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: 2019.06.06 at 04:31:20 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;/restriction>
 213  *               &lt;/complexContent>
 214  *             &lt;/complexType>
 215  *           &lt;/element>
 216  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 217  *             &lt;complexType>
 218  *               &lt;complexContent>
 219  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 220  *                   &lt;sequence>
 221  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 222  *                   &lt;/sequence>
 223  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 224  *                 &lt;/restriction>
 225  *               &lt;/complexContent>
 226  *             &lt;/complexType>
 227  *           &lt;/element>
 228  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 229  *             &lt;complexType>
 230  *               &lt;complexContent>
 231  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 232  *                   &lt;sequence minOccurs="0">
 233  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 234  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 235  *                   &lt;/sequence>
 236  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 237  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 238  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 239  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 240  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 241  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 242  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 243  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 244  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 245  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 246  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 247  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 248  *                 &lt;/restriction>
 249  *               &lt;/complexContent>
 250  *             &lt;/complexType>
 251  *           &lt;/element>
 252  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 253  *             &lt;complexType>
 254  *               &lt;complexContent>
 255  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 256  *                   &lt;sequence>
 257  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 258  *                       &lt;complexType>
 259  *                         &lt;complexContent>
 260  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 261  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 262  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 263  *                           &lt;/restriction>
 264  *                         &lt;/complexContent>
 265  *                       &lt;/complexType>
 266  *                     &lt;/element>
 267  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 268  *                       &lt;complexType>
 269  *                         &lt;complexContent>
 270  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 271  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 272  *                           &lt;/restriction>
 273  *                         &lt;/complexContent>
 274  *                       &lt;/complexType>
 275  *                     &lt;/element>
 276  *                     &lt;element name="seqPointMin">
 277  *                       &lt;complexType>
 278  *                         &lt;complexContent>
 279  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 280  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 281  *                           &lt;/restriction>
 282  *                         &lt;/complexContent>
 283  *                       &lt;/complexType>
 284  *                     &lt;/element>
 285  *                     &lt;element name="seqPointMax">
 286  *                       &lt;complexType>
 287  *                         &lt;complexContent>
 288  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 289  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 290  *                           &lt;/restriction>
 291  *                         &lt;/complexContent>
 292  *                       &lt;/complexType>
 293  *                     &lt;/element>
 294  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 295  *                   &lt;/sequence>
 296  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 297  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 298  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 299  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 300  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 301  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 302  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 303  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 304  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 305  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 306  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 307  *                 &lt;/restriction>
 308  *               &lt;/complexContent>
 309  *             &lt;/complexType>
 310  *           &lt;/element>
 311  *           &lt;element name="FeatureSettings" minOccurs="0">
 312  *             &lt;complexType>
 313  *               &lt;complexContent>
 314  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 315  *                   &lt;sequence>
 316  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 317  *                       &lt;complexType>
 318  *                         &lt;complexContent>
 319  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 320  *                             &lt;sequence>
 321  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 322  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 323  *                             &lt;/sequence>
 324  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 325  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 326  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 327  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 328  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 329  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 330  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 331  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 332  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 333  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 334  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 335  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 336  *                           &lt;/restriction>
 337  *                         &lt;/complexContent>
 338  *                       &lt;/complexType>
 339  *                     &lt;/element>
 340  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 341  *                       &lt;complexType>
 342  *                         &lt;complexContent>
 343  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 344  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 345  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 346  *                           &lt;/restriction>
 347  *                         &lt;/complexContent>
 348  *                       &lt;/complexType>
 349  *                     &lt;/element>
 350  *                   &lt;/sequence>
 351  *                 &lt;/restriction>
 352  *               &lt;/complexContent>
 353  *             &lt;/complexType>
 354  *           &lt;/element>
 355  *         &lt;/sequence>
 356  *       &lt;/sequence>
 357  *     &lt;/restriction>
 358  *   &lt;/complexContent>
 359  * &lt;/complexType>
 360  * </pre>
 361  *
 362  *
 363  */
 364 @XmlAccessorType(XmlAccessType.FIELD)
 365 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 366     "creationDate",
 367     "version",
 368     "vamsasModel",
 369     "jSeq",
 370     "jGroup",
 371     "viewport",
 372     "userColours",
 373     "tree",
 374     "pcaViewer",
 375     "featureSettings"
 376 })
 377 public class JalviewModel {
 378
 379     @XmlElement(required = true)
 380     @XmlSchemaType(name = "dateTime")
 381     protected XMLGregorianCalendar creationDate;
 382     @XmlElement(required = true)
 383     protected String version;
 384     @XmlElement(required = true)
 385     protected VAMSAS vamsasModel;
 386     @XmlElement(name = "JSeq")
 387     protected List<JalviewModel.JSeq> jSeq;
 388     @XmlElement(name = "JGroup")
 389     protected List<JalviewModel.JGroup> jGroup;
 390     @XmlElement(name = "Viewport")
 391     protected List<JalviewModel.Viewport> viewport;
 392     @XmlElement(name = "UserColours")
 393     protected List<JalviewModel.UserColours> userColours;
 394     protected List<JalviewModel.Tree> tree;
 395     @XmlElement(name = "PcaViewer")
 396     protected List<JalviewModel.PcaViewer> pcaViewer;
 397     @XmlElement(name = "FeatureSettings")
 398     protected JalviewModel.FeatureSettings featureSettings;
 399
 400     /**
 401      * Gets the value of the creationDate property.
 402      *
 403      * @return
 404      *     possible object is
 405      *     {@link XMLGregorianCalendar }
 406      *
 407      */
 408     public XMLGregorianCalendar getCreationDate() {
 409         return creationDate;
 410     }
 411
 412     /**
 413      * Sets the value of the creationDate property.
 414      *
 415      * @param value
 416      *     allowed object is
 417      *     {@link XMLGregorianCalendar }
 418      *
 419      */
 420     public void setCreationDate(XMLGregorianCalendar value) {
 421         this.creationDate = value;
 422     }
 423
 424     /**
 425      * Gets the value of the version property.
 426      *
 427      * @return
 428      *     possible object is
 429      *     {@link String }
 430      *
 431      */
 432     public String getVersion() {
 433         return version;
 434     }
 435
 436     /**
 437      * Sets the value of the version property.
 438      *
 439      * @param value
 440      *     allowed object is
 441      *     {@link String }
 442      *
 443      */
 444     public void setVersion(String value) {
 445         this.version = value;
 446     }
 447
 448     /**
 449      * Gets the value of the vamsasModel property.
 450      *
 451      * @return
 452      *     possible object is
 453      *     {@link VAMSAS }
 454      *
 455      */
 456     public VAMSAS getVamsasModel() {
 457         return vamsasModel;
 458     }
 459
 460     /**
 461      * Sets the value of the vamsasModel property.
 462      *
 463      * @param value
 464      *     allowed object is
 465      *     {@link VAMSAS }
 466      *
 467      */
 468     public void setVamsasModel(VAMSAS value) {
 469         this.vamsasModel = value;
 470     }
 471
 472     /**
 473      * Gets the value of the jSeq property.
 474      *
 475      * <p>
 476      * This accessor method returns a reference to the live list,
 477      * not a snapshot. Therefore any modification you make to the
 478      * returned list will be present inside the JAXB object.
 479      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 480      *
 481      * <p>
 482      * For example, to add a new item, do as follows:
 483      * <pre>
 484      *    getJSeq().add(newItem);
 485      * </pre>
 486      *
 487      *
 488      * <p>
 489      * Objects of the following type(s) are allowed in the list
 490      * {@link JalviewModel.JSeq }
 491      *
 492      *
 493      */
 494     public List<JalviewModel.JSeq> getJSeq() {
 495         if (jSeq == null) {
 496             jSeq = new ArrayList<JalviewModel.JSeq>();
 497         }
 498         return this.jSeq;
 499     }
 500
 501     /**
 502      * Gets the value of the jGroup property.
 503      *
 504      * <p>
 505      * This accessor method returns a reference to the live list,
 506      * not a snapshot. Therefore any modification you make to the
 507      * returned list will be present inside the JAXB object.
 508      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 509      *
 510      * <p>
 511      * For example, to add a new item, do as follows:
 512      * <pre>
 513      *    getJGroup().add(newItem);
 514      * </pre>
 515      *
 516      *
 517      * <p>
 518      * Objects of the following type(s) are allowed in the list
 519      * {@link JalviewModel.JGroup }
 520      *
 521      *
 522      */
 523     public List<JalviewModel.JGroup> getJGroup() {
 524         if (jGroup == null) {
 525             jGroup = new ArrayList<JalviewModel.JGroup>();
 526         }
 527         return this.jGroup;
 528     }
 529
 530     /**
 531      * Gets the value of the viewport property.
 532      *
 533      * <p>
 534      * This accessor method returns a reference to the live list,
 535      * not a snapshot. Therefore any modification you make to the
 536      * returned list will be present inside the JAXB object.
 537      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 538      *
 539      * <p>
 540      * For example, to add a new item, do as follows:
 541      * <pre>
 542      *    getViewport().add(newItem);
 543      * </pre>
 544      *
 545      *
 546      * <p>
 547      * Objects of the following type(s) are allowed in the list
 548      * {@link JalviewModel.Viewport }
 549      *
 550      *
 551      */
 552     public List<JalviewModel.Viewport> getViewport() {
 553         if (viewport == null) {
 554             viewport = new ArrayList<JalviewModel.Viewport>();
 555         }
 556         return this.viewport;
 557     }
 558
 559     /**
 560      * Gets the value of the userColours property.
 561      *
 562      * <p>
 563      * This accessor method returns a reference to the live list,
 564      * not a snapshot. Therefore any modification you make to the
 565      * returned list will be present inside the JAXB object.
 566      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 567      *
 568      * <p>
 569      * For example, to add a new item, do as follows:
 570      * <pre>
 571      *    getUserColours().add(newItem);
 572      * </pre>
 573      *
 574      *
 575      * <p>
 576      * Objects of the following type(s) are allowed in the list
 577      * {@link JalviewModel.UserColours }
 578      *
 579      *
 580      */
 581     public List<JalviewModel.UserColours> getUserColours() {
 582         if (userColours == null) {
 583             userColours = new ArrayList<JalviewModel.UserColours>();
 584         }
 585         return this.userColours;
 586     }
 587
 588     /**
 589      * Gets the value of the tree property.
 590      *
 591      * <p>
 592      * This accessor method returns a reference to the live list,
 593      * not a snapshot. Therefore any modification you make to the
 594      * returned list will be present inside the JAXB object.
 595      * This is why there is not a <CODE>set</CODE> method for the tree property.
 596      *
 597      * <p>
 598      * For example, to add a new item, do as follows:
 599      * <pre>
 600      *    getTree().add(newItem);
 601      * </pre>
 602      *
 603      *
 604      * <p>
 605      * Objects of the following type(s) are allowed in the list
 606      * {@link JalviewModel.Tree }
 607      *
 608      *
 609      */
 610     public List<JalviewModel.Tree> getTree() {
 611         if (tree == null) {
 612             tree = new ArrayList<JalviewModel.Tree>();
 613         }
 614         return this.tree;
 615     }
 616
 617     /**
 618      * Gets the value of the pcaViewer property.
 619      *
 620      * <p>
 621      * This accessor method returns a reference to the live list,
 622      * not a snapshot. Therefore any modification you make to the
 623      * returned list will be present inside the JAXB object.
 624      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 625      *
 626      * <p>
 627      * For example, to add a new item, do as follows:
 628      * <pre>
 629      *    getPcaViewer().add(newItem);
 630      * </pre>
 631      *
 632      *
 633      * <p>
 634      * Objects of the following type(s) are allowed in the list
 635      * {@link JalviewModel.PcaViewer }
 636      *
 637      *
 638      */
 639     public List<JalviewModel.PcaViewer> getPcaViewer() {
 640         if (pcaViewer == null) {
 641             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 642         }
 643         return this.pcaViewer;
 644     }
 645
 646     /**
 647      * Gets the value of the featureSettings property.
 648      *
 649      * @return
 650      *     possible object is
 651      *     {@link JalviewModel.FeatureSettings }
 652      *
 653      */
 654     public JalviewModel.FeatureSettings getFeatureSettings() {
 655         return featureSettings;
 656     }
 657
 658     /**
 659      * Sets the value of the featureSettings property.
 660      *
 661      * @param value
 662      *     allowed object is
 663      *     {@link JalviewModel.FeatureSettings }
 664      *
 665      */
 666     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 667         this.featureSettings = value;
 668     }
 669
 670
 671     /**
 672      * <p>Java class for anonymous complex type.
 673      *
 674      * <p>The following schema fragment specifies the expected content contained within this class.
 675      *
 676      * <pre>
 677      * &lt;complexType>
 678      *   &lt;complexContent>
 679      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 680      *       &lt;sequence>
 681      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 682      *           &lt;complexType>
 683      *             &lt;complexContent>
 684      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 685      *                 &lt;sequence>
 686      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 687      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 688      *                 &lt;/sequence>
 689      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 690      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 691      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 692      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 693      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 694      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 695      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 696      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 697      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 698      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 699      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 700      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 701      *               &lt;/restriction>
 702      *             &lt;/complexContent>
 703      *           &lt;/complexType>
 704      *         &lt;/element>
 705      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 706      *           &lt;complexType>
 707      *             &lt;complexContent>
 708      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 709      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 710      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 711      *               &lt;/restriction>
 712      *             &lt;/complexContent>
 713      *           &lt;/complexType>
 714      *         &lt;/element>
 715      *       &lt;/sequence>
 716      *     &lt;/restriction>
 717      *   &lt;/complexContent>
 718      * &lt;/complexType>
 719      * </pre>
 720      *
 721      *
 722      */
 723     @XmlAccessorType(XmlAccessType.FIELD)
 724     @XmlType(name = "", propOrder = {
 725         "setting",
 726         "group"
 727     })
 728     public static class FeatureSettings {
 729
 730         @XmlElement(namespace = "www.jalview.org")
 731         protected List<JalviewModel.FeatureSettings.Setting> setting;
 732         @XmlElement(namespace = "www.jalview.org")
 733         protected List<JalviewModel.FeatureSettings.Group> group;
 734
 735         /**
 736          * Gets the value of the setting property.
 737          *
 738          * <p>
 739          * This accessor method returns a reference to the live list,
 740          * not a snapshot. Therefore any modification you make to the
 741          * returned list will be present inside the JAXB object.
 742          * This is why there is not a <CODE>set</CODE> method for the setting property.
 743          *
 744          * <p>
 745          * For example, to add a new item, do as follows:
 746          * <pre>
 747          *    getSetting().add(newItem);
 748          * </pre>
 749          *
 750          *
 751          * <p>
 752          * Objects of the following type(s) are allowed in the list
 753          * {@link JalviewModel.FeatureSettings.Setting }
 754          *
 755          *
 756          */
 757         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 758             if (setting == null) {
 759                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 760             }
 761             return this.setting;
 762         }
 763
 764         /**
 765          * Gets the value of the group property.
 766          *
 767          * <p>
 768          * This accessor method returns a reference to the live list,
 769          * not a snapshot. Therefore any modification you make to the
 770          * returned list will be present inside the JAXB object.
 771          * This is why there is not a <CODE>set</CODE> method for the group property.
 772          *
 773          * <p>
 774          * For example, to add a new item, do as follows:
 775          * <pre>
 776          *    getGroup().add(newItem);
 777          * </pre>
 778          *
 779          *
 780          * <p>
 781          * Objects of the following type(s) are allowed in the list
 782          * {@link JalviewModel.FeatureSettings.Group }
 783          *
 784          *
 785          */
 786         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 787             if (group == null) {
 788                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 789             }
 790             return this.group;
 791         }
 792
 793
 794         /**
 795          * <p>Java class for anonymous complex type.
 796          *
 797          * <p>The following schema fragment specifies the expected content contained within this class.
 798          *
 799          * <pre>
 800          * &lt;complexType>
 801          *   &lt;complexContent>
 802          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 803          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 804          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 805          *     &lt;/restriction>
 806          *   &lt;/complexContent>
 807          * &lt;/complexType>
 808          * </pre>
 809          *
 810          *
 811          */
 812         @XmlAccessorType(XmlAccessType.FIELD)
 813         @XmlType(name = "")
 814         public static class Group {
 815
 816             @XmlAttribute(name = "name", required = true)
 817             protected String name;
 818             @XmlAttribute(name = "display", required = true)
 819             protected boolean display;
 820
 821             /**
 822              * Gets the value of the name property.
 823              *
 824              * @return
 825              *     possible object is
 826              *     {@link String }
 827              *
 828              */
 829             public String getName() {
 830                 return name;
 831             }
 832
 833             /**
 834              * Sets the value of the name property.
 835              *
 836              * @param value
 837              *     allowed object is
 838              *     {@link String }
 839              *
 840              */
 841             public void setName(String value) {
 842                 this.name = value;
 843             }
 844
 845             /**
 846              * Gets the value of the display property.
 847              *
 848              */
 849             public boolean isDisplay() {
 850                 return display;
 851             }
 852
 853             /**
 854              * Sets the value of the display property.
 855              *
 856              */
 857             public void setDisplay(boolean value) {
 858                 this.display = value;
 859             }
 860
 861         }
 862
 863
 864         /**
 865          * <p>Java class for anonymous complex type.
 866          *
 867          * <p>The following schema fragment specifies the expected content contained within this class.
 868          *
 869          * <pre>
 870          * &lt;complexType>
 871          *   &lt;complexContent>
 872          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 873          *       &lt;sequence>
 874          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 875          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 876          *       &lt;/sequence>
 877          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 878          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 879          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 880          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 881          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 882          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 883          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 884          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 885          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 886          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 887          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 888          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 889          *     &lt;/restriction>
 890          *   &lt;/complexContent>
 891          * &lt;/complexType>
 892          * </pre>
 893          *
 894          *
 895          */
 896         @XmlAccessorType(XmlAccessType.FIELD)
 897         @XmlType(name = "", propOrder = {
 898             "attributeName",
 899             "matcherSet"
 900         })
 901         public static class Setting {
 902
 903             @XmlElement(namespace = "www.jalview.org")
 904             protected List<String> attributeName;
 905             @XmlElement(namespace = "www.jalview.org")
 906             protected FeatureMatcherSet matcherSet;
 907             @XmlAttribute(name = "type", required = true)
 908             protected String type;
 909             @XmlAttribute(name = "colour", required = true)
 910             protected int colour;
 911             @XmlAttribute(name = "display", required = true)
 912             protected boolean display;
 913             @XmlAttribute(name = "order")
 914             protected Float order;
 915             @XmlAttribute(name = "mincolour")
 916             protected Integer mincolour;
 917             @XmlAttribute(name = "noValueColour")
 918             protected NoValueColour noValueColour;
 919             @XmlAttribute(name = "threshold")
 920             protected Float threshold;
 921             @XmlAttribute(name = "threshstate")
 922             protected Integer threshstate;
 923             @XmlAttribute(name = "max")
 924             protected Float max;
 925             @XmlAttribute(name = "min")
 926             protected Float min;
 927             @XmlAttribute(name = "colourByLabel")
 928             protected Boolean colourByLabel;
 929             @XmlAttribute(name = "autoScale")
 930             protected Boolean autoScale;
 931
 932             /**
 933              * Gets the value of the attributeName property.
 934              *
 935              * <p>
 936              * This accessor method returns a reference to the live list,
 937              * not a snapshot. Therefore any modification you make to the
 938              * returned list will be present inside the JAXB object.
 939              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 940              *
 941              * <p>
 942              * For example, to add a new item, do as follows:
 943              * <pre>
 944              *    getAttributeName().add(newItem);
 945              * </pre>
 946              *
 947              *
 948              * <p>
 949              * Objects of the following type(s) are allowed in the list
 950              * {@link String }
 951              *
 952              *
 953              */
 954             public List<String> getAttributeName() {
 955                 if (attributeName == null) {
 956                     attributeName = new ArrayList<String>();
 957                 }
 958                 return this.attributeName;
 959             }
 960
 961             /**
 962              * Gets the value of the matcherSet property.
 963              *
 964              * @return
 965              *     possible object is
 966              *     {@link FeatureMatcherSet }
 967              *
 968              */
 969             public FeatureMatcherSet getMatcherSet() {
 970                 return matcherSet;
 971             }
 972
 973             /**
 974              * Sets the value of the matcherSet property.
 975              *
 976              * @param value
 977              *     allowed object is
 978              *     {@link FeatureMatcherSet }
 979              *
 980              */
 981             public void setMatcherSet(FeatureMatcherSet value) {
 982                 this.matcherSet = value;
 983             }
 984
 985             /**
 986              * Gets the value of the type property.
 987              *
 988              * @return
 989              *     possible object is
 990              *     {@link String }
 991              *
 992              */
 993             public String getType() {
 994                 return type;
 995             }
 996
 997             /**
 998              * Sets the value of the type property.
 999              *
1000              * @param value
1001              *     allowed object is
1002              *     {@link String }
1003              *
1004              */
1005             public void setType(String value) {
1006                 this.type = value;
1007             }
1008
1009             /**
1010              * Gets the value of the colour property.
1011              *
1012              */
1013             public int getColour() {
1014                 return colour;
1015             }
1016
1017             /**
1018              * Sets the value of the colour property.
1019              *
1020              */
1021             public void setColour(int value) {
1022                 this.colour = value;
1023             }
1024
1025             /**
1026              * Gets the value of the display property.
1027              *
1028              */
1029             public boolean isDisplay() {
1030                 return display;
1031             }
1032
1033             /**
1034              * Sets the value of the display property.
1035              *
1036              */
1037             public void setDisplay(boolean value) {
1038                 this.display = value;
1039             }
1040
1041             /**
1042              * Gets the value of the order property.
1043              *
1044              * @return
1045              *     possible object is
1046              *     {@link Float }
1047              *
1048              */
1049             public Float getOrder() {
1050                 return order;
1051             }
1052
1053             /**
1054              * Sets the value of the order property.
1055              *
1056              * @param value
1057              *     allowed object is
1058              *     {@link Float }
1059              *
1060              */
1061             public void setOrder(Float value) {
1062                 this.order = value;
1063             }
1064
1065             /**
1066              * Gets the value of the mincolour property.
1067              *
1068              * @return
1069              *     possible object is
1070              *     {@link Integer }
1071              *
1072              */
1073             public Integer getMincolour() {
1074                 return mincolour;
1075             }
1076
1077             /**
1078              * Sets the value of the mincolour property.
1079              *
1080              * @param value
1081              *     allowed object is
1082              *     {@link Integer }
1083              *
1084              */
1085             public void setMincolour(Integer value) {
1086                 this.mincolour = value;
1087             }
1088
1089             /**
1090              * Gets the value of the noValueColour property.
1091              *
1092              * @return
1093              *     possible object is
1094              *     {@link NoValueColour }
1095              *
1096              */
1097             public NoValueColour getNoValueColour() {
1098                 if (noValueColour == null) {
1099                     return NoValueColour.MIN;
1100                 } else {
1101                     return noValueColour;
1102                 }
1103             }
1104
1105             /**
1106              * Sets the value of the noValueColour property.
1107              *
1108              * @param value
1109              *     allowed object is
1110              *     {@link NoValueColour }
1111              *
1112              */
1113             public void setNoValueColour(NoValueColour value) {
1114                 this.noValueColour = value;
1115             }
1116
1117             /**
1118              * Gets the value of the threshold property.
1119              *
1120              * @return
1121              *     possible object is
1122              *     {@link Float }
1123              *
1124              */
1125             public Float getThreshold() {
1126                 return threshold;
1127             }
1128
1129             /**
1130              * Sets the value of the threshold property.
1131              *
1132              * @param value
1133              *     allowed object is
1134              *     {@link Float }
1135              *
1136              */
1137             public void setThreshold(Float value) {
1138                 this.threshold = value;
1139             }
1140
1141             /**
1142              * Gets the value of the threshstate property.
1143              *
1144              * @return
1145              *     possible object is
1146              *     {@link Integer }
1147              *
1148              */
1149             public Integer getThreshstate() {
1150                 return threshstate;
1151             }
1152
1153             /**
1154              * Sets the value of the threshstate property.
1155              *
1156              * @param value
1157              *     allowed object is
1158              *     {@link Integer }
1159              *
1160              */
1161             public void setThreshstate(Integer value) {
1162                 this.threshstate = value;
1163             }
1164
1165             /**
1166              * Gets the value of the max property.
1167              *
1168              * @return
1169              *     possible object is
1170              *     {@link Float }
1171              *
1172              */
1173             public Float getMax() {
1174                 return max;
1175             }
1176
1177             /**
1178              * Sets the value of the max property.
1179              *
1180              * @param value
1181              *     allowed object is
1182              *     {@link Float }
1183              *
1184              */
1185             public void setMax(Float value) {
1186                 this.max = value;
1187             }
1188
1189             /**
1190              * Gets the value of the min property.
1191              *
1192              * @return
1193              *     possible object is
1194              *     {@link Float }
1195              *
1196              */
1197             public Float getMin() {
1198                 return min;
1199             }
1200
1201             /**
1202              * Sets the value of the min property.
1203              *
1204              * @param value
1205              *     allowed object is
1206              *     {@link Float }
1207              *
1208              */
1209             public void setMin(Float value) {
1210                 this.min = value;
1211             }
1212
1213             /**
1214              * Gets the value of the colourByLabel property.
1215              *
1216              * @return
1217              *     possible object is
1218              *     {@link Boolean }
1219              *
1220              */
1221             public Boolean isColourByLabel() {
1222                 return colourByLabel;
1223             }
1224
1225             /**
1226              * Sets the value of the colourByLabel property.
1227              *
1228              * @param value
1229              *     allowed object is
1230              *     {@link Boolean }
1231              *
1232              */
1233             public void setColourByLabel(Boolean value) {
1234                 this.colourByLabel = value;
1235             }
1236
1237             /**
1238              * Gets the value of the autoScale property.
1239              *
1240              * @return
1241              *     possible object is
1242              *     {@link Boolean }
1243              *
1244              */
1245             public Boolean isAutoScale() {
1246                 return autoScale;
1247             }
1248
1249             /**
1250              * Sets the value of the autoScale property.
1251              *
1252              * @param value
1253              *     allowed object is
1254              *     {@link Boolean }
1255              *
1256              */
1257             public void setAutoScale(Boolean value) {
1258                 this.autoScale = value;
1259             }
1260
1261         }
1262
1263     }
1264
1265
1266     /**
1267      * <p>Java class for anonymous complex type.
1268      *
1269      * <p>The following schema fragment specifies the expected content contained within this class.
1270      *
1271      * <pre>
1272      * &lt;complexType>
1273      *   &lt;complexContent>
1274      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1275      *       &lt;sequence>
1276      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1277      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1278      *       &lt;/sequence>
1279      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1280      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1281      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1282      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1283      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1284      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1285      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1286      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1287      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1288      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1289      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1290      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1291      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1292      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1293      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1294      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1295      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1296      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1297      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1298      *     &lt;/restriction>
1299      *   &lt;/complexContent>
1300      * &lt;/complexType>
1301      * </pre>
1302      *
1303      *
1304      */
1305     @XmlAccessorType(XmlAccessType.FIELD)
1306     @XmlType(name = "", propOrder = {
1307         "seq",
1308         "annotationColours"
1309     })
1310     public static class JGroup {
1311
1312         @XmlElement(namespace = "www.jalview.org", required = true)
1313         protected List<String> seq;
1314         @XmlElement(namespace = "www.jalview.org")
1315         protected AnnotationColourScheme annotationColours;
1316         @XmlAttribute(name = "start")
1317         protected Integer start;
1318         @XmlAttribute(name = "end")
1319         protected Integer end;
1320         @XmlAttribute(name = "name")
1321         protected String name;
1322         @XmlAttribute(name = "colour")
1323         protected String colour;
1324         @XmlAttribute(name = "consThreshold")
1325         protected Integer consThreshold;
1326         @XmlAttribute(name = "pidThreshold")
1327         protected Integer pidThreshold;
1328         @XmlAttribute(name = "outlineColour")
1329         protected Integer outlineColour;
1330         @XmlAttribute(name = "displayBoxes")
1331         protected Boolean displayBoxes;
1332         @XmlAttribute(name = "displayText")
1333         protected Boolean displayText;
1334         @XmlAttribute(name = "colourText")
1335         protected Boolean colourText;
1336         @XmlAttribute(name = "textCol1")
1337         protected Integer textCol1;
1338         @XmlAttribute(name = "textCol2")
1339         protected Integer textCol2;
1340         @XmlAttribute(name = "textColThreshold")
1341         protected Integer textColThreshold;
1342         @XmlAttribute(name = "showUnconserved")
1343         protected Boolean showUnconserved;
1344         @XmlAttribute(name = "ignoreGapsinConsensus")
1345         protected Boolean ignoreGapsinConsensus;
1346         @XmlAttribute(name = "showConsensusHistogram")
1347         protected Boolean showConsensusHistogram;
1348         @XmlAttribute(name = "showSequenceLogo")
1349         protected Boolean showSequenceLogo;
1350         @XmlAttribute(name = "normaliseSequenceLogo")
1351         protected Boolean normaliseSequenceLogo;
1352         @XmlAttribute(name = "id")
1353         protected String id;
1354
1355         /**
1356          * Gets the value of the seq property.
1357          *
1358          * <p>
1359          * This accessor method returns a reference to the live list,
1360          * not a snapshot. Therefore any modification you make to the
1361          * returned list will be present inside the JAXB object.
1362          * This is why there is not a <CODE>set</CODE> method for the seq property.
1363          *
1364          * <p>
1365          * For example, to add a new item, do as follows:
1366          * <pre>
1367          *    getSeq().add(newItem);
1368          * </pre>
1369          *
1370          *
1371          * <p>
1372          * Objects of the following type(s) are allowed in the list
1373          * {@link String }
1374          *
1375          *
1376          */
1377         public List<String> getSeq() {
1378             if (seq == null) {
1379                 seq = new ArrayList<String>();
1380             }
1381             return this.seq;
1382         }
1383
1384         /**
1385          * Gets the value of the annotationColours property.
1386          *
1387          * @return
1388          *     possible object is
1389          *     {@link AnnotationColourScheme }
1390          *
1391          */
1392         public AnnotationColourScheme getAnnotationColours() {
1393             return annotationColours;
1394         }
1395
1396         /**
1397          * Sets the value of the annotationColours property.
1398          *
1399          * @param value
1400          *     allowed object is
1401          *     {@link AnnotationColourScheme }
1402          *
1403          */
1404         public void setAnnotationColours(AnnotationColourScheme value) {
1405             this.annotationColours = value;
1406         }
1407
1408         /**
1409          * Gets the value of the start property.
1410          *
1411          * @return
1412          *     possible object is
1413          *     {@link Integer }
1414          *
1415          */
1416         public Integer getStart() {
1417             return start;
1418         }
1419
1420         /**
1421          * Sets the value of the start property.
1422          *
1423          * @param value
1424          *     allowed object is
1425          *     {@link Integer }
1426          *
1427          */
1428         public void setStart(Integer value) {
1429             this.start = value;
1430         }
1431
1432         /**
1433          * Gets the value of the end property.
1434          *
1435          * @return
1436          *     possible object is
1437          *     {@link Integer }
1438          *
1439          */
1440         public Integer getEnd() {
1441             return end;
1442         }
1443
1444         /**
1445          * Sets the value of the end property.
1446          *
1447          * @param value
1448          *     allowed object is
1449          *     {@link Integer }
1450          *
1451          */
1452         public void setEnd(Integer value) {
1453             this.end = value;
1454         }
1455
1456         /**
1457          * Gets the value of the name property.
1458          *
1459          * @return
1460          *     possible object is
1461          *     {@link String }
1462          *
1463          */
1464         public String getName() {
1465             return name;
1466         }
1467
1468         /**
1469          * Sets the value of the name property.
1470          *
1471          * @param value
1472          *     allowed object is
1473          *     {@link String }
1474          *
1475          */
1476         public void setName(String value) {
1477             this.name = value;
1478         }
1479
1480         /**
1481          * Gets the value of the colour property.
1482          *
1483          * @return
1484          *     possible object is
1485          *     {@link String }
1486          *
1487          */
1488         public String getColour() {
1489             return colour;
1490         }
1491
1492         /**
1493          * Sets the value of the colour property.
1494          *
1495          * @param value
1496          *     allowed object is
1497          *     {@link String }
1498          *
1499          */
1500         public void setColour(String value) {
1501             this.colour = value;
1502         }
1503
1504         /**
1505          * Gets the value of the consThreshold property.
1506          *
1507          * @return
1508          *     possible object is
1509          *     {@link Integer }
1510          *
1511          */
1512         public Integer getConsThreshold() {
1513             return consThreshold;
1514         }
1515
1516         /**
1517          * Sets the value of the consThreshold property.
1518          *
1519          * @param value
1520          *     allowed object is
1521          *     {@link Integer }
1522          *
1523          */
1524         public void setConsThreshold(Integer value) {
1525             this.consThreshold = value;
1526         }
1527
1528         /**
1529          * Gets the value of the pidThreshold property.
1530          *
1531          * @return
1532          *     possible object is
1533          *     {@link Integer }
1534          *
1535          */
1536         public Integer getPidThreshold() {
1537             return pidThreshold;
1538         }
1539
1540         /**
1541          * Sets the value of the pidThreshold property.
1542          *
1543          * @param value
1544          *     allowed object is
1545          *     {@link Integer }
1546          *
1547          */
1548         public void setPidThreshold(Integer value) {
1549             this.pidThreshold = value;
1550         }
1551
1552         /**
1553          * Gets the value of the outlineColour property.
1554          *
1555          * @return
1556          *     possible object is
1557          *     {@link Integer }
1558          *
1559          */
1560         public Integer getOutlineColour() {
1561             return outlineColour;
1562         }
1563
1564         /**
1565          * Sets the value of the outlineColour property.
1566          *
1567          * @param value
1568          *     allowed object is
1569          *     {@link Integer }
1570          *
1571          */
1572         public void setOutlineColour(Integer value) {
1573             this.outlineColour = value;
1574         }
1575
1576         /**
1577          * Gets the value of the displayBoxes property.
1578          *
1579          * @return
1580          *     possible object is
1581          *     {@link Boolean }
1582          *
1583          */
1584         public Boolean isDisplayBoxes() {
1585             return displayBoxes;
1586         }
1587
1588         /**
1589          * Sets the value of the displayBoxes property.
1590          *
1591          * @param value
1592          *     allowed object is
1593          *     {@link Boolean }
1594          *
1595          */
1596         public void setDisplayBoxes(Boolean value) {
1597             this.displayBoxes = value;
1598         }
1599
1600         /**
1601          * Gets the value of the displayText property.
1602          *
1603          * @return
1604          *     possible object is
1605          *     {@link Boolean }
1606          *
1607          */
1608         public Boolean isDisplayText() {
1609             return displayText;
1610         }
1611
1612         /**
1613          * Sets the value of the displayText property.
1614          *
1615          * @param value
1616          *     allowed object is
1617          *     {@link Boolean }
1618          *
1619          */
1620         public void setDisplayText(Boolean value) {
1621             this.displayText = value;
1622         }
1623
1624         /**
1625          * Gets the value of the colourText property.
1626          *
1627          * @return
1628          *     possible object is
1629          *     {@link Boolean }
1630          *
1631          */
1632         public Boolean isColourText() {
1633             return colourText;
1634         }
1635
1636         /**
1637          * Sets the value of the colourText property.
1638          *
1639          * @param value
1640          *     allowed object is
1641          *     {@link Boolean }
1642          *
1643          */
1644         public void setColourText(Boolean value) {
1645             this.colourText = value;
1646         }
1647
1648         /**
1649          * Gets the value of the textCol1 property.
1650          *
1651          * @return
1652          *     possible object is
1653          *     {@link Integer }
1654          *
1655          */
1656         public Integer getTextCol1() {
1657             return textCol1;
1658         }
1659
1660         /**
1661          * Sets the value of the textCol1 property.
1662          *
1663          * @param value
1664          *     allowed object is
1665          *     {@link Integer }
1666          *
1667          */
1668         public void setTextCol1(Integer value) {
1669             this.textCol1 = value;
1670         }
1671
1672         /**
1673          * Gets the value of the textCol2 property.
1674          *
1675          * @return
1676          *     possible object is
1677          *     {@link Integer }
1678          *
1679          */
1680         public Integer getTextCol2() {
1681             return textCol2;
1682         }
1683
1684         /**
1685          * Sets the value of the textCol2 property.
1686          *
1687          * @param value
1688          *     allowed object is
1689          *     {@link Integer }
1690          *
1691          */
1692         public void setTextCol2(Integer value) {
1693             this.textCol2 = value;
1694         }
1695
1696         /**
1697          * Gets the value of the textColThreshold property.
1698          *
1699          * @return
1700          *     possible object is
1701          *     {@link Integer }
1702          *
1703          */
1704         public Integer getTextColThreshold() {
1705             return textColThreshold;
1706         }
1707
1708         /**
1709          * Sets the value of the textColThreshold property.
1710          *
1711          * @param value
1712          *     allowed object is
1713          *     {@link Integer }
1714          *
1715          */
1716         public void setTextColThreshold(Integer value) {
1717             this.textColThreshold = value;
1718         }
1719
1720         /**
1721          * Gets the value of the showUnconserved property.
1722          *
1723          * @return
1724          *     possible object is
1725          *     {@link Boolean }
1726          *
1727          */
1728         public Boolean isShowUnconserved() {
1729             return showUnconserved;
1730         }
1731
1732         /**
1733          * Sets the value of the showUnconserved property.
1734          *
1735          * @param value
1736          *     allowed object is
1737          *     {@link Boolean }
1738          *
1739          */
1740         public void setShowUnconserved(Boolean value) {
1741             this.showUnconserved = value;
1742         }
1743
1744         /**
1745          * Gets the value of the ignoreGapsinConsensus property.
1746          *
1747          * @return
1748          *     possible object is
1749          *     {@link Boolean }
1750          *
1751          */
1752         public boolean isIgnoreGapsinConsensus() {
1753             if (ignoreGapsinConsensus == null) {
1754                 return true;
1755             } else {
1756                 return ignoreGapsinConsensus;
1757             }
1758         }
1759
1760         /**
1761          * Sets the value of the ignoreGapsinConsensus property.
1762          *
1763          * @param value
1764          *     allowed object is
1765          *     {@link Boolean }
1766          *
1767          */
1768         public void setIgnoreGapsinConsensus(Boolean value) {
1769             this.ignoreGapsinConsensus = value;
1770         }
1771
1772         /**
1773          * Gets the value of the showConsensusHistogram property.
1774          *
1775          * @return
1776          *     possible object is
1777          *     {@link Boolean }
1778          *
1779          */
1780         public boolean isShowConsensusHistogram() {
1781             if (showConsensusHistogram == null) {
1782                 return true;
1783             } else {
1784                 return showConsensusHistogram;
1785             }
1786         }
1787
1788         /**
1789          * Sets the value of the showConsensusHistogram property.
1790          *
1791          * @param value
1792          *     allowed object is
1793          *     {@link Boolean }
1794          *
1795          */
1796         public void setShowConsensusHistogram(Boolean value) {
1797             this.showConsensusHistogram = value;
1798         }
1799
1800         /**
1801          * Gets the value of the showSequenceLogo property.
1802          *
1803          * @return
1804          *     possible object is
1805          *     {@link Boolean }
1806          *
1807          */
1808         public boolean isShowSequenceLogo() {
1809             if (showSequenceLogo == null) {
1810                 return false;
1811             } else {
1812                 return showSequenceLogo;
1813             }
1814         }
1815
1816         /**
1817          * Sets the value of the showSequenceLogo property.
1818          *
1819          * @param value
1820          *     allowed object is
1821          *     {@link Boolean }
1822          *
1823          */
1824         public void setShowSequenceLogo(Boolean value) {
1825             this.showSequenceLogo = value;
1826         }
1827
1828         /**
1829          * Gets the value of the normaliseSequenceLogo property.
1830          *
1831          * @return
1832          *     possible object is
1833          *     {@link Boolean }
1834          *
1835          */
1836         public boolean isNormaliseSequenceLogo() {
1837             if (normaliseSequenceLogo == null) {
1838                 return false;
1839             } else {
1840                 return normaliseSequenceLogo;
1841             }
1842         }
1843
1844         /**
1845          * Sets the value of the normaliseSequenceLogo property.
1846          *
1847          * @param value
1848          *     allowed object is
1849          *     {@link Boolean }
1850          *
1851          */
1852         public void setNormaliseSequenceLogo(Boolean value) {
1853             this.normaliseSequenceLogo = value;
1854         }
1855
1856         /**
1857          * Gets the value of the id property.
1858          *
1859          * @return
1860          *     possible object is
1861          *     {@link String }
1862          *
1863          */
1864         public String getId() {
1865             return id;
1866         }
1867
1868         /**
1869          * Sets the value of the id property.
1870          *
1871          * @param value
1872          *     allowed object is
1873          *     {@link String }
1874          *
1875          */
1876         public void setId(String value) {
1877             this.id = value;
1878         }
1879
1880     }
1881
1882
1883     /**
1884      * <p>Java class for anonymous complex type.
1885      *
1886      * <p>The following schema fragment specifies the expected content contained within this class.
1887      *
1888      * <pre>
1889      * &lt;complexType>
1890      *   &lt;complexContent>
1891      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1892      *       &lt;sequence>
1893      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1894      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1895      *           &lt;complexType>
1896      *             &lt;complexContent>
1897      *               &lt;extension base="{www.jalview.org}pdbentry">
1898      *                 &lt;sequence>
1899      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1900      *                     &lt;complexType>
1901      *                       &lt;simpleContent>
1902      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1903      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1904      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1905      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1906      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1907      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1908      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1909      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1910      *                         &lt;/extension>
1911      *                       &lt;/simpleContent>
1912      *                     &lt;/complexType>
1913      *                   &lt;/element>
1914      *                 &lt;/sequence>
1915      *               &lt;/extension>
1916      *             &lt;/complexContent>
1917      *           &lt;/complexType>
1918      *         &lt;/element>
1919      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1920      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1921      *           &lt;complexType>
1922      *             &lt;complexContent>
1923      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1924      *                 &lt;sequence>
1925      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1926      *                     &lt;complexType>
1927      *                       &lt;complexContent>
1928      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1929      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1930      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1931      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1932      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1933      *                         &lt;/restriction>
1934      *                       &lt;/complexContent>
1935      *                     &lt;/complexType>
1936      *                   &lt;/element>
1937      *                 &lt;/sequence>
1938      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1939      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1940      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1941      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1942      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1943      *               &lt;/restriction>
1944      *             &lt;/complexContent>
1945      *           &lt;/complexType>
1946      *         &lt;/element>
1947      *         &lt;element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
1948      *       &lt;/sequence>
1949      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1950      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1951      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1952      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1953      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1954      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1955      *     &lt;/restriction>
1956      *   &lt;/complexContent>
1957      * &lt;/complexType>
1958      * </pre>
1959      *
1960      *
1961      */
1962     @XmlAccessorType(XmlAccessType.FIELD)
1963     @XmlType(name = "", propOrder = {
1964         "features",
1965         "pdbids",
1966         "hiddenSequences",
1967         "rnaViewer",
1968         "hmmerProfile"
1969     })
1970     public static class JSeq {
1971
1972         @XmlElement(namespace = "www.jalview.org")
1973         protected List<Feature> features;
1974         @XmlElement(namespace = "www.jalview.org")
1975         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1976         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1977         protected List<Integer> hiddenSequences;
1978         @XmlElement(namespace = "www.jalview.org")
1979         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1980         @XmlElement(namespace = "www.jalview.org")
1981         protected String hmmerProfile;
1982         @XmlAttribute(name = "colour")
1983         protected Integer colour;
1984         @XmlAttribute(name = "start", required = true)
1985         protected int start;
1986         @XmlAttribute(name = "end", required = true)
1987         protected int end;
1988         @XmlAttribute(name = "id", required = true)
1989         protected String id;
1990         @XmlAttribute(name = "hidden")
1991         protected Boolean hidden;
1992         @XmlAttribute(name = "viewreference")
1993         protected Boolean viewreference;
1994
1995         /**
1996          * Gets the value of the features property.
1997          *
1998          * <p>
1999          * This accessor method returns a reference to the live list,
2000          * not a snapshot. Therefore any modification you make to the
2001          * returned list will be present inside the JAXB object.
2002          * This is why there is not a <CODE>set</CODE> method for the features property.
2003          *
2004          * <p>
2005          * For example, to add a new item, do as follows:
2006          * <pre>
2007          *    getFeatures().add(newItem);
2008          * </pre>
2009          *
2010          *
2011          * <p>
2012          * Objects of the following type(s) are allowed in the list
2013          * {@link Feature }
2014          *
2015          *
2016          */
2017         public List<Feature> getFeatures() {
2018             if (features == null) {
2019                 features = new ArrayList<Feature>();
2020             }
2021             return this.features;
2022         }
2023
2024         /**
2025          * Gets the value of the pdbids property.
2026          *
2027          * <p>
2028          * This accessor method returns a reference to the live list,
2029          * not a snapshot. Therefore any modification you make to the
2030          * returned list will be present inside the JAXB object.
2031          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2032          *
2033          * <p>
2034          * For example, to add a new item, do as follows:
2035          * <pre>
2036          *    getPdbids().add(newItem);
2037          * </pre>
2038          *
2039          *
2040          * <p>
2041          * Objects of the following type(s) are allowed in the list
2042          * {@link JalviewModel.JSeq.Pdbids }
2043          *
2044          *
2045          */
2046         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2047             if (pdbids == null) {
2048                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2049             }
2050             return this.pdbids;
2051         }
2052
2053         /**
2054          * Gets the value of the hiddenSequences property.
2055          *
2056          * <p>
2057          * This accessor method returns a reference to the live list,
2058          * not a snapshot. Therefore any modification you make to the
2059          * returned list will be present inside the JAXB object.
2060          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2061          *
2062          * <p>
2063          * For example, to add a new item, do as follows:
2064          * <pre>
2065          *    getHiddenSequences().add(newItem);
2066          * </pre>
2067          *
2068          *
2069          * <p>
2070          * Objects of the following type(s) are allowed in the list
2071          * {@link Integer }
2072          *
2073          *
2074          */
2075         public List<Integer> getHiddenSequences() {
2076             if (hiddenSequences == null) {
2077                 hiddenSequences = new ArrayList<Integer>();
2078             }
2079             return this.hiddenSequences;
2080         }
2081
2082         /**
2083          * Gets the value of the rnaViewer property.
2084          *
2085          * <p>
2086          * This accessor method returns a reference to the live list,
2087          * not a snapshot. Therefore any modification you make to the
2088          * returned list will be present inside the JAXB object.
2089          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2090          *
2091          * <p>
2092          * For example, to add a new item, do as follows:
2093          * <pre>
2094          *    getRnaViewer().add(newItem);
2095          * </pre>
2096          *
2097          *
2098          * <p>
2099          * Objects of the following type(s) are allowed in the list
2100          * {@link JalviewModel.JSeq.RnaViewer }
2101          *
2102          *
2103          */
2104         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2105             if (rnaViewer == null) {
2106                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2107             }
2108             return this.rnaViewer;
2109         }
2110
2111         /**
2112          * Gets the value of the hmmerProfile property.
2113          *
2114          * @return
2115          *     possible object is
2116          *     {@link String }
2117          *
2118          */
2119         public String getHmmerProfile() {
2120             return hmmerProfile;
2121         }
2122
2123         /**
2124          * Sets the value of the hmmerProfile property.
2125          *
2126          * @param value
2127          *     allowed object is
2128          *     {@link String }
2129          *
2130          */
2131         public void setHmmerProfile(String value) {
2132             this.hmmerProfile = value;
2133         }
2134
2135         /**
2136          * Gets the value of the colour property.
2137          *
2138          * @return
2139          *     possible object is
2140          *     {@link Integer }
2141          *
2142          */
2143         public Integer getColour() {
2144             return colour;
2145         }
2146
2147         /**
2148          * Sets the value of the colour property.
2149          *
2150          * @param value
2151          *     allowed object is
2152          *     {@link Integer }
2153          *
2154          */
2155         public void setColour(Integer value) {
2156             this.colour = value;
2157         }
2158
2159         /**
2160          * Gets the value of the start property.
2161          *
2162          */
2163         public int getStart() {
2164             return start;
2165         }
2166
2167         /**
2168          * Sets the value of the start property.
2169          *
2170          */
2171         public void setStart(int value) {
2172             this.start = value;
2173         }
2174
2175         /**
2176          * Gets the value of the end property.
2177          *
2178          */
2179         public int getEnd() {
2180             return end;
2181         }
2182
2183         /**
2184          * Sets the value of the end property.
2185          *
2186          */
2187         public void setEnd(int value) {
2188             this.end = value;
2189         }
2190
2191         /**
2192          * Gets the value of the id property.
2193          *
2194          * @return
2195          *     possible object is
2196          *     {@link String }
2197          *
2198          */
2199         public String getId() {
2200             return id;
2201         }
2202
2203         /**
2204          * Sets the value of the id property.
2205          *
2206          * @param value
2207          *     allowed object is
2208          *     {@link String }
2209          *
2210          */
2211         public void setId(String value) {
2212             this.id = value;
2213         }
2214
2215         /**
2216          * Gets the value of the hidden property.
2217          *
2218          * @return
2219          *     possible object is
2220          *     {@link Boolean }
2221          *
2222          */
2223         public Boolean isHidden() {
2224             return hidden;
2225         }
2226
2227         /**
2228          * Sets the value of the hidden property.
2229          *
2230          * @param value
2231          *     allowed object is
2232          *     {@link Boolean }
2233          *
2234          */
2235         public void setHidden(Boolean value) {
2236             this.hidden = value;
2237         }
2238
2239         /**
2240          * Gets the value of the viewreference property.
2241          *
2242          * @return
2243          *     possible object is
2244          *     {@link Boolean }
2245          *
2246          */
2247         public Boolean isViewreference() {
2248             return viewreference;
2249         }
2250
2251         /**
2252          * Sets the value of the viewreference property.
2253          *
2254          * @param value
2255          *     allowed object is
2256          *     {@link Boolean }
2257          *
2258          */
2259         public void setViewreference(Boolean value) {
2260             this.viewreference = value;
2261         }
2262
2263
2264         /**
2265          * <p>Java class for anonymous complex type.
2266          *
2267          * <p>The following schema fragment specifies the expected content contained within this class.
2268          *
2269          * <pre>
2270          * &lt;complexType>
2271          *   &lt;complexContent>
2272          *     &lt;extension base="{www.jalview.org}pdbentry">
2273          *       &lt;sequence>
2274          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2275          *           &lt;complexType>
2276          *             &lt;simpleContent>
2277          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2278          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2279          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2280          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2281          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2282          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2283          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2284          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2285          *               &lt;/extension>
2286          *             &lt;/simpleContent>
2287          *           &lt;/complexType>
2288          *         &lt;/element>
2289          *       &lt;/sequence>
2290          *     &lt;/extension>
2291          *   &lt;/complexContent>
2292          * &lt;/complexType>
2293          * </pre>
2294          *
2295          *
2296          */
2297         @XmlAccessorType(XmlAccessType.FIELD)
2298         @XmlType(name = "", propOrder = {
2299             "structureState"
2300         })
2301         public static class Pdbids
2302             extends Pdbentry
2303         {
2304
2305             @XmlElement(namespace = "www.jalview.org")
2306             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2307
2308             /**
2309              * Gets the value of the structureState property.
2310              *
2311              * <p>
2312              * This accessor method returns a reference to the live list,
2313              * not a snapshot. Therefore any modification you make to the
2314              * returned list will be present inside the JAXB object.
2315              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2316              *
2317              * <p>
2318              * For example, to add a new item, do as follows:
2319              * <pre>
2320              *    getStructureState().add(newItem);
2321              * </pre>
2322              *
2323              *
2324              * <p>
2325              * Objects of the following type(s) are allowed in the list
2326              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2327              *
2328              *
2329              */
2330             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2331                 if (structureState == null) {
2332                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2333                 }
2334                 return this.structureState;
2335             }
2336
2337
2338             /**
2339              * <p>Java class for anonymous complex type.
2340              *
2341              * <p>The following schema fragment specifies the expected content contained within this class.
2342              *
2343              * <pre>
2344              * &lt;complexType>
2345              *   &lt;simpleContent>
2346              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2347              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2348              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2349              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2350              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2351              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2352              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2353              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2354              *     &lt;/extension>
2355              *   &lt;/simpleContent>
2356              * &lt;/complexType>
2357              * </pre>
2358              *
2359              *
2360              */
2361             @XmlAccessorType(XmlAccessType.FIELD)
2362             @XmlType(name = "", propOrder = {
2363                 "value"
2364             })
2365             public static class StructureState {
2366
2367                 @XmlValue
2368                 protected String value;
2369                 @XmlAttribute(name = "visible")
2370                 protected Boolean visible;
2371                 @XmlAttribute(name = "viewId")
2372                 protected String viewId;
2373                 @XmlAttribute(name = "alignwithAlignPanel")
2374                 protected Boolean alignwithAlignPanel;
2375                 @XmlAttribute(name = "colourwithAlignPanel")
2376                 protected Boolean colourwithAlignPanel;
2377                 @XmlAttribute(name = "colourByJmol")
2378                 protected Boolean colourByJmol;
2379                 @XmlAttribute(name = "type")
2380                 protected String type;
2381                 @XmlAttribute(name = "width")
2382                 protected Integer width;
2383                 @XmlAttribute(name = "height")
2384                 protected Integer height;
2385                 @XmlAttribute(name = "xpos")
2386                 protected Integer xpos;
2387                 @XmlAttribute(name = "ypos")
2388                 protected Integer ypos;
2389
2390                 /**
2391                  * Gets the value of the value property.
2392                  *
2393                  * @return
2394                  *     possible object is
2395                  *     {@link String }
2396                  *
2397                  */
2398                 public String getValue() {
2399                     return value;
2400                 }
2401
2402                 /**
2403                  * Sets the value of the value property.
2404                  *
2405                  * @param value
2406                  *     allowed object is
2407                  *     {@link String }
2408                  *
2409                  */
2410                 public void setValue(String value) {
2411                     this.value = value;
2412                 }
2413
2414                 /**
2415                  * Gets the value of the visible property.
2416                  *
2417                  * @return
2418                  *     possible object is
2419                  *     {@link Boolean }
2420                  *
2421                  */
2422                 public Boolean isVisible() {
2423                     return visible;
2424                 }
2425
2426                 /**
2427                  * Sets the value of the visible property.
2428                  *
2429                  * @param value
2430                  *     allowed object is
2431                  *     {@link Boolean }
2432                  *
2433                  */
2434                 public void setVisible(Boolean value) {
2435                     this.visible = value;
2436                 }
2437
2438                 /**
2439                  * Gets the value of the viewId property.
2440                  *
2441                  * @return
2442                  *     possible object is
2443                  *     {@link String }
2444                  *
2445                  */
2446                 public String getViewId() {
2447                     return viewId;
2448                 }
2449
2450                 /**
2451                  * Sets the value of the viewId property.
2452                  *
2453                  * @param value
2454                  *     allowed object is
2455                  *     {@link String }
2456                  *
2457                  */
2458                 public void setViewId(String value) {
2459                     this.viewId = value;
2460                 }
2461
2462                 /**
2463                  * Gets the value of the alignwithAlignPanel property.
2464                  *
2465                  * @return
2466                  *     possible object is
2467                  *     {@link Boolean }
2468                  *
2469                  */
2470                 public boolean isAlignwithAlignPanel() {
2471                     if (alignwithAlignPanel == null) {
2472                         return true;
2473                     } else {
2474                         return alignwithAlignPanel;
2475                     }
2476                 }
2477
2478                 /**
2479                  * Sets the value of the alignwithAlignPanel property.
2480                  *
2481                  * @param value
2482                  *     allowed object is
2483                  *     {@link Boolean }
2484                  *
2485                  */
2486                 public void setAlignwithAlignPanel(Boolean value) {
2487                     this.alignwithAlignPanel = value;
2488                 }
2489
2490                 /**
2491                  * Gets the value of the colourwithAlignPanel property.
2492                  *
2493                  * @return
2494                  *     possible object is
2495                  *     {@link Boolean }
2496                  *
2497                  */
2498                 public boolean isColourwithAlignPanel() {
2499                     if (colourwithAlignPanel == null) {
2500                         return false;
2501                     } else {
2502                         return colourwithAlignPanel;
2503                     }
2504                 }
2505
2506                 /**
2507                  * Sets the value of the colourwithAlignPanel property.
2508                  *
2509                  * @param value
2510                  *     allowed object is
2511                  *     {@link Boolean }
2512                  *
2513                  */
2514                 public void setColourwithAlignPanel(Boolean value) {
2515                     this.colourwithAlignPanel = value;
2516                 }
2517
2518                 /**
2519                  * Gets the value of the colourByJmol property.
2520                  *
2521                  * @return
2522                  *     possible object is
2523                  *     {@link Boolean }
2524                  *
2525                  */
2526                 public boolean isColourByJmol() {
2527                     if (colourByJmol == null) {
2528                         return true;
2529                     } else {
2530                         return colourByJmol;
2531                     }
2532                 }
2533
2534                 /**
2535                  * Sets the value of the colourByJmol property.
2536                  *
2537                  * @param value
2538                  *     allowed object is
2539                  *     {@link Boolean }
2540                  *
2541                  */
2542                 public void setColourByJmol(Boolean value) {
2543                     this.colourByJmol = value;
2544                 }
2545
2546                 /**
2547                  * Gets the value of the type property.
2548                  *
2549                  * @return
2550                  *     possible object is
2551                  *     {@link String }
2552                  *
2553                  */
2554                 public String getType() {
2555                     return type;
2556                 }
2557
2558                 /**
2559                  * Sets the value of the type property.
2560                  *
2561                  * @param value
2562                  *     allowed object is
2563                  *     {@link String }
2564                  *
2565                  */
2566                 public void setType(String value) {
2567                     this.type = value;
2568                 }
2569
2570                 /**
2571                  * Gets the value of the width property.
2572                  *
2573                  * @return
2574                  *     possible object is
2575                  *     {@link Integer }
2576                  *
2577                  */
2578                 public Integer getWidth() {
2579                     return width;
2580                 }
2581
2582                 /**
2583                  * Sets the value of the width property.
2584                  *
2585                  * @param value
2586                  *     allowed object is
2587                  *     {@link Integer }
2588                  *
2589                  */
2590                 public void setWidth(Integer value) {
2591                     this.width = value;
2592                 }
2593
2594                 /**
2595                  * Gets the value of the height property.
2596                  *
2597                  * @return
2598                  *     possible object is
2599                  *     {@link Integer }
2600                  *
2601                  */
2602                 public Integer getHeight() {
2603                     return height;
2604                 }
2605
2606                 /**
2607                  * Sets the value of the height property.
2608                  *
2609                  * @param value
2610                  *     allowed object is
2611                  *     {@link Integer }
2612                  *
2613                  */
2614                 public void setHeight(Integer value) {
2615                     this.height = value;
2616                 }
2617
2618                 /**
2619                  * Gets the value of the xpos property.
2620                  *
2621                  * @return
2622                  *     possible object is
2623                  *     {@link Integer }
2624                  *
2625                  */
2626                 public Integer getXpos() {
2627                     return xpos;
2628                 }
2629
2630                 /**
2631                  * Sets the value of the xpos property.
2632                  *
2633                  * @param value
2634                  *     allowed object is
2635                  *     {@link Integer }
2636                  *
2637                  */
2638                 public void setXpos(Integer value) {
2639                     this.xpos = value;
2640                 }
2641
2642                 /**
2643                  * Gets the value of the ypos property.
2644                  *
2645                  * @return
2646                  *     possible object is
2647                  *     {@link Integer }
2648                  *
2649                  */
2650                 public Integer getYpos() {
2651                     return ypos;
2652                 }
2653
2654                 /**
2655                  * Sets the value of the ypos property.
2656                  *
2657                  * @param value
2658                  *     allowed object is
2659                  *     {@link Integer }
2660                  *
2661                  */
2662                 public void setYpos(Integer value) {
2663                     this.ypos = value;
2664                 }
2665
2666             }
2667
2668         }
2669
2670
2671         /**
2672          * <p>Java class for anonymous complex type.
2673          *
2674          * <p>The following schema fragment specifies the expected content contained within this class.
2675          *
2676          * <pre>
2677          * &lt;complexType>
2678          *   &lt;complexContent>
2679          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2680          *       &lt;sequence>
2681          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2682          *           &lt;complexType>
2683          *             &lt;complexContent>
2684          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2685          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2686          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2687          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2688          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2689          *               &lt;/restriction>
2690          *             &lt;/complexContent>
2691          *           &lt;/complexType>
2692          *         &lt;/element>
2693          *       &lt;/sequence>
2694          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2695          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2696          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2697          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2698          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2699          *     &lt;/restriction>
2700          *   &lt;/complexContent>
2701          * &lt;/complexType>
2702          * </pre>
2703          *
2704          *
2705          */
2706         @XmlAccessorType(XmlAccessType.FIELD)
2707         @XmlType(name = "", propOrder = {
2708             "secondaryStructure"
2709         })
2710         public static class RnaViewer {
2711
2712             @XmlElement(namespace = "www.jalview.org", required = true)
2713             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2714             @XmlAttribute(name = "title")
2715             protected String title;
2716             @XmlAttribute(name = "viewId")
2717             protected String viewId;
2718             @XmlAttribute(name = "dividerLocation")
2719             protected Integer dividerLocation;
2720             @XmlAttribute(name = "selectedRna")
2721             protected Integer selectedRna;
2722             @XmlAttribute(name = "width")
2723             protected Integer width;
2724             @XmlAttribute(name = "height")
2725             protected Integer height;
2726             @XmlAttribute(name = "xpos")
2727             protected Integer xpos;
2728             @XmlAttribute(name = "ypos")
2729             protected Integer ypos;
2730
2731             /**
2732              * Gets the value of the secondaryStructure property.
2733              *
2734              * <p>
2735              * This accessor method returns a reference to the live list,
2736              * not a snapshot. Therefore any modification you make to the
2737              * returned list will be present inside the JAXB object.
2738              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2739              *
2740              * <p>
2741              * For example, to add a new item, do as follows:
2742              * <pre>
2743              *    getSecondaryStructure().add(newItem);
2744              * </pre>
2745              *
2746              *
2747              * <p>
2748              * Objects of the following type(s) are allowed in the list
2749              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2750              *
2751              *
2752              */
2753             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2754                 if (secondaryStructure == null) {
2755                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2756                 }
2757                 return this.secondaryStructure;
2758             }
2759
2760             /**
2761              * Gets the value of the title property.
2762              *
2763              * @return
2764              *     possible object is
2765              *     {@link String }
2766              *
2767              */
2768             public String getTitle() {
2769                 return title;
2770             }
2771
2772             /**
2773              * Sets the value of the title property.
2774              *
2775              * @param value
2776              *     allowed object is
2777              *     {@link String }
2778              *
2779              */
2780             public void setTitle(String value) {
2781                 this.title = value;
2782             }
2783
2784             /**
2785              * Gets the value of the viewId property.
2786              *
2787              * @return
2788              *     possible object is
2789              *     {@link String }
2790              *
2791              */
2792             public String getViewId() {
2793                 return viewId;
2794             }
2795
2796             /**
2797              * Sets the value of the viewId property.
2798              *
2799              * @param value
2800              *     allowed object is
2801              *     {@link String }
2802              *
2803              */
2804             public void setViewId(String value) {
2805                 this.viewId = value;
2806             }
2807
2808             /**
2809              * Gets the value of the dividerLocation property.
2810              *
2811              * @return
2812              *     possible object is
2813              *     {@link Integer }
2814              *
2815              */
2816             public Integer getDividerLocation() {
2817                 return dividerLocation;
2818             }
2819
2820             /**
2821              * Sets the value of the dividerLocation property.
2822              *
2823              * @param value
2824              *     allowed object is
2825              *     {@link Integer }
2826              *
2827              */
2828             public void setDividerLocation(Integer value) {
2829                 this.dividerLocation = value;
2830             }
2831
2832             /**
2833              * Gets the value of the selectedRna property.
2834              *
2835              * @return
2836              *     possible object is
2837              *     {@link Integer }
2838              *
2839              */
2840             public Integer getSelectedRna() {
2841                 return selectedRna;
2842             }
2843
2844             /**
2845              * Sets the value of the selectedRna property.
2846              *
2847              * @param value
2848              *     allowed object is
2849              *     {@link Integer }
2850              *
2851              */
2852             public void setSelectedRna(Integer value) {
2853                 this.selectedRna = value;
2854             }
2855
2856             /**
2857              * Gets the value of the width property.
2858              *
2859              * @return
2860              *     possible object is
2861              *     {@link Integer }
2862              *
2863              */
2864             public Integer getWidth() {
2865                 return width;
2866             }
2867
2868             /**
2869              * Sets the value of the width property.
2870              *
2871              * @param value
2872              *     allowed object is
2873              *     {@link Integer }
2874              *
2875              */
2876             public void setWidth(Integer value) {
2877                 this.width = value;
2878             }
2879
2880             /**
2881              * Gets the value of the height property.
2882              *
2883              * @return
2884              *     possible object is
2885              *     {@link Integer }
2886              *
2887              */
2888             public Integer getHeight() {
2889                 return height;
2890             }
2891
2892             /**
2893              * Sets the value of the height property.
2894              *
2895              * @param value
2896              *     allowed object is
2897              *     {@link Integer }
2898              *
2899              */
2900             public void setHeight(Integer value) {
2901                 this.height = value;
2902             }
2903
2904             /**
2905              * Gets the value of the xpos property.
2906              *
2907              * @return
2908              *     possible object is
2909              *     {@link Integer }
2910              *
2911              */
2912             public Integer getXpos() {
2913                 return xpos;
2914             }
2915
2916             /**
2917              * Sets the value of the xpos property.
2918              *
2919              * @param value
2920              *     allowed object is
2921              *     {@link Integer }
2922              *
2923              */
2924             public void setXpos(Integer value) {
2925                 this.xpos = value;
2926             }
2927
2928             /**
2929              * Gets the value of the ypos property.
2930              *
2931              * @return
2932              *     possible object is
2933              *     {@link Integer }
2934              *
2935              */
2936             public Integer getYpos() {
2937                 return ypos;
2938             }
2939
2940             /**
2941              * Sets the value of the ypos property.
2942              *
2943              * @param value
2944              *     allowed object is
2945              *     {@link Integer }
2946              *
2947              */
2948             public void setYpos(Integer value) {
2949                 this.ypos = value;
2950             }
2951
2952
2953             /**
2954              * <p>Java class for anonymous complex type.
2955              *
2956              * <p>The following schema fragment specifies the expected content contained within this class.
2957              *
2958              * <pre>
2959              * &lt;complexType>
2960              *   &lt;complexContent>
2961              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2962              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2963              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2964              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2965              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2966              *     &lt;/restriction>
2967              *   &lt;/complexContent>
2968              * &lt;/complexType>
2969              * </pre>
2970              *
2971              *
2972              */
2973             @XmlAccessorType(XmlAccessType.FIELD)
2974             @XmlType(name = "")
2975             public static class SecondaryStructure {
2976
2977                 @XmlAttribute(name = "title")
2978                 protected String title;
2979                 @XmlAttribute(name = "annotationId", required = true)
2980                 protected String annotationId;
2981                 @XmlAttribute(name = "gapped")
2982                 protected Boolean gapped;
2983                 @XmlAttribute(name = "viewerState")
2984                 protected String viewerState;
2985
2986                 /**
2987                  * Gets the value of the title property.
2988                  *
2989                  * @return
2990                  *     possible object is
2991                  *     {@link String }
2992                  *
2993                  */
2994                 public String getTitle() {
2995                     return title;
2996                 }
2997
2998                 /**
2999                  * Sets the value of the title property.
3000                  *
3001                  * @param value
3002                  *     allowed object is
3003                  *     {@link String }
3004                  *
3005                  */
3006                 public void setTitle(String value) {
3007                     this.title = value;
3008                 }
3009
3010                 /**
3011                  * Gets the value of the annotationId property.
3012                  *
3013                  * @return
3014                  *     possible object is
3015                  *     {@link String }
3016                  *
3017                  */
3018                 public String getAnnotationId() {
3019                     return annotationId;
3020                 }
3021
3022                 /**
3023                  * Sets the value of the annotationId property.
3024                  *
3025                  * @param value
3026                  *     allowed object is
3027                  *     {@link String }
3028                  *
3029                  */
3030                 public void setAnnotationId(String value) {
3031                     this.annotationId = value;
3032                 }
3033
3034                 /**
3035                  * Gets the value of the gapped property.
3036                  *
3037                  * @return
3038                  *     possible object is
3039                  *     {@link Boolean }
3040                  *
3041                  */
3042                 public Boolean isGapped() {
3043                     return gapped;
3044                 }
3045
3046                 /**
3047                  * Sets the value of the gapped property.
3048                  *
3049                  * @param value
3050                  *     allowed object is
3051                  *     {@link Boolean }
3052                  *
3053                  */
3054                 public void setGapped(Boolean value) {
3055                     this.gapped = value;
3056                 }
3057
3058                 /**
3059                  * Gets the value of the viewerState property.
3060                  *
3061                  * @return
3062                  *     possible object is
3063                  *     {@link String }
3064                  *
3065                  */
3066                 public String getViewerState() {
3067                     return viewerState;
3068                 }
3069
3070                 /**
3071                  * Sets the value of the viewerState property.
3072                  *
3073                  * @param value
3074                  *     allowed object is
3075                  *     {@link String }
3076                  *
3077                  */
3078                 public void setViewerState(String value) {
3079                     this.viewerState = value;
3080                 }
3081
3082             }
3083
3084         }
3085
3086     }
3087
3088
3089     /**
3090      * <p>Java class for anonymous complex type.
3091      *
3092      * <p>The following schema fragment specifies the expected content contained within this class.
3093      *
3094      * <pre>
3095      * &lt;complexType>
3096      *   &lt;complexContent>
3097      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3098      *       &lt;sequence>
3099      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3100      *           &lt;complexType>
3101      *             &lt;complexContent>
3102      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3103      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3104      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3105      *               &lt;/restriction>
3106      *             &lt;/complexContent>
3107      *           &lt;/complexType>
3108      *         &lt;/element>
3109      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3110      *           &lt;complexType>
3111      *             &lt;complexContent>
3112      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3113      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3114      *               &lt;/restriction>
3115      *             &lt;/complexContent>
3116      *           &lt;/complexType>
3117      *         &lt;/element>
3118      *         &lt;element name="seqPointMin">
3119      *           &lt;complexType>
3120      *             &lt;complexContent>
3121      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3122      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3123      *               &lt;/restriction>
3124      *             &lt;/complexContent>
3125      *           &lt;/complexType>
3126      *         &lt;/element>
3127      *         &lt;element name="seqPointMax">
3128      *           &lt;complexType>
3129      *             &lt;complexContent>
3130      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3131      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3132      *               &lt;/restriction>
3133      *             &lt;/complexContent>
3134      *           &lt;/complexType>
3135      *         &lt;/element>
3136      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3137      *       &lt;/sequence>
3138      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3139      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3140      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3141      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3142      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3143      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3144      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3145      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3146      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3147      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3148      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3149      *     &lt;/restriction>
3150      *   &lt;/complexContent>
3151      * &lt;/complexType>
3152      * </pre>
3153      *
3154      *
3155      */
3156     @XmlAccessorType(XmlAccessType.FIELD)
3157     @XmlType(name = "", propOrder = {
3158         "sequencePoint",
3159         "axis",
3160         "seqPointMin",
3161         "seqPointMax",
3162         "pcaData"
3163     })
3164     public static class PcaViewer {
3165
3166         @XmlElement(namespace = "www.jalview.org", required = true)
3167         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3168         @XmlElement(namespace = "www.jalview.org", required = true)
3169         protected List<JalviewModel.PcaViewer.Axis> axis;
3170         @XmlElement(namespace = "www.jalview.org", required = true)
3171         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3172         @XmlElement(namespace = "www.jalview.org", required = true)
3173         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3174         @XmlElement(namespace = "www.jalview.org", required = true)
3175         protected PcaDataType pcaData;
3176         @XmlAttribute(name = "title")
3177         protected String title;
3178         @XmlAttribute(name = "scoreModelName")
3179         protected String scoreModelName;
3180         @XmlAttribute(name = "xDim")
3181         protected Integer xDim;
3182         @XmlAttribute(name = "yDim")
3183         protected Integer yDim;
3184         @XmlAttribute(name = "zDim")
3185         protected Integer zDim;
3186         @XmlAttribute(name = "bgColour")
3187         protected Integer bgColour;
3188         @XmlAttribute(name = "scaleFactor")
3189         protected Float scaleFactor;
3190         @XmlAttribute(name = "showLabels")
3191         protected Boolean showLabels;
3192         @XmlAttribute(name = "linkToAllViews")
3193         protected Boolean linkToAllViews;
3194         @XmlAttribute(name = "width")
3195         protected Integer width;
3196         @XmlAttribute(name = "height")
3197         protected Integer height;
3198         @XmlAttribute(name = "xpos")
3199         protected Integer xpos;
3200         @XmlAttribute(name = "ypos")
3201         protected Integer ypos;
3202         @XmlAttribute(name = "includeGaps")
3203         protected Boolean includeGaps;
3204         @XmlAttribute(name = "matchGaps")
3205         protected Boolean matchGaps;
3206         @XmlAttribute(name = "includeGappedColumns")
3207         protected Boolean includeGappedColumns;
3208         @XmlAttribute(name = "denominateByShortestLength")
3209         protected Boolean denominateByShortestLength;
3210
3211         /**
3212          * Gets the value of the sequencePoint property.
3213          *
3214          * <p>
3215          * This accessor method returns a reference to the live list,
3216          * not a snapshot. Therefore any modification you make to the
3217          * returned list will be present inside the JAXB object.
3218          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3219          *
3220          * <p>
3221          * For example, to add a new item, do as follows:
3222          * <pre>
3223          *    getSequencePoint().add(newItem);
3224          * </pre>
3225          *
3226          *
3227          * <p>
3228          * Objects of the following type(s) are allowed in the list
3229          * {@link JalviewModel.PcaViewer.SequencePoint }
3230          *
3231          *
3232          */
3233         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3234             if (sequencePoint == null) {
3235                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3236             }
3237             return this.sequencePoint;
3238         }
3239
3240         /**
3241          * Gets the value of the axis property.
3242          *
3243          * <p>
3244          * This accessor method returns a reference to the live list,
3245          * not a snapshot. Therefore any modification you make to the
3246          * returned list will be present inside the JAXB object.
3247          * This is why there is not a <CODE>set</CODE> method for the axis property.
3248          *
3249          * <p>
3250          * For example, to add a new item, do as follows:
3251          * <pre>
3252          *    getAxis().add(newItem);
3253          * </pre>
3254          *
3255          *
3256          * <p>
3257          * Objects of the following type(s) are allowed in the list
3258          * {@link JalviewModel.PcaViewer.Axis }
3259          *
3260          *
3261          */
3262         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3263             if (axis == null) {
3264                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3265             }
3266             return this.axis;
3267         }
3268
3269         /**
3270          * Gets the value of the seqPointMin property.
3271          *
3272          * @return
3273          *     possible object is
3274          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3275          *
3276          */
3277         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3278             return seqPointMin;
3279         }
3280
3281         /**
3282          * Sets the value of the seqPointMin property.
3283          *
3284          * @param value
3285          *     allowed object is
3286          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3287          *
3288          */
3289         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3290             this.seqPointMin = value;
3291         }
3292
3293         /**
3294          * Gets the value of the seqPointMax property.
3295          *
3296          * @return
3297          *     possible object is
3298          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3299          *
3300          */
3301         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3302             return seqPointMax;
3303         }
3304
3305         /**
3306          * Sets the value of the seqPointMax property.
3307          *
3308          * @param value
3309          *     allowed object is
3310          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3311          *
3312          */
3313         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3314             this.seqPointMax = value;
3315         }
3316
3317         /**
3318          * Gets the value of the pcaData property.
3319          *
3320          * @return
3321          *     possible object is
3322          *     {@link PcaDataType }
3323          *
3324          */
3325         public PcaDataType getPcaData() {
3326             return pcaData;
3327         }
3328
3329         /**
3330          * Sets the value of the pcaData property.
3331          *
3332          * @param value
3333          *     allowed object is
3334          *     {@link PcaDataType }
3335          *
3336          */
3337         public void setPcaData(PcaDataType value) {
3338             this.pcaData = value;
3339         }
3340
3341         /**
3342          * Gets the value of the title property.
3343          *
3344          * @return
3345          *     possible object is
3346          *     {@link String }
3347          *
3348          */
3349         public String getTitle() {
3350             return title;
3351         }
3352
3353         /**
3354          * Sets the value of the title property.
3355          *
3356          * @param value
3357          *     allowed object is
3358          *     {@link String }
3359          *
3360          */
3361         public void setTitle(String value) {
3362             this.title = value;
3363         }
3364
3365         /**
3366          * Gets the value of the scoreModelName property.
3367          *
3368          * @return
3369          *     possible object is
3370          *     {@link String }
3371          *
3372          */
3373         public String getScoreModelName() {
3374             return scoreModelName;
3375         }
3376
3377         /**
3378          * Sets the value of the scoreModelName property.
3379          *
3380          * @param value
3381          *     allowed object is
3382          *     {@link String }
3383          *
3384          */
3385         public void setScoreModelName(String value) {
3386             this.scoreModelName = value;
3387         }
3388
3389         /**
3390          * Gets the value of the xDim property.
3391          *
3392          * @return
3393          *     possible object is
3394          *     {@link Integer }
3395          *
3396          */
3397         public Integer getXDim() {
3398             return xDim;
3399         }
3400
3401         /**
3402          * Sets the value of the xDim property.
3403          *
3404          * @param value
3405          *     allowed object is
3406          *     {@link Integer }
3407          *
3408          */
3409         public void setXDim(Integer value) {
3410             this.xDim = value;
3411         }
3412
3413         /**
3414          * Gets the value of the yDim property.
3415          *
3416          * @return
3417          *     possible object is
3418          *     {@link Integer }
3419          *
3420          */
3421         public Integer getYDim() {
3422             return yDim;
3423         }
3424
3425         /**
3426          * Sets the value of the yDim property.
3427          *
3428          * @param value
3429          *     allowed object is
3430          *     {@link Integer }
3431          *
3432          */
3433         public void setYDim(Integer value) {
3434             this.yDim = value;
3435         }
3436
3437         /**
3438          * Gets the value of the zDim property.
3439          *
3440          * @return
3441          *     possible object is
3442          *     {@link Integer }
3443          *
3444          */
3445         public Integer getZDim() {
3446             return zDim;
3447         }
3448
3449         /**
3450          * Sets the value of the zDim property.
3451          *
3452          * @param value
3453          *     allowed object is
3454          *     {@link Integer }
3455          *
3456          */
3457         public void setZDim(Integer value) {
3458             this.zDim = value;
3459         }
3460
3461         /**
3462          * Gets the value of the bgColour property.
3463          *
3464          * @return
3465          *     possible object is
3466          *     {@link Integer }
3467          *
3468          */
3469         public Integer getBgColour() {
3470             return bgColour;
3471         }
3472
3473         /**
3474          * Sets the value of the bgColour property.
3475          *
3476          * @param value
3477          *     allowed object is
3478          *     {@link Integer }
3479          *
3480          */
3481         public void setBgColour(Integer value) {
3482             this.bgColour = value;
3483         }
3484
3485         /**
3486          * Gets the value of the scaleFactor property.
3487          *
3488          * @return
3489          *     possible object is
3490          *     {@link Float }
3491          *
3492          */
3493         public Float getScaleFactor() {
3494             return scaleFactor;
3495         }
3496
3497         /**
3498          * Sets the value of the scaleFactor property.
3499          *
3500          * @param value
3501          *     allowed object is
3502          *     {@link Float }
3503          *
3504          */
3505         public void setScaleFactor(Float value) {
3506             this.scaleFactor = value;
3507         }
3508
3509         /**
3510          * Gets the value of the showLabels property.
3511          *
3512          * @return
3513          *     possible object is
3514          *     {@link Boolean }
3515          *
3516          */
3517         public Boolean isShowLabels() {
3518             return showLabels;
3519         }
3520
3521         /**
3522          * Sets the value of the showLabels property.
3523          *
3524          * @param value
3525          *     allowed object is
3526          *     {@link Boolean }
3527          *
3528          */
3529         public void setShowLabels(Boolean value) {
3530             this.showLabels = value;
3531         }
3532
3533         /**
3534          * Gets the value of the linkToAllViews property.
3535          *
3536          * @return
3537          *     possible object is
3538          *     {@link Boolean }
3539          *
3540          */
3541         public Boolean isLinkToAllViews() {
3542             return linkToAllViews;
3543         }
3544
3545         /**
3546          * Sets the value of the linkToAllViews property.
3547          *
3548          * @param value
3549          *     allowed object is
3550          *     {@link Boolean }
3551          *
3552          */
3553         public void setLinkToAllViews(Boolean value) {
3554             this.linkToAllViews = value;
3555         }
3556
3557         /**
3558          * Gets the value of the width property.
3559          *
3560          * @return
3561          *     possible object is
3562          *     {@link Integer }
3563          *
3564          */
3565         public Integer getWidth() {
3566             return width;
3567         }
3568
3569         /**
3570          * Sets the value of the width property.
3571          *
3572          * @param value
3573          *     allowed object is
3574          *     {@link Integer }
3575          *
3576          */
3577         public void setWidth(Integer value) {
3578             this.width = value;
3579         }
3580
3581         /**
3582          * Gets the value of the height property.
3583          *
3584          * @return
3585          *     possible object is
3586          *     {@link Integer }
3587          *
3588          */
3589         public Integer getHeight() {
3590             return height;
3591         }
3592
3593         /**
3594          * Sets the value of the height property.
3595          *
3596          * @param value
3597          *     allowed object is
3598          *     {@link Integer }
3599          *
3600          */
3601         public void setHeight(Integer value) {
3602             this.height = value;
3603         }
3604
3605         /**
3606          * Gets the value of the xpos property.
3607          *
3608          * @return
3609          *     possible object is
3610          *     {@link Integer }
3611          *
3612          */
3613         public Integer getXpos() {
3614             return xpos;
3615         }
3616
3617         /**
3618          * Sets the value of the xpos property.
3619          *
3620          * @param value
3621          *     allowed object is
3622          *     {@link Integer }
3623          *
3624          */
3625         public void setXpos(Integer value) {
3626             this.xpos = value;
3627         }
3628
3629         /**
3630          * Gets the value of the ypos property.
3631          *
3632          * @return
3633          *     possible object is
3634          *     {@link Integer }
3635          *
3636          */
3637         public Integer getYpos() {
3638             return ypos;
3639         }
3640
3641         /**
3642          * Sets the value of the ypos property.
3643          *
3644          * @param value
3645          *     allowed object is
3646          *     {@link Integer }
3647          *
3648          */
3649         public void setYpos(Integer value) {
3650             this.ypos = value;
3651         }
3652
3653         /**
3654          * Gets the value of the includeGaps property.
3655          *
3656          * @return
3657          *     possible object is
3658          *     {@link Boolean }
3659          *
3660          */
3661         public Boolean isIncludeGaps() {
3662             return includeGaps;
3663         }
3664
3665         /**
3666          * Sets the value of the includeGaps property.
3667          *
3668          * @param value
3669          *     allowed object is
3670          *     {@link Boolean }
3671          *
3672          */
3673         public void setIncludeGaps(Boolean value) {
3674             this.includeGaps = value;
3675         }
3676
3677         /**
3678          * Gets the value of the matchGaps property.
3679          *
3680          * @return
3681          *     possible object is
3682          *     {@link Boolean }
3683          *
3684          */
3685         public Boolean isMatchGaps() {
3686             return matchGaps;
3687         }
3688
3689         /**
3690          * Sets the value of the matchGaps property.
3691          *
3692          * @param value
3693          *     allowed object is
3694          *     {@link Boolean }
3695          *
3696          */
3697         public void setMatchGaps(Boolean value) {
3698             this.matchGaps = value;
3699         }
3700
3701         /**
3702          * Gets the value of the includeGappedColumns property.
3703          *
3704          * @return
3705          *     possible object is
3706          *     {@link Boolean }
3707          *
3708          */
3709         public Boolean isIncludeGappedColumns() {
3710             return includeGappedColumns;
3711         }
3712
3713         /**
3714          * Sets the value of the includeGappedColumns property.
3715          *
3716          * @param value
3717          *     allowed object is
3718          *     {@link Boolean }
3719          *
3720          */
3721         public void setIncludeGappedColumns(Boolean value) {
3722             this.includeGappedColumns = value;
3723         }
3724
3725         /**
3726          * Gets the value of the denominateByShortestLength property.
3727          *
3728          * @return
3729          *     possible object is
3730          *     {@link Boolean }
3731          *
3732          */
3733         public Boolean isDenominateByShortestLength() {
3734             return denominateByShortestLength;
3735         }
3736
3737         /**
3738          * Sets the value of the denominateByShortestLength property.
3739          *
3740          * @param value
3741          *     allowed object is
3742          *     {@link Boolean }
3743          *
3744          */
3745         public void setDenominateByShortestLength(Boolean value) {
3746             this.denominateByShortestLength = value;
3747         }
3748
3749
3750         /**
3751          * <p>Java class for anonymous complex type.
3752          *
3753          * <p>The following schema fragment specifies the expected content contained within this class.
3754          *
3755          * <pre>
3756          * &lt;complexType>
3757          *   &lt;complexContent>
3758          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3759          *       &lt;attGroup ref="{www.jalview.org}position"/>
3760          *     &lt;/restriction>
3761          *   &lt;/complexContent>
3762          * &lt;/complexType>
3763          * </pre>
3764          *
3765          *
3766          */
3767         @XmlAccessorType(XmlAccessType.FIELD)
3768         @XmlType(name = "")
3769         public static class Axis {
3770
3771             @XmlAttribute(name = "xPos")
3772             protected Float xPos;
3773             @XmlAttribute(name = "yPos")
3774             protected Float yPos;
3775             @XmlAttribute(name = "zPos")
3776             protected Float zPos;
3777
3778             /**
3779              * Gets the value of the xPos property.
3780              *
3781              * @return
3782              *     possible object is
3783              *     {@link Float }
3784              *
3785              */
3786             public Float getXPos() {
3787                 return xPos;
3788             }
3789
3790             /**
3791              * Sets the value of the xPos property.
3792              *
3793              * @param value
3794              *     allowed object is
3795              *     {@link Float }
3796              *
3797              */
3798             public void setXPos(Float value) {
3799                 this.xPos = value;
3800             }
3801
3802             /**
3803              * Gets the value of the yPos property.
3804              *
3805              * @return
3806              *     possible object is
3807              *     {@link Float }
3808              *
3809              */
3810             public Float getYPos() {
3811                 return yPos;
3812             }
3813
3814             /**
3815              * Sets the value of the yPos property.
3816              *
3817              * @param value
3818              *     allowed object is
3819              *     {@link Float }
3820              *
3821              */
3822             public void setYPos(Float value) {
3823                 this.yPos = value;
3824             }
3825
3826             /**
3827              * Gets the value of the zPos property.
3828              *
3829              * @return
3830              *     possible object is
3831              *     {@link Float }
3832              *
3833              */
3834             public Float getZPos() {
3835                 return zPos;
3836             }
3837
3838             /**
3839              * Sets the value of the zPos property.
3840              *
3841              * @param value
3842              *     allowed object is
3843              *     {@link Float }
3844              *
3845              */
3846             public void setZPos(Float value) {
3847                 this.zPos = value;
3848             }
3849
3850         }
3851
3852
3853         /**
3854          * <p>Java class for anonymous complex type.
3855          *
3856          * <p>The following schema fragment specifies the expected content contained within this class.
3857          *
3858          * <pre>
3859          * &lt;complexType>
3860          *   &lt;complexContent>
3861          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3862          *       &lt;attGroup ref="{www.jalview.org}position"/>
3863          *     &lt;/restriction>
3864          *   &lt;/complexContent>
3865          * &lt;/complexType>
3866          * </pre>
3867          *
3868          *
3869          */
3870         @XmlAccessorType(XmlAccessType.FIELD)
3871         @XmlType(name = "")
3872         public static class SeqPointMax {
3873
3874             @XmlAttribute(name = "xPos")
3875             protected Float xPos;
3876             @XmlAttribute(name = "yPos")
3877             protected Float yPos;
3878             @XmlAttribute(name = "zPos")
3879             protected Float zPos;
3880
3881             /**
3882              * Gets the value of the xPos property.
3883              *
3884              * @return
3885              *     possible object is
3886              *     {@link Float }
3887              *
3888              */
3889             public Float getXPos() {
3890                 return xPos;
3891             }
3892
3893             /**
3894              * Sets the value of the xPos property.
3895              *
3896              * @param value
3897              *     allowed object is
3898              *     {@link Float }
3899              *
3900              */
3901             public void setXPos(Float value) {
3902                 this.xPos = value;
3903             }
3904
3905             /**
3906              * Gets the value of the yPos property.
3907              *
3908              * @return
3909              *     possible object is
3910              *     {@link Float }
3911              *
3912              */
3913             public Float getYPos() {
3914                 return yPos;
3915             }
3916
3917             /**
3918              * Sets the value of the yPos property.
3919              *
3920              * @param value
3921              *     allowed object is
3922              *     {@link Float }
3923              *
3924              */
3925             public void setYPos(Float value) {
3926                 this.yPos = value;
3927             }
3928
3929             /**
3930              * Gets the value of the zPos property.
3931              *
3932              * @return
3933              *     possible object is
3934              *     {@link Float }
3935              *
3936              */
3937             public Float getZPos() {
3938                 return zPos;
3939             }
3940
3941             /**
3942              * Sets the value of the zPos property.
3943              *
3944              * @param value
3945              *     allowed object is
3946              *     {@link Float }
3947              *
3948              */
3949             public void setZPos(Float value) {
3950                 this.zPos = value;
3951             }
3952
3953         }
3954
3955
3956         /**
3957          * <p>Java class for anonymous complex type.
3958          *
3959          * <p>The following schema fragment specifies the expected content contained within this class.
3960          *
3961          * <pre>
3962          * &lt;complexType>
3963          *   &lt;complexContent>
3964          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3965          *       &lt;attGroup ref="{www.jalview.org}position"/>
3966          *     &lt;/restriction>
3967          *   &lt;/complexContent>
3968          * &lt;/complexType>
3969          * </pre>
3970          *
3971          *
3972          */
3973         @XmlAccessorType(XmlAccessType.FIELD)
3974         @XmlType(name = "")
3975         public static class SeqPointMin {
3976
3977             @XmlAttribute(name = "xPos")
3978             protected Float xPos;
3979             @XmlAttribute(name = "yPos")
3980             protected Float yPos;
3981             @XmlAttribute(name = "zPos")
3982             protected Float zPos;
3983
3984             /**
3985              * Gets the value of the xPos property.
3986              *
3987              * @return
3988              *     possible object is
3989              *     {@link Float }
3990              *
3991              */
3992             public Float getXPos() {
3993                 return xPos;
3994             }
3995
3996             /**
3997              * Sets the value of the xPos property.
3998              *
3999              * @param value
4000              *     allowed object is
4001              *     {@link Float }
4002              *
4003              */
4004             public void setXPos(Float value) {
4005                 this.xPos = value;
4006             }
4007
4008             /**
4009              * Gets the value of the yPos property.
4010              *
4011              * @return
4012              *     possible object is
4013              *     {@link Float }
4014              *
4015              */
4016             public Float getYPos() {
4017                 return yPos;
4018             }
4019
4020             /**
4021              * Sets the value of the yPos property.
4022              *
4023              * @param value
4024              *     allowed object is
4025              *     {@link Float }
4026              *
4027              */
4028             public void setYPos(Float value) {
4029                 this.yPos = value;
4030             }
4031
4032             /**
4033              * Gets the value of the zPos property.
4034              *
4035              * @return
4036              *     possible object is
4037              *     {@link Float }
4038              *
4039              */
4040             public Float getZPos() {
4041                 return zPos;
4042             }
4043
4044             /**
4045              * Sets the value of the zPos property.
4046              *
4047              * @param value
4048              *     allowed object is
4049              *     {@link Float }
4050              *
4051              */
4052             public void setZPos(Float value) {
4053                 this.zPos = value;
4054             }
4055
4056         }
4057
4058
4059         /**
4060          * <p>Java class for anonymous complex type.
4061          *
4062          * <p>The following schema fragment specifies the expected content contained within this class.
4063          *
4064          * <pre>
4065          * &lt;complexType>
4066          *   &lt;complexContent>
4067          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4068          *       &lt;attGroup ref="{www.jalview.org}position"/>
4069          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4070          *     &lt;/restriction>
4071          *   &lt;/complexContent>
4072          * &lt;/complexType>
4073          * </pre>
4074          *
4075          *
4076          */
4077         @XmlAccessorType(XmlAccessType.FIELD)
4078         @XmlType(name = "")
4079         public static class SequencePoint {
4080
4081             @XmlAttribute(name = "sequenceRef")
4082             protected String sequenceRef;
4083             @XmlAttribute(name = "xPos")
4084             protected Float xPos;
4085             @XmlAttribute(name = "yPos")
4086             protected Float yPos;
4087             @XmlAttribute(name = "zPos")
4088             protected Float zPos;
4089
4090             /**
4091              * Gets the value of the sequenceRef property.
4092              *
4093              * @return
4094              *     possible object is
4095              *     {@link String }
4096              *
4097              */
4098             public String getSequenceRef() {
4099                 return sequenceRef;
4100             }
4101
4102             /**
4103              * Sets the value of the sequenceRef property.
4104              *
4105              * @param value
4106              *     allowed object is
4107              *     {@link String }
4108              *
4109              */
4110             public void setSequenceRef(String value) {
4111                 this.sequenceRef = value;
4112             }
4113
4114             /**
4115              * Gets the value of the xPos property.
4116              *
4117              * @return
4118              *     possible object is
4119              *     {@link Float }
4120              *
4121              */
4122             public Float getXPos() {
4123                 return xPos;
4124             }
4125
4126             /**
4127              * Sets the value of the xPos property.
4128              *
4129              * @param value
4130              *     allowed object is
4131              *     {@link Float }
4132              *
4133              */
4134             public void setXPos(Float value) {
4135                 this.xPos = value;
4136             }
4137
4138             /**
4139              * Gets the value of the yPos property.
4140              *
4141              * @return
4142              *     possible object is
4143              *     {@link Float }
4144              *
4145              */
4146             public Float getYPos() {
4147                 return yPos;
4148             }
4149
4150             /**
4151              * Sets the value of the yPos property.
4152              *
4153              * @param value
4154              *     allowed object is
4155              *     {@link Float }
4156              *
4157              */
4158             public void setYPos(Float value) {
4159                 this.yPos = value;
4160             }
4161
4162             /**
4163              * Gets the value of the zPos property.
4164              *
4165              * @return
4166              *     possible object is
4167              *     {@link Float }
4168              *
4169              */
4170             public Float getZPos() {
4171                 return zPos;
4172             }
4173
4174             /**
4175              * Sets the value of the zPos property.
4176              *
4177              * @param value
4178              *     allowed object is
4179              *     {@link Float }
4180              *
4181              */
4182             public void setZPos(Float value) {
4183                 this.zPos = value;
4184             }
4185
4186         }
4187
4188     }
4189
4190
4191     /**
4192      * <p>Java class for anonymous complex type.
4193      *
4194      * <p>The following schema fragment specifies the expected content contained within this class.
4195      *
4196      * <pre>
4197      * &lt;complexType>
4198      *   &lt;complexContent>
4199      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4200      *       &lt;sequence minOccurs="0">
4201      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4202      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4203      *       &lt;/sequence>
4204      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4205      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4206      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4207      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4208      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4209      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4210      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4211      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4212      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4213      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4214      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4215      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4216      *     &lt;/restriction>
4217      *   &lt;/complexContent>
4218      * &lt;/complexType>
4219      * </pre>
4220      *
4221      *
4222      */
4223     @XmlAccessorType(XmlAccessType.FIELD)
4224     @XmlType(name = "", propOrder = {
4225         "title",
4226         "newick"
4227     })
4228     public static class Tree {
4229
4230         @XmlElement(namespace = "www.jalview.org")
4231         protected String title;
4232         @XmlElement(namespace = "www.jalview.org")
4233         protected String newick;
4234         @XmlAttribute(name = "fontName")
4235         protected String fontName;
4236         @XmlAttribute(name = "fontSize")
4237         protected Integer fontSize;
4238         @XmlAttribute(name = "fontStyle")
4239         protected Integer fontStyle;
4240         @XmlAttribute(name = "threshold")
4241         protected Float threshold;
4242         @XmlAttribute(name = "showBootstrap")
4243         protected Boolean showBootstrap;
4244         @XmlAttribute(name = "showDistances")
4245         protected Boolean showDistances;
4246         @XmlAttribute(name = "markUnlinked")
4247         protected Boolean markUnlinked;
4248         @XmlAttribute(name = "fitToWindow")
4249         protected Boolean fitToWindow;
4250         @XmlAttribute(name = "currentTree")
4251         protected Boolean currentTree;
4252         @XmlAttribute(name = "id")
4253         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4254         @XmlID
4255         @XmlSchemaType(name = "ID")
4256         protected String id;
4257         @XmlAttribute(name = "linkToAllViews")
4258         protected Boolean linkToAllViews;
4259         @XmlAttribute(name = "width")
4260         protected Integer width;
4261         @XmlAttribute(name = "height")
4262         protected Integer height;
4263         @XmlAttribute(name = "xpos")
4264         protected Integer xpos;
4265         @XmlAttribute(name = "ypos")
4266         protected Integer ypos;
4267
4268         /**
4269          * Gets the value of the title property.
4270          *
4271          * @return
4272          *     possible object is
4273          *     {@link String }
4274          *
4275          */
4276         public String getTitle() {
4277             return title;
4278         }
4279
4280         /**
4281          * Sets the value of the title property.
4282          *
4283          * @param value
4284          *     allowed object is
4285          *     {@link String }
4286          *
4287          */
4288         public void setTitle(String value) {
4289             this.title = value;
4290         }
4291
4292         /**
4293          * Gets the value of the newick property.
4294          *
4295          * @return
4296          *     possible object is
4297          *     {@link String }
4298          *
4299          */
4300         public String getNewick() {
4301             return newick;
4302         }
4303
4304         /**
4305          * Sets the value of the newick property.
4306          *
4307          * @param value
4308          *     allowed object is
4309          *     {@link String }
4310          *
4311          */
4312         public void setNewick(String value) {
4313             this.newick = value;
4314         }
4315
4316         /**
4317          * Gets the value of the fontName property.
4318          *
4319          * @return
4320          *     possible object is
4321          *     {@link String }
4322          *
4323          */
4324         public String getFontName() {
4325             return fontName;
4326         }
4327
4328         /**
4329          * Sets the value of the fontName property.
4330          *
4331          * @param value
4332          *     allowed object is
4333          *     {@link String }
4334          *
4335          */
4336         public void setFontName(String value) {
4337             this.fontName = value;
4338         }
4339
4340         /**
4341          * Gets the value of the fontSize property.
4342          *
4343          * @return
4344          *     possible object is
4345          *     {@link Integer }
4346          *
4347          */
4348         public Integer getFontSize() {
4349             return fontSize;
4350         }
4351
4352         /**
4353          * Sets the value of the fontSize property.
4354          *
4355          * @param value
4356          *     allowed object is
4357          *     {@link Integer }
4358          *
4359          */
4360         public void setFontSize(Integer value) {
4361             this.fontSize = value;
4362         }
4363
4364         /**
4365          * Gets the value of the fontStyle property.
4366          *
4367          * @return
4368          *     possible object is
4369          *     {@link Integer }
4370          *
4371          */
4372         public Integer getFontStyle() {
4373             return fontStyle;
4374         }
4375
4376         /**
4377          * Sets the value of the fontStyle property.
4378          *
4379          * @param value
4380          *     allowed object is
4381          *     {@link Integer }
4382          *
4383          */
4384         public void setFontStyle(Integer value) {
4385             this.fontStyle = value;
4386         }
4387
4388         /**
4389          * Gets the value of the threshold property.
4390          *
4391          * @return
4392          *     possible object is
4393          *     {@link Float }
4394          *
4395          */
4396         public Float getThreshold() {
4397             return threshold;
4398         }
4399
4400         /**
4401          * Sets the value of the threshold property.
4402          *
4403          * @param value
4404          *     allowed object is
4405          *     {@link Float }
4406          *
4407          */
4408         public void setThreshold(Float value) {
4409             this.threshold = value;
4410         }
4411
4412         /**
4413          * Gets the value of the showBootstrap property.
4414          *
4415          * @return
4416          *     possible object is
4417          *     {@link Boolean }
4418          *
4419          */
4420         public Boolean isShowBootstrap() {
4421             return showBootstrap;
4422         }
4423
4424         /**
4425          * Sets the value of the showBootstrap property.
4426          *
4427          * @param value
4428          *     allowed object is
4429          *     {@link Boolean }
4430          *
4431          */
4432         public void setShowBootstrap(Boolean value) {
4433             this.showBootstrap = value;
4434         }
4435
4436         /**
4437          * Gets the value of the showDistances property.
4438          *
4439          * @return
4440          *     possible object is
4441          *     {@link Boolean }
4442          *
4443          */
4444         public Boolean isShowDistances() {
4445             return showDistances;
4446         }
4447
4448         /**
4449          * Sets the value of the showDistances property.
4450          *
4451          * @param value
4452          *     allowed object is
4453          *     {@link Boolean }
4454          *
4455          */
4456         public void setShowDistances(Boolean value) {
4457             this.showDistances = value;
4458         }
4459
4460         /**
4461          * Gets the value of the markUnlinked property.
4462          *
4463          * @return
4464          *     possible object is
4465          *     {@link Boolean }
4466          *
4467          */
4468         public Boolean isMarkUnlinked() {
4469             return markUnlinked;
4470         }
4471
4472         /**
4473          * Sets the value of the markUnlinked property.
4474          *
4475          * @param value
4476          *     allowed object is
4477          *     {@link Boolean }
4478          *
4479          */
4480         public void setMarkUnlinked(Boolean value) {
4481             this.markUnlinked = value;
4482         }
4483
4484         /**
4485          * Gets the value of the fitToWindow property.
4486          *
4487          * @return
4488          *     possible object is
4489          *     {@link Boolean }
4490          *
4491          */
4492         public Boolean isFitToWindow() {
4493             return fitToWindow;
4494         }
4495
4496         /**
4497          * Sets the value of the fitToWindow property.
4498          *
4499          * @param value
4500          *     allowed object is
4501          *     {@link Boolean }
4502          *
4503          */
4504         public void setFitToWindow(Boolean value) {
4505             this.fitToWindow = value;
4506         }
4507
4508         /**
4509          * Gets the value of the currentTree property.
4510          *
4511          * @return
4512          *     possible object is
4513          *     {@link Boolean }
4514          *
4515          */
4516         public Boolean isCurrentTree() {
4517             return currentTree;
4518         }
4519
4520         /**
4521          * Sets the value of the currentTree property.
4522          *
4523          * @param value
4524          *     allowed object is
4525          *     {@link Boolean }
4526          *
4527          */
4528         public void setCurrentTree(Boolean value) {
4529             this.currentTree = value;
4530         }
4531
4532         /**
4533          * Gets the value of the id property.
4534          *
4535          * @return
4536          *     possible object is
4537          *     {@link String }
4538          *
4539          */
4540         public String getId() {
4541             return id;
4542         }
4543
4544         /**
4545          * Sets the value of the id property.
4546          *
4547          * @param value
4548          *     allowed object is
4549          *     {@link String }
4550          *
4551          */
4552         public void setId(String value) {
4553             this.id = value;
4554         }
4555
4556         /**
4557          * Gets the value of the linkToAllViews property.
4558          *
4559          * @return
4560          *     possible object is
4561          *     {@link Boolean }
4562          *
4563          */
4564         public boolean isLinkToAllViews() {
4565             if (linkToAllViews == null) {
4566                 return false;
4567             } else {
4568                 return linkToAllViews;
4569             }
4570         }
4571
4572         /**
4573          * Sets the value of the linkToAllViews property.
4574          *
4575          * @param value
4576          *     allowed object is
4577          *     {@link Boolean }
4578          *
4579          */
4580         public void setLinkToAllViews(Boolean value) {
4581             this.linkToAllViews = value;
4582         }
4583
4584         /**
4585          * Gets the value of the width property.
4586          *
4587          * @return
4588          *     possible object is
4589          *     {@link Integer }
4590          *
4591          */
4592         public Integer getWidth() {
4593             return width;
4594         }
4595
4596         /**
4597          * Sets the value of the width property.
4598          *
4599          * @param value
4600          *     allowed object is
4601          *     {@link Integer }
4602          *
4603          */
4604         public void setWidth(Integer value) {
4605             this.width = value;
4606         }
4607
4608         /**
4609          * Gets the value of the height property.
4610          *
4611          * @return
4612          *     possible object is
4613          *     {@link Integer }
4614          *
4615          */
4616         public Integer getHeight() {
4617             return height;
4618         }
4619
4620         /**
4621          * Sets the value of the height property.
4622          *
4623          * @param value
4624          *     allowed object is
4625          *     {@link Integer }
4626          *
4627          */
4628         public void setHeight(Integer value) {
4629             this.height = value;
4630         }
4631
4632         /**
4633          * Gets the value of the xpos property.
4634          *
4635          * @return
4636          *     possible object is
4637          *     {@link Integer }
4638          *
4639          */
4640         public Integer getXpos() {
4641             return xpos;
4642         }
4643
4644         /**
4645          * Sets the value of the xpos property.
4646          *
4647          * @param value
4648          *     allowed object is
4649          *     {@link Integer }
4650          *
4651          */
4652         public void setXpos(Integer value) {
4653             this.xpos = value;
4654         }
4655
4656         /**
4657          * Gets the value of the ypos property.
4658          *
4659          * @return
4660          *     possible object is
4661          *     {@link Integer }
4662          *
4663          */
4664         public Integer getYpos() {
4665             return ypos;
4666         }
4667
4668         /**
4669          * Sets the value of the ypos property.
4670          *
4671          * @param value
4672          *     allowed object is
4673          *     {@link Integer }
4674          *
4675          */
4676         public void setYpos(Integer value) {
4677             this.ypos = value;
4678         }
4679
4680     }
4681
4682
4683     /**
4684      * <p>Java class for anonymous complex type.
4685      *
4686      * <p>The following schema fragment specifies the expected content contained within this class.
4687      *
4688      * <pre>
4689      * &lt;complexType>
4690      *   &lt;complexContent>
4691      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4692      *       &lt;sequence>
4693      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4694      *       &lt;/sequence>
4695      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4696      *     &lt;/restriction>
4697      *   &lt;/complexContent>
4698      * &lt;/complexType>
4699      * </pre>
4700      *
4701      *
4702      */
4703     @XmlAccessorType(XmlAccessType.FIELD)
4704     @XmlType(name = "", propOrder = {
4705         "userColourScheme"
4706     })
4707     public static class UserColours {
4708
4709         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4710         protected JalviewUserColours userColourScheme;
4711         @XmlAttribute(name = "id")
4712         protected String id;
4713
4714         /**
4715          * Gets the value of the userColourScheme property.
4716          *
4717          * @return
4718          *     possible object is
4719          *     {@link JalviewUserColours }
4720          *
4721          */
4722         public JalviewUserColours getUserColourScheme() {
4723             return userColourScheme;
4724         }
4725
4726         /**
4727          * Sets the value of the userColourScheme property.
4728          *
4729          * @param value
4730          *     allowed object is
4731          *     {@link JalviewUserColours }
4732          *
4733          */
4734         public void setUserColourScheme(JalviewUserColours value) {
4735             this.userColourScheme = value;
4736         }
4737
4738         /**
4739          * Gets the value of the id property.
4740          *
4741          * @return
4742          *     possible object is
4743          *     {@link String }
4744          *
4745          */
4746         public String getId() {
4747             return id;
4748         }
4749
4750         /**
4751          * Sets the value of the id property.
4752          *
4753          * @param value
4754          *     allowed object is
4755          *     {@link String }
4756          *
4757          */
4758         public void setId(String value) {
4759             this.id = value;
4760         }
4761
4762     }
4763
4764
4765     /**
4766      * <p>Java class for anonymous complex type.
4767      *
4768      * <p>The following schema fragment specifies the expected content contained within this class.
4769      *
4770      * <pre>
4771      * &lt;complexType>
4772      *   &lt;complexContent>
4773      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4774      *       &lt;sequence>
4775      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4776      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4777      *           &lt;complexType>
4778      *             &lt;complexContent>
4779      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4780      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4781      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4782      *               &lt;/restriction>
4783      *             &lt;/complexContent>
4784      *           &lt;/complexType>
4785      *         &lt;/element>
4786      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4787      *           &lt;complexType>
4788      *             &lt;complexContent>
4789      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4790      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4791      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4792      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4793      *               &lt;/extension>
4794      *             &lt;/complexContent>
4795      *           &lt;/complexType>
4796      *         &lt;/element>
4797      *       &lt;/sequence>
4798      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4799      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4800      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4801      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4802      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4803      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4804      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4805      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4806      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4807      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4810      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4817      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4818      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4819      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4820      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4821      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4822      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4823      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4825      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4826      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4827      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4828      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4829      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4830      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4831      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4832      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4833      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4834      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4835      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4836      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4837      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4838      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4839      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4840      *     &lt;/restriction>
4841      *   &lt;/complexContent>
4842      * &lt;/complexType>
4843      * </pre>
4844      *
4845      *
4846      */
4847     @XmlAccessorType(XmlAccessType.FIELD)
4848     @XmlType(name = "", propOrder = {
4849         "annotationColours",
4850         "hiddenColumns",
4851         "calcIdParam"
4852     })
4853     public static class Viewport {
4854
4855         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4856         protected AnnotationColourScheme annotationColours;
4857         @XmlElement(namespace = "www.jalview.org")
4858         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4859         @XmlElement(namespace = "www.jalview.org")
4860         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4861         @XmlAttribute(name = "conservationSelected")
4862         protected Boolean conservationSelected;
4863         @XmlAttribute(name = "pidSelected")
4864         protected Boolean pidSelected;
4865         @XmlAttribute(name = "bgColour")
4866         protected String bgColour;
4867         @XmlAttribute(name = "consThreshold")
4868         protected Integer consThreshold;
4869         @XmlAttribute(name = "pidThreshold")
4870         protected Integer pidThreshold;
4871         @XmlAttribute(name = "title")
4872         protected String title;
4873         @XmlAttribute(name = "showFullId")
4874         protected Boolean showFullId;
4875         @XmlAttribute(name = "rightAlignIds")
4876         protected Boolean rightAlignIds;
4877         @XmlAttribute(name = "showText")
4878         protected Boolean showText;
4879         @XmlAttribute(name = "showColourText")
4880         protected Boolean showColourText;
4881         @XmlAttribute(name = "showUnconserved")
4882         protected Boolean showUnconserved;
4883         @XmlAttribute(name = "showBoxes")
4884         protected Boolean showBoxes;
4885         @XmlAttribute(name = "wrapAlignment")
4886         protected Boolean wrapAlignment;
4887         @XmlAttribute(name = "renderGaps")
4888         protected Boolean renderGaps;
4889         @XmlAttribute(name = "showSequenceFeatures")
4890         protected Boolean showSequenceFeatures;
4891         @XmlAttribute(name = "showNPfeatureTooltip")
4892         protected Boolean showNPfeatureTooltip;
4893         @XmlAttribute(name = "showDbRefTooltip")
4894         protected Boolean showDbRefTooltip;
4895         @XmlAttribute(name = "followHighlight")
4896         protected Boolean followHighlight;
4897         @XmlAttribute(name = "followSelection")
4898         protected Boolean followSelection;
4899         @XmlAttribute(name = "showAnnotation")
4900         protected Boolean showAnnotation;
4901         @XmlAttribute(name = "centreColumnLabels")
4902         protected Boolean centreColumnLabels;
4903         @XmlAttribute(name = "showGroupConservation")
4904         protected Boolean showGroupConservation;
4905         @XmlAttribute(name = "showGroupConsensus")
4906         protected Boolean showGroupConsensus;
4907         @XmlAttribute(name = "showConsensusHistogram")
4908         protected Boolean showConsensusHistogram;
4909         @XmlAttribute(name = "showSequenceLogo")
4910         protected Boolean showSequenceLogo;
4911         @XmlAttribute(name = "normaliseSequenceLogo")
4912         protected Boolean normaliseSequenceLogo;
4913         @XmlAttribute(name = "ignoreGapsinConsensus")
4914         protected Boolean ignoreGapsinConsensus;
4915         @XmlAttribute(name = "startRes")
4916         protected Integer startRes;
4917         @XmlAttribute(name = "startSeq")
4918         protected Integer startSeq;
4919         @XmlAttribute(name = "fontName")
4920         protected String fontName;
4921         @XmlAttribute(name = "fontSize")
4922         protected Integer fontSize;
4923         @XmlAttribute(name = "fontStyle")
4924         protected Integer fontStyle;
4925         @XmlAttribute(name = "scaleProteinAsCdna")
4926         protected Boolean scaleProteinAsCdna;
4927         @XmlAttribute(name = "viewName")
4928         protected String viewName;
4929         @XmlAttribute(name = "sequenceSetId")
4930         protected String sequenceSetId;
4931         @XmlAttribute(name = "gatheredViews")
4932         protected Boolean gatheredViews;
4933         @XmlAttribute(name = "textCol1")
4934         protected Integer textCol1;
4935         @XmlAttribute(name = "textCol2")
4936         protected Integer textCol2;
4937         @XmlAttribute(name = "textColThreshold")
4938         protected Integer textColThreshold;
4939         @XmlAttribute(name = "id")
4940         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4941         @XmlID
4942         @XmlSchemaType(name = "ID")
4943         protected String id;
4944         @XmlAttribute(name = "complementId")
4945         protected String complementId;
4946         @XmlAttribute(name = "width")
4947         protected Integer width;
4948         @XmlAttribute(name = "height")
4949         protected Integer height;
4950         @XmlAttribute(name = "xpos")
4951         protected Integer xpos;
4952         @XmlAttribute(name = "ypos")
4953         protected Integer ypos;
4954
4955         /**
4956          * Gets the value of the annotationColours property.
4957          *
4958          * @return
4959          *     possible object is
4960          *     {@link AnnotationColourScheme }
4961          *
4962          */
4963         public AnnotationColourScheme getAnnotationColours() {
4964             return annotationColours;
4965         }
4966
4967         /**
4968          * Sets the value of the annotationColours property.
4969          *
4970          * @param value
4971          *     allowed object is
4972          *     {@link AnnotationColourScheme }
4973          *
4974          */
4975         public void setAnnotationColours(AnnotationColourScheme value) {
4976             this.annotationColours = value;
4977         }
4978
4979         /**
4980          * Gets the value of the hiddenColumns property.
4981          *
4982          * <p>
4983          * This accessor method returns a reference to the live list,
4984          * not a snapshot. Therefore any modification you make to the
4985          * returned list will be present inside the JAXB object.
4986          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4987          *
4988          * <p>
4989          * For example, to add a new item, do as follows:
4990          * <pre>
4991          *    getHiddenColumns().add(newItem);
4992          * </pre>
4993          *
4994          *
4995          * <p>
4996          * Objects of the following type(s) are allowed in the list
4997          * {@link JalviewModel.Viewport.HiddenColumns }
4998          *
4999          *
5000          */
5001         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5002             if (hiddenColumns == null) {
5003                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5004             }
5005             return this.hiddenColumns;
5006         }
5007
5008         /**
5009          * Gets the value of the calcIdParam property.
5010          *
5011          * <p>
5012          * This accessor method returns a reference to the live list,
5013          * not a snapshot. Therefore any modification you make to the
5014          * returned list will be present inside the JAXB object.
5015          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5016          *
5017          * <p>
5018          * For example, to add a new item, do as follows:
5019          * <pre>
5020          *    getCalcIdParam().add(newItem);
5021          * </pre>
5022          *
5023          *
5024          * <p>
5025          * Objects of the following type(s) are allowed in the list
5026          * {@link JalviewModel.Viewport.CalcIdParam }
5027          *
5028          *
5029          */
5030         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5031             if (calcIdParam == null) {
5032                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5033             }
5034             return this.calcIdParam;
5035         }
5036
5037         /**
5038          * Gets the value of the conservationSelected property.
5039          *
5040          * @return
5041          *     possible object is
5042          *     {@link Boolean }
5043          *
5044          */
5045         public Boolean isConservationSelected() {
5046             return conservationSelected;
5047         }
5048
5049         /**
5050          * Sets the value of the conservationSelected property.
5051          *
5052          * @param value
5053          *     allowed object is
5054          *     {@link Boolean }
5055          *
5056          */
5057         public void setConservationSelected(Boolean value) {
5058             this.conservationSelected = value;
5059         }
5060
5061         /**
5062          * Gets the value of the pidSelected property.
5063          *
5064          * @return
5065          *     possible object is
5066          *     {@link Boolean }
5067          *
5068          */
5069         public Boolean isPidSelected() {
5070             return pidSelected;
5071         }
5072
5073         /**
5074          * Sets the value of the pidSelected property.
5075          *
5076          * @param value
5077          *     allowed object is
5078          *     {@link Boolean }
5079          *
5080          */
5081         public void setPidSelected(Boolean value) {
5082             this.pidSelected = value;
5083         }
5084
5085         /**
5086          * Gets the value of the bgColour property.
5087          *
5088          * @return
5089          *     possible object is
5090          *     {@link String }
5091          *
5092          */
5093         public String getBgColour() {
5094             return bgColour;
5095         }
5096
5097         /**
5098          * Sets the value of the bgColour property.
5099          *
5100          * @param value
5101          *     allowed object is
5102          *     {@link String }
5103          *
5104          */
5105         public void setBgColour(String value) {
5106             this.bgColour = value;
5107         }
5108
5109         /**
5110          * Gets the value of the consThreshold property.
5111          *
5112          * @return
5113          *     possible object is
5114          *     {@link Integer }
5115          *
5116          */
5117         public Integer getConsThreshold() {
5118             return consThreshold;
5119         }
5120
5121         /**
5122          * Sets the value of the consThreshold property.
5123          *
5124          * @param value
5125          *     allowed object is
5126          *     {@link Integer }
5127          *
5128          */
5129         public void setConsThreshold(Integer value) {
5130             this.consThreshold = value;
5131         }
5132
5133         /**
5134          * Gets the value of the pidThreshold property.
5135          *
5136          * @return
5137          *     possible object is
5138          *     {@link Integer }
5139          *
5140          */
5141         public Integer getPidThreshold() {
5142             return pidThreshold;
5143         }
5144
5145         /**
5146          * Sets the value of the pidThreshold property.
5147          *
5148          * @param value
5149          *     allowed object is
5150          *     {@link Integer }
5151          *
5152          */
5153         public void setPidThreshold(Integer value) {
5154             this.pidThreshold = value;
5155         }
5156
5157         /**
5158          * Gets the value of the title property.
5159          *
5160          * @return
5161          *     possible object is
5162          *     {@link String }
5163          *
5164          */
5165         public String getTitle() {
5166             return title;
5167         }
5168
5169         /**
5170          * Sets the value of the title property.
5171          *
5172          * @param value
5173          *     allowed object is
5174          *     {@link String }
5175          *
5176          */
5177         public void setTitle(String value) {
5178             this.title = value;
5179         }
5180
5181         /**
5182          * Gets the value of the showFullId property.
5183          *
5184          * @return
5185          *     possible object is
5186          *     {@link Boolean }
5187          *
5188          */
5189         public Boolean isShowFullId() {
5190             return showFullId;
5191         }
5192
5193         /**
5194          * Sets the value of the showFullId property.
5195          *
5196          * @param value
5197          *     allowed object is
5198          *     {@link Boolean }
5199          *
5200          */
5201         public void setShowFullId(Boolean value) {
5202             this.showFullId = value;
5203         }
5204
5205         /**
5206          * Gets the value of the rightAlignIds property.
5207          *
5208          * @return
5209          *     possible object is
5210          *     {@link Boolean }
5211          *
5212          */
5213         public Boolean isRightAlignIds() {
5214             return rightAlignIds;
5215         }
5216
5217         /**
5218          * Sets the value of the rightAlignIds property.
5219          *
5220          * @param value
5221          *     allowed object is
5222          *     {@link Boolean }
5223          *
5224          */
5225         public void setRightAlignIds(Boolean value) {
5226             this.rightAlignIds = value;
5227         }
5228
5229         /**
5230          * Gets the value of the showText property.
5231          *
5232          * @return
5233          *     possible object is
5234          *     {@link Boolean }
5235          *
5236          */
5237         public Boolean isShowText() {
5238             return showText;
5239         }
5240
5241         /**
5242          * Sets the value of the showText property.
5243          *
5244          * @param value
5245          *     allowed object is
5246          *     {@link Boolean }
5247          *
5248          */
5249         public void setShowText(Boolean value) {
5250             this.showText = value;
5251         }
5252
5253         /**
5254          * Gets the value of the showColourText property.
5255          *
5256          * @return
5257          *     possible object is
5258          *     {@link Boolean }
5259          *
5260          */
5261         public Boolean isShowColourText() {
5262             return showColourText;
5263         }
5264
5265         /**
5266          * Sets the value of the showColourText property.
5267          *
5268          * @param value
5269          *     allowed object is
5270          *     {@link Boolean }
5271          *
5272          */
5273         public void setShowColourText(Boolean value) {
5274             this.showColourText = value;
5275         }
5276
5277         /**
5278          * Gets the value of the showUnconserved property.
5279          *
5280          * @return
5281          *     possible object is
5282          *     {@link Boolean }
5283          *
5284          */
5285         public boolean isShowUnconserved() {
5286             if (showUnconserved == null) {
5287                 return false;
5288             } else {
5289                 return showUnconserved;
5290             }
5291         }
5292
5293         /**
5294          * Sets the value of the showUnconserved property.
5295          *
5296          * @param value
5297          *     allowed object is
5298          *     {@link Boolean }
5299          *
5300          */
5301         public void setShowUnconserved(Boolean value) {
5302             this.showUnconserved = value;
5303         }
5304
5305         /**
5306          * Gets the value of the showBoxes property.
5307          *
5308          * @return
5309          *     possible object is
5310          *     {@link Boolean }
5311          *
5312          */
5313         public Boolean isShowBoxes() {
5314             return showBoxes;
5315         }
5316
5317         /**
5318          * Sets the value of the showBoxes property.
5319          *
5320          * @param value
5321          *     allowed object is
5322          *     {@link Boolean }
5323          *
5324          */
5325         public void setShowBoxes(Boolean value) {
5326             this.showBoxes = value;
5327         }
5328
5329         /**
5330          * Gets the value of the wrapAlignment property.
5331          *
5332          * @return
5333          *     possible object is
5334          *     {@link Boolean }
5335          *
5336          */
5337         public Boolean isWrapAlignment() {
5338             return wrapAlignment;
5339         }
5340
5341         /**
5342          * Sets the value of the wrapAlignment property.
5343          *
5344          * @param value
5345          *     allowed object is
5346          *     {@link Boolean }
5347          *
5348          */
5349         public void setWrapAlignment(Boolean value) {
5350             this.wrapAlignment = value;
5351         }
5352
5353         /**
5354          * Gets the value of the renderGaps property.
5355          *
5356          * @return
5357          *     possible object is
5358          *     {@link Boolean }
5359          *
5360          */
5361         public Boolean isRenderGaps() {
5362             return renderGaps;
5363         }
5364
5365         /**
5366          * Sets the value of the renderGaps property.
5367          *
5368          * @param value
5369          *     allowed object is
5370          *     {@link Boolean }
5371          *
5372          */
5373         public void setRenderGaps(Boolean value) {
5374             this.renderGaps = value;
5375         }
5376
5377         /**
5378          * Gets the value of the showSequenceFeatures property.
5379          *
5380          * @return
5381          *     possible object is
5382          *     {@link Boolean }
5383          *
5384          */
5385         public Boolean isShowSequenceFeatures() {
5386             return showSequenceFeatures;
5387         }
5388
5389         /**
5390          * Sets the value of the showSequenceFeatures property.
5391          *
5392          * @param value
5393          *     allowed object is
5394          *     {@link Boolean }
5395          *
5396          */
5397         public void setShowSequenceFeatures(Boolean value) {
5398             this.showSequenceFeatures = value;
5399         }
5400
5401         /**
5402          * Gets the value of the showNPfeatureTooltip property.
5403          *
5404          * @return
5405          *     possible object is
5406          *     {@link Boolean }
5407          *
5408          */
5409         public Boolean isShowNPfeatureTooltip() {
5410             return showNPfeatureTooltip;
5411         }
5412
5413         /**
5414          * Sets the value of the showNPfeatureTooltip property.
5415          *
5416          * @param value
5417          *     allowed object is
5418          *     {@link Boolean }
5419          *
5420          */
5421         public void setShowNPfeatureTooltip(Boolean value) {
5422             this.showNPfeatureTooltip = value;
5423         }
5424
5425         /**
5426          * Gets the value of the showDbRefTooltip property.
5427          *
5428          * @return
5429          *     possible object is
5430          *     {@link Boolean }
5431          *
5432          */
5433         public Boolean isShowDbRefTooltip() {
5434             return showDbRefTooltip;
5435         }
5436
5437         /**
5438          * Sets the value of the showDbRefTooltip property.
5439          *
5440          * @param value
5441          *     allowed object is
5442          *     {@link Boolean }
5443          *
5444          */
5445         public void setShowDbRefTooltip(Boolean value) {
5446             this.showDbRefTooltip = value;
5447         }
5448
5449         /**
5450          * Gets the value of the followHighlight property.
5451          *
5452          * @return
5453          *     possible object is
5454          *     {@link Boolean }
5455          *
5456          */
5457         public boolean isFollowHighlight() {
5458             if (followHighlight == null) {
5459                 return true;
5460             } else {
5461                 return followHighlight;
5462             }
5463         }
5464
5465         /**
5466          * Sets the value of the followHighlight property.
5467          *
5468          * @param value
5469          *     allowed object is
5470          *     {@link Boolean }
5471          *
5472          */
5473         public void setFollowHighlight(Boolean value) {
5474             this.followHighlight = value;
5475         }
5476
5477         /**
5478          * Gets the value of the followSelection property.
5479          *
5480          * @return
5481          *     possible object is
5482          *     {@link Boolean }
5483          *
5484          */
5485         public boolean isFollowSelection() {
5486             if (followSelection == null) {
5487                 return true;
5488             } else {
5489                 return followSelection;
5490             }
5491         }
5492
5493         /**
5494          * Sets the value of the followSelection property.
5495          *
5496          * @param value
5497          *     allowed object is
5498          *     {@link Boolean }
5499          *
5500          */
5501         public void setFollowSelection(Boolean value) {
5502             this.followSelection = value;
5503         }
5504
5505         /**
5506          * Gets the value of the showAnnotation property.
5507          *
5508          * @return
5509          *     possible object is
5510          *     {@link Boolean }
5511          *
5512          */
5513         public Boolean isShowAnnotation() {
5514             return showAnnotation;
5515         }
5516
5517         /**
5518          * Sets the value of the showAnnotation property.
5519          *
5520          * @param value
5521          *     allowed object is
5522          *     {@link Boolean }
5523          *
5524          */
5525         public void setShowAnnotation(Boolean value) {
5526             this.showAnnotation = value;
5527         }
5528
5529         /**
5530          * Gets the value of the centreColumnLabels property.
5531          *
5532          * @return
5533          *     possible object is
5534          *     {@link Boolean }
5535          *
5536          */
5537         public boolean isCentreColumnLabels() {
5538             if (centreColumnLabels == null) {
5539                 return false;
5540             } else {
5541                 return centreColumnLabels;
5542             }
5543         }
5544
5545         /**
5546          * Sets the value of the centreColumnLabels property.
5547          *
5548          * @param value
5549          *     allowed object is
5550          *     {@link Boolean }
5551          *
5552          */
5553         public void setCentreColumnLabels(Boolean value) {
5554             this.centreColumnLabels = value;
5555         }
5556
5557         /**
5558          * Gets the value of the showGroupConservation property.
5559          *
5560          * @return
5561          *     possible object is
5562          *     {@link Boolean }
5563          *
5564          */
5565         public boolean isShowGroupConservation() {
5566             if (showGroupConservation == null) {
5567                 return false;
5568             } else {
5569                 return showGroupConservation;
5570             }
5571         }
5572
5573         /**
5574          * Sets the value of the showGroupConservation property.
5575          *
5576          * @param value
5577          *     allowed object is
5578          *     {@link Boolean }
5579          *
5580          */
5581         public void setShowGroupConservation(Boolean value) {
5582             this.showGroupConservation = value;
5583         }
5584
5585         /**
5586          * Gets the value of the showGroupConsensus property.
5587          *
5588          * @return
5589          *     possible object is
5590          *     {@link Boolean }
5591          *
5592          */
5593         public boolean isShowGroupConsensus() {
5594             if (showGroupConsensus == null) {
5595                 return false;
5596             } else {
5597                 return showGroupConsensus;
5598             }
5599         }
5600
5601         /**
5602          * Sets the value of the showGroupConsensus property.
5603          *
5604          * @param value
5605          *     allowed object is
5606          *     {@link Boolean }
5607          *
5608          */
5609         public void setShowGroupConsensus(Boolean value) {
5610             this.showGroupConsensus = value;
5611         }
5612
5613         /**
5614          * Gets the value of the showConsensusHistogram property.
5615          *
5616          * @return
5617          *     possible object is
5618          *     {@link Boolean }
5619          *
5620          */
5621         public boolean isShowConsensusHistogram() {
5622             if (showConsensusHistogram == null) {
5623                 return true;
5624             } else {
5625                 return showConsensusHistogram;
5626             }
5627         }
5628
5629         /**
5630          * Sets the value of the showConsensusHistogram property.
5631          *
5632          * @param value
5633          *     allowed object is
5634          *     {@link Boolean }
5635          *
5636          */
5637         public void setShowConsensusHistogram(Boolean value) {
5638             this.showConsensusHistogram = value;
5639         }
5640
5641         /**
5642          * Gets the value of the showSequenceLogo property.
5643          *
5644          * @return
5645          *     possible object is
5646          *     {@link Boolean }
5647          *
5648          */
5649         public boolean isShowSequenceLogo() {
5650             if (showSequenceLogo == null) {
5651                 return false;
5652             } else {
5653                 return showSequenceLogo;
5654             }
5655         }
5656
5657         /**
5658          * Sets the value of the showSequenceLogo property.
5659          *
5660          * @param value
5661          *     allowed object is
5662          *     {@link Boolean }
5663          *
5664          */
5665         public void setShowSequenceLogo(Boolean value) {
5666             this.showSequenceLogo = value;
5667         }
5668
5669         /**
5670          * Gets the value of the normaliseSequenceLogo property.
5671          *
5672          * @return
5673          *     possible object is
5674          *     {@link Boolean }
5675          *
5676          */
5677         public boolean isNormaliseSequenceLogo() {
5678             if (normaliseSequenceLogo == null) {
5679                 return false;
5680             } else {
5681                 return normaliseSequenceLogo;
5682             }
5683         }
5684
5685         /**
5686          * Sets the value of the normaliseSequenceLogo property.
5687          *
5688          * @param value
5689          *     allowed object is
5690          *     {@link Boolean }
5691          *
5692          */
5693         public void setNormaliseSequenceLogo(Boolean value) {
5694             this.normaliseSequenceLogo = value;
5695         }
5696
5697         /**
5698          * Gets the value of the ignoreGapsinConsensus property.
5699          *
5700          * @return
5701          *     possible object is
5702          *     {@link Boolean }
5703          *
5704          */
5705         public boolean isIgnoreGapsinConsensus() {
5706             if (ignoreGapsinConsensus == null) {
5707                 return true;
5708             } else {
5709                 return ignoreGapsinConsensus;
5710             }
5711         }
5712
5713         /**
5714          * Sets the value of the ignoreGapsinConsensus property.
5715          *
5716          * @param value
5717          *     allowed object is
5718          *     {@link Boolean }
5719          *
5720          */
5721         public void setIgnoreGapsinConsensus(Boolean value) {
5722             this.ignoreGapsinConsensus = value;
5723         }
5724
5725         /**
5726          * Gets the value of the startRes property.
5727          *
5728          * @return
5729          *     possible object is
5730          *     {@link Integer }
5731          *
5732          */
5733         public Integer getStartRes() {
5734             return startRes;
5735         }
5736
5737         /**
5738          * Sets the value of the startRes property.
5739          *
5740          * @param value
5741          *     allowed object is
5742          *     {@link Integer }
5743          *
5744          */
5745         public void setStartRes(Integer value) {
5746             this.startRes = value;
5747         }
5748
5749         /**
5750          * Gets the value of the startSeq property.
5751          *
5752          * @return
5753          *     possible object is
5754          *     {@link Integer }
5755          *
5756          */
5757         public Integer getStartSeq() {
5758             return startSeq;
5759         }
5760
5761         /**
5762          * Sets the value of the startSeq property.
5763          *
5764          * @param value
5765          *     allowed object is
5766          *     {@link Integer }
5767          *
5768          */
5769         public void setStartSeq(Integer value) {
5770             this.startSeq = value;
5771         }
5772
5773         /**
5774          * Gets the value of the fontName property.
5775          *
5776          * @return
5777          *     possible object is
5778          *     {@link String }
5779          *
5780          */
5781         public String getFontName() {
5782             return fontName;
5783         }
5784
5785         /**
5786          * Sets the value of the fontName property.
5787          *
5788          * @param value
5789          *     allowed object is
5790          *     {@link String }
5791          *
5792          */
5793         public void setFontName(String value) {
5794             this.fontName = value;
5795         }
5796
5797         /**
5798          * Gets the value of the fontSize property.
5799          *
5800          * @return
5801          *     possible object is
5802          *     {@link Integer }
5803          *
5804          */
5805         public Integer getFontSize() {
5806             return fontSize;
5807         }
5808
5809         /**
5810          * Sets the value of the fontSize property.
5811          *
5812          * @param value
5813          *     allowed object is
5814          *     {@link Integer }
5815          *
5816          */
5817         public void setFontSize(Integer value) {
5818             this.fontSize = value;
5819         }
5820
5821         /**
5822          * Gets the value of the fontStyle property.
5823          *
5824          * @return
5825          *     possible object is
5826          *     {@link Integer }
5827          *
5828          */
5829         public Integer getFontStyle() {
5830             return fontStyle;
5831         }
5832
5833         /**
5834          * Sets the value of the fontStyle property.
5835          *
5836          * @param value
5837          *     allowed object is
5838          *     {@link Integer }
5839          *
5840          */
5841         public void setFontStyle(Integer value) {
5842             this.fontStyle = value;
5843         }
5844
5845         /**
5846          * Gets the value of the scaleProteinAsCdna property.
5847          *
5848          * @return
5849          *     possible object is
5850          *     {@link Boolean }
5851          *
5852          */
5853         public boolean isScaleProteinAsCdna() {
5854             if (scaleProteinAsCdna == null) {
5855                 return true;
5856             } else {
5857                 return scaleProteinAsCdna;
5858             }
5859         }
5860
5861         /**
5862          * Sets the value of the scaleProteinAsCdna property.
5863          *
5864          * @param value
5865          *     allowed object is
5866          *     {@link Boolean }
5867          *
5868          */
5869         public void setScaleProteinAsCdna(Boolean value) {
5870             this.scaleProteinAsCdna = value;
5871         }
5872
5873         /**
5874          * Gets the value of the viewName property.
5875          *
5876          * @return
5877          *     possible object is
5878          *     {@link String }
5879          *
5880          */
5881         public String getViewName() {
5882             return viewName;
5883         }
5884
5885         /**
5886          * Sets the value of the viewName property.
5887          *
5888          * @param value
5889          *     allowed object is
5890          *     {@link String }
5891          *
5892          */
5893         public void setViewName(String value) {
5894             this.viewName = value;
5895         }
5896
5897         /**
5898          * Gets the value of the sequenceSetId property.
5899          *
5900          * @return
5901          *     possible object is
5902          *     {@link String }
5903          *
5904          */
5905         public String getSequenceSetId() {
5906             return sequenceSetId;
5907         }
5908
5909         /**
5910          * Sets the value of the sequenceSetId property.
5911          *
5912          * @param value
5913          *     allowed object is
5914          *     {@link String }
5915          *
5916          */
5917         public void setSequenceSetId(String value) {
5918             this.sequenceSetId = value;
5919         }
5920
5921         /**
5922          * Gets the value of the gatheredViews property.
5923          *
5924          * @return
5925          *     possible object is
5926          *     {@link Boolean }
5927          *
5928          */
5929         public Boolean isGatheredViews() {
5930             return gatheredViews;
5931         }
5932
5933         /**
5934          * Sets the value of the gatheredViews property.
5935          *
5936          * @param value
5937          *     allowed object is
5938          *     {@link Boolean }
5939          *
5940          */
5941         public void setGatheredViews(Boolean value) {
5942             this.gatheredViews = value;
5943         }
5944
5945         /**
5946          * Gets the value of the textCol1 property.
5947          *
5948          * @return
5949          *     possible object is
5950          *     {@link Integer }
5951          *
5952          */
5953         public Integer getTextCol1() {
5954             return textCol1;
5955         }
5956
5957         /**
5958          * Sets the value of the textCol1 property.
5959          *
5960          * @param value
5961          *     allowed object is
5962          *     {@link Integer }
5963          *
5964          */
5965         public void setTextCol1(Integer value) {
5966             this.textCol1 = value;
5967         }
5968
5969         /**
5970          * Gets the value of the textCol2 property.
5971          *
5972          * @return
5973          *     possible object is
5974          *     {@link Integer }
5975          *
5976          */
5977         public Integer getTextCol2() {
5978             return textCol2;
5979         }
5980
5981         /**
5982          * Sets the value of the textCol2 property.
5983          *
5984          * @param value
5985          *     allowed object is
5986          *     {@link Integer }
5987          *
5988          */
5989         public void setTextCol2(Integer value) {
5990             this.textCol2 = value;
5991         }
5992
5993         /**
5994          * Gets the value of the textColThreshold property.
5995          *
5996          * @return
5997          *     possible object is
5998          *     {@link Integer }
5999          *
6000          */
6001         public Integer getTextColThreshold() {
6002             return textColThreshold;
6003         }
6004
6005         /**
6006          * Sets the value of the textColThreshold property.
6007          *
6008          * @param value
6009          *     allowed object is
6010          *     {@link Integer }
6011          *
6012          */
6013         public void setTextColThreshold(Integer value) {
6014             this.textColThreshold = value;
6015         }
6016
6017         /**
6018          * Gets the value of the id property.
6019          *
6020          * @return
6021          *     possible object is
6022          *     {@link String }
6023          *
6024          */
6025         public String getId() {
6026             return id;
6027         }
6028
6029         /**
6030          * Sets the value of the id property.
6031          *
6032          * @param value
6033          *     allowed object is
6034          *     {@link String }
6035          *
6036          */
6037         public void setId(String value) {
6038             this.id = value;
6039         }
6040
6041         /**
6042          * Gets the value of the complementId property.
6043          *
6044          * @return
6045          *     possible object is
6046          *     {@link String }
6047          *
6048          */
6049         public String getComplementId() {
6050             return complementId;
6051         }
6052
6053         /**
6054          * Sets the value of the complementId property.
6055          *
6056          * @param value
6057          *     allowed object is
6058          *     {@link String }
6059          *
6060          */
6061         public void setComplementId(String value) {
6062             this.complementId = value;
6063         }
6064
6065         /**
6066          * Gets the value of the width property.
6067          *
6068          * @return
6069          *     possible object is
6070          *     {@link Integer }
6071          *
6072          */
6073         public Integer getWidth() {
6074             return width;
6075         }
6076
6077         /**
6078          * Sets the value of the width property.
6079          *
6080          * @param value
6081          *     allowed object is
6082          *     {@link Integer }
6083          *
6084          */
6085         public void setWidth(Integer value) {
6086             this.width = value;
6087         }
6088
6089         /**
6090          * Gets the value of the height property.
6091          *
6092          * @return
6093          *     possible object is
6094          *     {@link Integer }
6095          *
6096          */
6097         public Integer getHeight() {
6098             return height;
6099         }
6100
6101         /**
6102          * Sets the value of the height property.
6103          *
6104          * @param value
6105          *     allowed object is
6106          *     {@link Integer }
6107          *
6108          */
6109         public void setHeight(Integer value) {
6110             this.height = value;
6111         }
6112
6113         /**
6114          * Gets the value of the xpos property.
6115          *
6116          * @return
6117          *     possible object is
6118          *     {@link Integer }
6119          *
6120          */
6121         public Integer getXpos() {
6122             return xpos;
6123         }
6124
6125         /**
6126          * Sets the value of the xpos property.
6127          *
6128          * @param value
6129          *     allowed object is
6130          *     {@link Integer }
6131          *
6132          */
6133         public void setXpos(Integer value) {
6134             this.xpos = value;
6135         }
6136
6137         /**
6138          * Gets the value of the ypos property.
6139          *
6140          * @return
6141          *     possible object is
6142          *     {@link Integer }
6143          *
6144          */
6145         public Integer getYpos() {
6146             return ypos;
6147         }
6148
6149         /**
6150          * Sets the value of the ypos property.
6151          *
6152          * @param value
6153          *     allowed object is
6154          *     {@link Integer }
6155          *
6156          */
6157         public void setYpos(Integer value) {
6158             this.ypos = value;
6159         }
6160
6161
6162         /**
6163          * <p>Java class for anonymous complex type.
6164          *
6165          * <p>The following schema fragment specifies the expected content contained within this class.
6166          *
6167          * <pre>
6168          * &lt;complexType>
6169          *   &lt;complexContent>
6170          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6171          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6172          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6173          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6174          *     &lt;/extension>
6175          *   &lt;/complexContent>
6176          * &lt;/complexType>
6177          * </pre>
6178          *
6179          *
6180          */
6181         @XmlAccessorType(XmlAccessType.FIELD)
6182         @XmlType(name = "")
6183         public static class CalcIdParam
6184             extends WebServiceParameterSet
6185         {
6186
6187             @XmlAttribute(name = "calcId", required = true)
6188             protected String calcId;
6189             @XmlAttribute(name = "needsUpdate")
6190             protected Boolean needsUpdate;
6191             @XmlAttribute(name = "autoUpdate", required = true)
6192             protected boolean autoUpdate;
6193
6194             /**
6195              * Gets the value of the calcId property.
6196              *
6197              * @return
6198              *     possible object is
6199              *     {@link String }
6200              *
6201              */
6202             public String getCalcId() {
6203                 return calcId;
6204             }
6205
6206             /**
6207              * Sets the value of the calcId property.
6208              *
6209              * @param value
6210              *     allowed object is
6211              *     {@link String }
6212              *
6213              */
6214             public void setCalcId(String value) {
6215                 this.calcId = value;
6216             }
6217
6218             /**
6219              * Gets the value of the needsUpdate property.
6220              *
6221              * @return
6222              *     possible object is
6223              *     {@link Boolean }
6224              *
6225              */
6226             public boolean isNeedsUpdate() {
6227                 if (needsUpdate == null) {
6228                     return false;
6229                 } else {
6230                     return needsUpdate;
6231                 }
6232             }
6233
6234             /**
6235              * Sets the value of the needsUpdate property.
6236              *
6237              * @param value
6238              *     allowed object is
6239              *     {@link Boolean }
6240              *
6241              */
6242             public void setNeedsUpdate(Boolean value) {
6243                 this.needsUpdate = value;
6244             }
6245
6246             /**
6247              * Gets the value of the autoUpdate property.
6248              *
6249              */
6250             public boolean isAutoUpdate() {
6251                 return autoUpdate;
6252             }
6253
6254             /**
6255              * Sets the value of the autoUpdate property.
6256              *
6257              */
6258             public void setAutoUpdate(boolean value) {
6259                 this.autoUpdate = value;
6260             }
6261
6262         }
6263
6264
6265         /**
6266          * <p>Java class for anonymous complex type.
6267          *
6268          * <p>The following schema fragment specifies the expected content contained within this class.
6269          *
6270          * <pre>
6271          * &lt;complexType>
6272          *   &lt;complexContent>
6273          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6274          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6275          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6276          *     &lt;/restriction>
6277          *   &lt;/complexContent>
6278          * &lt;/complexType>
6279          * </pre>
6280          *
6281          *
6282          */
6283         @XmlAccessorType(XmlAccessType.FIELD)
6284         @XmlType(name = "")
6285         public static class HiddenColumns {
6286
6287             @XmlAttribute(name = "start")
6288             protected Integer start;
6289             @XmlAttribute(name = "end")
6290             protected Integer end;
6291
6292             /**
6293              * Gets the value of the start property.
6294              *
6295              * @return
6296              *     possible object is
6297              *     {@link Integer }
6298              *
6299              */
6300             public Integer getStart() {
6301                 return start;
6302             }
6303
6304             /**
6305              * Sets the value of the start property.
6306              *
6307              * @param value
6308              *     allowed object is
6309              *     {@link Integer }
6310              *
6311              */
6312             public void setStart(Integer value) {
6313                 this.start = value;
6314             }
6315
6316             /**
6317              * Gets the value of the end property.
6318              *
6319              * @return
6320              *     possible object is
6321              *     {@link Integer }
6322              *
6323              */
6324             public Integer getEnd() {
6325                 return end;
6326             }
6327
6328             /**
6329              * Sets the value of the end property.
6330              *
6331              * @param value
6332              *     allowed object is
6333              *     {@link Integer }
6334              *
6335              */
6336             public void setEnd(Integer value) {
6337                 this.end = value;
6338             }
6339
6340         }
6341
6342     }
6343
6344 }