snapshot. Therefore any modification you make to the
2090          * returned list will be present inside the JAXB object.
2091          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2092          *
2093          * <p>
2094          * For example, to add a new item, do as follows:
2095          * <pre>
2096          *    getRnaViewer().add(newItem);
2097          * </pre>
2098          *
2099          *
2100          * <p>
2101          * Objects of the following type(s) are allowed in the list
2102          * {@link JalviewModel.JSeq.RnaViewer }
2103          *
2104          *
2105          */
2106         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2107             if (rnaViewer == null) {
2108                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2109             }
2110             return this.rnaViewer;
2111         }
2112
2113         /**
2114          * Gets the value of the hmmerProfile property.
2115          *
2116          * @return
2117          *     possible object is
2118          *     {@link String }
2119          *
2120          */
2121         public String getHmmerProfile() {
2122             return hmmerProfile;
2123         }
2124
2125         /**
2126          * Sets the value of the hmmerProfile property.
2127          *
2128          * @param value
2129          *     allowed object is
2130          *     {@link String }
2131          *
2132          */
2133         public void setHmmerProfile(String value) {
2134             this.hmmerProfile = value;
2135         }
2136
2137         /**
2138          * Gets the value of the colour property.
2139          *
2140          * @return
2141          *     possible object is
2142          *     {@link Integer }
2143          *
2144          */
2145         public Integer getColour() {
2146             return colour;
2147         }
2148
2149         /**
2150          * Sets the value of the colour property.
2151          *
2152          * @param value
2153          *     allowed object is
2154          *     {@link Integer }
2155          *
2156          */
2157         public void setColour(Integer value) {
2158             this.colour = value;
2159         }
2160
2161         /**
2162          * Gets the value of the start property.
2163          *
2164          */
2165         public int getStart() {
2166             return start;
2167         }
2168
2169         /**
2170          * Sets the value of the start property.
2171          *
2172          */
2173         public void setStart(int value) {
2174             this.start = value;
2175         }
2176
2177         /**
2178          * Gets the value of the end property.
2179          *
2180          */
2181         public int getEnd() {
2182             return end;
2183         }
2184
2185         /**
2186          * Sets the value of the end property.
2187          *
2188          */
2189         public void setEnd(int value) {
2190             this.end = value;
2191         }
2192
2193         /**
2194          * Gets the value of the id property.
2195          *
2196          * @return
2197          *     possible object is
2198          *     {@link String }
2199          *
2200          */
2201         public String getId() {
2202             return id;
2203         }
2204
2205         /**
2206          * Sets the value of the id property.
2207          *
2208          * @param value
2209          *     allowed object is
2210          *     {@link String }
2211          *
2212          */
2213         public void setId(String value) {
2214             this.id = value;
2215         }
2216
2217         /**
2218          * Gets the value of the hidden property.
2219          *
2220          * @return
2221          *     possible object is
2222          *     {@link Boolean }
2223          *
2224          */
2225         public Boolean isHidden() {
2226             return hidden;
2227         }
2228
2229         /**
2230          * Sets the value of the hidden property.
2231          *
2232          * @param value
2233          *     allowed object is
2234          *     {@link Boolean }
2235          *
2236          */
2237         public void setHidden(Boolean value) {
2238             this.hidden = value;
2239         }
2240
2241         /**
2242          * Gets the value of the viewreference property.
2243          *
2244          * @return
2245          *     possible object is
2246          *     {@link Boolean }
2247          *
2248          */
2249         public Boolean isViewreference() {
2250             return viewreference;
2251         }
2252
2253         /**
2254          * Sets the value of the viewreference property.
2255          *
2256          * @param value
2257          *     allowed object is
2258          *     {@link Boolean }
2259          *
2260          */
2261         public void setViewreference(Boolean value) {
2262             this.viewreference = value;
2263         }
2264
2265
2266         /**
2267          * <p>Java class for anonymous complex type.
2268          *
2269          * <p>The following schema fragment specifies the expected content contained within this class.
2270          *
2271          * <pre>
2272          * &lt;complexType>
2273          *   &lt;complexContent>
2274          *     &lt;extension base="{www.jalview.org}pdbentry">
2275          *       &lt;sequence>
2276          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2277          *           &lt;complexType>
2278          *             &lt;simpleContent>
2279          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2280          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2281          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2282          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2283          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2284          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2285          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2286          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2287          *               &lt;/extension>
2288          *             &lt;/simpleContent>
2289          *           &lt;/complexType>
2290          *         &lt;/element>
2291          *       &lt;/sequence>
2292          *     &lt;/extension>
2293          *   &lt;/complexContent>
2294          * &lt;/complexType>
2295          * </pre>
2296          *
2297          *
2298          */
2299         @XmlAccessorType(XmlAccessType.FIELD)
2300         @XmlType(name = "", propOrder = {
2301             "structureState"
2302         })
2303         public static class Pdbids
2304             extends Pdbentry
2305         {
2306
2307             @XmlElement(namespace = "www.jalview.org")
2308             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2309
2310             /**
2311              * Gets the value of the structureState property.
2312              *
2313              * <p>
2314              * This accessor method returns a reference to the live list,
2315              * not a snapshot. Therefore any modification you make to the
2316              * returned list will be present inside the JAXB object.
2317              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2318              *
2319              * <p>
2320              * For example, to add a new item, do as follows:
2321              * <pre>
2322              *    getStructureState().add(newItem);
2323              * </pre>
2324              *
2325              *
2326              * <p>
2327              * Objects of the following type(s) are allowed in the list
2328              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2329              *
2330              *
2331              */
2332             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2333                 if (structureState == null) {
2334                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2335                 }
2336                 return this.structureState;
2337             }
2338
2339
2340             /**
2341              * <p>Java class for anonymous complex type.
2342              *
2343              * <p>The following schema fragment specifies the expected content contained within this class.
2344              *
2345              * <pre>
2346              * &lt;complexType>
2347              *   &lt;simpleContent>
2348              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2349              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2350              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2351              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2352              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2353              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2354              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2355              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2356              *     &lt;/extension>
2357              *   &lt;/simpleContent>
2358              * &lt;/complexType>
2359              * </pre>
2360              *
2361              *
2362              */
2363             @XmlAccessorType(XmlAccessType.FIELD)
2364             @XmlType(name = "", propOrder = {
2365                 "value"
2366             })
2367             public static class StructureState {
2368
2369                 @XmlValue
2370                 protected String value;
2371                 @XmlAttribute(name = "visible")
2372                 protected Boolean visible;
2373                 @XmlAttribute(name = "viewId")
2374                 protected String viewId;
2375                 @XmlAttribute(name = "alignwithAlignPanel")
2376                 protected Boolean alignwithAlignPanel;
2377                 @XmlAttribute(name = "colourwithAlignPanel")
2378                 protected Boolean colourwithAlignPanel;
2379                 @XmlAttribute(name = "colourByJmol")
2380                 protected Boolean colourByJmol;
2381                 @XmlAttribute(name = "type")
2382                 protected String type;
2383                 @XmlAttribute(name = "width")
2384                 protected Integer width;
2385                 @XmlAttribute(name = "height")
2386                 protected Integer height;
2387                 @XmlAttribute(name = "xpos")
2388                 protected Integer xpos;
2389                 @XmlAttribute(name = "ypos")
2390                 protected Integer ypos;
2391
2392                 /**
2393                  * Gets the value of the value property.
2394                  *
2395                  * @return
2396                  *     possible object is
2397                  *     {@link String }
2398                  *
2399                  */
2400                 public String getValue() {
2401                     return value;
2402                 }
2403
2404                 /**
2405                  * Sets the value of the value property.
2406                  *
2407                  * @param value
2408                  *     allowed object is
2409                  *     {@link String }
2410                  *
2411                  */
2412                 public void setValue(String value) {
2413                     this.value = value;
2414                 }
2415
2416                 /**
2417                  * Gets the value of the visible property.
2418                  *
2419                  * @return
2420                  *     possible object is
2421                  *     {@link Boolean }
2422                  *
2423                  */
2424                 public Boolean isVisible() {
2425                     return visible;
2426                 }
2427
2428                 /**
2429                  * Sets the value of the visible property.
2430                  *
2431                  * @param value
2432                  *     allowed object is
2433                  *     {@link Boolean }
2434                  *
2435                  */
2436                 public void setVisible(Boolean value) {
2437                     this.visible = value;
2438                 }
2439
2440                 /**
2441                  * Gets the value of the viewId property.
2442                  *
2443                  * @return
2444                  *     possible object is
2445                  *     {@link String }
2446                  *
2447                  */
2448                 public String getViewId() {
2449                     return viewId;
2450                 }
2451
2452                 /**
2453                  * Sets the value of the viewId property.
2454                  *
2455                  * @param value
2456                  *     allowed object is
2457                  *     {@link String }
2458                  *
2459                  */
2460                 public void setViewId(String value) {
2461                     this.viewId = value;
2462                 }
2463
2464                 /**
2465                  * Gets the value of the alignwithAlignPanel property.
2466                  *
2467                  * @return
2468                  *     possible object is
2469                  *     {@link Boolean }
2470                  *
2471                  */
2472                 public boolean isAlignwithAlignPanel() {
2473                     if (alignwithAlignPanel == null) {
2474                         return true;
2475                     } else {
2476                         return alignwithAlignPanel;
2477                     }
2478                 }
2479
2480                 /**
2481                  * Sets the value of the alignwithAlignPanel property.
2482                  *
2483                  * @param value
2484                  *     allowed object is
2485                  *     {@link Boolean }
2486                  *
2487                  */
2488                 public void setAlignwithAlignPanel(Boolean value) {
2489                     this.alignwithAlignPanel = value;
2490                 }
2491
2492                 /**
2493                  * Gets the value of the colourwithAlignPanel property.
2494                  *
2495                  * @return
2496                  *     possible object is
2497                  *     {@link Boolean }
2498                  *
2499                  */
2500                 public boolean isColourwithAlignPanel() {
2501                     if (colourwithAlignPanel == null) {
2502                         return false;
2503                     } else {
2504                         return colourwithAlignPanel;
2505                     }
2506                 }
2507
2508                 /**
2509                  * Sets the value of the colourwithAlignPanel property.
2510                  *
2511                  * @param value
2512                  *     allowed object is
2513                  *     {@link Boolean }
2514                  *
2515                  */
2516                 public void setColourwithAlignPanel(Boolean value) {
2517                     this.colourwithAlignPanel = value;
2518                 }
2519
2520                 /**
2521                  * Gets the value of the colourByJmol property.
2522                  *
2523                  * @return
2524                  *     possible object is
2525                  *     {@link Boolean }
2526                  *
2527                  */
2528                 public boolean isColourByJmol() {
2529                     if (colourByJmol == null) {
2530                         return true;
2531                     } else {
2532                         return colourByJmol;
2533                     }
2534                 }
2535
2536                 /**
2537                  * Sets the value of the colourByJmol property.
2538                  *
2539                  * @param value
2540                  *     allowed object is
2541                  *     {@link Boolean }
2542                  *
2543                  */
2544                 public void setColourByJmol(Boolean value) {
2545                     this.colourByJmol = value;
2546                 }
2547
2548                 /**
2549                  * Gets the value of the type property.
2550                  *
2551                  * @return
2552                  *     possible object is
2553                  *     {@link String }
2554                  *
2555                  */
2556                 public String getType() {
2557                     return type;
2558                 }
2559
2560                 /**
2561                  * Sets the value of the type property.
2562                  *
2563                  * @param value
2564                  *     allowed object is
2565                  *     {@link String }
2566                  *
2567                  */
2568                 public void setType(String value) {
2569                     this.type = value;
2570                 }
2571
2572                 /**
2573                  * Gets the value of the width property.
2574                  *
2575                  * @return
2576                  *     possible object is
2577                  *     {@link Integer }
2578                  *
2579                  */
2580                 public Integer getWidth() {
2581                     return width;
2582                 }
2583
2584                 /**
2585                  * Sets the value of the width property.
2586                  *
2587                  * @param value
2588                  *     allowed object is
2589                  *     {@link Integer }
2590                  *
2591                  */
2592                 public void setWidth(Integer value) {
2593                     this.width = value;
2594                 }
2595
2596                 /**
2597                  * Gets the value of the height property.
2598                  *
2599                  * @return
2600                  *     possible object is
2601                  *     {@link Integer }
2602                  *
2603                  */
2604                 public Integer getHeight() {
2605                     return height;
2606                 }
2607
2608                 /**
2609                  * Sets the value of the height property.
2610                  *
2611                  * @param value
2612                  *     allowed object is
2613                  *     {@link Integer }
2614                  *
2615                  */
2616                 public void setHeight(Integer value) {
2617                     this.height = value;
2618                 }
2619
2620                 /**
2621                  * Gets the value of the xpos property.
2622                  *
2623                  * @return
2624                  *     possible object is
2625                  *     {@link Integer }
2626                  *
2627                  */
2628                 public Integer getXpos() {
2629                     return xpos;
2630                 }
2631
2632                 /**
2633                  * Sets the value of the xpos property.
2634                  *
2635                  * @param value
2636                  *     allowed object is
2637                  *     {@link Integer }
2638                  *
2639                  */
2640                 public void setXpos(Integer value) {
2641                     this.xpos = value;
2642                 }
2643
2644                 /**
2645                  * Gets the value of the ypos property.
2646                  *
2647                  * @return
2648                  *     possible object is
2649                  *     {@link Integer }
2650                  *
2651                  */
2652                 public Integer getYpos() {
2653                     return ypos;
2654                 }
2655
2656                 /**
2657                  * Sets the value of the ypos property.
2658                  *
2659                  * @param value
2660                  *     allowed object is
2661                  *     {@link Integer }
2662                  *
2663                  */
2664                 public void setYpos(Integer value) {
2665                     this.ypos = value;
2666                 }
2667
2668             }
2669
2670         }
2671
2672
2673         /**
2674          * <p>Java class for anonymous complex type.
2675          *
2676          * <p>The following schema fragment specifies the expected content contained within this class.
2677          *
2678          * <pre>
2679          * &lt;complexType>
2680          *   &lt;complexContent>
2681          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2682          *       &lt;sequence>
2683          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2684          *           &lt;complexType>
2685          *             &lt;complexContent>
2686          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2687          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2688          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2689          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2690          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2691          *               &lt;/restriction>
2692          *             &lt;/complexContent>
2693          *           &lt;/complexType>
2694          *         &lt;/element>
2695          *       &lt;/sequence>
2696          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2697          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2698          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2699          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2700          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2701          *     &lt;/restriction>
2702          *   &lt;/complexContent>
2703          * &lt;/complexType>
2704          * </pre>
2705          *
2706          *
2707          */
2708         @XmlAccessorType(XmlAccessType.FIELD)
2709         @XmlType(name = "", propOrder = {
2710             "secondaryStructure"
2711         })
2712         public static class RnaViewer {
2713
2714             @XmlElement(namespace = "www.jalview.org", required = true)
2715             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2716             @XmlAttribute(name = "title")
2717             protected String title;
2718             @XmlAttribute(name = "viewId")
2719             protected String viewId;
2720             @XmlAttribute(name = "dividerLocation")
2721             protected Integer dividerLocation;
2722             @XmlAttribute(name = "selectedRna")
2723             protected Integer selectedRna;
2724             @XmlAttribute(name = "width")
2725             protected Integer width;
2726             @XmlAttribute(name = "height")
2727             protected Integer height;
2728             @XmlAttribute(name = "xpos")
2729             protected Integer xpos;
2730             @XmlAttribute(name = "ypos")
2731             protected Integer ypos;
2732
2733             /**
2734              * Gets the value of the secondaryStructure property.
2735              *
2736              * <p>
2737              * This accessor method returns a reference to the live list,
2738              * not a snapshot. Therefore any modification you make to the
2739              * returned list will be present inside the JAXB object.
2740              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2741              *
2742              * <p>
2743              * For example, to add a new item, do as follows:
2744              * <pre>
2745              *    getSecondaryStructure().add(newItem);
2746              * </pre>
2747              *
2748              *
2749              * <p>
2750              * Objects of the following type(s) are allowed in the list
2751              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2752              *
2753              *
2754              */
2755             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2756                 if (secondaryStructure == null) {
2757                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2758                 }
2759                 return this.secondaryStructure;
2760             }
2761
2762             /**
2763              * Gets the value of the title property.
2764              *
2765              * @return
2766              *     possible object is
2767              *     {@link String }
2768              *
2769              */
2770             public String getTitle() {
2771                 return title;
2772             }
2773
2774             /**
2775              * Sets the value of the title property.
2776              *
2777              * @param value
2778              *     allowed object is
2779              *     {@link String }
2780              *
2781              */
2782             public void setTitle(String value) {
2783                 this.title = value;
2784             }
2785
2786             /**
2787              * Gets the value of the viewId property.
2788              *
2789              * @return
2790              *     possible object is
2791              *     {@link String }
2792              *
2793              */
2794             public String getViewId() {
2795                 return viewId;
2796             }
2797
2798             /**
2799              * Sets the value of the viewId property.
2800              *
2801              * @param value
2802              *     allowed object is
2803              *     {@link String }
2804              *
2805              */
2806             public void setViewId(String value) {
2807                 this.viewId = value;
2808             }
2809
2810             /**
2811              * Gets the value of the dividerLocation property.
2812              *
2813              * @return
2814              *     possible object is
2815              *     {@link Integer }
2816              *
2817              */
2818             public Integer getDividerLocation() {
2819                 return dividerLocation;
2820             }
2821
2822             /**
2823              * Sets the value of the dividerLocation property.
2824              *
2825              * @param value
2826              *     allowed object is
2827              *     {@link Integer }
2828              *
2829              */
2830             public void setDividerLocation(Integer value) {
2831                 this.dividerLocation = value;
2832             }
2833
2834             /**
2835              * Gets the value of the selectedRna property.
2836              *
2837              * @return
2838              *     possible object is
2839              *     {@link Integer }
2840              *
2841              */
2842             public Integer getSelectedRna() {
2843                 return selectedRna;
2844             }
2845
2846             /**
2847              * Sets the value of the selectedRna property.
2848              *
2849              * @param value
2850              *     allowed object is
2851              *     {@link Integer }
2852              *
2853              */
2854             public void setSelectedRna(Integer value) {
2855                 this.selectedRna = value;
2856             }
2857
2858             /**
2859              * Gets the value of the width property.
2860              *
2861              * @return
2862              *     possible object is
2863              *     {@link Integer }
2864              *
2865              */
2866             public Integer getWidth() {
2867                 return width;
2868             }
2869
2870             /**
2871              * Sets the value of the width property.
2872              *
2873              * @param value
2874              *     allowed object is
2875              *     {@link Integer }
2876              *
2877              */
2878             public void setWidth(Integer value) {
2879                 this.width = value;
2880             }
2881
2882             /**
2883              * Gets the value of the height property.
2884              *
2885              * @return
2886              *     possible object is
2887              *     {@link Integer }
2888              *
2889              */
2890             public Integer getHeight() {
2891                 return height;
2892             }
2893
2894             /**
2895              * Sets the value of the height property.
2896              *
2897              * @param value
2898              *     allowed object is
2899              *     {@link Integer }
2900              *
2901              */
2902             public void setHeight(Integer value) {
2903                 this.height = value;
2904             }
2905
2906             /**
2907              * Gets the value of the xpos property.
2908              *
2909              * @return
2910              *     possible object is
2911              *     {@link Integer }
2912              *
2913              */
2914             public Integer getXpos() {
2915                 return xpos;
2916             }
2917
2918             /**
2919              * Sets the value of the xpos property.
2920              *
2921              * @param value
2922              *     allowed object is
2923              *     {@link Integer }
2924              *
2925              */
2926             public void setXpos(Integer value) {
2927                 this.xpos = value;
2928             }
2929
2930             /**
2931              * Gets the value of the ypos property.
2932              *
2933              * @return
2934              *     possible object is
2935              *     {@link Integer }
2936              *
2937              */
2938             public Integer getYpos() {
2939                 return ypos;
2940             }
2941
2942             /**
2943              * Sets the value of the ypos property.
2944              *
2945              * @param value
2946              *     allowed object is
2947              *     {@link Integer }
2948              *
2949              */
2950             public void setYpos(Integer value) {
2951                 this.ypos = value;
2952             }
2953
2954
2955             /**
2956              * <p>Java class for anonymous complex type.
2957              *
2958              * <p>The following schema fragment specifies the expected content contained within this class.
2959              *
2960              * <pre>
2961              * &lt;complexType>
2962              *   &lt;complexContent>
2963              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2964              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2965              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2966              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2967              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2968              *     &lt;/restriction>
2969              *   &lt;/complexContent>
2970              * &lt;/complexType>
2971              * </pre>
2972              *
2973              *
2974              */
2975             @XmlAccessorType(XmlAccessType.FIELD)
2976             @XmlType(name = "")
2977             public static class SecondaryStructure {
2978
2979                 @XmlAttribute(name = "title")
2980                 protected String title;
2981                 @XmlAttribute(name = "annotationId", required = true)
2982                 protected String annotationId;
2983                 @XmlAttribute(name = "gapped")
2984                 protected Boolean gapped;
2985                 @XmlAttribute(name = "viewerState")
2986                 protected String viewerState;
2987
2988                 /**
2989                  * Gets the value of the title property.
2990                  *
2991                  * @return
2992                  *     possible object is
2993                  *     {@link String }
2994                  *
2995                  */
2996                 public String getTitle() {
2997                     return title;
2998                 }
2999
3000                 /**
3001                  * Sets the value of the title property.
3002                  *
3003                  * @param value
3004                  *     allowed object is
3005                  *     {@link String }
3006                  *
3007                  */
3008                 public void setTitle(String value) {
3009                     this.title = value;
3010                 }
3011
3012                 /**
3013                  * Gets the value of the annotationId property.
3014                  *
3015                  * @return
3016                  *     possible object is
3017                  *     {@link String }
3018                  *
3019                  */
3020                 public String getAnnotationId() {
3021                     return annotationId;
3022                 }
3023
3024                 /**
3025                  * Sets the value of the annotationId property.
3026                  *
3027                  * @param value
3028                  *     allowed object is
3029                  *     {@link String }
3030                  *
3031                  */
3032                 public void setAnnotationId(String value) {
3033                     this.annotationId = value;
3034                 }
3035
3036                 /**
3037                  * Gets the value of the gapped property.
3038                  *
3039                  * @return
3040                  *     possible object is
3041                  *     {@link Boolean }
3042                  *
3043                  */
3044                 public Boolean isGapped() {
3045                     return gapped;
3046                 }
3047
3048                 /**
3049                  * Sets the value of the gapped property.
3050                  *
3051                  * @param value
3052                  *     allowed object is
3053                  *     {@link Boolean }
3054                  *
3055                  */
3056                 public void setGapped(Boolean value) {
3057                     this.gapped = value;
3058                 }
3059
3060                 /**
3061                  * Gets the value of the viewerState property.
3062                  *
3063                  * @return
3064                  *     possible object is
3065                  *     {@link String }
3066                  *
3067                  */
3068                 public String getViewerState() {
3069                     return viewerState;
3070                 }
3071
3072                 /**
3073                  * Sets the value of the viewerState property.
3074                  *
3075                  * @param value
3076                  *     allowed object is
3077                  *     {@link String }
3078                  *
3079                  */
3080                 public void setViewerState(String value) {
3081                     this.viewerState = value;
3082                 }
3083
3084             }
3085
3086         }
3087
3088     }
3089
3090
3091     /**
3092      * <p>Java class for anonymous complex type.
3093      *
3094      * <p>The following schema fragment specifies the expected content contained within this class.
3095      *
3096      * <pre>
3097      * &lt;complexType>
3098      *   &lt;complexContent>
3099      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3100      *       &lt;sequence>
3101      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3102      *           &lt;complexType>
3103      *             &lt;complexContent>
3104      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3105      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3106      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3107      *               &lt;/restriction>
3108      *             &lt;/complexContent>
3109      *           &lt;/complexType>
3110      *         &lt;/element>
3111      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3112      *           &lt;complexType>
3113      *             &lt;complexContent>
3114      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3115      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3116      *               &lt;/restriction>
3117      *             &lt;/complexContent>
3118      *           &lt;/complexType>
3119      *         &lt;/element>
3120      *         &lt;element name="seqPointMin">
3121      *           &lt;complexType>
3122      *             &lt;complexContent>
3123      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3124      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3125      *               &lt;/restriction>
3126      *             &lt;/complexContent>
3127      *           &lt;/complexType>
3128      *         &lt;/element>
3129      *         &lt;element name="seqPointMax">
3130      *           &lt;complexType>
3131      *             &lt;complexContent>
3132      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3133      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3134      *               &lt;/restriction>
3135      *             &lt;/complexContent>
3136      *           &lt;/complexType>
3137      *         &lt;/element>
3138      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3139      *       &lt;/sequence>
3140      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3141      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3142      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3143      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3144      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3145      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3146      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3147      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3148      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3149      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3150      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3151      *     &lt;/restriction>
3152      *   &lt;/complexContent>
3153      * &lt;/complexType>
3154      * </pre>
3155      *
3156      *
3157      */
3158     @XmlAccessorType(XmlAccessType.FIELD)
3159     @XmlType(name = "", propOrder = {
3160         "sequencePoint",
3161         "axis",
3162         "seqPointMin",
3163         "seqPointMax",
3164         "pcaData"
3165     })
3166     public static class PcaViewer {
3167
3168         @XmlElement(namespace = "www.jalview.org", required = true)
3169         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3170         @XmlElement(namespace = "www.jalview.org", required = true)
3171         protected List<JalviewModel.PcaViewer.Axis> axis;
3172         @XmlElement(namespace = "www.jalview.org", required = true)
3173         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3174         @XmlElement(namespace = "www.jalview.org", required = true)
3175         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3176         @XmlElement(namespace = "www.jalview.org", required = true)
3177         protected PcaDataType pcaData;
3178         @XmlAttribute(name = "title")
3179         protected String title;
3180         @XmlAttribute(name = "scoreModelName")
3181         protected String scoreModelName;
3182         @XmlAttribute(name = "xDim")
3183         protected Integer xDim;
3184         @XmlAttribute(name = "yDim")
3185         protected Integer yDim;
3186         @XmlAttribute(name = "zDim")
3187         protected Integer zDim;
3188         @XmlAttribute(name = "bgColour")
3189         protected Integer bgColour;
3190         @XmlAttribute(name = "scaleFactor")
3191         protected Float scaleFactor;
3192         @XmlAttribute(name = "showLabels")
3193         protected Boolean showLabels;
3194         @XmlAttribute(name = "linkToAllViews")
3195         protected Boolean linkToAllViews;
3196         @XmlAttribute(name = "width")
3197         protected Integer width;
3198         @XmlAttribute(name = "height")
3199         protected Integer height;
3200         @XmlAttribute(name = "xpos")
3201         protected Integer xpos;
3202         @XmlAttribute(name = "ypos")
3203         protected Integer ypos;
3204         @XmlAttribute(name = "includeGaps")
3205         protected Boolean includeGaps;
3206         @XmlAttribute(name = "matchGaps")
3207         protected Boolean matchGaps;
3208         @XmlAttribute(name = "includeGappedColumns")
3209         protected Boolean includeGappedColumns;
3210         @XmlAttribute(name = "denominateByShortestLength")
3211         protected Boolean denominateByShortestLength;
3212
3213         /**
3214          * Gets the value of the sequencePoint property.
3215          *
3216          * <p>
3217          * This accessor method returns a reference to the live list,
3218          * not a snapshot. Therefore any modification you make to the
3219          * returned list will be present inside the JAXB object.
3220          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3221          *
3222          * <p>
3223          * For example, to add a new item, do as follows:
3224          * <pre>
3225          *    getSequencePoint().add(newItem);
3226          * </pre>
3227          *
3228          *
3229          * <p>
3230          * Objects of the following type(s) are allowed in the list
3231          * {@link JalviewModel.PcaViewer.SequencePoint }
3232          *
3233          *
3234          */
3235         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3236             if (sequencePoint == null) {
3237                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3238             }
3239             return this.sequencePoint;
3240         }
3241
3242         /**
3243          * Gets the value of the axis property.
3244          *
3245          * <p>
3246          * This accessor method returns a reference to the live list,
3247          * not a snapshot. Therefore any modification you make to the
3248          * returned list will be present inside the JAXB object.
3249          * This is why there is not a <CODE>set</CODE> method for the axis property.
3250          *
3251          * <p>
3252          * For example, to add a new item, do as follows:
3253          * <pre>
3254          *    getAxis().add(newItem);
3255          * </pre>
3256          *
3257          *
3258          * <p>
3259          * Objects of the following type(s) are allowed in the list
3260          * {@link JalviewModel.PcaViewer.Axis }
3261          *
3262          *
3263          */
3264         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3265             if (axis == null) {
3266                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3267             }
3268             return this.axis;
3269         }
3270
3271         /**
3272          * Gets the value of the seqPointMin property.
3273          *
3274          * @return
3275          *     possible object is
3276          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3277          *
3278          */
3279         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3280             return seqPointMin;
3281         }
3282
3283         /**
3284          * Sets the value of the seqPointMin property.
3285          *
3286          * @param value
3287          *     allowed object is
3288          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3289          *
3290          */
3291         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3292             this.seqPointMin = value;
3293         }
3294
3295         /**
3296          * Gets the value of the seqPointMax property.
3297          *
3298          * @return
3299          *     possible object is
3300          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3301          *
3302          */
3303         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3304             return seqPointMax;
3305         }
3306
3307         /**
3308          * Sets the value of the seqPointMax property.
3309          *
3310          * @param value
3311          *     allowed object is
3312          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3313          *
3314          */
3315         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3316             this.seqPointMax = value;
3317         }
3318
3319         /**
3320          * Gets the value of the pcaData property.
3321          *
3322          * @return
3323          *     possible object is
3324          *     {@link PcaDataType }
3325          *
3326          */
3327         public PcaDataType getPcaData() {
3328             return pcaData;
3329         }
3330
3331         /**
3332          * Sets the value of the pcaData property.
3333          *
3334          * @param value
3335          *     allowed object is
3336          *     {@link PcaDataType }
3337          *
3338          */
3339         public void setPcaData(PcaDataType value) {
3340             this.pcaData = value;
3341         }
3342
3343         /**
3344          * Gets the value of the title property.
3345          *
3346          * @return
3347          *     possible object is
3348          *     {@link String }
3349          *
3350          */
3351         public String getTitle() {
3352             return title;
3353         }
3354
3355         /**
3356          * Sets the value of the title property.
3357          *
3358          * @param value
3359          *     allowed object is
3360          *     {@link String }
3361          *
3362          */
3363         public void setTitle(String value) {
3364             this.title = value;
3365         }
3366
3367         /**
3368          * Gets the value of the scoreModelName property.
3369          *
3370          * @return
3371          *     possible object is
3372          *     {@link String }
3373          *
3374          */
3375         public String getScoreModelName() {
3376             return scoreModelName;
3377         }
3378
3379         /**
3380          * Sets the value of the scoreModelName property.
3381          *
3382          * @param value
3383          *     allowed object is
3384          *     {@link String }
3385          *
3386          */
3387         public void setScoreModelName(String value) {
3388             this.scoreModelName = value;
3389         }
3390
3391         /**
3392          * Gets the value of the xDim property.
3393          *
3394          * @return
3395          *     possible object is
3396          *     {@link Integer }
3397          *
3398          */
3399         public Integer getXDim() {
3400             return xDim;
3401         }
3402
3403         /**
3404          * Sets the value of the xDim property.
3405          *
3406          * @param value
3407          *     allowed object is
3408          *     {@link Integer }
3409          *
3410          */
3411         public void setXDim(Integer value) {
3412             this.xDim = value;
3413         }
3414
3415         /**
3416          * Gets the value of the yDim property.
3417          *
3418          * @return
3419          *     possible object is
3420          *     {@link Integer }
3421          *
3422          */
3423         public Integer getYDim() {
3424             return yDim;
3425         }
3426
3427         /**
3428          * Sets the value of the yDim property.
3429          *
3430          * @param value
3431          *     allowed object is
3432          *     {@link Integer }
3433          *
3434          */
3435         public void setYDim(Integer value) {
3436             this.yDim = value;
3437         }
3438
3439         /**
3440          * Gets the value of the zDim property.
3441          *
3442          * @return
3443          *     possible object is
3444          *     {@link Integer }
3445          *
3446          */
3447         public Integer getZDim() {
3448             return zDim;
3449         }
3450
3451         /**
3452          * Sets the value of the zDim property.
3453          *
3454          * @param value
3455          *     allowed object is
3456          *     {@link Integer }
3457          *
3458          */
3459         public void setZDim(Integer value) {
3460             this.zDim = value;
3461         }
3462
3463         /**
3464          * Gets the value of the bgColour property.
3465          *
3466          * @return
3467          *     possible object is
3468          *     {@link Integer }
3469          *
3470          */
3471         public Integer getBgColour() {
3472             return bgColour;
3473         }
3474
3475         /**
3476          * Sets the value of the bgColour property.
3477          *
3478          * @param value
3479          *     allowed object is
3480          *     {@link Integer }
3481          *
3482          */
3483         public void setBgColour(Integer value) {
3484             this.bgColour = value;
3485         }
3486
3487         /**
3488          * Gets the value of the scaleFactor property.
3489          *
3490          * @return
3491          *     possible object is
3492          *     {@link Float }
3493          *
3494          */
3495         public Float getScaleFactor() {
3496             return scaleFactor;
3497         }
3498
3499         /**
3500          * Sets the value of the scaleFactor property.
3501          *
3502          * @param value
3503          *     allowed object is
3504          *     {@link Float }
3505          *
3506          */
3507         public void setScaleFactor(Float value) {
3508             this.scaleFactor = value;
3509         }
3510
3511         /**
3512          * Gets the value of the showLabels property.
3513          *
3514          * @return
3515          *     possible object is
3516          *     {@link Boolean }
3517          *
3518          */
3519         public Boolean isShowLabels() {
3520             return showLabels;
3521         }
3522
3523         /**
3524          * Sets the value of the showLabels property.
3525          *
3526          * @param value
3527          *     allowed object is
3528          *     {@link Boolean }
3529          *
3530          */
3531         public void setShowLabels(Boolean value) {
3532             this.showLabels = value;
3533         }
3534
3535         /**
3536          * Gets the value of the linkToAllViews property.
3537          *
3538          * @return
3539          *     possible object is
3540          *     {@link Boolean }
3541          *
3542          */
3543         public Boolean isLinkToAllViews() {
3544             return linkToAllViews;
3545         }
3546
3547         /**
3548          * Sets the value of the linkToAllViews property.
3549          *
3550          * @param value
3551          *     allowed object is
3552          *     {@link Boolean }
3553          *
3554          */
3555         public void setLinkToAllViews(Boolean value) {
3556             this.linkToAllViews = value;
3557         }
3558
3559         /**
3560          * Gets the value of the width property.
3561          *
3562          * @return
3563          *     possible object is
3564          *     {@link Integer }
3565          *
3566          */
3567         public Integer getWidth() {
3568             return width;
3569         }
3570
3571         /**
3572          * Sets the value of the width property.
3573          *
3574          * @param value
3575          *     allowed object is
3576          *     {@link Integer }
3577          *
3578          */
3579         public void setWidth(Integer value) {
3580             this.width = value;
3581         }
3582
3583         /**
3584          * Gets the value of the height property.
3585          *
3586          * @return
3587          *     possible object is
3588          *     {@link Integer }
3589          *
3590          */
3591         public Integer getHeight() {
3592             return height;
3593         }
3594
3595         /**
3596          * Sets the value of the height property.
3597          *
3598          * @param value
3599          *     allowed object is
3600          *     {@link Integer }
3601          *
3602          */
3603         public void setHeight(Integer value) {
3604             this.height = value;
3605         }
3606
3607         /**
3608          * Gets the value of the xpos property.
3609          *
3610          * @return
3611          *     possible object is
3612          *     {@link Integer }
3613          *
3614          */
3615         public Integer getXpos() {
3616             return xpos;
3617         }
3618
3619         /**
3620          * Sets the value of the xpos property.
3621          *
3622          * @param value
3623          *     allowed object is
3624          *     {@link Integer }
3625          *
3626          */
3627         public void setXpos(Integer value) {
3628             this.xpos = value;
3629         }
3630
3631         /**
3632          * Gets the value of the ypos property.
3633          *
3634          * @return
3635          *     possible object is
3636          *     {@link Integer }
3637          *
3638          */
3639         public Integer getYpos() {
3640             return ypos;
3641         }
3642
3643         /**
3644          * Sets the value of the ypos property.
3645          *
3646          * @param value
3647          *     allowed object is
3648          *     {@link Integer }
3649          *
3650          */
3651         public void setYpos(Integer value) {
3652             this.ypos = value;
3653         }
3654
3655         /**
3656          * Gets the value of the includeGaps property.
3657          *
3658          * @return
3659          *     possible object is
3660          *     {@link Boolean }
3661          *
3662          */
3663         public Boolean isIncludeGaps() {
3664             return includeGaps;
3665         }
3666
3667         /**
3668          * Sets the value of the includeGaps property.
3669          *
3670          * @param value
3671          *     allowed object is
3672          *     {@link Boolean }
3673          *
3674          */
3675         public void setIncludeGaps(Boolean value) {
3676             this.includeGaps = value;
3677         }
3678
3679         /**
3680          * Gets the value of the matchGaps property.
3681          *
3682          * @return
3683          *     possible object is
3684          *     {@link Boolean }
3685          *
3686          */
3687         public Boolean isMatchGaps() {
3688             return matchGaps;
3689         }
3690
3691         /**
3692          * Sets the value of the matchGaps property.
3693          *
3694          * @param value
3695          *     allowed object is
3696          *     {@link Boolean }
3697          *
3698          */
3699         public void setMatchGaps(Boolean value) {
3700             this.matchGaps = value;
3701         }
3702
3703         /**
3704          * Gets the value of the includeGappedColumns property.
3705          *
3706          * @return
3707          *     possible object is
3708          *     {@link Boolean }
3709          *
3710          */
3711         public Boolean isIncludeGappedColumns() {
3712             return includeGappedColumns;
3713         }
3714
3715         /**
3716          * Sets the value of the includeGappedColumns property.
3717          *
3718          * @param value
3719          *     allowed object is
3720          *     {@link Boolean }
3721          *
3722          */
3723         public void setIncludeGappedColumns(Boolean value) {
3724             this.includeGappedColumns = value;
3725         }
3726
3727         /**
3728          * Gets the value of the denominateByShortestLength property.
3729          *
3730          * @return
3731          *     possible object is
3732          *     {@link Boolean }
3733          *
3734          */
3735         public Boolean isDenominateByShortestLength() {
3736             return denominateByShortestLength;
3737         }
3738
3739         /**
3740          * Sets the value of the denominateByShortestLength property.
3741          *
3742          * @param value
3743          *     allowed object is
3744          *     {@link Boolean }
3745          *
3746          */
3747         public void setDenominateByShortestLength(Boolean value) {
3748             this.denominateByShortestLength = value;
3749         }
3750
3751
3752         /**
3753          * <p>Java class for anonymous complex type.
3754          *
3755          * <p>The following schema fragment specifies the expected content contained within this class.
3756          *
3757          * <pre>
3758          * &lt;complexType>
3759          *   &lt;complexContent>
3760          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3761          *       &lt;attGroup ref="{www.jalview.org}position"/>
3762          *     &lt;/restriction>
3763          *   &lt;/complexContent>
3764          * &lt;/complexType>
3765          * </pre>
3766          *
3767          *
3768          */
3769         @XmlAccessorType(XmlAccessType.FIELD)
3770         @XmlType(name = "")
3771         public static class Axis {
3772
3773             @XmlAttribute(name = "xPos")
3774             protected Float xPos;
3775             @XmlAttribute(name = "yPos")
3776             protected Float yPos;
3777             @XmlAttribute(name = "zPos")
3778             protected Float zPos;
3779
3780             /**
3781              * Gets the value of the xPos property.
3782              *
3783              * @return
3784              *     possible object is
3785              *     {@link Float }
3786              *
3787              */
3788             public Float getXPos() {
3789                 return xPos;
3790             }
3791
3792             /**
3793              * Sets the value of the xPos property.
3794              *
3795              * @param value
3796              *     allowed object is
3797              *     {@link Float }
3798              *
3799              */
3800             public void setXPos(Float value) {
3801                 this.xPos = value;
3802             }
3803
3804             /**
3805              * Gets the value of the yPos property.
3806              *
3807              * @return
3808              *     possible object is
3809              *     {@link Float }
3810              *
3811              */
3812             public Float getYPos() {
3813                 return yPos;
3814             }
3815
3816             /**
3817              * Sets the value of the yPos property.
3818              *
3819              * @param value
3820              *     allowed object is
3821              *     {@link Float }
3822              *
3823              */
3824             public void setYPos(Float value) {
3825                 this.yPos = value;
3826             }
3827
3828             /**
3829              * Gets the value of the zPos property.
3830              *
3831              * @return
3832              *     possible object is
3833              *     {@link Float }
3834              *
3835              */
3836             public Float getZPos() {
3837                 return zPos;
3838             }
3839
3840             /**
3841              * Sets the value of the zPos property.
3842              *
3843              * @param value
3844              *     allowed object is
3845              *     {@link Float }
3846              *
3847              */
3848             public void setZPos(Float value) {
3849                 this.zPos = value;
3850             }
3851
3852         }
3853
3854
3855         /**
3856          * <p>Java class for anonymous complex type.
3857          *
3858          * <p>The following schema fragment specifies the expected content contained within this class.
3859          *
3860          * <pre>
3861          * &lt;complexType>
3862          *   &lt;complexContent>
3863          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3864          *       &lt;attGroup ref="{www.jalview.org}position"/>
3865          *     &lt;/restriction>
3866          *   &lt;/complexContent>
3867          * &lt;/complexType>
3868          * </pre>
3869          *
3870          *
3871          */
3872         @XmlAccessorType(XmlAccessType.FIELD)
3873         @XmlType(name = "")
3874         public static class SeqPointMax {
3875
3876             @XmlAttribute(name = "xPos")
3877             protected Float xPos;
3878             @XmlAttribute(name = "yPos")
3879             protected Float yPos;
3880             @XmlAttribute(name = "zPos")
3881             protected Float zPos;
3882
3883             /**
3884              * Gets the value of the xPos property.
3885              *
3886              * @return
3887              *     possible object is
3888              *     {@link Float }
3889              *
3890              */
3891             public Float getXPos() {
3892                 return xPos;
3893             }
3894
3895             /**
3896              * Sets the value of the xPos property.
3897              *
3898              * @param value
3899              *     allowed object is
3900              *     {@link Float }
3901              *
3902              */
3903             public void setXPos(Float value) {
3904                 this.xPos = value;
3905             }
3906
3907             /**
3908              * Gets the value of the yPos property.
3909              *
3910              * @return
3911              *     possible object is
3912              *     {@link Float }
3913              *
3914              */
3915             public Float getYPos() {
3916                 return yPos;
3917             }
3918
3919             /**
3920              * Sets the value of the yPos property.
3921              *
3922              * @param value
3923              *     allowed object is
3924              *     {@link Float }
3925              *
3926              */
3927             public void setYPos(Float value) {
3928                 this.yPos = value;
3929             }
3930
3931             /**
3932              * Gets the value of the zPos property.
3933              *
3934              * @return
3935              *     possible object is
3936              *     {@link Float }
3937              *
3938              */
3939             public Float getZPos() {
3940                 return zPos;
3941             }
3942
3943             /**
3944              * Sets the value of the zPos property.
3945              *
3946              * @param value
3947              *     allowed object is
3948              *     {@link Float }
3949              *
3950              */
3951             public void setZPos(Float value) {
3952                 this.zPos = value;
3953             }
3954
3955         }
3956
3957
3958         /**
3959          * <p>Java class for anonymous complex type.
3960          *
3961          * <p>The following schema fragment specifies the expected content contained within this class.
3962          *
3963          * <pre>
3964          * &lt;complexType>
3965          *   &lt;complexContent>
3966          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3967          *       &lt;attGroup ref="{www.jalview.org}position"/>
3968          *     &lt;/restriction>
3969          *   &lt;/complexContent>
3970          * &lt;/complexType>
3971          * </pre>
3972          *
3973          *
3974          */
3975         @XmlAccessorType(XmlAccessType.FIELD)
3976         @XmlType(name = "")
3977         public static class SeqPointMin {
3978
3979             @XmlAttribute(name = "xPos")
3980             protected Float xPos;
3981             @XmlAttribute(name = "yPos")
3982             protected Float yPos;
3983             @XmlAttribute(name = "zPos")
3984             protected Float zPos;
3985
3986             /**
3987              * Gets the value of the xPos property.
3988              *
3989              * @return
3990              *     possible object is
3991              *     {@link Float }
3992              *
3993              */
3994             public Float getXPos() {
3995                 return xPos;
3996             }
3997
3998             /**
3999              * Sets the value of the xPos property.
4000              *
4001              * @param value
4002              *     allowed object is
4003              *     {@link Float }
4004              *
4005              */
4006             public void setXPos(Float value) {
4007                 this.xPos = value;
4008             }
4009
4010             /**
4011              * Gets the value of the yPos property.
4012              *
4013              * @return
4014              *     possible object is
4015              *     {@link Float }
4016              *
4017              */
4018             public Float getYPos() {
4019                 return yPos;
4020             }
4021
4022             /**
4023              * Sets the value of the yPos property.
4024              *
4025              * @param value
4026              *     allowed object is
4027              *     {@link Float }
4028              *
4029              */
4030             public void setYPos(Float value) {
4031                 this.yPos = value;
4032             }
4033
4034             /**
4035              * Gets the value of the zPos property.
4036              *
4037              * @return
4038              *     possible object is
4039              *     {@link Float }
4040              *
4041              */
4042             public Float getZPos() {
4043                 return zPos;
4044             }
4045
4046             /**
4047              * Sets the value of the zPos property.
4048              *
4049              * @param value
4050              *     allowed object is
4051              *     {@link Float }
4052              *
4053              */
4054             public void setZPos(Float value) {
4055                 this.zPos = value;
4056             }
4057
4058         }
4059
4060
4061         /**
4062          * <p>Java class for anonymous complex type.
4063          *
4064          * <p>The following schema fragment specifies the expected content contained within this class.
4065          *
4066          * <pre>
4067          * &lt;complexType>
4068          *   &lt;complexContent>
4069          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4070          *       &lt;attGroup ref="{www.jalview.org}position"/>
4071          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4072          *     &lt;/restriction>
4073          *   &lt;/complexContent>
4074          * &lt;/complexType>
4075          * </pre>
4076          *
4077          *
4078          */
4079         @XmlAccessorType(XmlAccessType.FIELD)
4080         @XmlType(name = "")
4081         public static class SequencePoint {
4082
4083             @XmlAttribute(name = "sequenceRef")
4084             protected String sequenceRef;
4085             @XmlAttribute(name = "xPos")
4086             protected Float xPos;
4087             @XmlAttribute(name = "yPos")
4088             protected Float yPos;
4089             @XmlAttribute(name = "zPos")
4090             protected Float zPos;
4091
4092             /**
4093              * Gets the value of the sequenceRef property.
4094              *
4095              * @return
4096              *     possible object is
4097              *     {@link String }
4098              *
4099              */
4100             public String getSequenceRef() {
4101                 return sequenceRef;
4102             }
4103
4104             /**
4105              * Sets the value of the sequenceRef property.
4106              *
4107              * @param value
4108              *     allowed object is
4109              *     {@link String }
4110              *
4111              */
4112             public void setSequenceRef(String value) {
4113                 this.sequenceRef = value;
4114             }
4115
4116             /**
4117              * Gets the value of the xPos property.
4118              *
4119              * @return
4120              *     possible object is
4121              *     {@link Float }
4122              *
4123              */
4124             public Float getXPos() {
4125                 return xPos;
4126             }
4127
4128             /**
4129              * Sets the value of the xPos property.
4130              *
4131              * @param value
4132              *     allowed object is
4133              *     {@link Float }
4134              *
4135              */
4136             public void setXPos(Float value) {
4137                 this.xPos = value;
4138             }
4139
4140             /**
4141              * Gets the value of the yPos property.
4142              *
4143              * @return
4144              *     possible object is
4145              *     {@link Float }
4146              *
4147              */
4148             public Float getYPos() {
4149                 return yPos;
4150             }
4151
4152             /**
4153              * Sets the value of the yPos property.
4154              *
4155              * @param value
4156              *     allowed object is
4157              *     {@link Float }
4158              *
4159              */
4160             public void setYPos(Float value) {
4161                 this.yPos = value;
4162             }
4163
4164             /**
4165              * Gets the value of the zPos property.
4166              *
4167              * @return
4168              *     possible object is
4169              *     {@link Float }
4170              *
4171              */
4172             public Float getZPos() {
4173                 return zPos;
4174             }
4175
4176             /**
4177              * Sets the value of the zPos property.
4178              *
4179              * @param value
4180              *     allowed object is
4181              *     {@link Float }
4182              *
4183              */
4184             public void setZPos(Float value) {
4185                 this.zPos = value;
4186             }
4187
4188         }
4189
4190     }
4191
4192
4193     /**
4194      * <p>Java class for anonymous complex type.
4195      *
4196      * <p>The following schema fragment specifies the expected content contained within this class.
4197      *
4198      * <pre>
4199      * &lt;complexType>
4200      *   &lt;complexContent>
4201      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4202      *       &lt;sequence minOccurs="0">
4203      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4204      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4205      *       &lt;/sequence>
4206      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4207      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4208      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4209      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4210      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4211      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4212      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4213      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4214      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4215      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4216      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4217      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4218      *     &lt;/restriction>
4219      *   &lt;/complexContent>
4220      * &lt;/complexType>
4221      * </pre>
4222      *
4223      *
4224      */
4225     @XmlAccessorType(XmlAccessType.FIELD)
4226     @XmlType(name = "", propOrder = {
4227         "title",
4228         "newick"
4229     })
4230     public static class Tree {
4231
4232         @XmlElement(namespace = "www.jalview.org")
4233         protected String title;
4234         @XmlElement(namespace = "www.jalview.org")
4235         protected String newick;
4236         @XmlAttribute(name = "fontName")
4237         protected String fontName;
4238         @XmlAttribute(name = "fontSize")
4239         protected Integer fontSize;
4240         @XmlAttribute(name = "fontStyle")
4241         protected Integer fontStyle;
4242         @XmlAttribute(name = "threshold")
4243         protected Float threshold;
4244         @XmlAttribute(name = "showBootstrap")
4245         protected Boolean showBootstrap;
4246         @XmlAttribute(name = "showDistances")
4247         protected Boolean showDistances;
4248         @XmlAttribute(name = "markUnlinked")
4249         protected Boolean markUnlinked;
4250         @XmlAttribute(name = "fitToWindow")
4251         protected Boolean fitToWindow;
4252         @XmlAttribute(name = "currentTree")
4253         protected Boolean currentTree;
4254         @XmlAttribute(name = "id")
4255         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4256         @XmlID
4257         @XmlSchemaType(name = "ID")
4258         protected String id;
4259         @XmlAttribute(name = "linkToAllViews")
4260         protected Boolean linkToAllViews;
4261         @XmlAttribute(name = "width")
4262         protected Integer width;
4263         @XmlAttribute(name = "height")
4264         protected Integer height;
4265         @XmlAttribute(name = "xpos")
4266         protected Integer xpos;
4267         @XmlAttribute(name = "ypos")
4268         protected Integer ypos;
4269
4270         /**
4271          * Gets the value of the title property.
4272          *
4273          * @return
4274          *     possible object is
4275          *     {@link String }
4276          *
4277          */
4278         public String getTitle() {
4279             return title;
4280         }
4281
4282         /**
4283          * Sets the value of the title property.
4284          *
4285          * @param value
4286          *     allowed object is
4287          *     {@link String }
4288          *
4289          */
4290         public void setTitle(String value) {
4291             this.title = value;
4292         }
4293
4294         /**
4295          * Gets the value of the newick property.
4296          *
4297          * @return
4298          *     possible object is
4299          *     {@link String }
4300          *
4301          */
4302         public String getNewick() {
4303             return newick;
4304         }
4305
4306         /**
4307          * Sets the value of the newick property.
4308          *
4309          * @param value
4310          *     allowed object is
4311          *     {@link String }
4312          *
4313          */
4314         public void setNewick(String value) {
4315             this.newick = value;
4316         }
4317
4318         /**
4319          * Gets the value of the fontName property.
4320          *
4321          * @return
4322          *     possible object is
4323          *     {@link String }
4324          *
4325          */
4326         public String getFontName() {
4327             return fontName;
4328         }
4329
4330         /**
4331          * Sets the value of the fontName property.
4332          *
4333          * @param value
4334          *     allowed object is
4335          *     {@link String }
4336          *
4337          */
4338         public void setFontName(String value) {
4339             this.fontName = value;
4340         }
4341
4342         /**
4343          * Gets the value of the fontSize property.
4344          *
4345          * @return
4346          *     possible object is
4347          *     {@link Integer }
4348          *
4349          */
4350         public Integer getFontSize() {
4351             return fontSize;
4352         }
4353
4354         /**
4355          * Sets the value of the fontSize property.
4356          *
4357          * @param value
4358          *     allowed object is
4359          *     {@link Integer }
4360          *
4361          */
4362         public void setFontSize(Integer value) {
4363             this.fontSize = value;
4364         }
4365
4366         /**
4367          * Gets the value of the fontStyle property.
4368          *
4369          * @return
4370          *     possible object is
4371          *     {@link Integer }
4372          *
4373          */
4374         public Integer getFontStyle() {
4375             return fontStyle;
4376         }
4377
4378         /**
4379          * Sets the value of the fontStyle property.
4380          *
4381          * @param value
4382          *     allowed object is
4383          *     {@link Integer }
4384          *
4385          */
4386         public void setFontStyle(Integer value) {
4387             this.fontStyle = value;
4388         }
4389
4390         /**
4391          * Gets the value of the threshold property.
4392          *
4393          * @return
4394          *     possible object is
4395          *     {@link Float }
4396          *
4397          */
4398         public Float getThreshold() {
4399             return threshold;
4400         }
4401
4402         /**
4403          * Sets the value of the threshold property.
4404          *
4405          * @param value
4406          *     allowed object is
4407          *     {@link Float }
4408          *
4409          */
4410         public void setThreshold(Float value) {
4411             this.threshold = value;
4412         }
4413
4414         /**
4415          * Gets the value of the showBootstrap property.
4416          *
4417          * @return
4418          *     possible object is
4419          *     {@link Boolean }
4420          *
4421          */
4422         public Boolean isShowBootstrap() {
4423             return showBootstrap;
4424         }
4425
4426         /**
4427          * Sets the value of the showBootstrap property.
4428          *
4429          * @param value
4430          *     allowed object is
4431          *     {@link Boolean }
4432          *
4433          */
4434         public void setShowBootstrap(Boolean value) {
4435             this.showBootstrap = value;
4436         }
4437
4438         /**
4439          * Gets the value of the showDistances property.
4440          *
4441          * @return
4442          *     possible object is
4443          *     {@link Boolean }
4444          *
4445          */
4446         public Boolean isShowDistances() {
4447             return showDistances;
4448         }
4449
4450         /**
4451          * Sets the value of the showDistances property.
4452          *
4453          * @param value
4454          *     allowed object is
4455          *     {@link Boolean }
4456          *
4457          */
4458         public void setShowDistances(Boolean value) {
4459             this.showDistances = value;
4460         }
4461
4462         /**
4463          * Gets the value of the markUnlinked property.
4464          *
4465          * @return
4466          *     possible object is
4467          *     {@link Boolean }
4468          *
4469          */
4470         public Boolean isMarkUnlinked() {
4471             return markUnlinked;
4472         }
4473
4474         /**
4475          * Sets the value of the markUnlinked property.
4476          *
4477          * @param value
4478          *     allowed object is
4479          *     {@link Boolean }
4480          *
4481          */
4482         public void setMarkUnlinked(Boolean value) {
4483             this.markUnlinked = value;
4484         }
4485
4486         /**
4487          * Gets the value of the fitToWindow property.
4488          *
4489          * @return
4490          *     possible object is
4491          *     {@link Boolean }
4492          *
4493          */
4494         public Boolean isFitToWindow() {
4495             return fitToWindow;
4496         }
4497
4498         /**
4499          * Sets the value of the fitToWindow property.
4500          *
4501          * @param value
4502          *     allowed object is
4503          *     {@link Boolean }
4504          *
4505          */
4506         public void setFitToWindow(Boolean value) {
4507             this.fitToWindow = value;
4508         }
4509
4510         /**
4511          * Gets the value of the currentTree property.
4512          *
4513          * @return
4514          *     possible object is
4515          *     {@link Boolean }
4516          *
4517          */
4518         public Boolean isCurrentTree() {
4519             return currentTree;
4520         }
4521
4522         /**
4523          * Sets the value of the currentTree property.
4524          *
4525          * @param value
4526          *     allowed object is
4527          *     {@link Boolean }
4528          *
4529          */
4530         public void setCurrentTree(Boolean value) {
4531             this.currentTree = value;
4532         }
4533
4534         /**
4535          * Gets the value of the id property.
4536          *
4537          * @return
4538          *     possible object is
4539          *     {@link String }
4540          *
4541          */
4542         public String getId() {
4543             return id;
4544         }
4545
4546         /**
4547          * Sets the value of the id property.
4548          *
4549          * @param value
4550          *     allowed object is
4551          *     {@link String }
4552          *
4553          */
4554         public void setId(String value) {
4555             this.id = value;
4556         }
4557
4558         /**
4559          * Gets the value of the linkToAllViews property.
4560          *
4561          * @return
4562          *     possible object is
4563          *     {@link Boolean }
4564          *
4565          */
4566         public boolean isLinkToAllViews() {
4567             if (linkToAllViews == null) {
4568                 return false;
4569             } else {
4570                 return linkToAllViews;
4571             }
4572         }
4573
4574         /**
4575          * Sets the value of the linkToAllViews property.
4576          *
4577          * @param value
4578          *     allowed object is
4579          *     {@link Boolean }
4580          *
4581          */
4582         public void setLinkToAllViews(Boolean value) {
4583             this.linkToAllViews = value;
4584         }
4585
4586         /**
4587          * Gets the value of the width property.
4588          *
4589          * @return
4590          *     possible object is
4591          *     {@link Integer }
4592          *
4593          */
4594         public Integer getWidth() {
4595             return width;
4596         }
4597
4598         /**
4599          * Sets the value of the width property.
4600          *
4601          * @param value
4602          *     allowed object is
4603          *     {@link Integer }
4604          *
4605          */
4606         public void setWidth(Integer value) {
4607             this.width = value;
4608         }
4609
4610         /**
4611          * Gets the value of the height property.
4612          *
4613          * @return
4614          *     possible object is
4615          *     {@link Integer }
4616          *
4617          */
4618         public Integer getHeight() {
4619             return height;
4620         }
4621
4622         /**
4623          * Sets the value of the height property.
4624          *
4625          * @param value
4626          *     allowed object is
4627          *     {@link Integer }
4628          *
4629          */
4630         public void setHeight(Integer value) {
4631             this.height = value;
4632         }
4633
4634         /**
4635          * Gets the value of the xpos property.
4636          *
4637          * @return
4638          *     possible object is
4639          *     {@link Integer }
4640          *
4641          */
4642         public Integer getXpos() {
4643             return xpos;
4644         }
4645
4646         /**
4647          * Sets the value of the xpos property.
4648          *
4649          * @param value
4650          *     allowed object is
4651          *     {@link Integer }
4652          *
4653          */
4654         public void setXpos(Integer value) {
4655             this.xpos = value;
4656         }
4657
4658         /**
4659          * Gets the value of the ypos property.
4660          *
4661          * @return
4662          *     possible object is
4663          *     {@link Integer }
4664          *
4665          */
4666         public Integer getYpos() {
4667             return ypos;
4668         }
4669
4670         /**
4671          * Sets the value of the ypos property.
4672          *
4673          * @param value
4674          *     allowed object is
4675          *     {@link Integer }
4676          *
4677          */
4678         public void setYpos(Integer value) {
4679             this.ypos = value;
4680         }
4681
4682     }
4683
4684
4685     /**
4686      * <p>Java class for anonymous complex type.
4687      *
4688      * <p>The following schema fragment specifies the expected content contained within this class.
4689      *
4690      * <pre>
4691      * &lt;complexType>
4692      *   &lt;complexContent>
4693      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4694      *       &lt;sequence>
4695      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4696      *       &lt;/sequence>
4697      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4698      *     &lt;/restriction>
4699      *   &lt;/complexContent>
4700      * &lt;/complexType>
4701      * </pre>
4702      *
4703      *
4704      */
4705     @XmlAccessorType(XmlAccessType.FIELD)
4706     @XmlType(name = "", propOrder = {
4707         "userColourScheme"
4708     })
4709     public static class UserColours {
4710
4711         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4712         protected JalviewUserColours userColourScheme;
4713         @XmlAttribute(name = "id")
4714         protected String id;
4715
4716         /**
4717          * Gets the value of the userColourScheme property.
4718          *
4719          * @return
4720          *     possible object is
4721          *     {@link JalviewUserColours }
4722          *
4723          */
4724         public JalviewUserColours getUserColourScheme() {
4725             return userColourScheme;
4726         }
4727
4728         /**
4729          * Sets the value of the userColourScheme property.
4730          *
4731          * @param value
4732          *     allowed object is
4733          *     {@link JalviewUserColours }
4734          *
4735          */
4736         public void setUserColourScheme(JalviewUserColours value) {
4737             this.userColourScheme = value;
4738         }
4739
4740         /**
4741          * Gets the value of the id property.
4742          *
4743          * @return
4744          *     possible object is
4745          *     {@link String }
4746          *
4747          */
4748         public String getId() {
4749             return id;
4750         }
4751
4752         /**
4753          * Sets the value of the id property.
4754          *
4755          * @param value
4756          *     allowed object is
4757          *     {@link String }
4758          *
4759          */
4760         public void setId(String value) {
4761             this.id = value;
4762         }
4763
4764     }
4765
4766
4767     /**
4768      * <p>Java class for anonymous complex type.
4769      *
4770      * <p>The following schema fragment specifies the expected content contained within this class.
4771      *
4772      * <pre>
4773      * &lt;complexType>
4774      *   &lt;complexContent>
4775      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4776      *       &lt;sequence>
4777      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4778      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4779      *           &lt;complexType>
4780      *             &lt;complexContent>
4781      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4782      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4783      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4784      *               &lt;/restriction>
4785      *             &lt;/complexContent>
4786      *           &lt;/complexType>
4787      *         &lt;/element>
4788      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4789      *           &lt;complexType>
4790      *             &lt;complexContent>
4791      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4792      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4793      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4794      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4795      *               &lt;/extension>
4796      *             &lt;/complexContent>
4797      *           &lt;/complexType>
4798      *         &lt;/element>
4799      *       &lt;/sequence>
4800      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4801      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4802      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4803      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4804      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4805      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4806      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4807      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4812      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4817      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4818      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4819      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4820      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4821      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4822      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4825      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4826      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4827      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4828      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4829      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4830      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4831      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4832      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4833      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4834      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4835      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4836      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4837      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4838      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4839      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4840      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4841      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4842      *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4843      *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4844      *     &lt;/restriction>
4845      *   &lt;/complexContent>
4846      * &lt;/complexType>
4847      * </pre>
4848      *
4849      *
4850      */
4851     @XmlAccessorType(XmlAccessType.FIELD)
4852     @XmlType(name = "", propOrder = {
4853         "annotationColours",
4854         "hiddenColumns",
4855         "calcIdParam"
4856     })
4857     public static class Viewport {
4858
4859         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4860         protected AnnotationColourScheme annotationColours;
4861         @XmlElement(namespace = "www.jalview.org")
4862         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4863         @XmlElement(namespace = "www.jalview.org")
4864         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
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 conservationSelected property.
5047          *
5048          * @return
5049          *     possible object is
5050          *     {@link Boolean }
5051          *
5052          */
5053         public Boolean isConservationSelected() {
5054             return conservationSelected;
5055         }
5056
5057         /**
5058          * Sets the value of the conservationSelected property.
5059          *
5060          * @param value
5061          *     allowed object is
5062          *     {@link Boolean }
5063          *
5064          */
5065         public void setConservationSelected(Boolean value) {
5066             this.conservationSelected = value;
5067         }
5068
5069         /**
5070          * Gets the value of the pidSelected property.
5071          *
5072          * @return
5073          *     possible object is
5074          *     {@link Boolean }
5075          *
5076          */
5077         public Boolean isPidSelected() {
5078             return pidSelected;
5079         }
5080
5081         /**
5082          * Sets the value of the pidSelected property.
5083          *
5084          * @param value
5085          *     allowed object is
5086          *     {@link Boolean }
5087          *
5088          */
5089         public void setPidSelected(Boolean value) {
5090             this.pidSelected = value;
5091         }
5092
5093         /**
5094          * Gets the value of the bgColour property.
5095          *
5096          * @return
5097          *     possible object is
5098          *     {@link String }
5099          *
5100          */
5101         public String getBgColour() {
5102             return bgColour;
5103         }
5104
5105         /**
5106          * Sets the value of the bgColour property.
5107          *
5108          * @param value
5109          *     allowed object is
5110          *     {@link String }
5111          *
5112          */
5113         public void setBgColour(String value) {
5114             this.bgColour = value;
5115         }
5116
5117         /**
5118          * Gets the value of the consThreshold property.
5119          *
5120          * @return
5121          *     possible object is
5122          *     {@link Integer }
5123          *
5124          */
5125         public Integer getConsThreshold() {
5126             return consThreshold;
5127         }
5128
5129         /**
5130          * Sets the value of the consThreshold property.
5131          *
5132          * @param value
5133          *     allowed object is
5134          *     {@link Integer }
5135          *
5136          */
5137         public void setConsThreshold(Integer value) {
5138             this.consThreshold = value;
5139         }
5140
5141         /**
5142          * Gets the value of the pidThreshold property.
5143          *
5144          * @return
5145          *     possible object is
5146          *     {@link Integer }
5147          *
5148          */
5149         public Integer getPidThreshold() {
5150             return pidThreshold;
5151         }
5152
5153         /**
5154          * Sets the value of the pidThreshold property.
5155          *
5156          * @param value
5157          *     allowed object is
5158          *     {@link Integer }
5159          *
5160          */
5161         public void setPidThreshold(Integer value) {
5162             this.pidThreshold = value;
5163         }
5164
5165         /**
5166          * Gets the value of the title property.
5167          *
5168          * @return
5169          *     possible object is
5170          *     {@link String }
5171          *
5172          */
5173         public String getTitle() {
5174             return title;
5175         }
5176
5177         /**
5178          * Sets the value of the title property.
5179          *
5180          * @param value
5181          *     allowed object is
5182          *     {@link String }
5183          *
5184          */
5185         public void setTitle(String value) {
5186             this.title = value;
5187         }
5188
5189         /**
5190          * Gets the value of the showFullId property.
5191          *
5192          * @return
5193          *     possible object is
5194          *     {@link Boolean }
5195          *
5196          */
5197         public Boolean isShowFullId() {
5198             return showFullId;
5199         }
5200
5201         /**
5202          * Sets the value of the showFullId property.
5203          *
5204          * @param value
5205          *     allowed object is
5206          *     {@link Boolean }
5207          *
5208          */
5209         public void setShowFullId(Boolean value) {
5210             this.showFullId = value;
5211         }
5212
5213         /**
5214          * Gets the value of the rightAlignIds property.
5215          *
5216          * @return
5217          *     possible object is
5218          *     {@link Boolean }
5219          *
5220          */
5221         public Boolean isRightAlignIds() {
5222             return rightAlignIds;
5223         }
5224
5225         /**
5226          * Sets the value of the rightAlignIds property.
5227          *
5228          * @param value
5229          *     allowed object is
5230          *     {@link Boolean }
5231          *
5232          */
5233         public void setRightAlignIds(Boolean value) {
5234             this.rightAlignIds = value;
5235         }
5236
5237         /**
5238          * Gets the value of the showText property.
5239          *
5240          * @return
5241          *     possible object is
5242          *     {@link Boolean }
5243          *
5244          */
5245         public Boolean isShowText() {
5246             return showText;
5247         }
5248
5249         /**
5250          * Sets the value of the showText property.
5251          *
5252          * @param value
5253          *     allowed object is
5254          *     {@link Boolean }
5255          *
5256          */
5257         public void setShowText(Boolean value) {
5258             this.showText = value;
5259         }
5260
5261         /**
5262          * Gets the value of the showColourText property.
5263          *
5264          * @return
5265          *     possible object is
5266          *     {@link Boolean }
5267          *
5268          */
5269         public Boolean isShowColourText() {
5270             return showColourText;
5271         }
5272
5273         /**
5274          * Sets the value of the showColourText property.
5275          *
5276          * @param value
5277          *     allowed object is
5278          *     {@link Boolean }
5279          *
5280          */
5281         public void setShowColourText(Boolean value) {
5282             this.showColourText = value;
5283         }
5284
5285         /**
5286          * Gets the value of the showUnconserved property.
5287          *
5288          * @return
5289          *     possible object is
5290          *     {@link Boolean }
5291          *
5292          */
5293         public boolean isShowUnconserved() {
5294             if (showUnconserved == null) {
5295                 return false;
5296             } else {
5297                 return showUnconserved;
5298             }
5299         }
5300
5301         /**
5302          * Sets the value of the showUnconserved property.
5303          *
5304          * @param value
5305          *     allowed object is
5306          *     {@link Boolean }
5307          *
5308          */
5309         public void setShowUnconserved(Boolean value) {
5310             this.showUnconserved = value;
5311         }
5312
5313         /**
5314          * Gets the value of the showBoxes property.
5315          *
5316          * @return
5317          *     possible object is
5318          *     {@link Boolean }
5319          *
5320          */
5321         public Boolean isShowBoxes() {
5322             return showBoxes;
5323         }
5324
5325         /**
5326          * Sets the value of the showBoxes property.
5327          *
5328          * @param value
5329          *     allowed object is
5330          *     {@link Boolean }
5331          *
5332          */
5333         public void setShowBoxes(Boolean value) {
5334             this.showBoxes = value;
5335         }
5336
5337         /**
5338          * Gets the value of the wrapAlignment property.
5339          *
5340          * @return
5341          *     possible object is
5342          *     {@link Boolean }
5343          *
5344          */
5345         public Boolean isWrapAlignment() {
5346             return wrapAlignment;
5347         }
5348
5349         /**
5350          * Sets the value of the wrapAlignment property.
5351          *
5352          * @param value
5353          *     allowed object is
5354          *     {@link Boolean }
5355          *
5356          */
5357         public void setWrapAlignment(Boolean value) {
5358             this.wrapAlignment = value;
5359         }
5360
5361         /**
5362          * Gets the value of the renderGaps property.
5363          *
5364          * @return
5365          *     possible object is
5366          *     {@link Boolean }
5367          *
5368          */
5369         public Boolean isRenderGaps() {
5370             return renderGaps;
5371         }
5372
5373         /**
5374          * Sets the value of the renderGaps property.
5375          *
5376          * @param value
5377          *     allowed object is
5378          *     {@link Boolean }
5379          *
5380          */
5381         public void setRenderGaps(Boolean value) {
5382             this.renderGaps = value;
5383         }
5384
5385         /**
5386          * Gets the value of the showSequenceFeatures property.
5387          *
5388          * @return
5389          *     possible object is
5390          *     {@link Boolean }
5391          *
5392          */
5393         public Boolean isShowSequenceFeatures() {
5394             return showSequenceFeatures;
5395         }
5396
5397         /**
5398          * Sets the value of the showSequenceFeatures property.
5399          *
5400          * @param value
5401          *     allowed object is
5402          *     {@link Boolean }
5403          *
5404          */
5405         public void setShowSequenceFeatures(Boolean value) {
5406             this.showSequenceFeatures = value;
5407         }
5408
5409         /**
5410          * Gets the value of the showNPfeatureTooltip property.
5411          *
5412          * @return
5413          *     possible object is
5414          *     {@link Boolean }
5415          *
5416          */
5417         public Boolean isShowNPfeatureTooltip() {
5418             return showNPfeatureTooltip;
5419         }
5420
5421         /**
5422          * Sets the value of the showNPfeatureTooltip property.
5423          *
5424          * @param value
5425          *     allowed object is
5426          *     {@link Boolean }
5427          *
5428          */
5429         public void setShowNPfeatureTooltip(Boolean value) {
5430             this.showNPfeatureTooltip = value;
5431         }
5432
5433         /**
5434          * Gets the value of the showDbRefTooltip property.
5435          *
5436          * @return
5437          *     possible object is
5438          *     {@link Boolean }
5439          *
5440          */
5441         public Boolean isShowDbRefTooltip() {
5442             return showDbRefTooltip;
5443         }
5444
5445         /**
5446          * Sets the value of the showDbRefTooltip property.
5447          *
5448          * @param value
5449          *     allowed object is
5450          *     {@link Boolean }
5451          *
5452          */
5453         public void setShowDbRefTooltip(Boolean value) {
5454             this.showDbRefTooltip = value;
5455         }
5456
5457         /**
5458          * Gets the value of the followHighlight property.
5459          *
5460          * @return
5461          *     possible object is
5462          *     {@link Boolean }
5463          *
5464          */
5465         public boolean isFollowHighlight() {
5466             if (followHighlight == null) {
5467                 return true;
5468             } else {
5469                 return followHighlight;
5470             }
5471         }
5472
5473         /**
5474          * Sets the value of the followHighlight property.
5475          *
5476          * @param value
5477          *     allowed object is
5478          *     {@link Boolean }
5479          *
5480          */
5481         public void setFollowHighlight(Boolean value) {
5482             this.followHighlight = value;
5483         }
5484
5485         /**
5486          * Gets the value of the followSelection property.
5487          *
5488          * @return
5489          *     possible object is
5490          *     {@link Boolean }
5491          *
5492          */
5493         public boolean isFollowSelection() {
5494             if (followSelection == null) {
5495                 return true;
5496             } else {
5497                 return followSelection;
5498             }
5499         }
5500
5501         /**
5502          * Sets the value of the followSelection property.
5503          *
5504          * @param value
5505          *     allowed object is
5506          *     {@link Boolean }
5507          *
5508          */
5509         public void setFollowSelection(Boolean value) {
5510             this.followSelection = value;
5511         }
5512
5513         /**
5514          * Gets the value of the showAnnotation property.
5515          *
5516          * @return
5517          *     possible object is
5518          *     {@link Boolean }
5519          *
5520          */
5521         public Boolean isShowAnnotation() {
5522             return showAnnotation;
5523         }
5524
5525         /**
5526          * Sets the value of the showAnnotation property.
5527          *
5528          * @param value
5529          *     allowed object is
5530          *     {@link Boolean }
5531          *
5532          */
5533         public void setShowAnnotation(Boolean value) {
5534             this.showAnnotation = value;
5535         }
5536
5537         /**
5538          * Gets the value of the centreColumnLabels property.
5539          *
5540          * @return
5541          *     possible object is
5542          *     {@link Boolean }
5543          *
5544          */
5545         public boolean isCentreColumnLabels() {
5546             if (centreColumnLabels == null) {
5547                 return false;
5548             } else {
5549                 return centreColumnLabels;
5550             }
5551         }
5552
5553         /**
5554          * Sets the value of the centreColumnLabels property.
5555          *
5556          * @param value
5557          *     allowed object is
5558          *     {@link Boolean }
5559          *
5560          */
5561         public void setCentreColumnLabels(Boolean value) {
5562             this.centreColumnLabels = value;
5563         }
5564
5565         /**
5566          * Gets the value of the showGroupConservation property.
5567          *
5568          * @return
5569          *     possible object is
5570          *     {@link Boolean }
5571          *
5572          */
5573         public boolean isShowGroupConservation() {
5574             if (showGroupConservation == null) {
5575                 return false;
5576             } else {
5577                 return showGroupConservation;
5578             }
5579         }
5580
5581         /**
5582          * Sets the value of the showGroupConservation property.
5583          *
5584          * @param value
5585          *     allowed object is
5586          *     {@link Boolean }
5587          *
5588          */
5589         public void setShowGroupConservation(Boolean value) {
5590             this.showGroupConservation = value;
5591         }
5592
5593         /**
5594          * Gets the value of the showGroupConsensus property.
5595          *
5596          * @return
5597          *     possible object is
5598          *     {@link Boolean }
5599          *
5600          */
5601         public boolean isShowGroupConsensus() {
5602             if (showGroupConsensus == null) {
5603                 return false;
5604             } else {
5605                 return showGroupConsensus;
5606             }
5607         }
5608
5609         /**
5610          * Sets the value of the showGroupConsensus property.
5611          *
5612          * @param value
5613          *     allowed object is
5614          *     {@link Boolean }
5615          *
5616          */
5617         public void setShowGroupConsensus(Boolean value) {
5618             this.showGroupConsensus = value;
5619         }
5620
5621         /**
5622          * Gets the value of the showConsensusHistogram property.
5623          *
5624          * @return
5625          *     possible object is
5626          *     {@link Boolean }
5627          *
5628          */
5629         public boolean isShowConsensusHistogram() {
5630             if (showConsensusHistogram == null) {
5631                 return true;
5632             } else {
5633                 return showConsensusHistogram;
5634             }
5635         }
5636
5637         /**
5638          * Sets the value of the showConsensusHistogram property.
5639          *
5640          * @param value
5641          *     allowed object is
5642          *     {@link Boolean }
5643          *
5644          */
5645         public void setShowConsensusHistogram(Boolean value) {
5646             this.showConsensusHistogram = value;
5647         }
5648
5649         /**
5650          * Gets the value of the showSequenceLogo property.
5651          *
5652          * @return
5653          *     possible object is
5654          *     {@link Boolean }
5655          *
5656          */
5657         public boolean isShowSequenceLogo() {
5658             if (showSequenceLogo == null) {
5659                 return false;
5660             } else {
5661                 return showSequenceLogo;
5662             }
5663         }
5664
5665         /**
5666          * Sets the value of the showSequenceLogo property.
5667          *
5668          * @param value
5669          *     allowed object is
5670          *     {@link Boolean }
5671          *
5672          */
5673         public void setShowSequenceLogo(Boolean value) {
5674             this.showSequenceLogo = value;
5675         }
5676
5677         /**
5678          * Gets the value of the normaliseSequenceLogo property.
5679          *
5680          * @return
5681          *     possible object is
5682          *     {@link Boolean }
5683          *
5684          */
5685         public boolean isNormaliseSequenceLogo() {
5686             if (normaliseSequenceLogo == null) {
5687                 return false;
5688             } else {
5689                 return normaliseSequenceLogo;
5690             }
5691         }
5692
5693         /**
5694          * Sets the value of the normaliseSequenceLogo property.
5695          *
5696          * @param value
5697          *     allowed object is
5698          *     {@link Boolean }
5699          *
5700          */
5701         public void setNormaliseSequenceLogo(Boolean value) {
5702             this.normaliseSequenceLogo = value;
5703         }
5704
5705         /**
5706          * Gets the value of the ignoreGapsinConsensus property.
5707          *
5708          * @return
5709          *     possible object is
5710          *     {@link Boolean }
5711          *
5712          */
5713         public boolean isIgnoreGapsinConsensus() {
5714             if (ignoreGapsinConsensus == null) {
5715                 return true;
5716             } else {
5717                 return ignoreGapsinConsensus;
5718             }
5719         }
5720
5721         /**
5722          * Sets the value of the ignoreGapsinConsensus property.
5723          *
5724          * @param value
5725          *     allowed object is
5726          *     {@link Boolean }
5727          *
5728          */
5729         public void setIgnoreGapsinConsensus(Boolean value) {
5730             this.ignoreGapsinConsensus = value;
5731         }
5732
5733         /**
5734          * Gets the value of the startRes property.
5735          *
5736          * @return
5737          *     possible object is
5738          *     {@link Integer }
5739          *
5740          */
5741         public Integer getStartRes() {
5742             return startRes;
5743         }
5744
5745         /**
5746          * Sets the value of the startRes property.
5747          *
5748          * @param value
5749          *     allowed object is
5750          *     {@link Integer }
5751          *
5752          */
5753         public void setStartRes(Integer value) {
5754             this.startRes = value;
5755         }
5756
5757         /**
5758          * Gets the value of the startSeq property.
5759          *
5760          * @return
5761          *     possible object is
5762          *     {@link Integer }
5763          *
5764          */
5765         public Integer getStartSeq() {
5766             return startSeq;
5767         }
5768
5769         /**
5770          * Sets the value of the startSeq property.
5771          *
5772          * @param value
5773          *     allowed object is
5774          *     {@link Integer }
5775          *
5776          */
5777         public void setStartSeq(Integer value) {
5778             this.startSeq = value;
5779         }
5780
5781         /**
5782          * Gets the value of the fontName property.
5783          *
5784          * @return
5785          *     possible object is
5786          *     {@link String }
5787          *
5788          */
5789         public String getFontName() {
5790             return fontName;
5791         }
5792
5793         /**
5794          * Sets the value of the fontName property.
5795          *
5796          * @param value
5797          *     allowed object is
5798          *     {@link String }
5799          *
5800          */
5801         public void setFontName(String value) {
5802             this.fontName = value;
5803         }
5804
5805         /**
5806          * Gets the value of the fontSize property.
5807          *
5808          * @return
5809          *     possible object is
5810          *     {@link Integer }
5811          *
5812          */
5813         public Integer getFontSize() {
5814             return fontSize;
5815         }
5816
5817         /**
5818          * Sets the value of the fontSize property.
5819          *
5820          * @param value
5821          *     allowed object is
5822          *     {@link Integer }
5823          *
5824          */
5825         public void setFontSize(Integer value) {
5826             this.fontSize = value;
5827         }
5828
5829         /**
5830          * Gets the value of the fontStyle property.
5831          *
5832          * @return
5833          *     possible object is
5834          *     {@link Integer }
5835          *
5836          */
5837         public Integer getFontStyle() {
5838             return fontStyle;
5839         }
5840
5841         /**
5842          * Sets the value of the fontStyle property.
5843          *
5844          * @param value
5845          *     allowed object is
5846          *     {@link Integer }
5847          *
5848          */
5849         public void setFontStyle(Integer value) {
5850             this.fontStyle = value;
5851         }
5852
5853         /**
5854          * Gets the value of the scaleProteinAsCdna property.
5855          *
5856          * @return
5857          *     possible object is
5858          *     {@link Boolean }
5859          *
5860          */
5861         public boolean isScaleProteinAsCdna() {
5862             if (scaleProteinAsCdna == null) {
5863                 return true;
5864             } else {
5865                 return scaleProteinAsCdna;
5866             }
5867         }
5868
5869         /**
5870          * Sets the value of the scaleProteinAsCdna property.
5871          *
5872          * @param value
5873          *     allowed object is
5874          *     {@link Boolean }
5875          *
5876          */
5877         public void setScaleProteinAsCdna(Boolean value) {
5878             this.scaleProteinAsCdna = value;
5879         }
5880
5881         /**
5882          * Gets the value of the viewName property.
5883          *
5884          * @return
5885          *     possible object is
5886          *     {@link String }
5887          *
5888          */
5889         public String getViewName() {
5890             return viewName;
5891         }
5892
5893         /**
5894          * Sets the value of the viewName property.
5895          *
5896          * @param value
5897          *     allowed object is
5898          *     {@link String }
5899          *
5900          */
5901         public void setViewName(String value) {
5902             this.viewName = value;
5903         }
5904
5905         /**
5906          * Gets the value of the sequenceSetId property.
5907          *
5908          * @return
5909          *     possible object is
5910          *     {@link String }
5911          *
5912          */
5913         public String getSequenceSetId() {
5914             return sequenceSetId;
5915         }
5916
5917         /**
5918          * Sets the value of the sequenceSetId property.
5919          *
5920          * @param value
5921          *     allowed object is
5922          *     {@link String }
5923          *
5924          */
5925         public void setSequenceSetId(String value) {
5926             this.sequenceSetId = value;
5927         }
5928
5929         /**
5930          * Gets the value of the gatheredViews property.
5931          *
5932          * @return
5933          *     possible object is
5934          *     {@link Boolean }
5935          *
5936          */
5937         public Boolean isGatheredViews() {
5938             return gatheredViews;
5939         }
5940
5941         /**
5942          * Sets the value of the gatheredViews property.
5943          *
5944          * @param value
5945          *     allowed object is
5946          *     {@link Boolean }
5947          *
5948          */
5949         public void setGatheredViews(Boolean value) {
5950             this.gatheredViews = value;
5951         }
5952
5953         /**
5954          * Gets the value of the textCol1 property.
5955          *
5956          * @return
5957          *     possible object is
5958          *     {@link Integer }
5959          *
5960          */
5961         public Integer getTextCol1() {
5962             return textCol1;
5963         }
5964
5965         /**
5966          * Sets the value of the textCol1 property.
5967          *
5968          * @param value
5969          *     allowed object is
5970          *     {@link Integer }
5971          *
5972          */
5973         public void setTextCol1(Integer value) {
5974             this.textCol1 = value;
5975         }
5976
5977         /**
5978          * Gets the value of the textCol2 property.
5979          *
5980          * @return
5981          *     possible object is
5982          *     {@link Integer }
5983          *
5984          */
5985         public Integer getTextCol2() {
5986             return textCol2;
5987         }
5988
5989         /**
5990          * Sets the value of the textCol2 property.
5991          *
5992          * @param value
5993          *     allowed object is
5994          *     {@link Integer }
5995          *
5996          */
5997         public void setTextCol2(Integer value) {
5998             this.textCol2 = value;
5999         }
6000
6001         /**
6002          * Gets the value of the textColThreshold property.
6003          *
6004          * @return
6005          *     possible object is
6006          *     {@link Integer }
6007          *
6008          */
6009         public Integer getTextColThreshold() {
6010             return textColThreshold;
6011         }
6012
6013         /**
6014          * Sets the value of the textColThreshold property.
6015          *
6016          * @param value
6017          *     allowed object is
6018          *     {@link Integer }
6019          *
6020          */
6021         public void setTextColThreshold(Integer value) {
6022             this.textColThreshold = value;
6023         }
6024
6025         /**
6026          * Gets the value of the id property.
6027          *
6028          * @return
6029          *     possible object is
6030          *     {@link String }
6031          *
6032          */
6033         public String getId() {
6034             return id;
6035         }
6036
6037         /**
6038          * Sets the value of the id property.
6039          *
6040          * @param value
6041          *     allowed object is
6042          *     {@link String }
6043          *
6044          */
6045         public void setId(String value) {
6046             this.id = value;
6047         }
6048
6049         /**
6050          * Gets the value of the complementId property.
6051          *
6052          * @return
6053          *     possible object is
6054          *     {@link String }
6055          *
6056          */
6057         public String getComplementId() {
6058             return complementId;
6059         }
6060
6061         /**
6062          * Sets the value of the complementId property.
6063          *
6064          * @param value
6065          *     allowed object is
6066          *     {@link String }
6067          *
6068          */
6069         public void setComplementId(String value) {
6070             this.complementId = value;
6071         }
6072
6073         /**
6074          * Gets the value of the showComplementFeatures property.
6075          *
6076          * @return
6077          *     possible object is
6078          *     {@link Boolean }
6079          *
6080          */
6081         public boolean isShowComplementFeatures() {
6082             if (showComplementFeatures == null) {
6083                 return false;
6084             } else {
6085                 return showComplementFeatures;
6086             }
6087         }
6088
6089         /**
6090          * Sets the value of the showComplementFeatures property.
6091          *
6092          * @param value
6093          *     allowed object is
6094          *     {@link Boolean }
6095          *
6096          */
6097         public void setShowComplementFeatures(Boolean value) {
6098             this.showComplementFeatures = value;
6099         }
6100
6101         /**
6102          * Gets the value of the showComplementFeaturesOnTop property.
6103          *
6104          * @return
6105          *     possible object is
6106          *     {@link Boolean }
6107          *
6108          */
6109         public boolean isShowComplementFeaturesOnTop() {
6110             if (showComplementFeaturesOnTop == null) {
6111                 return false;
6112             } else {
6113                 return showComplementFeaturesOnTop;
6114             }
6115         }
6116
6117         /**
6118          * Sets the value of the showComplementFeaturesOnTop property.
6119          *
6120          * @param value
6121          *     allowed object is
6122          *     {@link Boolean }
6123          *
6124          */
6125         public void setShowComplementFeaturesOnTop(Boolean value) {
6126             this.showComplementFeaturesOnTop = value;
6127         }
6128
6129         /**
6130          * Gets the value of the width property.
6131          *
6132          * @return
6133          *     possible object is
6134          *     {@link Integer }
6135          *
6136          */
6137         public Integer getWidth() {
6138             return width;
6139         }
6140
6141         /**
6142          * Sets the value of the width property.
6143          *
6144          * @param value
6145          *     allowed object is
6146          *     {@link Integer }
6147          *
6148          */
6149         public void setWidth(Integer value) {
6150             this.width = value;
6151         }
6152
6153         /**
6154          * Gets the value of the height property.
6155          *
6156          * @return
6157          *     possible object is
6158          *     {@link Integer }
6159          *
6160          */
6161         public Integer getHeight() {
6162             return height;
6163         }
6164
6165         /**
6166          * Sets the value of the height property.
6167          *
6168          * @param value
6169          *     allowed object is
6170          *     {@link Integer }
6171          *
6172          */
6173         public void setHeight(Integer value) {
6174             this.height = value;
6175         }
6176
6177         /**
6178          * Gets the value of the xpos property.
6179          *
6180          * @return
6181          *     possible object is
6182          *     {@link Integer }
6183          *
6184          */
6185         public Integer getXpos() {
6186             return xpos;
6187         }
6188
6189         /**
6190          * Sets the value of the xpos property.
6191          *
6192          * @param value
6193          *     allowed object is
6194          *     {@link Integer }
6195          *
6196          */
6197         public void setXpos(Integer value) {
6198             this.xpos = value;
6199         }
6200
6201         /**
6202          * Gets the value of the ypos property.
6203          *
6204          * @return
6205          *     possible object is
6206          *     {@link Integer }
6207          *
6208          */
6209         public Integer getYpos() {
6210             return ypos;
6211         }
6212
6213         /**
6214          * Sets the value of the ypos property.
6215          *
6216          * @param value
6217          *     allowed object is
6218          *     {@link Integer }
6219          *
6220          */
6221         public void setYpos(Integer value) {
6222             this.ypos = value;
6223         }
6224
6225
6226         /**
6227          * <p>Java class for anonymous complex type.
6228          *
6229          * <p>The following schema fragment specifies the expected content contained within this class.
6230          *
6231          * <pre>
6232          * &lt;complexType>
6233          *   &lt;complexContent>
6234          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6235          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6236          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6237          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6238          *     &lt;/extension>
6239          *   &lt;/complexContent>
6240          * &lt;/complexType>
6241          * </pre>
6242          *
6243          *
6244          */
6245         @XmlAccessorType(XmlAccessType.FIELD)
6246         @XmlType(name = "")
6247         public static class CalcIdParam
6248             extends WebServiceParameterSet
6249         {
6250
6251             @XmlAttribute(name = "calcId", required = true)
6252             protected String calcId;
6253             @XmlAttribute(name = "needsUpdate")
6254             protected Boolean needsUpdate;
6255             @XmlAttribute(name = "autoUpdate", required = true)
6256             protected boolean autoUpdate;
6257
6258             /**
6259              * Gets the value of the calcId property.
6260              *
6261              * @return
6262              *     possible object is
6263              *     {@link String }
6264              *
6265              */
6266             public String getCalcId() {
6267                 return calcId;
6268             }
6269
6270             /**
6271              * Sets the value of the calcId property.
6272              *
6273              * @param value
6274              *     allowed object is
6275              *     {@link String }
6276              *
6277              */
6278             public void setCalcId(String value) {
6279                 this.calcId = value;
6280             }
6281
6282             /**
6283              * Gets the value of the needsUpdate property.
6284              *
6285              * @return
6286              *     possible object is
6287              *     {@link Boolean }
6288              *
6289              */
6290             public boolean isNeedsUpdate() {
6291                 if (needsUpdate == null) {
6292                     return false;
6293                 } else {
6294                     return needsUpdate;
6295                 }
6296             }
6297
6298             /**
6299              * Sets the value of the needsUpdate property.
6300              *
6301              * @param value
6302              *     allowed object is
6303              *     {@link Boolean }
6304              *
6305              */
6306             public void setNeedsUpdate(Boolean value) {
6307                 this.needsUpdate = value;
6308             }
6309
6310             /**
6311              * Gets the value of the autoUpdate property.
6312              *
6313              */
6314             public boolean isAutoUpdate() {
6315                 return autoUpdate;
6316             }
6317
6318             /**
6319              * Sets the value of the autoUpdate property.
6320              *
6321              */
6322             public void setAutoUpdate(boolean value) {
6323                 this.autoUpdate = value;
6324             }
6325
6326         }
6327
6328
6329         /**
6330          * <p>Java class for anonymous complex type.
6331          *
6332          * <p>The following schema fragment specifies the expected content contained within this class.
6333          *
6334          * <pre>
6335          * &lt;complexType>
6336          *   &lt;complexContent>
6337          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6338          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6339          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6340          *     &lt;/restriction>
6341          *   &lt;/complexContent>
6342          * &lt;/complexType>
6343          * </pre>
6344          *
6345          *
6346          */
6347         @XmlAccessorType(XmlAccessType.FIELD)
6348         @XmlType(name = "")
6349         public static class HiddenColumns {
6350
6351             @XmlAttribute(name = "start")
6352             protected Integer start;
6353             @XmlAttribute(name = "end")
6354             protected Integer end;
6355
6356             /**
6357              * Gets the value of the start property.
6358              *
6359              * @return
6360              *     possible object is
6361              *     {@link Integer }
6362              *
6363              */
6364             public Integer getStart() {
6365                 return start;
6366             }
6367
6368             /**
6369              * Sets the value of the start property.
6370              *
6371              * @param value
6372              *     allowed object is
6373              *     {@link Integer }
6374              *
6375              */
6376             public void setStart(Integer value) {
6377                 this.start = value;
6378             }
6379
6380             /**
6381              * Gets the value of the end property.
6382              *
6383              * @return
6384              *     possible object is
6385              *     {@link Integer }
6386              *
6387              */
6388             public Integer getEnd() {
6389                 return end;
6390             }
6391
6392             /**
6393              * Sets the value of the end property.
6394              *
6395              * @param value
6396              *     allowed object is
6397              *     {@link Integer }
6398              *
6399              */
6400             public void setEnd(Integer value) {
6401                 this.end = value;
6402             }
6403
6404         }
6405
6406     }
6407
6408 }