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: 2019.06.07 at 02:14:40 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;/sequence>
 100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                 &lt;/restriction>
 107  *               &lt;/complexContent>
 108  *             &lt;/complexType>
 109  *           &lt;/element>
 110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 111  *             &lt;complexType>
 112  *               &lt;complexContent>
 113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 114  *                   &lt;sequence>
 115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 117  *                   &lt;/sequence>
 118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 137  *                 &lt;/restriction>
 138  *               &lt;/complexContent>
 139  *             &lt;/complexType>
 140  *           &lt;/element>
 141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 142  *             &lt;complexType>
 143  *               &lt;complexContent>
 144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 145  *                   &lt;sequence>
 146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 148  *                       &lt;complexType>
 149  *                         &lt;complexContent>
 150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                           &lt;/restriction>
 154  *                         &lt;/complexContent>
 155  *                       &lt;/complexType>
 156  *                     &lt;/element>
 157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 158  *                       &lt;complexType>
 159  *                         &lt;complexContent>
 160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 164  *                           &lt;/extension>
 165  *                         &lt;/complexContent>
 166  *                       &lt;/complexType>
 167  *                     &lt;/element>
 168  *                   &lt;/sequence>
 169  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 170  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 171  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 172  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 173  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 174  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 175  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 176  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 177  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 178  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 179  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 180  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 181  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 182  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 183  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 184  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 185  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 186  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 187  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 188  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 189  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 190  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 191  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 192  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 193  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 194  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 195  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 196  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 197  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 198  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 199  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 200  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 201  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 202  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 203  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 204  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 205  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 206  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 207  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 208  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 209  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 210  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 211  *                 &lt;/restriction>
 212  *               &lt;/complexContent>
 213  *             &lt;/complexType>
 214  *           &lt;/element>
 215  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 216  *             &lt;complexType>
 217  *               &lt;complexContent>
 218  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 219  *                   &lt;sequence>
 220  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 221  *                   &lt;/sequence>
 222  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 223  *                 &lt;/restriction>
 224  *               &lt;/complexContent>
 225  *             &lt;/complexType>
 226  *           &lt;/element>
 227  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 228  *             &lt;complexType>
 229  *               &lt;complexContent>
 230  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 231  *                   &lt;sequence minOccurs="0">
 232  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 233  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 234  *                   &lt;/sequence>
 235  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 236  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 237  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 238  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 239  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 240  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 241  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 242  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 243  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 244  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 245  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 246  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 247  *                 &lt;/restriction>
 248  *               &lt;/complexContent>
 249  *             &lt;/complexType>
 250  *           &lt;/element>
 251  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 252  *             &lt;complexType>
 253  *               &lt;complexContent>
 254  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 255  *                   &lt;sequence>
 256  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 257  *                       &lt;complexType>
 258  *                         &lt;complexContent>
 259  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 260  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 261  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 262  *                           &lt;/restriction>
 263  *                         &lt;/complexContent>
 264  *                       &lt;/complexType>
 265  *                     &lt;/element>
 266  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 267  *                       &lt;complexType>
 268  *                         &lt;complexContent>
 269  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 270  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 271  *                           &lt;/restriction>
 272  *                         &lt;/complexContent>
 273  *                       &lt;/complexType>
 274  *                     &lt;/element>
 275  *                     &lt;element name="seqPointMin">
 276  *                       &lt;complexType>
 277  *                         &lt;complexContent>
 278  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 279  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 280  *                           &lt;/restriction>
 281  *                         &lt;/complexContent>
 282  *                       &lt;/complexType>
 283  *                     &lt;/element>
 284  *                     &lt;element name="seqPointMax">
 285  *                       &lt;complexType>
 286  *                         &lt;complexContent>
 287  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 288  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 289  *                           &lt;/restriction>
 290  *                         &lt;/complexContent>
 291  *                       &lt;/complexType>
 292  *                     &lt;/element>
 293  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 294  *                   &lt;/sequence>
 295  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 296  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 297  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 298  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 299  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 300  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 301  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 302  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 303  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 304  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 305  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 306  *                 &lt;/restriction>
 307  *               &lt;/complexContent>
 308  *             &lt;/complexType>
 309  *           &lt;/element>
 310  *           &lt;element name="FeatureSettings" minOccurs="0">
 311  *             &lt;complexType>
 312  *               &lt;complexContent>
 313  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 314  *                   &lt;sequence>
 315  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 316  *                       &lt;complexType>
 317  *                         &lt;complexContent>
 318  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 319  *                             &lt;sequence>
 320  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 321  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 322  *                             &lt;/sequence>
 323  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 324  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 325  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 326  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 327  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 328  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 329  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 330  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 331  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 332  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 333  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 334  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 335  *                           &lt;/restriction>
 336  *                         &lt;/complexContent>
 337  *                       &lt;/complexType>
 338  *                     &lt;/element>
 339  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 340  *                       &lt;complexType>
 341  *                         &lt;complexContent>
 342  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 343  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 344  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 345  *                           &lt;/restriction>
 346  *                         &lt;/complexContent>
 347  *                       &lt;/complexType>
 348  *                     &lt;/element>
 349  *                   &lt;/sequence>
 350  *                 &lt;/restriction>
 351  *               &lt;/complexContent>
 352  *             &lt;/complexType>
 353  *           &lt;/element>
 354  *         &lt;/sequence>
 355  *       &lt;/sequence>
 356  *     &lt;/restriction>
 357  *   &lt;/complexContent>
 358  * &lt;/complexType>
 359  * </pre>
 360  *
 361  *
 362  */
 363 @XmlAccessorType(XmlAccessType.FIELD)
 364 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 365     "creationDate",
 366     "version",
 367     "vamsasModel",
 368     "jSeq",
 369     "jGroup",
 370     "viewport",
 371     "userColours",
 372     "tree",
 373     "pcaViewer",
 374     "featureSettings"
 375 })
 376 public class JalviewModel {
 377
 378     @XmlElement(required = true)
 379     @XmlSchemaType(name = "dateTime")
 380     protected XMLGregorianCalendar creationDate;
 381     @XmlElement(required = true)
 382     protected String version;
 383     @XmlElement(required = true)
 384     protected VAMSAS vamsasModel;
 385     @XmlElement(name = "JSeq")
 386     protected List<JalviewModel.JSeq> jSeq;
 387     @XmlElement(name = "JGroup")
 388     protected List<JalviewModel.JGroup> jGroup;
 389     @XmlElement(name = "Viewport")
 390     protected List<JalviewModel.Viewport> viewport;
 391     @XmlElement(name = "UserColours")
 392     protected List<JalviewModel.UserColours> userColours;
 393     protected List<JalviewModel.Tree> tree;
 394     @XmlElement(name = "PcaViewer")
 395     protected List<JalviewModel.PcaViewer> pcaViewer;
 396     @XmlElement(name = "FeatureSettings")
 397     protected JalviewModel.FeatureSettings featureSettings;
 398
 399     /**
 400      * Gets the value of the creationDate property.
 401      *
 402      * @return
 403      *     possible object is
 404      *     {@link XMLGregorianCalendar }
 405      *
 406      */
 407     public XMLGregorianCalendar getCreationDate() {
 408         return creationDate;
 409     }
 410
 411     /**
 412      * Sets the value of the creationDate property.
 413      *
 414      * @param value
 415      *     allowed object is
 416      *     {@link XMLGregorianCalendar }
 417      *
 418      */
 419     public void setCreationDate(XMLGregorianCalendar value) {
 420         this.creationDate = value;
 421     }
 422
 423     /**
 424      * Gets the value of the version property.
 425      *
 426      * @return
 427      *     possible object is
 428      *     {@link String }
 429      *
 430      */
 431     public String getVersion() {
 432         return version;
 433     }
 434
 435     /**
 436      * Sets the value of the version property.
 437      *
 438      * @param value
 439      *     allowed object is
 440      *     {@link String }
 441      *
 442      */
 443     public void setVersion(String value) {
 444         this.version = value;
 445     }
 446
 447     /**
 448      * Gets the value of the vamsasModel property.
 449      *
 450      * @return
 451      *     possible object is
 452      *     {@link VAMSAS }
 453      *
 454      */
 455     public VAMSAS getVamsasModel() {
 456         return vamsasModel;
 457     }
 458
 459     /**
 460      * Sets the value of the vamsasModel property.
 461      *
 462      * @param value
 463      *     allowed object is
 464      *     {@link VAMSAS }
 465      *
 466      */
 467     public void setVamsasModel(VAMSAS value) {
 468         this.vamsasModel = value;
 469     }
 470
 471     /**
 472      * Gets the value of the jSeq property.
 473      *
 474      * <p>
 475      * This accessor method returns a reference to the live list,
 476      * not a snapshot. Therefore any modification you make to the
 477      * returned list will be present inside the JAXB object.
 478      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 479      *
 480      * <p>
 481      * For example, to add a new item, do as follows:
 482      * <pre>
 483      *    getJSeq().add(newItem);
 484      * </pre>
 485      *
 486      *
 487      * <p>
 488      * Objects of the following type(s) are allowed in the list
 489      * {@link JalviewModel.JSeq }
 490      *
 491      *
 492      */
 493     public List<JalviewModel.JSeq> getJSeq() {
 494         if (jSeq == null) {
 495             jSeq = new ArrayList<JalviewModel.JSeq>();
 496         }
 497         return this.jSeq;
 498     }
 499
 500     /**
 501      * Gets the value of the jGroup property.
 502      *
 503      * <p>
 504      * This accessor method returns a reference to the live list,
 505      * not a snapshot. Therefore any modification you make to the
 506      * returned list will be present inside the JAXB object.
 507      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 508      *
 509      * <p>
 510      * For example, to add a new item, do as follows:
 511      * <pre>
 512      *    getJGroup().add(newItem);
 513      * </pre>
 514      *
 515      *
 516      * <p>
 517      * Objects of the following type(s) are allowed in the list
 518      * {@link JalviewModel.JGroup }
 519      *
 520      *
 521      */
 522     public List<JalviewModel.JGroup> getJGroup() {
 523         if (jGroup == null) {
 524             jGroup = new ArrayList<JalviewModel.JGroup>();
 525         }
 526         return this.jGroup;
 527     }
 528
 529     /**
 530      * Gets the value of the viewport property.
 531      *
 532      * <p>
 533      * This accessor method returns a reference to the live list,
 534      * not a snapshot. Therefore any modification you make to the
 535      * returned list will be present inside the JAXB object.
 536      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 537      *
 538      * <p>
 539      * For example, to add a new item, do as follows:
 540      * <pre>
 541      *    getViewport().add(newItem);
 542      * </pre>
 543      *
 544      *
 545      * <p>
 546      * Objects of the following type(s) are allowed in the list
 547      * {@link JalviewModel.Viewport }
 548      *
 549      *
 550      */
 551     public List<JalviewModel.Viewport> getViewport() {
 552         if (viewport == null) {
 553             viewport = new ArrayList<JalviewModel.Viewport>();
 554         }
 555         return this.viewport;
 556     }
 557
 558     /**
 559      * Gets the value of the userColours property.
 560      *
 561      * <p>
 562      * This accessor method returns a reference to the live list,
 563      * not a snapshot. Therefore any modification you make to the
 564      * returned list will be present inside the JAXB object.
 565      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 566      *
 567      * <p>
 568      * For example, to add a new item, do as follows:
 569      * <pre>
 570      *    getUserColours().add(newItem);
 571      * </pre>
 572      *
 573      *
 574      * <p>
 575      * Objects of the following type(s) are allowed in the list
 576      * {@link JalviewModel.UserColours }
 577      *
 578      *
 579      */
 580     public List<JalviewModel.UserColours> getUserColours() {
 581         if (userColours == null) {
 582             userColours = new ArrayList<JalviewModel.UserColours>();
 583         }
 584         return this.userColours;
 585     }
 586
 587     /**
 588      * Gets the value of the tree property.
 589      *
 590      * <p>
 591      * This accessor method returns a reference to the live list,
 592      * not a snapshot. Therefore any modification you make to the
 593      * returned list will be present inside the JAXB object.
 594      * This is why there is not a <CODE>set</CODE> method for the tree property.
 595      *
 596      * <p>
 597      * For example, to add a new item, do as follows:
 598      * <pre>
 599      *    getTree().add(newItem);
 600      * </pre>
 601      *
 602      *
 603      * <p>
 604      * Objects of the following type(s) are allowed in the list
 605      * {@link JalviewModel.Tree }
 606      *
 607      *
 608      */
 609     public List<JalviewModel.Tree> getTree() {
 610         if (tree == null) {
 611             tree = new ArrayList<JalviewModel.Tree>();
 612         }
 613         return this.tree;
 614     }
 615
 616     /**
 617      * Gets the value of the pcaViewer property.
 618      *
 619      * <p>
 620      * This accessor method returns a reference to the live list,
 621      * not a snapshot. Therefore any modification you make to the
 622      * returned list will be present inside the JAXB object.
 623      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 624      *
 625      * <p>
 626      * For example, to add a new item, do as follows:
 627      * <pre>
 628      *    getPcaViewer().add(newItem);
 629      * </pre>
 630      *
 631      *
 632      * <p>
 633      * Objects of the following type(s) are allowed in the list
 634      * {@link JalviewModel.PcaViewer }
 635      *
 636      *
 637      */
 638     public List<JalviewModel.PcaViewer> getPcaViewer() {
 639         if (pcaViewer == null) {
 640             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 641         }
 642         return this.pcaViewer;
 643     }
 644
 645     /**
 646      * Gets the value of the featureSettings property.
 647      *
 648      * @return
 649      *     possible object is
 650      *     {@link JalviewModel.FeatureSettings }
 651      *
 652      */
 653     public JalviewModel.FeatureSettings getFeatureSettings() {
 654         return featureSettings;
 655     }
 656
 657     /**
 658      * Sets the value of the featureSettings property.
 659      *
 660      * @param value
 661      *     allowed object is
 662      *     {@link JalviewModel.FeatureSettings }
 663      *
 664      */
 665     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 666         this.featureSettings = value;
 667     }
 668
 669
 670     /**
 671      * <p>Java class for anonymous complex type.
 672      *
 673      * <p>The following schema fragment specifies the expected content contained within this class.
 674      *
 675      * <pre>
 676      * &lt;complexType>
 677      *   &lt;complexContent>
 678      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 679      *       &lt;sequence>
 680      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 681      *           &lt;complexType>
 682      *             &lt;complexContent>
 683      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 684      *                 &lt;sequence>
 685      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 686      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 687      *                 &lt;/sequence>
 688      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 689      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 690      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 691      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 692      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 693      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 694      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 695      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 696      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 697      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 698      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 699      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 700      *               &lt;/restriction>
 701      *             &lt;/complexContent>
 702      *           &lt;/complexType>
 703      *         &lt;/element>
 704      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 705      *           &lt;complexType>
 706      *             &lt;complexContent>
 707      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 708      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 709      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 710      *               &lt;/restriction>
 711      *             &lt;/complexContent>
 712      *           &lt;/complexType>
 713      *         &lt;/element>
 714      *       &lt;/sequence>
 715      *     &lt;/restriction>
 716      *   &lt;/complexContent>
 717      * &lt;/complexType>
 718      * </pre>
 719      *
 720      *
 721      */
 722     @XmlAccessorType(XmlAccessType.FIELD)
 723     @XmlType(name = "", propOrder = {
 724         "setting",
 725         "group"
 726     })
 727     public static class FeatureSettings {
 728
 729         @XmlElement(namespace = "www.jalview.org")
 730         protected List<JalviewModel.FeatureSettings.Setting> setting;
 731         @XmlElement(namespace = "www.jalview.org")
 732         protected List<JalviewModel.FeatureSettings.Group> group;
 733
 734         /**
 735          * Gets the value of the setting property.
 736          *
 737          * <p>
 738          * This accessor method returns a reference to the live list,
 739          * not a snapshot. Therefore any modification you make to the
 740          * returned list will be present inside the JAXB object.
 741          * This is why there is not a <CODE>set</CODE> method for the setting property.
 742          *
 743          * <p>
 744          * For example, to add a new item, do as follows:
 745          * <pre>
 746          *    getSetting().add(newItem);
 747          * </pre>
 748          *
 749          *
 750          * <p>
 751          * Objects of the following type(s) are allowed in the list
 752          * {@link JalviewModel.FeatureSettings.Setting }
 753          *
 754          *
 755          */
 756         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 757             if (setting == null) {
 758                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 759             }
 760             return this.setting;
 761         }
 762
 763         /**
 764          * Gets the value of the group property.
 765          *
 766          * <p>
 767          * This accessor method returns a reference to the live list,
 768          * not a snapshot. Therefore any modification you make to the
 769          * returned list will be present inside the JAXB object.
 770          * This is why there is not a <CODE>set</CODE> method for the group property.
 771          *
 772          * <p>
 773          * For example, to add a new item, do as follows:
 774          * <pre>
 775          *    getGroup().add(newItem);
 776          * </pre>
 777          *
 778          *
 779          * <p>
 780          * Objects of the following type(s) are allowed in the list
 781          * {@link JalviewModel.FeatureSettings.Group }
 782          *
 783          *
 784          */
 785         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 786             if (group == null) {
 787                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 788             }
 789             return this.group;
 790         }
 791
 792
 793         /**
 794          * <p>Java class for anonymous complex type.
 795          *
 796          * <p>The following schema fragment specifies the expected content contained within this class.
 797          *
 798          * <pre>
 799          * &lt;complexType>
 800          *   &lt;complexContent>
 801          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 802          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 803          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 804          *     &lt;/restriction>
 805          *   &lt;/complexContent>
 806          * &lt;/complexType>
 807          * </pre>
 808          *
 809          *
 810          */
 811         @XmlAccessorType(XmlAccessType.FIELD)
 812         @XmlType(name = "")
 813         public static class Group {
 814
 815             @XmlAttribute(name = "name", required = true)
 816             protected String name;
 817             @XmlAttribute(name = "display", required = true)
 818             protected boolean display;
 819
 820             /**
 821              * Gets the value of the name property.
 822              *
 823              * @return
 824              *     possible object is
 825              *     {@link String }
 826              *
 827              */
 828             public String getName() {
 829                 return name;
 830             }
 831
 832             /**
 833              * Sets the value of the name property.
 834              *
 835              * @param value
 836              *     allowed object is
 837              *     {@link String }
 838              *
 839              */
 840             public void setName(String value) {
 841                 this.name = value;
 842             }
 843
 844             /**
 845              * Gets the value of the display property.
 846              *
 847              */
 848             public boolean isDisplay() {
 849                 return display;
 850             }
 851
 852             /**
 853              * Sets the value of the display property.
 854              *
 855              */
 856             public void setDisplay(boolean value) {
 857                 this.display = value;
 858             }
 859
 860         }
 861
 862
 863         /**
 864          * <p>Java class for anonymous complex type.
 865          *
 866          * <p>The following schema fragment specifies the expected content contained within this class.
 867          *
 868          * <pre>
 869          * &lt;complexType>
 870          *   &lt;complexContent>
 871          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 872          *       &lt;sequence>
 873          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 874          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 875          *       &lt;/sequence>
 876          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 877          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 878          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 879          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 880          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 881          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 882          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 883          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 884          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 885          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 886          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 887          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 888          *     &lt;/restriction>
 889          *   &lt;/complexContent>
 890          * &lt;/complexType>
 891          * </pre>
 892          *
 893          *
 894          */
 895         @XmlAccessorType(XmlAccessType.FIELD)
 896         @XmlType(name = "", propOrder = {
 897             "attributeName",
 898             "matcherSet"
 899         })
 900         public static class Setting {
 901
 902             @XmlElement(namespace = "www.jalview.org")
 903             protected List<String> attributeName;
 904             @XmlElement(namespace = "www.jalview.org")
 905             protected FeatureMatcherSet matcherSet;
 906             @XmlAttribute(name = "type", required = true)
 907             protected String type;
 908             @XmlAttribute(name = "colour", required = true)
 909             protected int colour;
 910             @XmlAttribute(name = "display", required = true)
 911             protected boolean display;
 912             @XmlAttribute(name = "order")
 913             protected Float order;
 914             @XmlAttribute(name = "mincolour")
 915             protected Integer mincolour;
 916             @XmlAttribute(name = "noValueColour")
 917             protected NoValueColour noValueColour;
 918             @XmlAttribute(name = "threshold")
 919             protected Float threshold;
 920             @XmlAttribute(name = "threshstate")
 921             protected Integer threshstate;
 922             @XmlAttribute(name = "max")
 923             protected Float max;
 924             @XmlAttribute(name = "min")
 925             protected Float min;
 926             @XmlAttribute(name = "colourByLabel")
 927             protected Boolean colourByLabel;
 928             @XmlAttribute(name = "autoScale")
 929             protected Boolean autoScale;
 930
 931             /**
 932              * Gets the value of the attributeName property.
 933              *
 934              * <p>
 935              * This accessor method returns a reference to the live list,
 936              * not a snapshot. Therefore any modification you make to the
 937              * returned list will be present inside the JAXB object.
 938              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 939              *
 940              * <p>
 941              * For example, to add a new item, do as follows:
 942              * <pre>
 943              *    getAttributeName().add(newItem);
 944              * </pre>
 945              *
 946              *
 947              * <p>
 948              * Objects of the following type(s) are allowed in the list
 949              * {@link String }
 950              *
 951              *
 952              */
 953             public List<String> getAttributeName() {
 954                 if (attributeName == null) {
 955                     attributeName = new ArrayList<String>();
 956                 }
 957                 return this.attributeName;
 958             }
 959
 960             /**
 961              * Gets the value of the matcherSet property.
 962              *
 963              * @return
 964              *     possible object is
 965              *     {@link FeatureMatcherSet }
 966              *
 967              */
 968             public FeatureMatcherSet getMatcherSet() {
 969                 return matcherSet;
 970             }
 971
 972             /**
 973              * Sets the value of the matcherSet property.
 974              *
 975              * @param value
 976              *     allowed object is
 977              *     {@link FeatureMatcherSet }
 978              *
 979              */
 980             public void setMatcherSet(FeatureMatcherSet value) {
 981                 this.matcherSet = value;
 982             }
 983
 984             /**
 985              * Gets the value of the type property.
 986              *
 987              * @return
 988              *     possible object is
 989              *     {@link String }
 990              *
 991              */
 992             public String getType() {
 993                 return type;
 994             }
 995
 996             /**
 997              * Sets the value of the type property.
 998              *
 999              * @param value
1000              *     allowed object is
1001              *     {@link String }
1002              *
1003              */
1004             public void setType(String value) {
1005                 this.type = value;
1006             }
1007
1008             /**
1009              * Gets the value of the colour property.
1010              *
1011              */
1012             public int getColour() {
1013                 return colour;
1014             }
1015
1016             /**
1017              * Sets the value of the colour property.
1018              *
1019              */
1020             public void setColour(int value) {
1021                 this.colour = value;
1022             }
1023
1024             /**
1025              * Gets the value of the display property.
1026              *
1027              */
1028             public boolean isDisplay() {
1029                 return display;
1030             }
1031
1032             /**
1033              * Sets the value of the display property.
1034              *
1035              */
1036             public void setDisplay(boolean value) {
1037                 this.display = value;
1038             }
1039
1040             /**
1041              * Gets the value of the order property.
1042              *
1043              * @return
1044              *     possible object is
1045              *     {@link Float }
1046              *
1047              */
1048             public Float getOrder() {
1049                 return order;
1050             }
1051
1052             /**
1053              * Sets the value of the order property.
1054              *
1055              * @param value
1056              *     allowed object is
1057              *     {@link Float }
1058              *
1059              */
1060             public void setOrder(Float value) {
1061                 this.order = value;
1062             }
1063
1064             /**
1065              * Gets the value of the mincolour property.
1066              *
1067              * @return
1068              *     possible object is
1069              *     {@link Integer }
1070              *
1071              */
1072             public Integer getMincolour() {
1073                 return mincolour;
1074             }
1075
1076             /**
1077              * Sets the value of the mincolour property.
1078              *
1079              * @param value
1080              *     allowed object is
1081              *     {@link Integer }
1082              *
1083              */
1084             public void setMincolour(Integer value) {
1085                 this.mincolour = value;
1086             }
1087
1088             /**
1089              * Gets the value of the noValueColour property.
1090              *
1091              * @return
1092              *     possible object is
1093              *     {@link NoValueColour }
1094              *
1095              */
1096             public NoValueColour getNoValueColour() {
1097                 if (noValueColour == null) {
1098                     return NoValueColour.MIN;
1099                 } else {
1100                     return noValueColour;
1101                 }
1102             }
1103
1104             /**
1105              * Sets the value of the noValueColour property.
1106              *
1107              * @param value
1108              *     allowed object is
1109              *     {@link NoValueColour }
1110              *
1111              */
1112             public void setNoValueColour(NoValueColour value) {
1113                 this.noValueColour = value;
1114             }
1115
1116             /**
1117              * Gets the value of the threshold property.
1118              *
1119              * @return
1120              *     possible object is
1121              *     {@link Float }
1122              *
1123              */
1124             public Float getThreshold() {
1125                 return threshold;
1126             }
1127
1128             /**
1129              * Sets the value of the threshold property.
1130              *
1131              * @param value
1132              *     allowed object is
1133              *     {@link Float }
1134              *
1135              */
1136             public void setThreshold(Float value) {
1137                 this.threshold = value;
1138             }
1139
1140             /**
1141              * Gets the value of the threshstate property.
1142              *
1143              * @return
1144              *     possible object is
1145              *     {@link Integer }
1146              *
1147              */
1148             public Integer getThreshstate() {
1149                 return threshstate;
1150             }
1151
1152             /**
1153              * Sets the value of the threshstate property.
1154              *
1155              * @param value
1156              *     allowed object is
1157              *     {@link Integer }
1158              *
1159              */
1160             public void setThreshstate(Integer value) {
1161                 this.threshstate = value;
1162             }
1163
1164             /**
1165              * Gets the value of the max property.
1166              *
1167              * @return
1168              *     possible object is
1169              *     {@link Float }
1170              *
1171              */
1172             public Float getMax() {
1173                 return max;
1174             }
1175
1176             /**
1177              * Sets the value of the max property.
1178              *
1179              * @param value
1180              *     allowed object is
1181              *     {@link Float }
1182              *
1183              */
1184             public void setMax(Float value) {
1185                 this.max = value;
1186             }
1187
1188             /**
1189              * Gets the value of the min property.
1190              *
1191              * @return
1192              *     possible object is
1193              *     {@link Float }
1194              *
1195              */
1196             public Float getMin() {
1197                 return min;
1198             }
1199
1200             /**
1201              * Sets the value of the min property.
1202              *
1203              * @param value
1204              *     allowed object is
1205              *     {@link Float }
1206              *
1207              */
1208             public void setMin(Float value) {
1209                 this.min = value;
1210             }
1211
1212             /**
1213              * Gets the value of the colourByLabel property.
1214              *
1215              * @return
1216              *     possible object is
1217              *     {@link Boolean }
1218              *
1219              */
1220             public Boolean isColourByLabel() {
1221                 return colourByLabel;
1222             }
1223
1224             /**
1225              * Sets the value of the colourByLabel property.
1226              *
1227              * @param value
1228              *     allowed object is
1229              *     {@link Boolean }
1230              *
1231              */
1232             public void setColourByLabel(Boolean value) {
1233                 this.colourByLabel = value;
1234             }
1235
1236             /**
1237              * Gets the value of the autoScale property.
1238              *
1239              * @return
1240              *     possible object is
1241              *     {@link Boolean }
1242              *
1243              */
1244             public Boolean isAutoScale() {
1245                 return autoScale;
1246             }
1247
1248             /**
1249              * Sets the value of the autoScale property.
1250              *
1251              * @param value
1252              *     allowed object is
1253              *     {@link Boolean }
1254              *
1255              */
1256             public void setAutoScale(Boolean value) {
1257                 this.autoScale = value;
1258             }
1259
1260         }
1261
1262     }
1263
1264
1265     /**
1266      * <p>Java class for anonymous complex type.
1267      *
1268      * <p>The following schema fragment specifies the expected content contained within this class.
1269      *
1270      * <pre>
1271      * &lt;complexType>
1272      *   &lt;complexContent>
1273      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1274      *       &lt;sequence>
1275      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1276      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1277      *       &lt;/sequence>
1278      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1279      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1280      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1281      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1282      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1283      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1284      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1285      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1286      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1287      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1288      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1289      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1290      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1291      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1292      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1293      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1294      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1295      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1296      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1297      *     &lt;/restriction>
1298      *   &lt;/complexContent>
1299      * &lt;/complexType>
1300      * </pre>
1301      *
1302      *
1303      */
1304     @XmlAccessorType(XmlAccessType.FIELD)
1305     @XmlType(name = "", propOrder = {
1306         "seq",
1307         "annotationColours"
1308     })
1309     public static class JGroup {
1310
1311         @XmlElement(namespace = "www.jalview.org", required = true)
1312         protected List<String> seq;
1313         @XmlElement(namespace = "www.jalview.org")
1314         protected AnnotationColourScheme annotationColours;
1315         @XmlAttribute(name = "start")
1316         protected Integer start;
1317         @XmlAttribute(name = "end")
1318         protected Integer end;
1319         @XmlAttribute(name = "name")
1320         protected String name;
1321         @XmlAttribute(name = "colour")
1322         protected String colour;
1323         @XmlAttribute(name = "consThreshold")
1324         protected Integer consThreshold;
1325         @XmlAttribute(name = "pidThreshold")
1326         protected Integer pidThreshold;
1327         @XmlAttribute(name = "outlineColour")
1328         protected Integer outlineColour;
1329         @XmlAttribute(name = "displayBoxes")
1330         protected Boolean displayBoxes;
1331         @XmlAttribute(name = "displayText")
1332         protected Boolean displayText;
1333         @XmlAttribute(name = "colourText")
1334         protected Boolean colourText;
1335         @XmlAttribute(name = "textCol1")
1336         protected Integer textCol1;
1337         @XmlAttribute(name = "textCol2")
1338         protected Integer textCol2;
1339         @XmlAttribute(name = "textColThreshold")
1340         protected Integer textColThreshold;
1341         @XmlAttribute(name = "showUnconserved")
1342         protected Boolean showUnconserved;
1343         @XmlAttribute(name = "ignoreGapsinConsensus")
1344         protected Boolean ignoreGapsinConsensus;
1345         @XmlAttribute(name = "showConsensusHistogram")
1346         protected Boolean showConsensusHistogram;
1347         @XmlAttribute(name = "showSequenceLogo")
1348         protected Boolean showSequenceLogo;
1349         @XmlAttribute(name = "normaliseSequenceLogo")
1350         protected Boolean normaliseSequenceLogo;
1351         @XmlAttribute(name = "id")
1352         protected String id;
1353
1354         /**
1355          * Gets the value of the seq property.
1356          *
1357          * <p>
1358          * This accessor method returns a reference to the live list,
1359          * not a snapshot. Therefore any modification you make to the
1360          * returned list will be present inside the JAXB object.
1361          * This is why there is not a <CODE>set</CODE> method for the seq property.
1362          *
1363          * <p>
1364          * For example, to add a new item, do as follows:
1365          * <pre>
1366          *    getSeq().add(newItem);
1367          * </pre>
1368          *
1369          *
1370          * <p>
1371          * Objects of the following type(s) are allowed in the list
1372          * {@link String }
1373          *
1374          *
1375          */
1376         public List<String> getSeq() {
1377             if (seq == null) {
1378                 seq = new ArrayList<String>();
1379             }
1380             return this.seq;
1381         }
1382
1383         /**
1384          * Gets the value of the annotationColours property.
1385          *
1386          * @return
1387          *     possible object is
1388          *     {@link AnnotationColourScheme }
1389          *
1390          */
1391         public AnnotationColourScheme getAnnotationColours() {
1392             return annotationColours;
1393         }
1394
1395         /**
1396          * Sets the value of the annotationColours property.
1397          *
1398          * @param value
1399          *     allowed object is
1400          *     {@link AnnotationColourScheme }
1401          *
1402          */
1403         public void setAnnotationColours(AnnotationColourScheme value) {
1404             this.annotationColours = value;
1405         }
1406
1407         /**
1408          * Gets the value of the start property.
1409          *
1410          * @return
1411          *     possible object is
1412          *     {@link Integer }
1413          *
1414          */
1415         public Integer getStart() {
1416             return start;
1417         }
1418
1419         /**
1420          * Sets the value of the start property.
1421          *
1422          * @param value
1423          *     allowed object is
1424          *     {@link Integer }
1425          *
1426          */
1427         public void setStart(Integer value) {
1428             this.start = value;
1429         }
1430
1431         /**
1432          * Gets the value of the end property.
1433          *
1434          * @return
1435          *     possible object is
1436          *     {@link Integer }
1437          *
1438          */
1439         public Integer getEnd() {
1440             return end;
1441         }
1442
1443         /**
1444          * Sets the value of the end property.
1445          *
1446          * @param value
1447          *     allowed object is
1448          *     {@link Integer }
1449          *
1450          */
1451         public void setEnd(Integer value) {
1452             this.end = value;
1453         }
1454
1455         /**
1456          * Gets the value of the name property.
1457          *
1458          * @return
1459          *     possible object is
1460          *     {@link String }
1461          *
1462          */
1463         public String getName() {
1464             return name;
1465         }
1466
1467         /**
1468          * Sets the value of the name property.
1469          *
1470          * @param value
1471          *     allowed object is
1472          *     {@link String }
1473          *
1474          */
1475         public void setName(String value) {
1476             this.name = value;
1477         }
1478
1479         /**
1480          * Gets the value of the colour property.
1481          *
1482          * @return
1483          *     possible object is
1484          *     {@link String }
1485          *
1486          */
1487         public String getColour() {
1488             return colour;
1489         }
1490
1491         /**
1492          * Sets the value of the colour property.
1493          *
1494          * @param value
1495          *     allowed object is
1496          *     {@link String }
1497          *
1498          */
1499         public void setColour(String value) {
1500             this.colour = value;
1501         }
1502
1503         /**
1504          * Gets the value of the consThreshold property.
1505          *
1506          * @return
1507          *     possible object is
1508          *     {@link Integer }
1509          *
1510          */
1511         public Integer getConsThreshold() {
1512             return consThreshold;
1513         }
1514
1515         /**
1516          * Sets the value of the consThreshold property.
1517          *
1518          * @param value
1519          *     allowed object is
1520          *     {@link Integer }
1521          *
1522          */
1523         public void setConsThreshold(Integer value) {
1524             this.consThreshold = value;
1525         }
1526
1527         /**
1528          * Gets the value of the pidThreshold property.
1529          *
1530          * @return
1531          *     possible object is
1532          *     {@link Integer }
1533          *
1534          */
1535         public Integer getPidThreshold() {
1536             return pidThreshold;
1537         }
1538
1539         /**
1540          * Sets the value of the pidThreshold property.
1541          *
1542          * @param value
1543          *     allowed object is
1544          *     {@link Integer }
1545          *
1546          */
1547         public void setPidThreshold(Integer value) {
1548             this.pidThreshold = value;
1549         }
1550
1551         /**
1552          * Gets the value of the outlineColour property.
1553          *
1554          * @return
1555          *     possible object is
1556          *     {@link Integer }
1557          *
1558          */
1559         public Integer getOutlineColour() {
1560             return outlineColour;
1561         }
1562
1563         /**
1564          * Sets the value of the outlineColour property.
1565          *
1566          * @param value
1567          *     allowed object is
1568          *     {@link Integer }
1569          *
1570          */
1571         public void setOutlineColour(Integer value) {
1572             this.outlineColour = value;
1573         }
1574
1575         /**
1576          * Gets the value of the displayBoxes property.
1577          *
1578          * @return
1579          *     possible object is
1580          *     {@link Boolean }
1581          *
1582          */
1583         public Boolean isDisplayBoxes() {
1584             return displayBoxes;
1585         }
1586
1587         /**
1588          * Sets the value of the displayBoxes property.
1589          *
1590          * @param value
1591          *     allowed object is
1592          *     {@link Boolean }
1593          *
1594          */
1595         public void setDisplayBoxes(Boolean value) {
1596             this.displayBoxes = value;
1597         }
1598
1599         /**
1600          * Gets the value of the displayText property.
1601          *
1602          * @return
1603          *     possible object is
1604          *     {@link Boolean }
1605          *
1606          */
1607         public Boolean isDisplayText() {
1608             return displayText;
1609         }
1610
1611         /**
1612          * Sets the value of the displayText property.
1613          *
1614          * @param value
1615          *     allowed object is
1616          *     {@link Boolean }
1617          *
1618          */
1619         public void setDisplayText(Boolean value) {
1620             this.displayText = value;
1621         }
1622
1623         /**
1624          * Gets the value of the colourText property.
1625          *
1626          * @return
1627          *     possible object is
1628          *     {@link Boolean }
1629          *
1630          */
1631         public Boolean isColourText() {
1632             return colourText;
1633         }
1634
1635         /**
1636          * Sets the value of the colourText property.
1637          *
1638          * @param value
1639          *     allowed object is
1640          *     {@link Boolean }
1641          *
1642          */
1643         public void setColourText(Boolean value) {
1644             this.colourText = value;
1645         }
1646
1647         /**
1648          * Gets the value of the textCol1 property.
1649          *
1650          * @return
1651          *     possible object is
1652          *     {@link Integer }
1653          *
1654          */
1655         public Integer getTextCol1() {
1656             return textCol1;
1657         }
1658
1659         /**
1660          * Sets the value of the textCol1 property.
1661          *
1662          * @param value
1663          *     allowed object is
1664          *     {@link Integer }
1665          *
1666          */
1667         public void setTextCol1(Integer value) {
1668             this.textCol1 = value;
1669         }
1670
1671         /**
1672          * Gets the value of the textCol2 property.
1673          *
1674          * @return
1675          *     possible object is
1676          *     {@link Integer }
1677          *
1678          */
1679         public Integer getTextCol2() {
1680             return textCol2;
1681         }
1682
1683         /**
1684          * Sets the value of the textCol2 property.
1685          *
1686          * @param value
1687          *     allowed object is
1688          *     {@link Integer }
1689          *
1690          */
1691         public void setTextCol2(Integer value) {
1692             this.textCol2 = value;
1693         }
1694
1695         /**
1696          * Gets the value of the textColThreshold property.
1697          *
1698          * @return
1699          *     possible object is
1700          *     {@link Integer }
1701          *
1702          */
1703         public Integer getTextColThreshold() {
1704             return textColThreshold;
1705         }
1706
1707         /**
1708          * Sets the value of the textColThreshold property.
1709          *
1710          * @param value
1711          *     allowed object is
1712          *     {@link Integer }
1713          *
1714          */
1715         public void setTextColThreshold(Integer value) {
1716             this.textColThreshold = value;
1717         }
1718
1719         /**
1720          * Gets the value of the showUnconserved property.
1721          *
1722          * @return
1723          *     possible object is
1724          *     {@link Boolean }
1725          *
1726          */
1727         public Boolean isShowUnconserved() {
1728             return showUnconserved;
1729         }
1730
1731         /**
1732          * Sets the value of the showUnconserved property.
1733          *
1734          * @param value
1735          *     allowed object is
1736          *     {@link Boolean }
1737          *
1738          */
1739         public void setShowUnconserved(Boolean value) {
1740             this.showUnconserved = value;
1741         }
1742
1743         /**
1744          * Gets the value of the ignoreGapsinConsensus property.
1745          *
1746          * @return
1747          *     possible object is
1748          *     {@link Boolean }
1749          *
1750          */
1751         public boolean isIgnoreGapsinConsensus() {
1752             if (ignoreGapsinConsensus == null) {
1753                 return true;
1754             } else {
1755                 return ignoreGapsinConsensus;
1756             }
1757         }
1758
1759         /**
1760          * Sets the value of the ignoreGapsinConsensus property.
1761          *
1762          * @param value
1763          *     allowed object is
1764          *     {@link Boolean }
1765          *
1766          */
1767         public void setIgnoreGapsinConsensus(Boolean value) {
1768             this.ignoreGapsinConsensus = value;
1769         }
1770
1771         /**
1772          * Gets the value of the showConsensusHistogram property.
1773          *
1774          * @return
1775          *     possible object is
1776          *     {@link Boolean }
1777          *
1778          */
1779         public boolean isShowConsensusHistogram() {
1780             if (showConsensusHistogram == null) {
1781                 return true;
1782             } else {
1783                 return showConsensusHistogram;
1784             }
1785         }
1786
1787         /**
1788          * Sets the value of the showConsensusHistogram property.
1789          *
1790          * @param value
1791          *     allowed object is
1792          *     {@link Boolean }
1793          *
1794          */
1795         public void setShowConsensusHistogram(Boolean value) {
1796             this.showConsensusHistogram = value;
1797         }
1798
1799         /**
1800          * Gets the value of the showSequenceLogo property.
1801          *
1802          * @return
1803          *     possible object is
1804          *     {@link Boolean }
1805          *
1806          */
1807         public boolean isShowSequenceLogo() {
1808             if (showSequenceLogo == null) {
1809                 return false;
1810             } else {
1811                 return showSequenceLogo;
1812             }
1813         }
1814
1815         /**
1816          * Sets the value of the showSequenceLogo property.
1817          *
1818          * @param value
1819          *     allowed object is
1820          *     {@link Boolean }
1821          *
1822          */
1823         public void setShowSequenceLogo(Boolean value) {
1824             this.showSequenceLogo = value;
1825         }
1826
1827         /**
1828          * Gets the value of the normaliseSequenceLogo property.
1829          *
1830          * @return
1831          *     possible object is
1832          *     {@link Boolean }
1833          *
1834          */
1835         public boolean isNormaliseSequenceLogo() {
1836             if (normaliseSequenceLogo == null) {
1837                 return false;
1838             } else {
1839                 return normaliseSequenceLogo;
1840             }
1841         }
1842
1843         /**
1844          * Sets the value of the normaliseSequenceLogo property.
1845          *
1846          * @param value
1847          *     allowed object is
1848          *     {@link Boolean }
1849          *
1850          */
1851         public void setNormaliseSequenceLogo(Boolean value) {
1852             this.normaliseSequenceLogo = value;
1853         }
1854
1855         /**
1856          * Gets the value of the id property.
1857          *
1858          * @return
1859          *     possible object is
1860          *     {@link String }
1861          *
1862          */
1863         public String getId() {
1864             return id;
1865         }
1866
1867         /**
1868          * Sets the value of the id property.
1869          *
1870          * @param value
1871          *     allowed object is
1872          *     {@link String }
1873          *
1874          */
1875         public void setId(String value) {
1876             this.id = value;
1877         }
1878
1879     }
1880
1881
1882     /**
1883      * <p>Java class for anonymous complex type.
1884      *
1885      * <p>The following schema fragment specifies the expected content contained within this class.
1886      *
1887      * <pre>
1888      * &lt;complexType>
1889      *   &lt;complexContent>
1890      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1891      *       &lt;sequence>
1892      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1893      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1894      *           &lt;complexType>
1895      *             &lt;complexContent>
1896      *               &lt;extension base="{www.jalview.org}pdbentry">
1897      *                 &lt;sequence>
1898      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1899      *                     &lt;complexType>
1900      *                       &lt;simpleContent>
1901      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1902      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1903      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1904      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1905      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1906      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1907      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1908      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1909      *                         &lt;/extension>
1910      *                       &lt;/simpleContent>
1911      *                     &lt;/complexType>
1912      *                   &lt;/element>
1913      *                 &lt;/sequence>
1914      *               &lt;/extension>
1915      *             &lt;/complexContent>
1916      *           &lt;/complexType>
1917      *         &lt;/element>
1918      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1919      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1920      *           &lt;complexType>
1921      *             &lt;complexContent>
1922      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1923      *                 &lt;sequence>
1924      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1925      *                     &lt;complexType>
1926      *                       &lt;complexContent>
1927      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1928      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1929      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1930      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1931      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1932      *                         &lt;/restriction>
1933      *                       &lt;/complexContent>
1934      *                     &lt;/complexType>
1935      *                   &lt;/element>
1936      *                 &lt;/sequence>
1937      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1938      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1939      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1940      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1941      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1942      *               &lt;/restriction>
1943      *             &lt;/complexContent>
1944      *           &lt;/complexType>
1945      *         &lt;/element>
1946      *       &lt;/sequence>
1947      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1948      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1949      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1950      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1951      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1952      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1953      *     &lt;/restriction>
1954      *   &lt;/complexContent>
1955      * &lt;/complexType>
1956      * </pre>
1957      *
1958      *
1959      */
1960     @XmlAccessorType(XmlAccessType.FIELD)
1961     @XmlType(name = "", propOrder = {
1962         "features",
1963         "pdbids",
1964         "hiddenSequences",
1965         "rnaViewer"
1966     })
1967     public static class JSeq {
1968
1969         @XmlElement(namespace = "www.jalview.org")
1970         protected List<Feature> features;
1971         @XmlElement(namespace = "www.jalview.org")
1972         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1973         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1974         protected List<Integer> hiddenSequences;
1975         @XmlElement(namespace = "www.jalview.org")
1976         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1977         @XmlAttribute(name = "colour")
1978         protected Integer colour;
1979         @XmlAttribute(name = "start", required = true)
1980         protected int start;
1981         @XmlAttribute(name = "end", required = true)
1982         protected int end;
1983         @XmlAttribute(name = "id", required = true)
1984         protected String id;
1985         @XmlAttribute(name = "hidden")
1986         protected Boolean hidden;
1987         @XmlAttribute(name = "viewreference")
1988         protected Boolean viewreference;
1989
1990         /**
1991          * Gets the value of the features property.
1992          *
1993          * <p>
1994          * This accessor method returns a reference to the live list,
1995          * not a snapshot. Therefore any modification you make to the
1996          * returned list will be present inside the JAXB object.
1997          * This is why there is not a <CODE>set</CODE> method for the features property.
1998          *
1999          * <p>
2000          * For example, to add a new item, do as follows:
2001          * <pre>
2002          *    getFeatures().add(newItem);
2003          * </pre>
2004          *
2005          *
2006          * <p>
2007          * Objects of the following type(s) are allowed in the list
2008          * {@link Feature }
2009          *
2010          *
2011          */
2012         public List<Feature> getFeatures() {
2013             if (features == null) {
2014                 features = new ArrayList<Feature>();
2015             }
2016             return this.features;
2017         }
2018
2019         /**
2020          * Gets the value of the pdbids property.
2021          *
2022          * <p>
2023          * This accessor method returns a reference to the live list,
2024          * not a snapshot. Therefore any modification you make to the
2025          * returned list will be present inside the JAXB object.
2026          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2027          *
2028          * <p>
2029          * For example, to add a new item, do as follows:
2030          * <pre>
2031          *    getPdbids().add(newItem);
2032          * </pre>
2033          *
2034          *
2035          * <p>
2036          * Objects of the following type(s) are allowed in the list
2037          * {@link JalviewModel.JSeq.Pdbids }
2038          *
2039          *
2040          */
2041         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2042             if (pdbids == null) {
2043                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2044             }
2045             return this.pdbids;
2046         }
2047
2048         /**
2049          * Gets the value of the hiddenSequences property.
2050          *
2051          * <p>
2052          * This accessor method returns a reference to the live list,
2053          * not a snapshot. Therefore any modification you make to the
2054          * returned list will be present inside the JAXB object.
2055          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2056          *
2057          * <p>
2058          * For example, to add a new item, do as follows:
2059          * <pre>
2060          *    getHiddenSequences().add(newItem);
2061          * </pre>
2062          *
2063          *
2064          * <p>
2065          * Objects of the following type(s) are allowed in the list
2066          * {@link Integer }
2067          *
2068          *
2069          */
2070         public List<Integer> getHiddenSequences() {
2071             if (hiddenSequences == null) {
2072                 hiddenSequences = new ArrayList<Integer>();
2073             }
2074             return this.hiddenSequences;
2075         }
2076
2077         /**
2078          * Gets the value of the rnaViewer property.
2079          *
2080          * <p>
2081          * This accessor method returns a reference to the live list,
2082          * not a snapshot. Therefore any modification you make to the
2083          * returned list will be present inside the JAXB object.
2084          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2085          *
2086          * <p>
2087          * For example, to add a new item, do as follows:
2088          * <pre>
2089          *    getRnaViewer().add(newItem);
2090          * </pre>
2091          *
2092          *
2093          * <p>
2094          * Objects of the following type(s) are allowed in the list
2095          * {@link JalviewModel.JSeq.RnaViewer }
2096          *
2097          *
2098          */
2099         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2100             if (rnaViewer == null) {
2101                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2102             }
2103             return this.rnaViewer;
2104         }
2105
2106         /**
2107          * Gets the value of the colour property.
2108          *
2109          * @return
2110          *     possible object is
2111          *     {@link Integer }
2112          *
2113          */
2114         public Integer getColour() {
2115             return colour;
2116         }
2117
2118         /**
2119          * Sets the value of the colour property.
2120          *
2121          * @param value
2122          *     allowed object is
2123          *     {@link Integer }
2124          *
2125          */
2126         public void setColour(Integer value) {
2127             this.colour = value;
2128         }
2129
2130         /**
2131          * Gets the value of the start property.
2132          *
2133          */
2134         public int getStart() {
2135             return start;
2136         }
2137
2138         /**
2139          * Sets the value of the start property.
2140          *
2141          */
2142         public void setStart(int value) {
2143             this.start = value;
2144         }
2145
2146         /**
2147          * Gets the value of the end property.
2148          *
2149          */
2150         public int getEnd() {
2151             return end;
2152         }
2153
2154         /**
2155          * Sets the value of the end property.
2156          *
2157          */
2158         public void setEnd(int value) {
2159             this.end = value;
2160         }
2161
2162         /**
2163          * Gets the value of the id property.
2164          *
2165          * @return
2166          *     possible object is
2167          *     {@link String }
2168          *
2169          */
2170         public String getId() {
2171             return id;
2172         }
2173
2174         /**
2175          * Sets the value of the id property.
2176          *
2177          * @param value
2178          *     allowed object is
2179          *     {@link String }
2180          *
2181          */
2182         public void setId(String value) {
2183             this.id = value;
2184         }
2185
2186         /**
2187          * Gets the value of the hidden property.
2188          *
2189          * @return
2190          *     possible object is
2191          *     {@link Boolean }
2192          *
2193          */
2194         public Boolean isHidden() {
2195             return hidden;
2196         }
2197
2198         /**
2199          * Sets the value of the hidden property.
2200          *
2201          * @param value
2202          *     allowed object is
2203          *     {@link Boolean }
2204          *
2205          */
2206         public void setHidden(Boolean value) {
2207             this.hidden = value;
2208         }
2209
2210         /**
2211          * Gets the value of the viewreference property.
2212          *
2213          * @return
2214          *     possible object is
2215          *     {@link Boolean }
2216          *
2217          */
2218         public Boolean isViewreference() {
2219             return viewreference;
2220         }
2221
2222         /**
2223          * Sets the value of the viewreference property.
2224          *
2225          * @param value
2226          *     allowed object is
2227          *     {@link Boolean }
2228          *
2229          */
2230         public void setViewreference(Boolean value) {
2231             this.viewreference = value;
2232         }
2233
2234
2235         /**
2236          * <p>Java class for anonymous complex type.
2237          *
2238          * <p>The following schema fragment specifies the expected content contained within this class.
2239          *
2240          * <pre>
2241          * &lt;complexType>
2242          *   &lt;complexContent>
2243          *     &lt;extension base="{www.jalview.org}pdbentry">
2244          *       &lt;sequence>
2245          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2246          *           &lt;complexType>
2247          *             &lt;simpleContent>
2248          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2249          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2250          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2251          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2252          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2253          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2254          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2255          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2256          *               &lt;/extension>
2257          *             &lt;/simpleContent>
2258          *           &lt;/complexType>
2259          *         &lt;/element>
2260          *       &lt;/sequence>
2261          *     &lt;/extension>
2262          *   &lt;/complexContent>
2263          * &lt;/complexType>
2264          * </pre>
2265          *
2266          *
2267          */
2268         @XmlAccessorType(XmlAccessType.FIELD)
2269         @XmlType(name = "", propOrder = {
2270             "structureState"
2271         })
2272         public static class Pdbids
2273             extends Pdbentry
2274         {
2275
2276             @XmlElement(namespace = "www.jalview.org")
2277             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2278
2279             /**
2280              * Gets the value of the structureState property.
2281              *
2282              * <p>
2283              * This accessor method returns a reference to the live list,
2284              * not a snapshot. Therefore any modification you make to the
2285              * returned list will be present inside the JAXB object.
2286              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2287              *
2288              * <p>
2289              * For example, to add a new item, do as follows:
2290              * <pre>
2291              *    getStructureState().add(newItem);
2292              * </pre>
2293              *
2294              *
2295              * <p>
2296              * Objects of the following type(s) are allowed in the list
2297              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2298              *
2299              *
2300              */
2301             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2302                 if (structureState == null) {
2303                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2304                 }
2305                 return this.structureState;
2306             }
2307
2308
2309             /**
2310              * <p>Java class for anonymous complex type.
2311              *
2312              * <p>The following schema fragment specifies the expected content contained within this class.
2313              *
2314              * <pre>
2315              * &lt;complexType>
2316              *   &lt;simpleContent>
2317              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2318              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2319              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2320              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2321              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2322              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2323              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2324              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2325              *     &lt;/extension>
2326              *   &lt;/simpleContent>
2327              * &lt;/complexType>
2328              * </pre>
2329              *
2330              *
2331              */
2332             @XmlAccessorType(XmlAccessType.FIELD)
2333             @XmlType(name = "", propOrder = {
2334                 "value"
2335             })
2336             public static class StructureState {
2337
2338                 @XmlValue
2339                 protected String value;
2340                 @XmlAttribute(name = "visible")
2341                 protected Boolean visible;
2342                 @XmlAttribute(name = "viewId")
2343                 protected String viewId;
2344                 @XmlAttribute(name = "alignwithAlignPanel")
2345                 protected Boolean alignwithAlignPanel;
2346                 @XmlAttribute(name = "colourwithAlignPanel")
2347                 protected Boolean colourwithAlignPanel;
2348                 @XmlAttribute(name = "colourByJmol")
2349                 protected Boolean colourByJmol;
2350                 @XmlAttribute(name = "type")
2351                 protected String type;
2352                 @XmlAttribute(name = "width")
2353                 protected Integer width;
2354                 @XmlAttribute(name = "height")
2355                 protected Integer height;
2356                 @XmlAttribute(name = "xpos")
2357                 protected Integer xpos;
2358                 @XmlAttribute(name = "ypos")
2359                 protected Integer ypos;
2360
2361                 /**
2362                  * Gets the value of the value property.
2363                  *
2364                  * @return
2365                  *     possible object is
2366                  *     {@link String }
2367                  *
2368                  */
2369                 public String getValue() {
2370                     return value;
2371                 }
2372
2373                 /**
2374                  * Sets the value of the value property.
2375                  *
2376                  * @param value
2377                  *     allowed object is
2378                  *     {@link String }
2379                  *
2380                  */
2381                 public void setValue(String value) {
2382                     this.value = value;
2383                 }
2384
2385                 /**
2386                  * Gets the value of the visible property.
2387                  *
2388                  * @return
2389                  *     possible object is
2390                  *     {@link Boolean }
2391                  *
2392                  */
2393                 public Boolean isVisible() {
2394                     return visible;
2395                 }
2396
2397                 /**
2398                  * Sets the value of the visible property.
2399                  *
2400                  * @param value
2401                  *     allowed object is
2402                  *     {@link Boolean }
2403                  *
2404                  */
2405                 public void setVisible(Boolean value) {
2406                     this.visible = value;
2407                 }
2408
2409                 /**
2410                  * Gets the value of the viewId property.
2411                  *
2412                  * @return
2413                  *     possible object is
2414                  *     {@link String }
2415                  *
2416                  */
2417                 public String getViewId() {
2418                     return viewId;
2419                 }
2420
2421                 /**
2422                  * Sets the value of the viewId property.
2423                  *
2424                  * @param value
2425                  *     allowed object is
2426                  *     {@link String }
2427                  *
2428                  */
2429                 public void setViewId(String value) {
2430                     this.viewId = value;
2431                 }
2432
2433                 /**
2434                  * Gets the value of the alignwithAlignPanel property.
2435                  *
2436                  * @return
2437                  *     possible object is
2438                  *     {@link Boolean }
2439                  *
2440                  */
2441                 public boolean isAlignwithAlignPanel() {
2442                     if (alignwithAlignPanel == null) {
2443                         return true;
2444                     } else {
2445                         return alignwithAlignPanel;
2446                     }
2447                 }
2448
2449                 /**
2450                  * Sets the value of the alignwithAlignPanel property.
2451                  *
2452                  * @param value
2453                  *     allowed object is
2454                  *     {@link Boolean }
2455                  *
2456                  */
2457                 public void setAlignwithAlignPanel(Boolean value) {
2458                     this.alignwithAlignPanel = value;
2459                 }
2460
2461                 /**
2462                  * Gets the value of the colourwithAlignPanel property.
2463                  *
2464                  * @return
2465                  *     possible object is
2466                  *     {@link Boolean }
2467                  *
2468                  */
2469                 public boolean isColourwithAlignPanel() {
2470                     if (colourwithAlignPanel == null) {
2471                         return false;
2472                     } else {
2473                         return colourwithAlignPanel;
2474                     }
2475                 }
2476
2477                 /**
2478                  * Sets the value of the colourwithAlignPanel property.
2479                  *
2480                  * @param value
2481                  *     allowed object is
2482                  *     {@link Boolean }
2483                  *
2484                  */
2485                 public void setColourwithAlignPanel(Boolean value) {
2486                     this.colourwithAlignPanel = value;
2487                 }
2488
2489                 /**
2490                  * Gets the value of the colourByJmol property.
2491                  *
2492                  * @return
2493                  *     possible object is
2494                  *     {@link Boolean }
2495                  *
2496                  */
2497                 public boolean isColourByJmol() {
2498                     if (colourByJmol == null) {
2499                         return true;
2500                     } else {
2501                         return colourByJmol;
2502                     }
2503                 }
2504
2505                 /**
2506                  * Sets the value of the colourByJmol property.
2507                  *
2508                  * @param value
2509                  *     allowed object is
2510                  *     {@link Boolean }
2511                  *
2512                  */
2513                 public void setColourByJmol(Boolean value) {
2514                     this.colourByJmol = value;
2515                 }
2516
2517                 /**
2518                  * Gets the value of the type property.
2519                  *
2520                  * @return
2521                  *     possible object is
2522                  *     {@link String }
2523                  *
2524                  */
2525                 public String getType() {
2526                     return type;
2527                 }
2528
2529                 /**
2530                  * Sets the value of the type property.
2531                  *
2532                  * @param value
2533                  *     allowed object is
2534                  *     {@link String }
2535                  *
2536                  */
2537                 public void setType(String value) {
2538                     this.type = value;
2539                 }
2540
2541                 /**
2542                  * Gets the value of the width property.
2543                  *
2544                  * @return
2545                  *     possible object is
2546                  *     {@link Integer }
2547                  *
2548                  */
2549                 public Integer getWidth() {
2550                     return width;
2551                 }
2552
2553                 /**
2554                  * Sets the value of the width property.
2555                  *
2556                  * @param value
2557                  *     allowed object is
2558                  *     {@link Integer }
2559                  *
2560                  */
2561                 public void setWidth(Integer value) {
2562                     this.width = value;
2563                 }
2564
2565                 /**
2566                  * Gets the value of the height property.
2567                  *
2568                  * @return
2569                  *     possible object is
2570                  *     {@link Integer }
2571                  *
2572                  */
2573                 public Integer getHeight() {
2574                     return height;
2575                 }
2576
2577                 /**
2578                  * Sets the value of the height property.
2579                  *
2580                  * @param value
2581                  *     allowed object is
2582                  *     {@link Integer }
2583                  *
2584                  */
2585                 public void setHeight(Integer value) {
2586                     this.height = value;
2587                 }
2588
2589                 /**
2590                  * Gets the value of the xpos property.
2591                  *
2592                  * @return
2593                  *     possible object is
2594                  *     {@link Integer }
2595                  *
2596                  */
2597                 public Integer getXpos() {
2598                     return xpos;
2599                 }
2600
2601                 /**
2602                  * Sets the value of the xpos property.
2603                  *
2604                  * @param value
2605                  *     allowed object is
2606                  *     {@link Integer }
2607                  *
2608                  */
2609                 public void setXpos(Integer value) {
2610                     this.xpos = value;
2611                 }
2612
2613                 /**
2614                  * Gets the value of the ypos property.
2615                  *
2616                  * @return
2617                  *     possible object is
2618                  *     {@link Integer }
2619                  *
2620                  */
2621                 public Integer getYpos() {
2622                     return ypos;
2623                 }
2624
2625                 /**
2626                  * Sets the value of the ypos property.
2627                  *
2628                  * @param value
2629                  *     allowed object is
2630                  *     {@link Integer }
2631                  *
2632                  */
2633                 public void setYpos(Integer value) {
2634                     this.ypos = value;
2635                 }
2636
2637             }
2638
2639         }
2640
2641
2642         /**
2643          * <p>Java class for anonymous complex type.
2644          *
2645          * <p>The following schema fragment specifies the expected content contained within this class.
2646          *
2647          * <pre>
2648          * &lt;complexType>
2649          *   &lt;complexContent>
2650          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2651          *       &lt;sequence>
2652          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2653          *           &lt;complexType>
2654          *             &lt;complexContent>
2655          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2656          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2657          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2658          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2659          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2660          *               &lt;/restriction>
2661          *             &lt;/complexContent>
2662          *           &lt;/complexType>
2663          *         &lt;/element>
2664          *       &lt;/sequence>
2665          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2666          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2667          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2668          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2669          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2670          *     &lt;/restriction>
2671          *   &lt;/complexContent>
2672          * &lt;/complexType>
2673          * </pre>
2674          *
2675          *
2676          */
2677         @XmlAccessorType(XmlAccessType.FIELD)
2678         @XmlType(name = "", propOrder = {
2679             "secondaryStructure"
2680         })
2681         public static class RnaViewer {
2682
2683             @XmlElement(namespace = "www.jalview.org", required = true)
2684             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2685             @XmlAttribute(name = "title")
2686             protected String title;
2687             @XmlAttribute(name = "viewId")
2688             protected String viewId;
2689             @XmlAttribute(name = "dividerLocation")
2690             protected Integer dividerLocation;
2691             @XmlAttribute(name = "selectedRna")
2692             protected Integer selectedRna;
2693             @XmlAttribute(name = "width")
2694             protected Integer width;
2695             @XmlAttribute(name = "height")
2696             protected Integer height;
2697             @XmlAttribute(name = "xpos")
2698             protected Integer xpos;
2699             @XmlAttribute(name = "ypos")
2700             protected Integer ypos;
2701
2702             /**
2703              * Gets the value of the secondaryStructure property.
2704              *
2705              * <p>
2706              * This accessor method returns a reference to the live list,
2707              * not a snapshot. Therefore any modification you make to the
2708              * returned list will be present inside the JAXB object.
2709              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2710              *
2711              * <p>
2712              * For example, to add a new item, do as follows:
2713              * <pre>
2714              *    getSecondaryStructure().add(newItem);
2715              * </pre>
2716              *
2717              *
2718              * <p>
2719              * Objects of the following type(s) are allowed in the list
2720              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2721              *
2722              *
2723              */
2724             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2725                 if (secondaryStructure == null) {
2726                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2727                 }
2728                 return this.secondaryStructure;
2729             }
2730
2731             /**
2732              * Gets the value of the title property.
2733              *
2734              * @return
2735              *     possible object is
2736              *     {@link String }
2737              *
2738              */
2739             public String getTitle() {
2740                 return title;
2741             }
2742
2743             /**
2744              * Sets the value of the title property.
2745              *
2746              * @param value
2747              *     allowed object is
2748              *     {@link String }
2749              *
2750              */
2751             public void setTitle(String value) {
2752                 this.title = value;
2753             }
2754
2755             /**
2756              * Gets the value of the viewId property.
2757              *
2758              * @return
2759              *     possible object is
2760              *     {@link String }
2761              *
2762              */
2763             public String getViewId() {
2764                 return viewId;
2765             }
2766
2767             /**
2768              * Sets the value of the viewId property.
2769              *
2770              * @param value
2771              *     allowed object is
2772              *     {@link String }
2773              *
2774              */
2775             public void setViewId(String value) {
2776                 this.viewId = value;
2777             }
2778
2779             /**
2780              * Gets the value of the dividerLocation property.
2781              *
2782              * @return
2783              *     possible object is
2784              *     {@link Integer }
2785              *
2786              */
2787             public Integer getDividerLocation() {
2788                 return dividerLocation;
2789             }
2790
2791             /**
2792              * Sets the value of the dividerLocation property.
2793              *
2794              * @param value
2795              *     allowed object is
2796              *     {@link Integer }
2797              *
2798              */
2799             public void setDividerLocation(Integer value) {
2800                 this.dividerLocation = value;
2801             }
2802
2803             /**
2804              * Gets the value of the selectedRna property.
2805              *
2806              * @return
2807              *     possible object is
2808              *     {@link Integer }
2809              *
2810              */
2811             public Integer getSelectedRna() {
2812                 return selectedRna;
2813             }
2814
2815             /**
2816              * Sets the value of the selectedRna property.
2817              *
2818              * @param value
2819              *     allowed object is
2820              *     {@link Integer }
2821              *
2822              */
2823             public void setSelectedRna(Integer value) {
2824                 this.selectedRna = value;
2825             }
2826
2827             /**
2828              * Gets the value of the width property.
2829              *
2830              * @return
2831              *     possible object is
2832              *     {@link Integer }
2833              *
2834              */
2835             public Integer getWidth() {
2836                 return width;
2837             }
2838
2839             /**
2840              * Sets the value of the width property.
2841              *
2842              * @param value
2843              *     allowed object is
2844              *     {@link Integer }
2845              *
2846              */
2847             public void setWidth(Integer value) {
2848                 this.width = value;
2849             }
2850
2851             /**
2852              * Gets the value of the height property.
2853              *
2854              * @return
2855              *     possible object is
2856              *     {@link Integer }
2857              *
2858              */
2859             public Integer getHeight() {
2860                 return height;
2861             }
2862
2863             /**
2864              * Sets the value of the height property.
2865              *
2866              * @param value
2867              *     allowed object is
2868              *     {@link Integer }
2869              *
2870              */
2871             public void setHeight(Integer value) {
2872                 this.height = value;
2873             }
2874
2875             /**
2876              * Gets the value of the xpos property.
2877              *
2878              * @return
2879              *     possible object is
2880              *     {@link Integer }
2881              *
2882              */
2883             public Integer getXpos() {
2884                 return xpos;
2885             }
2886
2887             /**
2888              * Sets the value of the xpos property.
2889              *
2890              * @param value
2891              *     allowed object is
2892              *     {@link Integer }
2893              *
2894              */
2895             public void setXpos(Integer value) {
2896                 this.xpos = value;
2897             }
2898
2899             /**
2900              * Gets the value of the ypos property.
2901              *
2902              * @return
2903              *     possible object is
2904              *     {@link Integer }
2905              *
2906              */
2907             public Integer getYpos() {
2908                 return ypos;
2909             }
2910
2911             /**
2912              * Sets the value of the ypos property.
2913              *
2914              * @param value
2915              *     allowed object is
2916              *     {@link Integer }
2917              *
2918              */
2919             public void setYpos(Integer value) {
2920                 this.ypos = value;
2921             }
2922
2923
2924             /**
2925              * <p>Java class for anonymous complex type.
2926              *
2927              * <p>The following schema fragment specifies the expected content contained within this class.
2928              *
2929              * <pre>
2930              * &lt;complexType>
2931              *   &lt;complexContent>
2932              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2933              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2934              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2935              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2936              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2937              *     &lt;/restriction>
2938              *   &lt;/complexContent>
2939              * &lt;/complexType>
2940              * </pre>
2941              *
2942              *
2943              */
2944             @XmlAccessorType(XmlAccessType.FIELD)
2945             @XmlType(name = "")
2946             public static class SecondaryStructure {
2947
2948                 @XmlAttribute(name = "title")
2949                 protected String title;
2950                 @XmlAttribute(name = "annotationId", required = true)
2951                 protected String annotationId;
2952                 @XmlAttribute(name = "gapped")
2953                 protected Boolean gapped;
2954                 @XmlAttribute(name = "viewerState")
2955                 protected String viewerState;
2956
2957                 /**
2958                  * Gets the value of the title property.
2959                  *
2960                  * @return
2961                  *     possible object is
2962                  *     {@link String }
2963                  *
2964                  */
2965                 public String getTitle() {
2966                     return title;
2967                 }
2968
2969                 /**
2970                  * Sets the value of the title property.
2971                  *
2972                  * @param value
2973                  *     allowed object is
2974                  *     {@link String }
2975                  *
2976                  */
2977                 public void setTitle(String value) {
2978                     this.title = value;
2979                 }
2980
2981                 /**
2982                  * Gets the value of the annotationId property.
2983                  *
2984                  * @return
2985                  *     possible object is
2986                  *     {@link String }
2987                  *
2988                  */
2989                 public String getAnnotationId() {
2990                     return annotationId;
2991                 }
2992
2993                 /**
2994                  * Sets the value of the annotationId property.
2995                  *
2996                  * @param value
2997                  *     allowed object is
2998                  *     {@link String }
2999                  *
3000                  */
3001                 public void setAnnotationId(String value) {
3002                     this.annotationId = value;
3003                 }
3004
3005                 /**
3006                  * Gets the value of the gapped property.
3007                  *
3008                  * @return
3009                  *     possible object is
3010                  *     {@link Boolean }
3011                  *
3012                  */
3013                 public Boolean isGapped() {
3014                     return gapped;
3015                 }
3016
3017                 /**
3018                  * Sets the value of the gapped property.
3019                  *
3020                  * @param value
3021                  *     allowed object is
3022                  *     {@link Boolean }
3023                  *
3024                  */
3025                 public void setGapped(Boolean value) {
3026                     this.gapped = value;
3027                 }
3028
3029                 /**
3030                  * Gets the value of the viewerState property.
3031                  *
3032                  * @return
3033                  *     possible object is
3034                  *     {@link String }
3035                  *
3036                  */
3037                 public String getViewerState() {
3038                     return viewerState;
3039                 }
3040
3041                 /**
3042                  * Sets the value of the viewerState property.
3043                  *
3044                  * @param value
3045                  *     allowed object is
3046                  *     {@link String }
3047                  *
3048                  */
3049                 public void setViewerState(String value) {
3050                     this.viewerState = value;
3051                 }
3052
3053             }
3054
3055         }
3056
3057     }
3058
3059
3060     /**
3061      * <p>Java class for anonymous complex type.
3062      *
3063      * <p>The following schema fragment specifies the expected content contained within this class.
3064      *
3065      * <pre>
3066      * &lt;complexType>
3067      *   &lt;complexContent>
3068      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3069      *       &lt;sequence>
3070      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3071      *           &lt;complexType>
3072      *             &lt;complexContent>
3073      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3074      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3075      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3076      *               &lt;/restriction>
3077      *             &lt;/complexContent>
3078      *           &lt;/complexType>
3079      *         &lt;/element>
3080      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3081      *           &lt;complexType>
3082      *             &lt;complexContent>
3083      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3084      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3085      *               &lt;/restriction>
3086      *             &lt;/complexContent>
3087      *           &lt;/complexType>
3088      *         &lt;/element>
3089      *         &lt;element name="seqPointMin">
3090      *           &lt;complexType>
3091      *             &lt;complexContent>
3092      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3093      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3094      *               &lt;/restriction>
3095      *             &lt;/complexContent>
3096      *           &lt;/complexType>
3097      *         &lt;/element>
3098      *         &lt;element name="seqPointMax">
3099      *           &lt;complexType>
3100      *             &lt;complexContent>
3101      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3102      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3103      *               &lt;/restriction>
3104      *             &lt;/complexContent>
3105      *           &lt;/complexType>
3106      *         &lt;/element>
3107      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3108      *       &lt;/sequence>
3109      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3110      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3111      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3112      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3113      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3114      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3115      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3116      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3117      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3118      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3119      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3120      *     &lt;/restriction>
3121      *   &lt;/complexContent>
3122      * &lt;/complexType>
3123      * </pre>
3124      *
3125      *
3126      */
3127     @XmlAccessorType(XmlAccessType.FIELD)
3128     @XmlType(name = "", propOrder = {
3129         "sequencePoint",
3130         "axis",
3131         "seqPointMin",
3132         "seqPointMax",
3133         "pcaData"
3134     })
3135     public static class PcaViewer {
3136
3137         @XmlElement(namespace = "www.jalview.org", required = true)
3138         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3139         @XmlElement(namespace = "www.jalview.org", required = true)
3140         protected List<JalviewModel.PcaViewer.Axis> axis;
3141         @XmlElement(namespace = "www.jalview.org", required = true)
3142         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3143         @XmlElement(namespace = "www.jalview.org", required = true)
3144         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3145         @XmlElement(namespace = "www.jalview.org", required = true)
3146         protected PcaDataType pcaData;
3147         @XmlAttribute(name = "title")
3148         protected String title;
3149         @XmlAttribute(name = "scoreModelName")
3150         protected String scoreModelName;
3151         @XmlAttribute(name = "xDim")
3152         protected Integer xDim;
3153         @XmlAttribute(name = "yDim")
3154         protected Integer yDim;
3155         @XmlAttribute(name = "zDim")
3156         protected Integer zDim;
3157         @XmlAttribute(name = "bgColour")
3158         protected Integer bgColour;
3159         @XmlAttribute(name = "scaleFactor")
3160         protected Float scaleFactor;
3161         @XmlAttribute(name = "showLabels")
3162         protected Boolean showLabels;
3163         @XmlAttribute(name = "linkToAllViews")
3164         protected Boolean linkToAllViews;
3165         @XmlAttribute(name = "width")
3166         protected Integer width;
3167         @XmlAttribute(name = "height")
3168         protected Integer height;
3169         @XmlAttribute(name = "xpos")
3170         protected Integer xpos;
3171         @XmlAttribute(name = "ypos")
3172         protected Integer ypos;
3173         @XmlAttribute(name = "includeGaps")
3174         protected Boolean includeGaps;
3175         @XmlAttribute(name = "matchGaps")
3176         protected Boolean matchGaps;
3177         @XmlAttribute(name = "includeGappedColumns")
3178         protected Boolean includeGappedColumns;
3179         @XmlAttribute(name = "denominateByShortestLength")
3180         protected Boolean denominateByShortestLength;
3181
3182         /**
3183          * Gets the value of the sequencePoint property.
3184          *
3185          * <p>
3186          * This accessor method returns a reference to the live list,
3187          * not a snapshot. Therefore any modification you make to the
3188          * returned list will be present inside the JAXB object.
3189          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3190          *
3191          * <p>
3192          * For example, to add a new item, do as follows:
3193          * <pre>
3194          *    getSequencePoint().add(newItem);
3195          * </pre>
3196          *
3197          *
3198          * <p>
3199          * Objects of the following type(s) are allowed in the list
3200          * {@link JalviewModel.PcaViewer.SequencePoint }
3201          *
3202          *
3203          */
3204         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3205             if (sequencePoint == null) {
3206                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3207             }
3208             return this.sequencePoint;
3209         }
3210
3211         /**
3212          * Gets the value of the axis 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 axis property.
3219          *
3220          * <p>
3221          * For example, to add a new item, do as follows:
3222          * <pre>
3223          *    getAxis().add(newItem);
3224          * </pre>
3225          *
3226          *
3227          * <p>
3228          * Objects of the following type(s) are allowed in the list
3229          * {@link JalviewModel.PcaViewer.Axis }
3230          *
3231          *
3232          */
3233         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3234             if (axis == null) {
3235                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3236             }
3237             return this.axis;
3238         }
3239
3240         /**
3241          * Gets the value of the seqPointMin property.
3242          *
3243          * @return
3244          *     possible object is
3245          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3246          *
3247          */
3248         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3249             return seqPointMin;
3250         }
3251
3252         /**
3253          * Sets the value of the seqPointMin property.
3254          *
3255          * @param value
3256          *     allowed object is
3257          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3258          *
3259          */
3260         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3261             this.seqPointMin = value;
3262         }
3263
3264         /**
3265          * Gets the value of the seqPointMax property.
3266          *
3267          * @return
3268          *     possible object is
3269          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3270          *
3271          */
3272         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3273             return seqPointMax;
3274         }
3275
3276         /**
3277          * Sets the value of the seqPointMax property.
3278          *
3279          * @param value
3280          *     allowed object is
3281          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3282          *
3283          */
3284         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3285             this.seqPointMax = value;
3286         }
3287
3288         /**
3289          * Gets the value of the pcaData property.
3290          *
3291          * @return
3292          *     possible object is
3293          *     {@link PcaDataType }
3294          *
3295          */
3296         public PcaDataType getPcaData() {
3297             return pcaData;
3298         }
3299
3300         /**
3301          * Sets the value of the pcaData property.
3302          *
3303          * @param value
3304          *     allowed object is
3305          *     {@link PcaDataType }
3306          *
3307          */
3308         public void setPcaData(PcaDataType value) {
3309             this.pcaData = value;
3310         }
3311
3312         /**
3313          * Gets the value of the title property.
3314          *
3315          * @return
3316          *     possible object is
3317          *     {@link String }
3318          *
3319          */
3320         public String getTitle() {
3321             return title;
3322         }
3323
3324         /**
3325          * Sets the value of the title property.
3326          *
3327          * @param value
3328          *     allowed object is
3329          *     {@link String }
3330          *
3331          */
3332         public void setTitle(String value) {
3333             this.title = value;
3334         }
3335
3336         /**
3337          * Gets the value of the scoreModelName property.
3338          *
3339          * @return
3340          *     possible object is
3341          *     {@link String }
3342          *
3343          */
3344         public String getScoreModelName() {
3345             return scoreModelName;
3346         }
3347
3348         /**
3349          * Sets the value of the scoreModelName property.
3350          *
3351          * @param value
3352          *     allowed object is
3353          *     {@link String }
3354          *
3355          */
3356         public void setScoreModelName(String value) {
3357             this.scoreModelName = value;
3358         }
3359
3360         /**
3361          * Gets the value of the xDim property.
3362          *
3363          * @return
3364          *     possible object is
3365          *     {@link Integer }
3366          *
3367          */
3368         public Integer getXDim() {
3369             return xDim;
3370         }
3371
3372         /**
3373          * Sets the value of the xDim property.
3374          *
3375          * @param value
3376          *     allowed object is
3377          *     {@link Integer }
3378          *
3379          */
3380         public void setXDim(Integer value) {
3381             this.xDim = value;
3382         }
3383
3384         /**
3385          * Gets the value of the yDim property.
3386          *
3387          * @return
3388          *     possible object is
3389          *     {@link Integer }
3390          *
3391          */
3392         public Integer getYDim() {
3393             return yDim;
3394         }
3395
3396         /**
3397          * Sets the value of the yDim property.
3398          *
3399          * @param value
3400          *     allowed object is
3401          *     {@link Integer }
3402          *
3403          */
3404         public void setYDim(Integer value) {
3405             this.yDim = value;
3406         }
3407
3408         /**
3409          * Gets the value of the zDim property.
3410          *
3411          * @return
3412          *     possible object is
3413          *     {@link Integer }
3414          *
3415          */
3416         public Integer getZDim() {
3417             return zDim;
3418         }
3419
3420         /**
3421          * Sets the value of the zDim property.
3422          *
3423          * @param value
3424          *     allowed object is
3425          *     {@link Integer }
3426          *
3427          */
3428         public void setZDim(Integer value) {
3429             this.zDim = value;
3430         }
3431
3432         /**
3433          * Gets the value of the bgColour property.
3434          *
3435          * @return
3436          *     possible object is
3437          *     {@link Integer }
3438          *
3439          */
3440         public Integer getBgColour() {
3441             return bgColour;
3442         }
3443
3444         /**
3445          * Sets the value of the bgColour property.
3446          *
3447          * @param value
3448          *     allowed object is
3449          *     {@link Integer }
3450          *
3451          */
3452         public void setBgColour(Integer value) {
3453             this.bgColour = value;
3454         }
3455
3456         /**
3457          * Gets the value of the scaleFactor property.
3458          *
3459          * @return
3460          *     possible object is
3461          *     {@link Float }
3462          *
3463          */
3464         public Float getScaleFactor() {
3465             return scaleFactor;
3466         }
3467
3468         /**
3469          * Sets the value of the scaleFactor property.
3470          *
3471          * @param value
3472          *     allowed object is
3473          *     {@link Float }
3474          *
3475          */
3476         public void setScaleFactor(Float value) {
3477             this.scaleFactor = value;
3478         }
3479
3480         /**
3481          * Gets the value of the showLabels property.
3482          *
3483          * @return
3484          *     possible object is
3485          *     {@link Boolean }
3486          *
3487          */
3488         public Boolean isShowLabels() {
3489             return showLabels;
3490         }
3491
3492         /**
3493          * Sets the value of the showLabels property.
3494          *
3495          * @param value
3496          *     allowed object is
3497          *     {@link Boolean }
3498          *
3499          */
3500         public void setShowLabels(Boolean value) {
3501             this.showLabels = value;
3502         }
3503
3504         /**
3505          * Gets the value of the linkToAllViews property.
3506          *
3507          * @return
3508          *     possible object is
3509          *     {@link Boolean }
3510          *
3511          */
3512         public Boolean isLinkToAllViews() {
3513             return linkToAllViews;
3514         }
3515
3516         /**
3517          * Sets the value of the linkToAllViews property.
3518          *
3519          * @param value
3520          *     allowed object is
3521          *     {@link Boolean }
3522          *
3523          */
3524         public void setLinkToAllViews(Boolean value) {
3525             this.linkToAllViews = value;
3526         }
3527
3528         /**
3529          * Gets the value of the width property.
3530          *
3531          * @return
3532          *     possible object is
3533          *     {@link Integer }
3534          *
3535          */
3536         public Integer getWidth() {
3537             return width;
3538         }
3539
3540         /**
3541          * Sets the value of the width property.
3542          *
3543          * @param value
3544          *     allowed object is
3545          *     {@link Integer }
3546          *
3547          */
3548         public void setWidth(Integer value) {
3549             this.width = value;
3550         }
3551
3552         /**
3553          * Gets the value of the height property.
3554          *
3555          * @return
3556          *     possible object is
3557          *     {@link Integer }
3558          *
3559          */
3560         public Integer getHeight() {
3561             return height;
3562         }
3563
3564         /**
3565          * Sets the value of the height property.
3566          *
3567          * @param value
3568          *     allowed object is
3569          *     {@link Integer }
3570          *
3571          */
3572         public void setHeight(Integer value) {
3573             this.height = value;
3574         }
3575
3576         /**
3577          * Gets the value of the xpos property.
3578          *
3579          * @return
3580          *     possible object is
3581          *     {@link Integer }
3582          *
3583          */
3584         public Integer getXpos() {
3585             return xpos;
3586         }
3587
3588         /**
3589          * Sets the value of the xpos property.
3590          *
3591          * @param value
3592          *     allowed object is
3593          *     {@link Integer }
3594          *
3595          */
3596         public void setXpos(Integer value) {
3597             this.xpos = value;
3598         }
3599
3600         /**
3601          * Gets the value of the ypos property.
3602          *
3603          * @return
3604          *     possible object is
3605          *     {@link Integer }
3606          *
3607          */
3608         public Integer getYpos() {
3609             return ypos;
3610         }
3611
3612         /**
3613          * Sets the value of the ypos property.
3614          *
3615          * @param value
3616          *     allowed object is
3617          *     {@link Integer }
3618          *
3619          */
3620         public void setYpos(Integer value) {
3621             this.ypos = value;
3622         }
3623
3624         /**
3625          * Gets the value of the includeGaps property.
3626          *
3627          * @return
3628          *     possible object is
3629          *     {@link Boolean }
3630          *
3631          */
3632         public Boolean isIncludeGaps() {
3633             return includeGaps;
3634         }
3635
3636         /**
3637          * Sets the value of the includeGaps property.
3638          *
3639          * @param value
3640          *     allowed object is
3641          *     {@link Boolean }
3642          *
3643          */
3644         public void setIncludeGaps(Boolean value) {
3645             this.includeGaps = value;
3646         }
3647
3648         /**
3649          * Gets the value of the matchGaps property.
3650          *
3651          * @return
3652          *     possible object is
3653          *     {@link Boolean }
3654          *
3655          */
3656         public Boolean isMatchGaps() {
3657             return matchGaps;
3658         }
3659
3660         /**
3661          * Sets the value of the matchGaps property.
3662          *
3663          * @param value
3664          *     allowed object is
3665          *     {@link Boolean }
3666          *
3667          */
3668         public void setMatchGaps(Boolean value) {
3669             this.matchGaps = value;
3670         }
3671
3672         /**
3673          * Gets the value of the includeGappedColumns property.
3674          *
3675          * @return
3676          *     possible object is
3677          *     {@link Boolean }
3678          *
3679          */
3680         public Boolean isIncludeGappedColumns() {
3681             return includeGappedColumns;
3682         }
3683
3684         /**
3685          * Sets the value of the includeGappedColumns property.
3686          *
3687          * @param value
3688          *     allowed object is
3689          *     {@link Boolean }
3690          *
3691          */
3692         public void setIncludeGappedColumns(Boolean value) {
3693             this.includeGappedColumns = value;
3694         }
3695
3696         /**
3697          * Gets the value of the denominateByShortestLength property.
3698          *
3699          * @return
3700          *     possible object is
3701          *     {@link Boolean }
3702          *
3703          */
3704         public Boolean isDenominateByShortestLength() {
3705             return denominateByShortestLength;
3706         }
3707
3708         /**
3709          * Sets the value of the denominateByShortestLength property.
3710          *
3711          * @param value
3712          *     allowed object is
3713          *     {@link Boolean }
3714          *
3715          */
3716         public void setDenominateByShortestLength(Boolean value) {
3717             this.denominateByShortestLength = value;
3718         }
3719
3720
3721         /**
3722          * <p>Java class for anonymous complex type.
3723          *
3724          * <p>The following schema fragment specifies the expected content contained within this class.
3725          *
3726          * <pre>
3727          * &lt;complexType>
3728          *   &lt;complexContent>
3729          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3730          *       &lt;attGroup ref="{www.jalview.org}position"/>
3731          *     &lt;/restriction>
3732          *   &lt;/complexContent>
3733          * &lt;/complexType>
3734          * </pre>
3735          *
3736          *
3737          */
3738         @XmlAccessorType(XmlAccessType.FIELD)
3739         @XmlType(name = "")
3740         public static class Axis {
3741
3742             @XmlAttribute(name = "xPos")
3743             protected Float xPos;
3744             @XmlAttribute(name = "yPos")
3745             protected Float yPos;
3746             @XmlAttribute(name = "zPos")
3747             protected Float zPos;
3748
3749             /**
3750              * Gets the value of the xPos property.
3751              *
3752              * @return
3753              *     possible object is
3754              *     {@link Float }
3755              *
3756              */
3757             public Float getXPos() {
3758                 return xPos;
3759             }
3760
3761             /**
3762              * Sets the value of the xPos property.
3763              *
3764              * @param value
3765              *     allowed object is
3766              *     {@link Float }
3767              *
3768              */
3769             public void setXPos(Float value) {
3770                 this.xPos = value;
3771             }
3772
3773             /**
3774              * Gets the value of the yPos property.
3775              *
3776              * @return
3777              *     possible object is
3778              *     {@link Float }
3779              *
3780              */
3781             public Float getYPos() {
3782                 return yPos;
3783             }
3784
3785             /**
3786              * Sets the value of the yPos property.
3787              *
3788              * @param value
3789              *     allowed object is
3790              *     {@link Float }
3791              *
3792              */
3793             public void setYPos(Float value) {
3794                 this.yPos = value;
3795             }
3796
3797             /**
3798              * Gets the value of the zPos property.
3799              *
3800              * @return
3801              *     possible object is
3802              *     {@link Float }
3803              *
3804              */
3805             public Float getZPos() {
3806                 return zPos;
3807             }
3808
3809             /**
3810              * Sets the value of the zPos property.
3811              *
3812              * @param value
3813              *     allowed object is
3814              *     {@link Float }
3815              *
3816              */
3817             public void setZPos(Float value) {
3818                 this.zPos = value;
3819             }
3820
3821         }
3822
3823
3824         /**
3825          * <p>Java class for anonymous complex type.
3826          *
3827          * <p>The following schema fragment specifies the expected content contained within this class.
3828          *
3829          * <pre>
3830          * &lt;complexType>
3831          *   &lt;complexContent>
3832          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3833          *       &lt;attGroup ref="{www.jalview.org}position"/>
3834          *     &lt;/restriction>
3835          *   &lt;/complexContent>
3836          * &lt;/complexType>
3837          * </pre>
3838          *
3839          *
3840          */
3841         @XmlAccessorType(XmlAccessType.FIELD)
3842         @XmlType(name = "")
3843         public static class SeqPointMax {
3844
3845             @XmlAttribute(name = "xPos")
3846             protected Float xPos;
3847             @XmlAttribute(name = "yPos")
3848             protected Float yPos;
3849             @XmlAttribute(name = "zPos")
3850             protected Float zPos;
3851
3852             /**
3853              * Gets the value of the xPos property.
3854              *
3855              * @return
3856              *     possible object is
3857              *     {@link Float }
3858              *
3859              */
3860             public Float getXPos() {
3861                 return xPos;
3862             }
3863
3864             /**
3865              * Sets the value of the xPos property.
3866              *
3867              * @param value
3868              *     allowed object is
3869              *     {@link Float }
3870              *
3871              */
3872             public void setXPos(Float value) {
3873                 this.xPos = value;
3874             }
3875
3876             /**
3877              * Gets the value of the yPos property.
3878              *
3879              * @return
3880              *     possible object is
3881              *     {@link Float }
3882              *
3883              */
3884             public Float getYPos() {
3885                 return yPos;
3886             }
3887
3888             /**
3889              * Sets the value of the yPos property.
3890              *
3891              * @param value
3892              *     allowed object is
3893              *     {@link Float }
3894              *
3895              */
3896             public void setYPos(Float value) {
3897                 this.yPos = value;
3898             }
3899
3900             /**
3901              * Gets the value of the zPos property.
3902              *
3903              * @return
3904              *     possible object is
3905              *     {@link Float }
3906              *
3907              */
3908             public Float getZPos() {
3909                 return zPos;
3910             }
3911
3912             /**
3913              * Sets the value of the zPos property.
3914              *
3915              * @param value
3916              *     allowed object is
3917              *     {@link Float }
3918              *
3919              */
3920             public void setZPos(Float value) {
3921                 this.zPos = value;
3922             }
3923
3924         }
3925
3926
3927         /**
3928          * <p>Java class for anonymous complex type.
3929          *
3930          * <p>The following schema fragment specifies the expected content contained within this class.
3931          *
3932          * <pre>
3933          * &lt;complexType>
3934          *   &lt;complexContent>
3935          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3936          *       &lt;attGroup ref="{www.jalview.org}position"/>
3937          *     &lt;/restriction>
3938          *   &lt;/complexContent>
3939          * &lt;/complexType>
3940          * </pre>
3941          *
3942          *
3943          */
3944         @XmlAccessorType(XmlAccessType.FIELD)
3945         @XmlType(name = "")
3946         public static class SeqPointMin {
3947
3948             @XmlAttribute(name = "xPos")
3949             protected Float xPos;
3950             @XmlAttribute(name = "yPos")
3951             protected Float yPos;
3952             @XmlAttribute(name = "zPos")
3953             protected Float zPos;
3954
3955             /**
3956              * Gets the value of the xPos property.
3957              *
3958              * @return
3959              *     possible object is
3960              *     {@link Float }
3961              *
3962              */
3963             public Float getXPos() {
3964                 return xPos;
3965             }
3966
3967             /**
3968              * Sets the value of the xPos property.
3969              *
3970              * @param value
3971              *     allowed object is
3972              *     {@link Float }
3973              *
3974              */
3975             public void setXPos(Float value) {
3976                 this.xPos = value;
3977             }
3978
3979             /**
3980              * Gets the value of the yPos property.
3981              *
3982              * @return
3983              *     possible object is
3984              *     {@link Float }
3985              *
3986              */
3987             public Float getYPos() {
3988                 return yPos;
3989             }
3990
3991             /**
3992              * Sets the value of the yPos property.
3993              *
3994              * @param value
3995              *     allowed object is
3996              *     {@link Float }
3997              *
3998              */
3999             public void setYPos(Float value) {
4000                 this.yPos = value;
4001             }
4002
4003             /**
4004              * Gets the value of the zPos property.
4005              *
4006              * @return
4007              *     possible object is
4008              *     {@link Float }
4009              *
4010              */
4011             public Float getZPos() {
4012                 return zPos;
4013             }
4014
4015             /**
4016              * Sets the value of the zPos property.
4017              *
4018              * @param value
4019              *     allowed object is
4020              *     {@link Float }
4021              *
4022              */
4023             public void setZPos(Float value) {
4024                 this.zPos = value;
4025             }
4026
4027         }
4028
4029
4030         /**
4031          * <p>Java class for anonymous complex type.
4032          *
4033          * <p>The following schema fragment specifies the expected content contained within this class.
4034          *
4035          * <pre>
4036          * &lt;complexType>
4037          *   &lt;complexContent>
4038          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4039          *       &lt;attGroup ref="{www.jalview.org}position"/>
4040          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4041          *     &lt;/restriction>
4042          *   &lt;/complexContent>
4043          * &lt;/complexType>
4044          * </pre>
4045          *
4046          *
4047          */
4048         @XmlAccessorType(XmlAccessType.FIELD)
4049         @XmlType(name = "")
4050         public static class SequencePoint {
4051
4052             @XmlAttribute(name = "sequenceRef")
4053             protected String sequenceRef;
4054             @XmlAttribute(name = "xPos")
4055             protected Float xPos;
4056             @XmlAttribute(name = "yPos")
4057             protected Float yPos;
4058             @XmlAttribute(name = "zPos")
4059             protected Float zPos;
4060
4061             /**
4062              * Gets the value of the sequenceRef property.
4063              *
4064              * @return
4065              *     possible object is
4066              *     {@link String }
4067              *
4068              */
4069             public String getSequenceRef() {
4070                 return sequenceRef;
4071             }
4072
4073             /**
4074              * Sets the value of the sequenceRef property.
4075              *
4076              * @param value
4077              *     allowed object is
4078              *     {@link String }
4079              *
4080              */
4081             public void setSequenceRef(String value) {
4082                 this.sequenceRef = value;
4083             }
4084
4085             /**
4086              * Gets the value of the xPos property.
4087              *
4088              * @return
4089              *     possible object is
4090              *     {@link Float }
4091              *
4092              */
4093             public Float getXPos() {
4094                 return xPos;
4095             }
4096
4097             /**
4098              * Sets the value of the xPos property.
4099              *
4100              * @param value
4101              *     allowed object is
4102              *     {@link Float }
4103              *
4104              */
4105             public void setXPos(Float value) {
4106                 this.xPos = value;
4107             }
4108
4109             /**
4110              * Gets the value of the yPos property.
4111              *
4112              * @return
4113              *     possible object is
4114              *     {@link Float }
4115              *
4116              */
4117             public Float getYPos() {
4118                 return yPos;
4119             }
4120
4121             /**
4122              * Sets the value of the yPos property.
4123              *
4124              * @param value
4125              *     allowed object is
4126              *     {@link Float }
4127              *
4128              */
4129             public void setYPos(Float value) {
4130                 this.yPos = value;
4131             }
4132
4133             /**
4134              * Gets the value of the zPos property.
4135              *
4136              * @return
4137              *     possible object is
4138              *     {@link Float }
4139              *
4140              */
4141             public Float getZPos() {
4142                 return zPos;
4143             }
4144
4145             /**
4146              * Sets the value of the zPos property.
4147              *
4148              * @param value
4149              *     allowed object is
4150              *     {@link Float }
4151              *
4152              */
4153             public void setZPos(Float value) {
4154                 this.zPos = value;
4155             }
4156
4157         }
4158
4159     }
4160
4161
4162     /**
4163      * <p>Java class for anonymous complex type.
4164      *
4165      * <p>The following schema fragment specifies the expected content contained within this class.
4166      *
4167      * <pre>
4168      * &lt;complexType>
4169      *   &lt;complexContent>
4170      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4171      *       &lt;sequence minOccurs="0">
4172      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4173      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4174      *       &lt;/sequence>
4175      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4176      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4177      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4178      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4179      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4180      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4181      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4182      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4183      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4184      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4185      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4186      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4187      *     &lt;/restriction>
4188      *   &lt;/complexContent>
4189      * &lt;/complexType>
4190      * </pre>
4191      *
4192      *
4193      */
4194     @XmlAccessorType(XmlAccessType.FIELD)
4195     @XmlType(name = "", propOrder = {
4196         "title",
4197         "newick"
4198     })
4199     public static class Tree {
4200
4201         @XmlElement(namespace = "www.jalview.org")
4202         protected String title;
4203         @XmlElement(namespace = "www.jalview.org")
4204         protected String newick;
4205         @XmlAttribute(name = "fontName")
4206         protected String fontName;
4207         @XmlAttribute(name = "fontSize")
4208         protected Integer fontSize;
4209         @XmlAttribute(name = "fontStyle")
4210         protected Integer fontStyle;
4211         @XmlAttribute(name = "threshold")
4212         protected Float threshold;
4213         @XmlAttribute(name = "showBootstrap")
4214         protected Boolean showBootstrap;
4215         @XmlAttribute(name = "showDistances")
4216         protected Boolean showDistances;
4217         @XmlAttribute(name = "markUnlinked")
4218         protected Boolean markUnlinked;
4219         @XmlAttribute(name = "fitToWindow")
4220         protected Boolean fitToWindow;
4221         @XmlAttribute(name = "currentTree")
4222         protected Boolean currentTree;
4223         @XmlAttribute(name = "id")
4224         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4225         @XmlID
4226         @XmlSchemaType(name = "ID")
4227         protected String id;
4228         @XmlAttribute(name = "linkToAllViews")
4229         protected Boolean linkToAllViews;
4230         @XmlAttribute(name = "width")
4231         protected Integer width;
4232         @XmlAttribute(name = "height")
4233         protected Integer height;
4234         @XmlAttribute(name = "xpos")
4235         protected Integer xpos;
4236         @XmlAttribute(name = "ypos")
4237         protected Integer ypos;
4238
4239         /**
4240          * Gets the value of the title property.
4241          *
4242          * @return
4243          *     possible object is
4244          *     {@link String }
4245          *
4246          */
4247         public String getTitle() {
4248             return title;
4249         }
4250
4251         /**
4252          * Sets the value of the title property.
4253          *
4254          * @param value
4255          *     allowed object is
4256          *     {@link String }
4257          *
4258          */
4259         public void setTitle(String value) {
4260             this.title = value;
4261         }
4262
4263         /**
4264          * Gets the value of the newick property.
4265          *
4266          * @return
4267          *     possible object is
4268          *     {@link String }
4269          *
4270          */
4271         public String getNewick() {
4272             return newick;
4273         }
4274
4275         /**
4276          * Sets the value of the newick property.
4277          *
4278          * @param value
4279          *     allowed object is
4280          *     {@link String }
4281          *
4282          */
4283         public void setNewick(String value) {
4284             this.newick = value;
4285         }
4286
4287         /**
4288          * Gets the value of the fontName property.
4289          *
4290          * @return
4291          *     possible object is
4292          *     {@link String }
4293          *
4294          */
4295         public String getFontName() {
4296             return fontName;
4297         }
4298
4299         /**
4300          * Sets the value of the fontName property.
4301          *
4302          * @param value
4303          *     allowed object is
4304          *     {@link String }
4305          *
4306          */
4307         public void setFontName(String value) {
4308             this.fontName = value;
4309         }
4310
4311         /**
4312          * Gets the value of the fontSize property.
4313          *
4314          * @return
4315          *     possible object is
4316          *     {@link Integer }
4317          *
4318          */
4319         public Integer getFontSize() {
4320             return fontSize;
4321         }
4322
4323         /**
4324          * Sets the value of the fontSize property.
4325          *
4326          * @param value
4327          *     allowed object is
4328          *     {@link Integer }
4329          *
4330          */
4331         public void setFontSize(Integer value) {
4332             this.fontSize = value;
4333         }
4334
4335         /**
4336          * Gets the value of the fontStyle property.
4337          *
4338          * @return
4339          *     possible object is
4340          *     {@link Integer }
4341          *
4342          */
4343         public Integer getFontStyle() {
4344             return fontStyle;
4345         }
4346
4347         /**
4348          * Sets the value of the fontStyle property.
4349          *
4350          * @param value
4351          *     allowed object is
4352          *     {@link Integer }
4353          *
4354          */
4355         public void setFontStyle(Integer value) {
4356             this.fontStyle = value;
4357         }
4358
4359         /**
4360          * Gets the value of the threshold property.
4361          *
4362          * @return
4363          *     possible object is
4364          *     {@link Float }
4365          *
4366          */
4367         public Float getThreshold() {
4368             return threshold;
4369         }
4370
4371         /**
4372          * Sets the value of the threshold property.
4373          *
4374          * @param value
4375          *     allowed object is
4376          *     {@link Float }
4377          *
4378          */
4379         public void setThreshold(Float value) {
4380             this.threshold = value;
4381         }
4382
4383         /**
4384          * Gets the value of the showBootstrap property.
4385          *
4386          * @return
4387          *     possible object is
4388          *     {@link Boolean }
4389          *
4390          */
4391         public Boolean isShowBootstrap() {
4392             return showBootstrap;
4393         }
4394
4395         /**
4396          * Sets the value of the showBootstrap property.
4397          *
4398          * @param value
4399          *     allowed object is
4400          *     {@link Boolean }
4401          *
4402          */
4403         public void setShowBootstrap(Boolean value) {
4404             this.showBootstrap = value;
4405         }
4406
4407         /**
4408          * Gets the value of the showDistances property.
4409          *
4410          * @return
4411          *     possible object is
4412          *     {@link Boolean }
4413          *
4414          */
4415         public Boolean isShowDistances() {
4416             return showDistances;
4417         }
4418
4419         /**
4420          * Sets the value of the showDistances property.
4421          *
4422          * @param value
4423          *     allowed object is
4424          *     {@link Boolean }
4425          *
4426          */
4427         public void setShowDistances(Boolean value) {
4428             this.showDistances = value;
4429         }
4430
4431         /**
4432          * Gets the value of the markUnlinked property.
4433          *
4434          * @return
4435          *     possible object is
4436          *     {@link Boolean }
4437          *
4438          */
4439         public Boolean isMarkUnlinked() {
4440             return markUnlinked;
4441         }
4442
4443         /**
4444          * Sets the value of the markUnlinked property.
4445          *
4446          * @param value
4447          *     allowed object is
4448          *     {@link Boolean }
4449          *
4450          */
4451         public void setMarkUnlinked(Boolean value) {
4452             this.markUnlinked = value;
4453         }
4454
4455         /**
4456          * Gets the value of the fitToWindow property.
4457          *
4458          * @return
4459          *     possible object is
4460          *     {@link Boolean }
4461          *
4462          */
4463         public Boolean isFitToWindow() {
4464             return fitToWindow;
4465         }
4466
4467         /**
4468          * Sets the value of the fitToWindow property.
4469          *
4470          * @param value
4471          *     allowed object is
4472          *     {@link Boolean }
4473          *
4474          */
4475         public void setFitToWindow(Boolean value) {
4476             this.fitToWindow = value;
4477         }
4478
4479         /**
4480          * Gets the value of the currentTree property.
4481          *
4482          * @return
4483          *     possible object is
4484          *     {@link Boolean }
4485          *
4486          */
4487         public Boolean isCurrentTree() {
4488             return currentTree;
4489         }
4490
4491         /**
4492          * Sets the value of the currentTree property.
4493          *
4494          * @param value
4495          *     allowed object is
4496          *     {@link Boolean }
4497          *
4498          */
4499         public void setCurrentTree(Boolean value) {
4500             this.currentTree = value;
4501         }
4502
4503         /**
4504          * Gets the value of the id property.
4505          *
4506          * @return
4507          *     possible object is
4508          *     {@link String }
4509          *
4510          */
4511         public String getId() {
4512             return id;
4513         }
4514
4515         /**
4516          * Sets the value of the id property.
4517          *
4518          * @param value
4519          *     allowed object is
4520          *     {@link String }
4521          *
4522          */
4523         public void setId(String value) {
4524             this.id = value;
4525         }
4526
4527         /**
4528          * Gets the value of the linkToAllViews property.
4529          *
4530          * @return
4531          *     possible object is
4532          *     {@link Boolean }
4533          *
4534          */
4535         public boolean isLinkToAllViews() {
4536             if (linkToAllViews == null) {
4537                 return false;
4538             } else {
4539                 return linkToAllViews;
4540             }
4541         }
4542
4543         /**
4544          * Sets the value of the linkToAllViews property.
4545          *
4546          * @param value
4547          *     allowed object is
4548          *     {@link Boolean }
4549          *
4550          */
4551         public void setLinkToAllViews(Boolean value) {
4552             this.linkToAllViews = value;
4553         }
4554
4555         /**
4556          * Gets the value of the width property.
4557          *
4558          * @return
4559          *     possible object is
4560          *     {@link Integer }
4561          *
4562          */
4563         public Integer getWidth() {
4564             return width;
4565         }
4566
4567         /**
4568          * Sets the value of the width property.
4569          *
4570          * @param value
4571          *     allowed object is
4572          *     {@link Integer }
4573          *
4574          */
4575         public void setWidth(Integer value) {
4576             this.width = value;
4577         }
4578
4579         /**
4580          * Gets the value of the height property.
4581          *
4582          * @return
4583          *     possible object is
4584          *     {@link Integer }
4585          *
4586          */
4587         public Integer getHeight() {
4588             return height;
4589         }
4590
4591         /**
4592          * Sets the value of the height property.
4593          *
4594          * @param value
4595          *     allowed object is
4596          *     {@link Integer }
4597          *
4598          */
4599         public void setHeight(Integer value) {
4600             this.height = value;
4601         }
4602
4603         /**
4604          * Gets the value of the xpos property.
4605          *
4606          * @return
4607          *     possible object is
4608          *     {@link Integer }
4609          *
4610          */
4611         public Integer getXpos() {
4612             return xpos;
4613         }
4614
4615         /**
4616          * Sets the value of the xpos property.
4617          *
4618          * @param value
4619          *     allowed object is
4620          *     {@link Integer }
4621          *
4622          */
4623         public void setXpos(Integer value) {
4624             this.xpos = value;
4625         }
4626
4627         /**
4628          * Gets the value of the ypos property.
4629          *
4630          * @return
4631          *     possible object is
4632          *     {@link Integer }
4633          *
4634          */
4635         public Integer getYpos() {
4636             return ypos;
4637         }
4638
4639         /**
4640          * Sets the value of the ypos property.
4641          *
4642          * @param value
4643          *     allowed object is
4644          *     {@link Integer }
4645          *
4646          */
4647         public void setYpos(Integer value) {
4648             this.ypos = value;
4649         }
4650
4651     }
4652
4653
4654     /**
4655      * <p>Java class for anonymous complex type.
4656      *
4657      * <p>The following schema fragment specifies the expected content contained within this class.
4658      *
4659      * <pre>
4660      * &lt;complexType>
4661      *   &lt;complexContent>
4662      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4663      *       &lt;sequence>
4664      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4665      *       &lt;/sequence>
4666      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4667      *     &lt;/restriction>
4668      *   &lt;/complexContent>
4669      * &lt;/complexType>
4670      * </pre>
4671      *
4672      *
4673      */
4674     @XmlAccessorType(XmlAccessType.FIELD)
4675     @XmlType(name = "", propOrder = {
4676         "userColourScheme"
4677     })
4678     public static class UserColours {
4679
4680         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4681         protected JalviewUserColours userColourScheme;
4682         @XmlAttribute(name = "id")
4683         protected String id;
4684
4685         /**
4686          * Gets the value of the userColourScheme property.
4687          *
4688          * @return
4689          *     possible object is
4690          *     {@link JalviewUserColours }
4691          *
4692          */
4693         public JalviewUserColours getUserColourScheme() {
4694             return userColourScheme;
4695         }
4696
4697         /**
4698          * Sets the value of the userColourScheme property.
4699          *
4700          * @param value
4701          *     allowed object is
4702          *     {@link JalviewUserColours }
4703          *
4704          */
4705         public void setUserColourScheme(JalviewUserColours value) {
4706             this.userColourScheme = value;
4707         }
4708
4709         /**
4710          * Gets the value of the id property.
4711          *
4712          * @return
4713          *     possible object is
4714          *     {@link String }
4715          *
4716          */
4717         public String getId() {
4718             return id;
4719         }
4720
4721         /**
4722          * Sets the value of the id property.
4723          *
4724          * @param value
4725          *     allowed object is
4726          *     {@link String }
4727          *
4728          */
4729         public void setId(String value) {
4730             this.id = value;
4731         }
4732
4733     }
4734
4735
4736     /**
4737      * <p>Java class for anonymous complex type.
4738      *
4739      * <p>The following schema fragment specifies the expected content contained within this class.
4740      *
4741      * <pre>
4742      * &lt;complexType>
4743      *   &lt;complexContent>
4744      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4745      *       &lt;sequence>
4746      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4747      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4748      *           &lt;complexType>
4749      *             &lt;complexContent>
4750      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4751      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4752      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4753      *               &lt;/restriction>
4754      *             &lt;/complexContent>
4755      *           &lt;/complexType>
4756      *         &lt;/element>
4757      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4758      *           &lt;complexType>
4759      *             &lt;complexContent>
4760      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4761      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4762      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4763      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4764      *               &lt;/extension>
4765      *             &lt;/complexContent>
4766      *           &lt;/complexType>
4767      *         &lt;/element>
4768      *       &lt;/sequence>
4769      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4770      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4771      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4772      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4773      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4774      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4775      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4776      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4777      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4778      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4779      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4780      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4781      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4782      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4783      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4784      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4785      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4786      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4787      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4788      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4789      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4790      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4791      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4792      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4793      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4794      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4795      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4796      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4797      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4798      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4799      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4800      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4801      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4802      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4803      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4804      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4805      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4806      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4807      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4808      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4809      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4810      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4811      *     &lt;/restriction>
4812      *   &lt;/complexContent>
4813      * &lt;/complexType>
4814      * </pre>
4815      *
4816      *
4817      */
4818     @XmlAccessorType(XmlAccessType.FIELD)
4819     @XmlType(name = "", propOrder = {
4820         "annotationColours",
4821         "hiddenColumns",
4822         "calcIdParam"
4823     })
4824     public static class Viewport {
4825
4826         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4827         protected AnnotationColourScheme annotationColours;
4828         @XmlElement(namespace = "www.jalview.org")
4829         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4830         @XmlElement(namespace = "www.jalview.org")
4831         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4832         @XmlAttribute(name = "conservationSelected")
4833         protected Boolean conservationSelected;
4834         @XmlAttribute(name = "pidSelected")
4835         protected Boolean pidSelected;
4836         @XmlAttribute(name = "bgColour")
4837         protected String bgColour;
4838         @XmlAttribute(name = "consThreshold")
4839         protected Integer consThreshold;
4840         @XmlAttribute(name = "pidThreshold")
4841         protected Integer pidThreshold;
4842         @XmlAttribute(name = "title")
4843         protected String title;
4844         @XmlAttribute(name = "showFullId")
4845         protected Boolean showFullId;
4846         @XmlAttribute(name = "rightAlignIds")
4847         protected Boolean rightAlignIds;
4848         @XmlAttribute(name = "showText")
4849         protected Boolean showText;
4850         @XmlAttribute(name = "showColourText")
4851         protected Boolean showColourText;
4852         @XmlAttribute(name = "showUnconserved")
4853         protected Boolean showUnconserved;
4854         @XmlAttribute(name = "showBoxes")
4855         protected Boolean showBoxes;
4856         @XmlAttribute(name = "wrapAlignment")
4857         protected Boolean wrapAlignment;
4858         @XmlAttribute(name = "renderGaps")
4859         protected Boolean renderGaps;
4860         @XmlAttribute(name = "showSequenceFeatures")
4861         protected Boolean showSequenceFeatures;
4862         @XmlAttribute(name = "showNPfeatureTooltip")
4863         protected Boolean showNPfeatureTooltip;
4864         @XmlAttribute(name = "showDbRefTooltip")
4865         protected Boolean showDbRefTooltip;
4866         @XmlAttribute(name = "followHighlight")
4867         protected Boolean followHighlight;
4868         @XmlAttribute(name = "followSelection")
4869         protected Boolean followSelection;
4870         @XmlAttribute(name = "showAnnotation")
4871         protected Boolean showAnnotation;
4872         @XmlAttribute(name = "centreColumnLabels")
4873         protected Boolean centreColumnLabels;
4874         @XmlAttribute(name = "showGroupConservation")
4875         protected Boolean showGroupConservation;
4876         @XmlAttribute(name = "showGroupConsensus")
4877         protected Boolean showGroupConsensus;
4878         @XmlAttribute(name = "showConsensusHistogram")
4879         protected Boolean showConsensusHistogram;
4880         @XmlAttribute(name = "showSequenceLogo")
4881         protected Boolean showSequenceLogo;
4882         @XmlAttribute(name = "normaliseSequenceLogo")
4883         protected Boolean normaliseSequenceLogo;
4884         @XmlAttribute(name = "ignoreGapsinConsensus")
4885         protected Boolean ignoreGapsinConsensus;
4886         @XmlAttribute(name = "startRes")
4887         protected Integer startRes;
4888         @XmlAttribute(name = "startSeq")
4889         protected Integer startSeq;
4890         @XmlAttribute(name = "fontName")
4891         protected String fontName;
4892         @XmlAttribute(name = "fontSize")
4893         protected Integer fontSize;
4894         @XmlAttribute(name = "fontStyle")
4895         protected Integer fontStyle;
4896         @XmlAttribute(name = "scaleProteinAsCdna")
4897         protected Boolean scaleProteinAsCdna;
4898         @XmlAttribute(name = "viewName")
4899         protected String viewName;
4900         @XmlAttribute(name = "sequenceSetId")
4901         protected String sequenceSetId;
4902         @XmlAttribute(name = "gatheredViews")
4903         protected Boolean gatheredViews;
4904         @XmlAttribute(name = "textCol1")
4905         protected Integer textCol1;
4906         @XmlAttribute(name = "textCol2")
4907         protected Integer textCol2;
4908         @XmlAttribute(name = "textColThreshold")
4909         protected Integer textColThreshold;
4910         @XmlAttribute(name = "id")
4911         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4912         @XmlID
4913         @XmlSchemaType(name = "ID")
4914         protected String id;
4915         @XmlAttribute(name = "complementId")
4916         protected String complementId;
4917         @XmlAttribute(name = "width")
4918         protected Integer width;
4919         @XmlAttribute(name = "height")
4920         protected Integer height;
4921         @XmlAttribute(name = "xpos")
4922         protected Integer xpos;
4923         @XmlAttribute(name = "ypos")
4924         protected Integer ypos;
4925
4926         /**
4927          * Gets the value of the annotationColours property.
4928          *
4929          * @return
4930          *     possible object is
4931          *     {@link AnnotationColourScheme }
4932          *
4933          */
4934         public AnnotationColourScheme getAnnotationColours() {
4935             return annotationColours;
4936         }
4937
4938         /**
4939          * Sets the value of the annotationColours property.
4940          *
4941          * @param value
4942          *     allowed object is
4943          *     {@link AnnotationColourScheme }
4944          *
4945          */
4946         public void setAnnotationColours(AnnotationColourScheme value) {
4947             this.annotationColours = value;
4948         }
4949
4950         /**
4951          * Gets the value of the hiddenColumns property.
4952          *
4953          * <p>
4954          * This accessor method returns a reference to the live list,
4955          * not a snapshot. Therefore any modification you make to the
4956          * returned list will be present inside the JAXB object.
4957          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4958          *
4959          * <p>
4960          * For example, to add a new item, do as follows:
4961          * <pre>
4962          *    getHiddenColumns().add(newItem);
4963          * </pre>
4964          *
4965          *
4966          * <p>
4967          * Objects of the following type(s) are allowed in the list
4968          * {@link JalviewModel.Viewport.HiddenColumns }
4969          *
4970          *
4971          */
4972         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
4973             if (hiddenColumns == null) {
4974                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
4975             }
4976             return this.hiddenColumns;
4977         }
4978
4979         /**
4980          * Gets the value of the calcIdParam 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 calcIdParam property.
4987          *
4988          * <p>
4989          * For example, to add a new item, do as follows:
4990          * <pre>
4991          *    getCalcIdParam().add(newItem);
4992          * </pre>
4993          *
4994          *
4995          * <p>
4996          * Objects of the following type(s) are allowed in the list
4997          * {@link JalviewModel.Viewport.CalcIdParam }
4998          *
4999          *
5000          */
5001         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5002             if (calcIdParam == null) {
5003                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5004             }
5005             return this.calcIdParam;
5006         }
5007
5008         /**
5009          * Gets the value of the conservationSelected property.
5010          *
5011          * @return
5012          *     possible object is
5013          *     {@link Boolean }
5014          *
5015          */
5016         public Boolean isConservationSelected() {
5017             return conservationSelected;
5018         }
5019
5020         /**
5021          * Sets the value of the conservationSelected property.
5022          *
5023          * @param value
5024          *     allowed object is
5025          *     {@link Boolean }
5026          *
5027          */
5028         public void setConservationSelected(Boolean value) {
5029             this.conservationSelected = value;
5030         }
5031
5032         /**
5033          * Gets the value of the pidSelected property.
5034          *
5035          * @return
5036          *     possible object is
5037          *     {@link Boolean }
5038          *
5039          */
5040         public Boolean isPidSelected() {
5041             return pidSelected;
5042         }
5043
5044         /**
5045          * Sets the value of the pidSelected property.
5046          *
5047          * @param value
5048          *     allowed object is
5049          *     {@link Boolean }
5050          *
5051          */
5052         public void setPidSelected(Boolean value) {
5053             this.pidSelected = value;
5054         }
5055
5056         /**
5057          * Gets the value of the bgColour property.
5058          *
5059          * @return
5060          *     possible object is
5061          *     {@link String }
5062          *
5063          */
5064         public String getBgColour() {
5065             return bgColour;
5066         }
5067
5068         /**
5069          * Sets the value of the bgColour property.
5070          *
5071          * @param value
5072          *     allowed object is
5073          *     {@link String }
5074          *
5075          */
5076         public void setBgColour(String value) {
5077             this.bgColour = value;
5078         }
5079
5080         /**
5081          * Gets the value of the consThreshold property.
5082          *
5083          * @return
5084          *     possible object is
5085          *     {@link Integer }
5086          *
5087          */
5088         public Integer getConsThreshold() {
5089             return consThreshold;
5090         }
5091
5092         /**
5093          * Sets the value of the consThreshold property.
5094          *
5095          * @param value
5096          *     allowed object is
5097          *     {@link Integer }
5098          *
5099          */
5100         public void setConsThreshold(Integer value) {
5101             this.consThreshold = value;
5102         }
5103
5104         /**
5105          * Gets the value of the pidThreshold property.
5106          *
5107          * @return
5108          *     possible object is
5109          *     {@link Integer }
5110          *
5111          */
5112         public Integer getPidThreshold() {
5113             return pidThreshold;
5114         }
5115
5116         /**
5117          * Sets the value of the pidThreshold property.
5118          *
5119          * @param value
5120          *     allowed object is
5121          *     {@link Integer }
5122          *
5123          */
5124         public void setPidThreshold(Integer value) {
5125             this.pidThreshold = value;
5126         }
5127
5128         /**
5129          * Gets the value of the title property.
5130          *
5131          * @return
5132          *     possible object is
5133          *     {@link String }
5134          *
5135          */
5136         public String getTitle() {
5137             return title;
5138         }
5139
5140         /**
5141          * Sets the value of the title property.
5142          *
5143          * @param value
5144          *     allowed object is
5145          *     {@link String }
5146          *
5147          */
5148         public void setTitle(String value) {
5149             this.title = value;
5150         }
5151
5152         /**
5153          * Gets the value of the showFullId property.
5154          *
5155          * @return
5156          *     possible object is
5157          *     {@link Boolean }
5158          *
5159          */
5160         public Boolean isShowFullId() {
5161             return showFullId;
5162         }
5163
5164         /**
5165          * Sets the value of the showFullId property.
5166          *
5167          * @param value
5168          *     allowed object is
5169          *     {@link Boolean }
5170          *
5171          */
5172         public void setShowFullId(Boolean value) {
5173             this.showFullId = value;
5174         }
5175
5176         /**
5177          * Gets the value of the rightAlignIds property.
5178          *
5179          * @return
5180          *     possible object is
5181          *     {@link Boolean }
5182          *
5183          */
5184         public Boolean isRightAlignIds() {
5185             return rightAlignIds;
5186         }
5187
5188         /**
5189          * Sets the value of the rightAlignIds property.
5190          *
5191          * @param value
5192          *     allowed object is
5193          *     {@link Boolean }
5194          *
5195          */
5196         public void setRightAlignIds(Boolean value) {
5197             this.rightAlignIds = value;
5198         }
5199
5200         /**
5201          * Gets the value of the showText property.
5202          *
5203          * @return
5204          *     possible object is
5205          *     {@link Boolean }
5206          *
5207          */
5208         public Boolean isShowText() {
5209             return showText;
5210         }
5211
5212         /**
5213          * Sets the value of the showText property.
5214          *
5215          * @param value
5216          *     allowed object is
5217          *     {@link Boolean }
5218          *
5219          */
5220         public void setShowText(Boolean value) {
5221             this.showText = value;
5222         }
5223
5224         /**
5225          * Gets the value of the showColourText property.
5226          *
5227          * @return
5228          *     possible object is
5229          *     {@link Boolean }
5230          *
5231          */
5232         public Boolean isShowColourText() {
5233             return showColourText;
5234         }
5235
5236         /**
5237          * Sets the value of the showColourText property.
5238          *
5239          * @param value
5240          *     allowed object is
5241          *     {@link Boolean }
5242          *
5243          */
5244         public void setShowColourText(Boolean value) {
5245             this.showColourText = value;
5246         }
5247
5248         /**
5249          * Gets the value of the showUnconserved property.
5250          *
5251          * @return
5252          *     possible object is
5253          *     {@link Boolean }
5254          *
5255          */
5256         public boolean isShowUnconserved() {
5257             if (showUnconserved == null) {
5258                 return false;
5259             } else {
5260                 return showUnconserved;
5261             }
5262         }
5263
5264         /**
5265          * Sets the value of the showUnconserved property.
5266          *
5267          * @param value
5268          *     allowed object is
5269          *     {@link Boolean }
5270          *
5271          */
5272         public void setShowUnconserved(Boolean value) {
5273             this.showUnconserved = value;
5274         }
5275
5276         /**
5277          * Gets the value of the showBoxes property.
5278          *
5279          * @return
5280          *     possible object is
5281          *     {@link Boolean }
5282          *
5283          */
5284         public Boolean isShowBoxes() {
5285             return showBoxes;
5286         }
5287
5288         /**
5289          * Sets the value of the showBoxes property.
5290          *
5291          * @param value
5292          *     allowed object is
5293          *     {@link Boolean }
5294          *
5295          */
5296         public void setShowBoxes(Boolean value) {
5297             this.showBoxes = value;
5298         }
5299
5300         /**
5301          * Gets the value of the wrapAlignment property.
5302          *
5303          * @return
5304          *     possible object is
5305          *     {@link Boolean }
5306          *
5307          */
5308         public Boolean isWrapAlignment() {
5309             return wrapAlignment;
5310         }
5311
5312         /**
5313          * Sets the value of the wrapAlignment property.
5314          *
5315          * @param value
5316          *     allowed object is
5317          *     {@link Boolean }
5318          *
5319          */
5320         public void setWrapAlignment(Boolean value) {
5321             this.wrapAlignment = value;
5322         }
5323
5324         /**
5325          * Gets the value of the renderGaps property.
5326          *
5327          * @return
5328          *     possible object is
5329          *     {@link Boolean }
5330          *
5331          */
5332         public Boolean isRenderGaps() {
5333             return renderGaps;
5334         }
5335
5336         /**
5337          * Sets the value of the renderGaps property.
5338          *
5339          * @param value
5340          *     allowed object is
5341          *     {@link Boolean }
5342          *
5343          */
5344         public void setRenderGaps(Boolean value) {
5345             this.renderGaps = value;
5346         }
5347
5348         /**
5349          * Gets the value of the showSequenceFeatures property.
5350          *
5351          * @return
5352          *     possible object is
5353          *     {@link Boolean }
5354          *
5355          */
5356         public Boolean isShowSequenceFeatures() {
5357             return showSequenceFeatures;
5358         }
5359
5360         /**
5361          * Sets the value of the showSequenceFeatures property.
5362          *
5363          * @param value
5364          *     allowed object is
5365          *     {@link Boolean }
5366          *
5367          */
5368         public void setShowSequenceFeatures(Boolean value) {
5369             this.showSequenceFeatures = value;
5370         }
5371
5372         /**
5373          * Gets the value of the showNPfeatureTooltip property.
5374          *
5375          * @return
5376          *     possible object is
5377          *     {@link Boolean }
5378          *
5379          */
5380         public Boolean isShowNPfeatureTooltip() {
5381             return showNPfeatureTooltip;
5382         }
5383
5384         /**
5385          * Sets the value of the showNPfeatureTooltip property.
5386          *
5387          * @param value
5388          *     allowed object is
5389          *     {@link Boolean }
5390          *
5391          */
5392         public void setShowNPfeatureTooltip(Boolean value) {
5393             this.showNPfeatureTooltip = value;
5394         }
5395
5396         /**
5397          * Gets the value of the showDbRefTooltip property.
5398          *
5399          * @return
5400          *     possible object is
5401          *     {@link Boolean }
5402          *
5403          */
5404         public Boolean isShowDbRefTooltip() {
5405             return showDbRefTooltip;
5406         }
5407
5408         /**
5409          * Sets the value of the showDbRefTooltip property.
5410          *
5411          * @param value
5412          *     allowed object is
5413          *     {@link Boolean }
5414          *
5415          */
5416         public void setShowDbRefTooltip(Boolean value) {
5417             this.showDbRefTooltip = value;
5418         }
5419
5420         /**
5421          * Gets the value of the followHighlight property.
5422          *
5423          * @return
5424          *     possible object is
5425          *     {@link Boolean }
5426          *
5427          */
5428         public boolean isFollowHighlight() {
5429             if (followHighlight == null) {
5430                 return true;
5431             } else {
5432                 return followHighlight;
5433             }
5434         }
5435
5436         /**
5437          * Sets the value of the followHighlight property.
5438          *
5439          * @param value
5440          *     allowed object is
5441          *     {@link Boolean }
5442          *
5443          */
5444         public void setFollowHighlight(Boolean value) {
5445             this.followHighlight = value;
5446         }
5447
5448         /**
5449          * Gets the value of the followSelection property.
5450          *
5451          * @return
5452          *     possible object is
5453          *     {@link Boolean }
5454          *
5455          */
5456         public boolean isFollowSelection() {
5457             if (followSelection == null) {
5458                 return true;
5459             } else {
5460                 return followSelection;
5461             }
5462         }
5463
5464         /**
5465          * Sets the value of the followSelection property.
5466          *
5467          * @param value
5468          *     allowed object is
5469          *     {@link Boolean }
5470          *
5471          */
5472         public void setFollowSelection(Boolean value) {
5473             this.followSelection = value;
5474         }
5475
5476         /**
5477          * Gets the value of the showAnnotation property.
5478          *
5479          * @return
5480          *     possible object is
5481          *     {@link Boolean }
5482          *
5483          */
5484         public Boolean isShowAnnotation() {
5485             return showAnnotation;
5486         }
5487
5488         /**
5489          * Sets the value of the showAnnotation property.
5490          *
5491          * @param value
5492          *     allowed object is
5493          *     {@link Boolean }
5494          *
5495          */
5496         public void setShowAnnotation(Boolean value) {
5497             this.showAnnotation = value;
5498         }
5499
5500         /**
5501          * Gets the value of the centreColumnLabels property.
5502          *
5503          * @return
5504          *     possible object is
5505          *     {@link Boolean }
5506          *
5507          */
5508         public boolean isCentreColumnLabels() {
5509             if (centreColumnLabels == null) {
5510                 return false;
5511             } else {
5512                 return centreColumnLabels;
5513             }
5514         }
5515
5516         /**
5517          * Sets the value of the centreColumnLabels property.
5518          *
5519          * @param value
5520          *     allowed object is
5521          *     {@link Boolean }
5522          *
5523          */
5524         public void setCentreColumnLabels(Boolean value) {
5525             this.centreColumnLabels = value;
5526         }
5527
5528         /**
5529          * Gets the value of the showGroupConservation property.
5530          *
5531          * @return
5532          *     possible object is
5533          *     {@link Boolean }
5534          *
5535          */
5536         public boolean isShowGroupConservation() {
5537             if (showGroupConservation == null) {
5538                 return false;
5539             } else {
5540                 return showGroupConservation;
5541             }
5542         }
5543
5544         /**
5545          * Sets the value of the showGroupConservation property.
5546          *
5547          * @param value
5548          *     allowed object is
5549          *     {@link Boolean }
5550          *
5551          */
5552         public void setShowGroupConservation(Boolean value) {
5553             this.showGroupConservation = value;
5554         }
5555
5556         /**
5557          * Gets the value of the showGroupConsensus property.
5558          *
5559          * @return
5560          *     possible object is
5561          *     {@link Boolean }
5562          *
5563          */
5564         public boolean isShowGroupConsensus() {
5565             if (showGroupConsensus == null) {
5566                 return false;
5567             } else {
5568                 return showGroupConsensus;
5569             }
5570         }
5571
5572         /**
5573          * Sets the value of the showGroupConsensus property.
5574          *
5575          * @param value
5576          *     allowed object is
5577          *     {@link Boolean }
5578          *
5579          */
5580         public void setShowGroupConsensus(Boolean value) {
5581             this.showGroupConsensus = value;
5582         }
5583
5584         /**
5585          * Gets the value of the showConsensusHistogram property.
5586          *
5587          * @return
5588          *     possible object is
5589          *     {@link Boolean }
5590          *
5591          */
5592         public boolean isShowConsensusHistogram() {
5593             if (showConsensusHistogram == null) {
5594                 return true;
5595             } else {
5596                 return showConsensusHistogram;
5597             }
5598         }
5599
5600         /**
5601          * Sets the value of the showConsensusHistogram property.
5602          *
5603          * @param value
5604          *     allowed object is
5605          *     {@link Boolean }
5606          *
5607          */
5608         public void setShowConsensusHistogram(Boolean value) {
5609             this.showConsensusHistogram = value;
5610         }
5611
5612         /**
5613          * Gets the value of the showSequenceLogo property.
5614          *
5615          * @return
5616          *     possible object is
5617          *     {@link Boolean }
5618          *
5619          */
5620         public boolean isShowSequenceLogo() {
5621             if (showSequenceLogo == null) {
5622                 return false;
5623             } else {
5624                 return showSequenceLogo;
5625             }
5626         }
5627
5628         /**
5629          * Sets the value of the showSequenceLogo property.
5630          *
5631          * @param value
5632          *     allowed object is
5633          *     {@link Boolean }
5634          *
5635          */
5636         public void setShowSequenceLogo(Boolean value) {
5637             this.showSequenceLogo = value;
5638         }
5639
5640         /**
5641          * Gets the value of the normaliseSequenceLogo property.
5642          *
5643          * @return
5644          *     possible object is
5645          *     {@link Boolean }
5646          *
5647          */
5648         public boolean isNormaliseSequenceLogo() {
5649             if (normaliseSequenceLogo == null) {
5650                 return false;
5651             } else {
5652                 return normaliseSequenceLogo;
5653             }
5654         }
5655
5656         /**
5657          * Sets the value of the normaliseSequenceLogo property.
5658          *
5659          * @param value
5660          *     allowed object is
5661          *     {@link Boolean }
5662          *
5663          */
5664         public void setNormaliseSequenceLogo(Boolean value) {
5665             this.normaliseSequenceLogo = value;
5666         }
5667
5668         /**
5669          * Gets the value of the ignoreGapsinConsensus property.
5670          *
5671          * @return
5672          *     possible object is
5673          *     {@link Boolean }
5674          *
5675          */
5676         public boolean isIgnoreGapsinConsensus() {
5677             if (ignoreGapsinConsensus == null) {
5678                 return true;
5679             } else {
5680                 return ignoreGapsinConsensus;
5681             }
5682         }
5683
5684         /**
5685          * Sets the value of the ignoreGapsinConsensus property.
5686          *
5687          * @param value
5688          *     allowed object is
5689          *     {@link Boolean }
5690          *
5691          */
5692         public void setIgnoreGapsinConsensus(Boolean value) {
5693             this.ignoreGapsinConsensus = value;
5694         }
5695
5696         /**
5697          * Gets the value of the startRes property.
5698          *
5699          * @return
5700          *     possible object is
5701          *     {@link Integer }
5702          *
5703          */
5704         public Integer getStartRes() {
5705             return startRes;
5706         }
5707
5708         /**
5709          * Sets the value of the startRes property.
5710          *
5711          * @param value
5712          *     allowed object is
5713          *     {@link Integer }
5714          *
5715          */
5716         public void setStartRes(Integer value) {
5717             this.startRes = value;
5718         }
5719
5720         /**
5721          * Gets the value of the startSeq property.
5722          *
5723          * @return
5724          *     possible object is
5725          *     {@link Integer }
5726          *
5727          */
5728         public Integer getStartSeq() {
5729             return startSeq;
5730         }
5731
5732         /**
5733          * Sets the value of the startSeq property.
5734          *
5735          * @param value
5736          *     allowed object is
5737          *     {@link Integer }
5738          *
5739          */
5740         public void setStartSeq(Integer value) {
5741             this.startSeq = value;
5742         }
5743
5744         /**
5745          * Gets the value of the fontName property.
5746          *
5747          * @return
5748          *     possible object is
5749          *     {@link String }
5750          *
5751          */
5752         public String getFontName() {
5753             return fontName;
5754         }
5755
5756         /**
5757          * Sets the value of the fontName property.
5758          *
5759          * @param value
5760          *     allowed object is
5761          *     {@link String }
5762          *
5763          */
5764         public void setFontName(String value) {
5765             this.fontName = value;
5766         }
5767
5768         /**
5769          * Gets the value of the fontSize property.
5770          *
5771          * @return
5772          *     possible object is
5773          *     {@link Integer }
5774          *
5775          */
5776         public Integer getFontSize() {
5777             return fontSize;
5778         }
5779
5780         /**
5781          * Sets the value of the fontSize property.
5782          *
5783          * @param value
5784          *     allowed object is
5785          *     {@link Integer }
5786          *
5787          */
5788         public void setFontSize(Integer value) {
5789             this.fontSize = value;
5790         }
5791
5792         /**
5793          * Gets the value of the fontStyle property.
5794          *
5795          * @return
5796          *     possible object is
5797          *     {@link Integer }
5798          *
5799          */
5800         public Integer getFontStyle() {
5801             return fontStyle;
5802         }
5803
5804         /**
5805          * Sets the value of the fontStyle property.
5806          *
5807          * @param value
5808          *     allowed object is
5809          *     {@link Integer }
5810          *
5811          */
5812         public void setFontStyle(Integer value) {
5813             this.fontStyle = value;
5814         }
5815
5816         /**
5817          * Gets the value of the scaleProteinAsCdna property.
5818          *
5819          * @return
5820          *     possible object is
5821          *     {@link Boolean }
5822          *
5823          */
5824         public boolean isScaleProteinAsCdna() {
5825             if (scaleProteinAsCdna == null) {
5826                 return true;
5827             } else {
5828                 return scaleProteinAsCdna;
5829             }
5830         }
5831
5832         /**
5833          * Sets the value of the scaleProteinAsCdna property.
5834          *
5835          * @param value
5836          *     allowed object is
5837          *     {@link Boolean }
5838          *
5839          */
5840         public void setScaleProteinAsCdna(Boolean value) {
5841             this.scaleProteinAsCdna = value;
5842         }
5843
5844         /**
5845          * Gets the value of the viewName property.
5846          *
5847          * @return
5848          *     possible object is
5849          *     {@link String }
5850          *
5851          */
5852         public String getViewName() {
5853             return viewName;
5854         }
5855
5856         /**
5857          * Sets the value of the viewName property.
5858          *
5859          * @param value
5860          *     allowed object is
5861          *     {@link String }
5862          *
5863          */
5864         public void setViewName(String value) {
5865             this.viewName = value;
5866         }
5867
5868         /**
5869          * Gets the value of the sequenceSetId property.
5870          *
5871          * @return
5872          *     possible object is
5873          *     {@link String }
5874          *
5875          */
5876         public String getSequenceSetId() {
5877             return sequenceSetId;
5878         }
5879
5880         /**
5881          * Sets the value of the sequenceSetId property.
5882          *
5883          * @param value
5884          *     allowed object is
5885          *     {@link String }
5886          *
5887          */
5888         public void setSequenceSetId(String value) {
5889             this.sequenceSetId = value;
5890         }
5891
5892         /**
5893          * Gets the value of the gatheredViews property.
5894          *
5895          * @return
5896          *     possible object is
5897          *     {@link Boolean }
5898          *
5899          */
5900         public Boolean isGatheredViews() {
5901             return gatheredViews;
5902         }
5903
5904         /**
5905          * Sets the value of the gatheredViews property.
5906          *
5907          * @param value
5908          *     allowed object is
5909          *     {@link Boolean }
5910          *
5911          */
5912         public void setGatheredViews(Boolean value) {
5913             this.gatheredViews = value;
5914         }
5915
5916         /**
5917          * Gets the value of the textCol1 property.
5918          *
5919          * @return
5920          *     possible object is
5921          *     {@link Integer }
5922          *
5923          */
5924         public Integer getTextCol1() {
5925             return textCol1;
5926         }
5927
5928         /**
5929          * Sets the value of the textCol1 property.
5930          *
5931          * @param value
5932          *     allowed object is
5933          *     {@link Integer }
5934          *
5935          */
5936         public void setTextCol1(Integer value) {
5937             this.textCol1 = value;
5938         }
5939
5940         /**
5941          * Gets the value of the textCol2 property.
5942          *
5943          * @return
5944          *     possible object is
5945          *     {@link Integer }
5946          *
5947          */
5948         public Integer getTextCol2() {
5949             return textCol2;
5950         }
5951
5952         /**
5953          * Sets the value of the textCol2 property.
5954          *
5955          * @param value
5956          *     allowed object is
5957          *     {@link Integer }
5958          *
5959          */
5960         public void setTextCol2(Integer value) {
5961             this.textCol2 = value;
5962         }
5963
5964         /**
5965          * Gets the value of the textColThreshold property.
5966          *
5967          * @return
5968          *     possible object is
5969          *     {@link Integer }
5970          *
5971          */
5972         public Integer getTextColThreshold() {
5973             return textColThreshold;
5974         }
5975
5976         /**
5977          * Sets the value of the textColThreshold property.
5978          *
5979          * @param value
5980          *     allowed object is
5981          *     {@link Integer }
5982          *
5983          */
5984         public void setTextColThreshold(Integer value) {
5985             this.textColThreshold = value;
5986         }
5987
5988         /**
5989          * Gets the value of the id property.
5990          *
5991          * @return
5992          *     possible object is
5993          *     {@link String }
5994          *
5995          */
5996         public String getId() {
5997             return id;
5998         }
5999
6000         /**
6001          * Sets the value of the id property.
6002          *
6003          * @param value
6004          *     allowed object is
6005          *     {@link String }
6006          *
6007          */
6008         public void setId(String value) {
6009             this.id = value;
6010         }
6011
6012         /**
6013          * Gets the value of the complementId property.
6014          *
6015          * @return
6016          *     possible object is
6017          *     {@link String }
6018          *
6019          */
6020         public String getComplementId() {
6021             return complementId;
6022         }
6023
6024         /**
6025          * Sets the value of the complementId property.
6026          *
6027          * @param value
6028          *     allowed object is
6029          *     {@link String }
6030          *
6031          */
6032         public void setComplementId(String value) {
6033             this.complementId = value;
6034         }
6035
6036         /**
6037          * Gets the value of the width property.
6038          *
6039          * @return
6040          *     possible object is
6041          *     {@link Integer }
6042          *
6043          */
6044         public Integer getWidth() {
6045             return width;
6046         }
6047
6048         /**
6049          * Sets the value of the width property.
6050          *
6051          * @param value
6052          *     allowed object is
6053          *     {@link Integer }
6054          *
6055          */
6056         public void setWidth(Integer value) {
6057             this.width = value;
6058         }
6059
6060         /**
6061          * Gets the value of the height property.
6062          *
6063          * @return
6064          *     possible object is
6065          *     {@link Integer }
6066          *
6067          */
6068         public Integer getHeight() {
6069             return height;
6070         }
6071
6072         /**
6073          * Sets the value of the height property.
6074          *
6075          * @param value
6076          *     allowed object is
6077          *     {@link Integer }
6078          *
6079          */
6080         public void setHeight(Integer value) {
6081             this.height = value;
6082         }
6083
6084         /**
6085          * Gets the value of the xpos property.
6086          *
6087          * @return
6088          *     possible object is
6089          *     {@link Integer }
6090          *
6091          */
6092         public Integer getXpos() {
6093             return xpos;
6094         }
6095
6096         /**
6097          * Sets the value of the xpos property.
6098          *
6099          * @param value
6100          *     allowed object is
6101          *     {@link Integer }
6102          *
6103          */
6104         public void setXpos(Integer value) {
6105             this.xpos = value;
6106         }
6107
6108         /**
6109          * Gets the value of the ypos property.
6110          *
6111          * @return
6112          *     possible object is
6113          *     {@link Integer }
6114          *
6115          */
6116         public Integer getYpos() {
6117             return ypos;
6118         }
6119
6120         /**
6121          * Sets the value of the ypos property.
6122          *
6123          * @param value
6124          *     allowed object is
6125          *     {@link Integer }
6126          *
6127          */
6128         public void setYpos(Integer value) {
6129             this.ypos = value;
6130         }
6131
6132
6133         /**
6134          * <p>Java class for anonymous complex type.
6135          *
6136          * <p>The following schema fragment specifies the expected content contained within this class.
6137          *
6138          * <pre>
6139          * &lt;complexType>
6140          *   &lt;complexContent>
6141          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6142          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6143          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6144          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6145          *     &lt;/extension>
6146          *   &lt;/complexContent>
6147          * &lt;/complexType>
6148          * </pre>
6149          *
6150          *
6151          */
6152         @XmlAccessorType(XmlAccessType.FIELD)
6153         @XmlType(name = "")
6154         public static class CalcIdParam
6155             extends WebServiceParameterSet
6156         {
6157
6158             @XmlAttribute(name = "calcId", required = true)
6159             protected String calcId;
6160             @XmlAttribute(name = "needsUpdate")
6161             protected Boolean needsUpdate;
6162             @XmlAttribute(name = "autoUpdate", required = true)
6163             protected boolean autoUpdate;
6164
6165             /**
6166              * Gets the value of the calcId property.
6167              *
6168              * @return
6169              *     possible object is
6170              *     {@link String }
6171              *
6172              */
6173             public String getCalcId() {
6174                 return calcId;
6175             }
6176
6177             /**
6178              * Sets the value of the calcId property.
6179              *
6180              * @param value
6181              *     allowed object is
6182              *     {@link String }
6183              *
6184              */
6185             public void setCalcId(String value) {
6186                 this.calcId = value;
6187             }
6188
6189             /**
6190              * Gets the value of the needsUpdate property.
6191              *
6192              * @return
6193              *     possible object is
6194              *     {@link Boolean }
6195              *
6196              */
6197             public boolean isNeedsUpdate() {
6198                 if (needsUpdate == null) {
6199                     return false;
6200                 } else {
6201                     return needsUpdate;
6202                 }
6203             }
6204
6205             /**
6206              * Sets the value of the needsUpdate property.
6207              *
6208              * @param value
6209              *     allowed object is
6210              *     {@link Boolean }
6211              *
6212              */
6213             public void setNeedsUpdate(Boolean value) {
6214                 this.needsUpdate = value;
6215             }
6216
6217             /**
6218              * Gets the value of the autoUpdate property.
6219              *
6220              */
6221             public boolean isAutoUpdate() {
6222                 return autoUpdate;
6223             }
6224
6225             /**
6226              * Sets the value of the autoUpdate property.
6227              *
6228              */
6229             public void setAutoUpdate(boolean value) {
6230                 this.autoUpdate = value;
6231             }
6232
6233         }
6234
6235
6236         /**
6237          * <p>Java class for anonymous complex type.
6238          *
6239          * <p>The following schema fragment specifies the expected content contained within this class.
6240          *
6241          * <pre>
6242          * &lt;complexType>
6243          *   &lt;complexContent>
6244          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6245          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6246          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6247          *     &lt;/restriction>
6248          *   &lt;/complexContent>
6249          * &lt;/complexType>
6250          * </pre>
6251          *
6252          *
6253          */
6254         @XmlAccessorType(XmlAccessType.FIELD)
6255         @XmlType(name = "")
6256         public static class HiddenColumns {
6257
6258             @XmlAttribute(name = "start")
6259             protected Integer start;
6260             @XmlAttribute(name = "end")
6261             protected Integer end;
6262
6263             /**
6264              * Gets the value of the start property.
6265              *
6266              * @return
6267              *     possible object is
6268              *     {@link Integer }
6269              *
6270              */
6271             public Integer getStart() {
6272                 return start;
6273             }
6274
6275             /**
6276              * Sets the value of the start property.
6277              *
6278              * @param value
6279              *     allowed object is
6280              *     {@link Integer }
6281              *
6282              */
6283             public void setStart(Integer value) {
6284                 this.start = value;
6285             }
6286
6287             /**
6288              * Gets the value of the end property.
6289              *
6290              * @return
6291              *     possible object is
6292              *     {@link Integer }
6293              *
6294              */
6295             public Integer getEnd() {
6296                 return end;
6297             }
6298
6299             /**
6300              * Sets the value of the end property.
6301              *
6302              * @param value
6303              *     allowed object is
6304              *     {@link Integer }
6305              *
6306              */
6307             public void setEnd(Integer value) {
6308                 this.end = value;
6309             }
6310
6311         }
6312
6313     }
6314
6315 }