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

   1 //
   2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
   3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
   4 // Any modifications to this file will be lost upon recompilation of the source schema.
   5 // Generated on: 2020.12.10 at 03:00:06 PM GMT
   6 //
   7
   8
   9 package jalview.xml.binding.jalview;
  10
  11 import java.util.ArrayList;
  12 import java.util.List;
  13 import javax.xml.bind.annotation.XmlAccessType;
  14 import javax.xml.bind.annotation.XmlAccessorType;
  15 import javax.xml.bind.annotation.XmlAttribute;
  16 import javax.xml.bind.annotation.XmlElement;
  17 import javax.xml.bind.annotation.XmlID;
  18 import javax.xml.bind.annotation.XmlSchemaType;
  19 import javax.xml.bind.annotation.XmlType;
  20 import javax.xml.bind.annotation.XmlValue;
  21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
  22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  23 import javax.xml.datatype.XMLGregorianCalendar;
  24
  25
  26 /**
  27  * <p>Java class for JalviewModel complex type.
  28  *
  29  * <p>The following schema fragment specifies the expected content contained within this class.
  30  *
  31  * <pre>
  32  * &lt;complexType name="JalviewModel">
  33  *   &lt;complexContent>
  34  *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  35  *       &lt;sequence>
  36  *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
  37  *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
  38  *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
  39  *         &lt;sequence>
  40  *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  41  *             &lt;complexType>
  42  *               &lt;complexContent>
  43  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  44  *                   &lt;sequence>
  45  *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
  46  *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
  47  *                       &lt;complexType>
  48  *                         &lt;complexContent>
  49  *                           &lt;extension base="{www.jalview.org}pdbentry">
  50  *                             &lt;sequence>
  51  *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
  52  *                                 &lt;complexType>
  53  *                                   &lt;simpleContent>
  54  *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
  55  *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  56  *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  57  *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  58  *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  59  *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  60  *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  61  *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
  62  *                                     &lt;/extension>
  63  *                                   &lt;/simpleContent>
  64  *                                 &lt;/complexType>
  65  *                               &lt;/element>
  66  *                             &lt;/sequence>
  67  *                           &lt;/extension>
  68  *                         &lt;/complexContent>
  69  *                       &lt;/complexType>
  70  *                     &lt;/element>
  71  *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
  72  *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
  73  *                       &lt;complexType>
  74  *                         &lt;complexContent>
  75  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  76  *                             &lt;sequence>
  77  *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
  78  *                                 &lt;complexType>
  79  *                                   &lt;complexContent>
  80  *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  81  *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  82  *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  83  *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  84  *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
  85  *                                     &lt;/restriction>
  86  *                                   &lt;/complexContent>
  87  *                                 &lt;/complexType>
  88  *                               &lt;/element>
  89  *                             &lt;/sequence>
  90  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  91  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  92  *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  93  *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
  94  *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
  95  *                           &lt;/restriction>
  96  *                         &lt;/complexContent>
  97  *                       &lt;/complexType>
  98  *                     &lt;/element>
  99  *                   &lt;/sequence>
 100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                 &lt;/restriction>
 107  *               &lt;/complexContent>
 108  *             &lt;/complexType>
 109  *           &lt;/element>
 110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 111  *             &lt;complexType>
 112  *               &lt;complexContent>
 113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 114  *                   &lt;sequence>
 115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 117  *                   &lt;/sequence>
 118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 137  *                 &lt;/restriction>
 138  *               &lt;/complexContent>
 139  *             &lt;/complexType>
 140  *           &lt;/element>
 141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 142  *             &lt;complexType>
 143  *               &lt;complexContent>
 144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 145  *                   &lt;sequence>
 146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 148  *                       &lt;complexType>
 149  *                         &lt;complexContent>
 150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                           &lt;/restriction>
 154  *                         &lt;/complexContent>
 155  *                       &lt;/complexType>
 156  *                     &lt;/element>
 157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 158  *                       &lt;complexType>
 159  *                         &lt;complexContent>
 160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 164  *                           &lt;/extension>
 165  *                         &lt;/complexContent>
 166  *                       &lt;/complexType>
 167  *                     &lt;/element>
 168  *                     &lt;element name="overview" minOccurs="0">
 169  *                       &lt;complexType>
 170  *                         &lt;complexContent>
 171  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 172  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 173  *                             &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 174  *                             &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 175  *                             &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 176  *                             &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 177  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 178  *                           &lt;/restriction>
 179  *                         &lt;/complexContent>
 180  *                       &lt;/complexType>
 181  *                     &lt;/element>
 182  *                   &lt;/sequence>
 183  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 184  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 185  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 186  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 187  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 188  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 189  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 190  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 191  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 192  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 193  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 194  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 195  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 196  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 197  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 198  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 199  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 200  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 201  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 202  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 203  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 204  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 205  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 206  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 207  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 208  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 209  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 210  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 211  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 212  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 213  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 214  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 215  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 216  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 217  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 218  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 219  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 220  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 221  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 222  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 223  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 224  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 225  *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 226  *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 227  *                 &lt;/restriction>
 228  *               &lt;/complexContent>
 229  *             &lt;/complexType>
 230  *           &lt;/element>
 231  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 232  *             &lt;complexType>
 233  *               &lt;complexContent>
 234  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 235  *                   &lt;sequence>
 236  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 237  *                   &lt;/sequence>
 238  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 239  *                 &lt;/restriction>
 240  *               &lt;/complexContent>
 241  *             &lt;/complexType>
 242  *           &lt;/element>
 243  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 244  *             &lt;complexType>
 245  *               &lt;complexContent>
 246  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 247  *                   &lt;sequence minOccurs="0">
 248  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 249  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 250  *                   &lt;/sequence>
 251  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 252  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 253  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 254  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 255  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 256  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 257  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 258  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 259  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 260  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 261  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 262  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 263  *                 &lt;/restriction>
 264  *               &lt;/complexContent>
 265  *             &lt;/complexType>
 266  *           &lt;/element>
 267  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 268  *             &lt;complexType>
 269  *               &lt;complexContent>
 270  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 271  *                   &lt;sequence>
 272  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 273  *                       &lt;complexType>
 274  *                         &lt;complexContent>
 275  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 276  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 277  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 278  *                           &lt;/restriction>
 279  *                         &lt;/complexContent>
 280  *                       &lt;/complexType>
 281  *                     &lt;/element>
 282  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 283  *                       &lt;complexType>
 284  *                         &lt;complexContent>
 285  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 286  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 287  *                           &lt;/restriction>
 288  *                         &lt;/complexContent>
 289  *                       &lt;/complexType>
 290  *                     &lt;/element>
 291  *                     &lt;element name="seqPointMin">
 292  *                       &lt;complexType>
 293  *                         &lt;complexContent>
 294  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 295  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 296  *                           &lt;/restriction>
 297  *                         &lt;/complexContent>
 298  *                       &lt;/complexType>
 299  *                     &lt;/element>
 300  *                     &lt;element name="seqPointMax">
 301  *                       &lt;complexType>
 302  *                         &lt;complexContent>
 303  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 304  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 305  *                           &lt;/restriction>
 306  *                         &lt;/complexContent>
 307  *                       &lt;/complexType>
 308  *                     &lt;/element>
 309  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 310  *                   &lt;/sequence>
 311  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 312  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 313  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 314  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 315  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 316  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 317  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 318  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 319  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 320  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 321  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 322  *                 &lt;/restriction>
 323  *               &lt;/complexContent>
 324  *             &lt;/complexType>
 325  *           &lt;/element>
 326  *           &lt;element name="FeatureSettings" minOccurs="0">
 327  *             &lt;complexType>
 328  *               &lt;complexContent>
 329  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 330  *                   &lt;sequence>
 331  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 332  *                       &lt;complexType>
 333  *                         &lt;complexContent>
 334  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 335  *                             &lt;sequence>
 336  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 337  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 338  *                             &lt;/sequence>
 339  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 340  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 341  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 342  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 343  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 344  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 345  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 346  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 347  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 348  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 349  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 350  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 351  *                           &lt;/restriction>
 352  *                         &lt;/complexContent>
 353  *                       &lt;/complexType>
 354  *                     &lt;/element>
 355  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 356  *                       &lt;complexType>
 357  *                         &lt;complexContent>
 358  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 359  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 360  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 361  *                           &lt;/restriction>
 362  *                         &lt;/complexContent>
 363  *                       &lt;/complexType>
 364  *                     &lt;/element>
 365  *                   &lt;/sequence>
 366  *                 &lt;/restriction>
 367  *               &lt;/complexContent>
 368  *             &lt;/complexType>
 369  *           &lt;/element>
 370  *         &lt;/sequence>
 371  *       &lt;/sequence>
 372  *     &lt;/restriction>
 373  *   &lt;/complexContent>
 374  * &lt;/complexType>
 375  * </pre>
 376  *
 377  *
 378  */
 379 @XmlAccessorType(XmlAccessType.FIELD)
 380 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 381     "creationDate",
 382     "version",
 383     "vamsasModel",
 384     "jSeq",
 385     "jGroup",
 386     "viewport",
 387     "userColours",
 388     "tree",
 389     "pcaViewer",
 390     "featureSettings"
 391 })
 392 public class JalviewModel {
 393
 394     @XmlElement(required = true)
 395     @XmlSchemaType(name = "dateTime")
 396     protected XMLGregorianCalendar creationDate;
 397     @XmlElement(required = true)
 398     protected String version;
 399     @XmlElement(required = true)
 400     protected VAMSAS vamsasModel;
 401     @XmlElement(name = "JSeq")
 402     protected List<JalviewModel.JSeq> jSeq;
 403     @XmlElement(name = "JGroup")
 404     protected List<JalviewModel.JGroup> jGroup;
 405     @XmlElement(name = "Viewport")
 406     protected List<JalviewModel.Viewport> viewport;
 407     @XmlElement(name = "UserColours")
 408     protected List<JalviewModel.UserColours> userColours;
 409     protected List<JalviewModel.Tree> tree;
 410     @XmlElement(name = "PcaViewer")
 411     protected List<JalviewModel.PcaViewer> pcaViewer;
 412     @XmlElement(name = "FeatureSettings")
 413     protected JalviewModel.FeatureSettings featureSettings;
 414
 415     /**
 416      * Gets the value of the creationDate property.
 417      *
 418      * @return
 419      *     possible object is
 420      *     {@link XMLGregorianCalendar }
 421      *
 422      */
 423     public XMLGregorianCalendar getCreationDate() {
 424         return creationDate;
 425     }
 426
 427     /**
 428      * Sets the value of the creationDate property.
 429      *
 430      * @param value
 431      *     allowed object is
 432      *     {@link XMLGregorianCalendar }
 433      *
 434      */
 435     public void setCreationDate(XMLGregorianCalendar value) {
 436         this.creationDate = value;
 437     }
 438
 439     /**
 440      * Gets the value of the version property.
 441      *
 442      * @return
 443      *     possible object is
 444      *     {@link String }
 445      *
 446      */
 447     public String getVersion() {
 448         return version;
 449     }
 450
 451     /**
 452      * Sets the value of the version property.
 453      *
 454      * @param value
 455      *     allowed object is
 456      *     {@link String }
 457      *
 458      */
 459     public void setVersion(String value) {
 460         this.version = value;
 461     }
 462
 463     /**
 464      * Gets the value of the vamsasModel property.
 465      *
 466      * @return
 467      *     possible object is
 468      *     {@link VAMSAS }
 469      *
 470      */
 471     public VAMSAS getVamsasModel() {
 472         return vamsasModel;
 473     }
 474
 475     /**
 476      * Sets the value of the vamsasModel property.
 477      *
 478      * @param value
 479      *     allowed object is
 480      *     {@link VAMSAS }
 481      *
 482      */
 483     public void setVamsasModel(VAMSAS value) {
 484         this.vamsasModel = value;
 485     }
 486
 487     /**
 488      * Gets the value of the jSeq property.
 489      *
 490      * <p>
 491      * This accessor method returns a reference to the live list,
 492      * not a snapshot. Therefore any modification you make to the
 493      * returned list will be present inside the JAXB object.
 494      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 495      *
 496      * <p>
 497      * For example, to add a new item, do as follows:
 498      * <pre>
 499      *    getJSeq().add(newItem);
 500      * </pre>
 501      *
 502      *
 503      * <p>
 504      * Objects of the following type(s) are allowed in the list
 505      * {@link JalviewModel.JSeq }
 506      *
 507      *
 508      */
 509     public List<JalviewModel.JSeq> getJSeq() {
 510         if (jSeq == null) {
 511             jSeq = new ArrayList<JalviewModel.JSeq>();
 512         }
 513         return this.jSeq;
 514     }
 515
 516     /**
 517      * Gets the value of the jGroup property.
 518      *
 519      * <p>
 520      * This accessor method returns a reference to the live list,
 521      * not a snapshot. Therefore any modification you make to the
 522      * returned list will be present inside the JAXB object.
 523      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 524      *
 525      * <p>
 526      * For example, to add a new item, do as follows:
 527      * <pre>
 528      *    getJGroup().add(newItem);
 529      * </pre>
 530      *
 531      *
 532      * <p>
 533      * Objects of the following type(s) are allowed in the list
 534      * {@link JalviewModel.JGroup }
 535      *
 536      *
 537      */
 538     public List<JalviewModel.JGroup> getJGroup() {
 539         if (jGroup == null) {
 540             jGroup = new ArrayList<JalviewModel.JGroup>();
 541         }
 542         return this.jGroup;
 543     }
 544
 545     /**
 546      * Gets the value of the viewport property.
 547      *
 548      * <p>
 549      * This accessor method returns a reference to the live list,
 550      * not a snapshot. Therefore any modification you make to the
 551      * returned list will be present inside the JAXB object.
 552      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 553      *
 554      * <p>
 555      * For example, to add a new item, do as follows:
 556      * <pre>
 557      *    getViewport().add(newItem);
 558      * </pre>
 559      *
 560      *
 561      * <p>
 562      * Objects of the following type(s) are allowed in the list
 563      * {@link JalviewModel.Viewport }
 564      *
 565      *
 566      */
 567     public List<JalviewModel.Viewport> getViewport() {
 568         if (viewport == null) {
 569             viewport = new ArrayList<JalviewModel.Viewport>();
 570         }
 571         return this.viewport;
 572     }
 573
 574     /**
 575      * Gets the value of the userColours property.
 576      *
 577      * <p>
 578      * This accessor method returns a reference to the live list,
 579      * not a snapshot. Therefore any modification you make to the
 580      * returned list will be present inside the JAXB object.
 581      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 582      *
 583      * <p>
 584      * For example, to add a new item, do as follows:
 585      * <pre>
 586      *    getUserColours().add(newItem);
 587      * </pre>
 588      *
 589      *
 590      * <p>
 591      * Objects of the following type(s) are allowed in the list
 592      * {@link JalviewModel.UserColours }
 593      *
 594      *
 595      */
 596     public List<JalviewModel.UserColours> getUserColours() {
 597         if (userColours == null) {
 598             userColours = new ArrayList<JalviewModel.UserColours>();
 599         }
 600         return this.userColours;
 601     }
 602
 603     /**
 604      * Gets the value of the tree property.
 605      *
 606      * <p>
 607      * This accessor method returns a reference to the live list,
 608      * not a snapshot. Therefore any modification you make to the
 609      * returned list will be present inside the JAXB object.
 610      * This is why there is not a <CODE>set</CODE> method for the tree property.
 611      *
 612      * <p>
 613      * For example, to add a new item, do as follows:
 614      * <pre>
 615      *    getTree().add(newItem);
 616      * </pre>
 617      *
 618      *
 619      * <p>
 620      * Objects of the following type(s) are allowed in the list
 621      * {@link JalviewModel.Tree }
 622      *
 623      *
 624      */
 625     public List<JalviewModel.Tree> getTree() {
 626         if (tree == null) {
 627             tree = new ArrayList<JalviewModel.Tree>();
 628         }
 629         return this.tree;
 630     }
 631
 632     /**
 633      * Gets the value of the pcaViewer property.
 634      *
 635      * <p>
 636      * This accessor method returns a reference to the live list,
 637      * not a snapshot. Therefore any modification you make to the
 638      * returned list will be present inside the JAXB object.
 639      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 640      *
 641      * <p>
 642      * For example, to add a new item, do as follows:
 643      * <pre>
 644      *    getPcaViewer().add(newItem);
 645      * </pre>
 646      *
 647      *
 648      * <p>
 649      * Objects of the following type(s) are allowed in the list
 650      * {@link JalviewModel.PcaViewer }
 651      *
 652      *
 653      */
 654     public List<JalviewModel.PcaViewer> getPcaViewer() {
 655         if (pcaViewer == null) {
 656             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 657         }
 658         return this.pcaViewer;
 659     }
 660
 661     /**
 662      * Gets the value of the featureSettings property.
 663      *
 664      * @return
 665      *     possible object is
 666      *     {@link JalviewModel.FeatureSettings }
 667      *
 668      */
 669     public JalviewModel.FeatureSettings getFeatureSettings() {
 670         return featureSettings;
 671     }
 672
 673     /**
 674      * Sets the value of the featureSettings property.
 675      *
 676      * @param value
 677      *     allowed object is
 678      *     {@link JalviewModel.FeatureSettings }
 679      *
 680      */
 681     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 682         this.featureSettings = value;
 683     }
 684
 685
 686     /**
 687      * <p>Java class for anonymous complex type.
 688      *
 689      * <p>The following schema fragment specifies the expected content contained within this class.
 690      *
 691      * <pre>
 692      * &lt;complexType>
 693      *   &lt;complexContent>
 694      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 695      *       &lt;sequence>
 696      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 697      *           &lt;complexType>
 698      *             &lt;complexContent>
 699      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 700      *                 &lt;sequence>
 701      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 702      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 703      *                 &lt;/sequence>
 704      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 705      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 706      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 707      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 708      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 709      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 710      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 711      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 712      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 713      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 714      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 715      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 716      *               &lt;/restriction>
 717      *             &lt;/complexContent>
 718      *           &lt;/complexType>
 719      *         &lt;/element>
 720      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 721      *           &lt;complexType>
 722      *             &lt;complexContent>
 723      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 724      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 725      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 726      *               &lt;/restriction>
 727      *             &lt;/complexContent>
 728      *           &lt;/complexType>
 729      *         &lt;/element>
 730      *       &lt;/sequence>
 731      *     &lt;/restriction>
 732      *   &lt;/complexContent>
 733      * &lt;/complexType>
 734      * </pre>
 735      *
 736      *
 737      */
 738     @XmlAccessorType(XmlAccessType.FIELD)
 739     @XmlType(name = "", propOrder = {
 740         "setting",
 741         "group"
 742     })
 743     public static class FeatureSettings {
 744
 745         @XmlElement(namespace = "www.jalview.org")
 746         protected List<JalviewModel.FeatureSettings.Setting> setting;
 747         @XmlElement(namespace = "www.jalview.org")
 748         protected List<JalviewModel.FeatureSettings.Group> group;
 749
 750         /**
 751          * Gets the value of the setting property.
 752          *
 753          * <p>
 754          * This accessor method returns a reference to the live list,
 755          * not a snapshot. Therefore any modification you make to the
 756          * returned list will be present inside the JAXB object.
 757          * This is why there is not a <CODE>set</CODE> method for the setting property.
 758          *
 759          * <p>
 760          * For example, to add a new item, do as follows:
 761          * <pre>
 762          *    getSetting().add(newItem);
 763          * </pre>
 764          *
 765          *
 766          * <p>
 767          * Objects of the following type(s) are allowed in the list
 768          * {@link JalviewModel.FeatureSettings.Setting }
 769          *
 770          *
 771          */
 772         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 773             if (setting == null) {
 774                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 775             }
 776             return this.setting;
 777         }
 778
 779         /**
 780          * Gets the value of the group property.
 781          *
 782          * <p>
 783          * This accessor method returns a reference to the live list,
 784          * not a snapshot. Therefore any modification you make to the
 785          * returned list will be present inside the JAXB object.
 786          * This is why there is not a <CODE>set</CODE> method for the group property.
 787          *
 788          * <p>
 789          * For example, to add a new item, do as follows:
 790          * <pre>
 791          *    getGroup().add(newItem);
 792          * </pre>
 793          *
 794          *
 795          * <p>
 796          * Objects of the following type(s) are allowed in the list
 797          * {@link JalviewModel.FeatureSettings.Group }
 798          *
 799          *
 800          */
 801         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 802             if (group == null) {
 803                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 804             }
 805             return this.group;
 806         }
 807
 808
 809         /**
 810          * <p>Java class for anonymous complex type.
 811          *
 812          * <p>The following schema fragment specifies the expected content contained within this class.
 813          *
 814          * <pre>
 815          * &lt;complexType>
 816          *   &lt;complexContent>
 817          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 818          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 819          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 820          *     &lt;/restriction>
 821          *   &lt;/complexContent>
 822          * &lt;/complexType>
 823          * </pre>
 824          *
 825          *
 826          */
 827         @XmlAccessorType(XmlAccessType.FIELD)
 828         @XmlType(name = "")
 829         public static class Group {
 830
 831             @XmlAttribute(name = "name", required = true)
 832             protected String name;
 833             @XmlAttribute(name = "display", required = true)
 834             protected boolean display;
 835
 836             /**
 837              * Gets the value of the name property.
 838              *
 839              * @return
 840              *     possible object is
 841              *     {@link String }
 842              *
 843              */
 844             public String getName() {
 845                 return name;
 846             }
 847
 848             /**
 849              * Sets the value of the name property.
 850              *
 851              * @param value
 852              *     allowed object is
 853              *     {@link String }
 854              *
 855              */
 856             public void setName(String value) {
 857                 this.name = value;
 858             }
 859
 860             /**
 861              * Gets the value of the display property.
 862              *
 863              */
 864             public boolean isDisplay() {
 865                 return display;
 866             }
 867
 868             /**
 869              * Sets the value of the display property.
 870              *
 871              */
 872             public void setDisplay(boolean value) {
 873                 this.display = value;
 874             }
 875
 876         }
 877
 878
 879         /**
 880          * <p>Java class for anonymous complex type.
 881          *
 882          * <p>The following schema fragment specifies the expected content contained within this class.
 883          *
 884          * <pre>
 885          * &lt;complexType>
 886          *   &lt;complexContent>
 887          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 888          *       &lt;sequence>
 889          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 890          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 891          *       &lt;/sequence>
 892          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 893          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 894          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 895          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 896          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 897          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 898          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 899          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 900          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 901          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 902          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 903          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 904          *     &lt;/restriction>
 905          *   &lt;/complexContent>
 906          * &lt;/complexType>
 907          * </pre>
 908          *
 909          *
 910          */
 911         @XmlAccessorType(XmlAccessType.FIELD)
 912         @XmlType(name = "", propOrder = {
 913             "attributeName",
 914             "matcherSet"
 915         })
 916         public static class Setting {
 917
 918             @XmlElement(namespace = "www.jalview.org")
 919             protected List<String> attributeName;
 920             @XmlElement(namespace = "www.jalview.org")
 921             protected FeatureMatcherSet matcherSet;
 922             @XmlAttribute(name = "type", required = true)
 923             protected String type;
 924             @XmlAttribute(name = "colour", required = true)
 925             protected int colour;
 926             @XmlAttribute(name = "display", required = true)
 927             protected boolean display;
 928             @XmlAttribute(name = "order")
 929             protected Float order;
 930             @XmlAttribute(name = "mincolour")
 931             protected Integer mincolour;
 932             @XmlAttribute(name = "noValueColour")
 933             protected NoValueColour noValueColour;
 934             @XmlAttribute(name = "threshold")
 935             protected Float threshold;
 936             @XmlAttribute(name = "threshstate")
 937             protected Integer threshstate;
 938             @XmlAttribute(name = "max")
 939             protected Float max;
 940             @XmlAttribute(name = "min")
 941             protected Float min;
 942             @XmlAttribute(name = "colourByLabel")
 943             protected Boolean colourByLabel;
 944             @XmlAttribute(name = "autoScale")
 945             protected Boolean autoScale;
 946
 947             /**
 948              * Gets the value of the attributeName property.
 949              *
 950              * <p>
 951              * This accessor method returns a reference to the live list,
 952              * not a snapshot. Therefore any modification you make to the
 953              * returned list will be present inside the JAXB object.
 954              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 955              *
 956              * <p>
 957              * For example, to add a new item, do as follows:
 958              * <pre>
 959              *    getAttributeName().add(newItem);
 960              * </pre>
 961              *
 962              *
 963              * <p>
 964              * Objects of the following type(s) are allowed in the list
 965              * {@link String }
 966              *
 967              *
 968              */
 969             public List<String> getAttributeName() {
 970                 if (attributeName == null) {
 971                     attributeName = new ArrayList<String>();
 972                 }
 973                 return this.attributeName;
 974             }
 975
 976             /**
 977              * Gets the value of the matcherSet property.
 978              *
 979              * @return
 980              *     possible object is
 981              *     {@link FeatureMatcherSet }
 982              *
 983              */
 984             public FeatureMatcherSet getMatcherSet() {
 985                 return matcherSet;
 986             }
 987
 988             /**
 989              * Sets the value of the matcherSet property.
 990              *
 991              * @param value
 992              *     allowed object is
 993              *     {@link FeatureMatcherSet }
 994              *
 995              */
 996             public void setMatcherSet(FeatureMatcherSet value) {
 997                 this.matcherSet = value;
 998             }
 999
1000             /**
1001              * Gets the value of the type property.
1002              *
1003              * @return
1004              *     possible object is
1005              *     {@link String }
1006              *
1007              */
1008             public String getType() {
1009                 return type;
1010             }
1011
1012             /**
1013              * Sets the value of the type property.
1014              *
1015              * @param value
1016              *     allowed object is
1017              *     {@link String }
1018              *
1019              */
1020             public void setType(String value) {
1021                 this.type = value;
1022             }
1023
1024             /**
1025              * Gets the value of the colour property.
1026              *
1027              */
1028             public int getColour() {
1029                 return colour;
1030             }
1031
1032             /**
1033              * Sets the value of the colour property.
1034              *
1035              */
1036             public void setColour(int value) {
1037                 this.colour = value;
1038             }
1039
1040             /**
1041              * Gets the value of the display property.
1042              *
1043              */
1044             public boolean isDisplay() {
1045                 return display;
1046             }
1047
1048             /**
1049              * Sets the value of the display property.
1050              *
1051              */
1052             public void setDisplay(boolean value) {
1053                 this.display = value;
1054             }
1055
1056             /**
1057              * Gets the value of the order property.
1058              *
1059              * @return
1060              *     possible object is
1061              *     {@link Float }
1062              *
1063              */
1064             public Float getOrder() {
1065                 return order;
1066             }
1067
1068             /**
1069              * Sets the value of the order property.
1070              *
1071              * @param value
1072              *     allowed object is
1073              *     {@link Float }
1074              *
1075              */
1076             public void setOrder(Float value) {
1077                 this.order = value;
1078             }
1079
1080             /**
1081              * Gets the value of the mincolour property.
1082              *
1083              * @return
1084              *     possible object is
1085              *     {@link Integer }
1086              *
1087              */
1088             public Integer getMincolour() {
1089                 return mincolour;
1090             }
1091
1092             /**
1093              * Sets the value of the mincolour property.
1094              *
1095              * @param value
1096              *     allowed object is
1097              *     {@link Integer }
1098              *
1099              */
1100             public void setMincolour(Integer value) {
1101                 this.mincolour = value;
1102             }
1103
1104             /**
1105              * Gets the value of the noValueColour property.
1106              *
1107              * @return
1108              *     possible object is
1109              *     {@link NoValueColour }
1110              *
1111              */
1112             public NoValueColour getNoValueColour() {
1113                 if (noValueColour == null) {
1114                     return NoValueColour.MIN;
1115                 } else {
1116                     return noValueColour;
1117                 }
1118             }
1119
1120             /**
1121              * Sets the value of the noValueColour property.
1122              *
1123              * @param value
1124              *     allowed object is
1125              *     {@link NoValueColour }
1126              *
1127              */
1128             public void setNoValueColour(NoValueColour value) {
1129                 this.noValueColour = value;
1130             }
1131
1132             /**
1133              * Gets the value of the threshold property.
1134              *
1135              * @return
1136              *     possible object is
1137              *     {@link Float }
1138              *
1139              */
1140             public Float getThreshold() {
1141                 return threshold;
1142             }
1143
1144             /**
1145              * Sets the value of the threshold property.
1146              *
1147              * @param value
1148              *     allowed object is
1149              *     {@link Float }
1150              *
1151              */
1152             public void setThreshold(Float value) {
1153                 this.threshold = value;
1154             }
1155
1156             /**
1157              * Gets the value of the threshstate property.
1158              *
1159              * @return
1160              *     possible object is
1161              *     {@link Integer }
1162              *
1163              */
1164             public Integer getThreshstate() {
1165                 return threshstate;
1166             }
1167
1168             /**
1169              * Sets the value of the threshstate property.
1170              *
1171              * @param value
1172              *     allowed object is
1173              *     {@link Integer }
1174              *
1175              */
1176             public void setThreshstate(Integer value) {
1177                 this.threshstate = value;
1178             }
1179
1180             /**
1181              * Gets the value of the max property.
1182              *
1183              * @return
1184              *     possible object is
1185              *     {@link Float }
1186              *
1187              */
1188             public Float getMax() {
1189                 return max;
1190             }
1191
1192             /**
1193              * Sets the value of the max property.
1194              *
1195              * @param value
1196              *     allowed object is
1197              *     {@link Float }
1198              *
1199              */
1200             public void setMax(Float value) {
1201                 this.max = value;
1202             }
1203
1204             /**
1205              * Gets the value of the min property.
1206              *
1207              * @return
1208              *     possible object is
1209              *     {@link Float }
1210              *
1211              */
1212             public Float getMin() {
1213                 return min;
1214             }
1215
1216             /**
1217              * Sets the value of the min property.
1218              *
1219              * @param value
1220              *     allowed object is
1221              *     {@link Float }
1222              *
1223              */
1224             public void setMin(Float value) {
1225                 this.min = value;
1226             }
1227
1228             /**
1229              * Gets the value of the colourByLabel property.
1230              *
1231              * @return
1232              *     possible object is
1233              *     {@link Boolean }
1234              *
1235              */
1236             public Boolean isColourByLabel() {
1237                 return colourByLabel;
1238             }
1239
1240             /**
1241              * Sets the value of the colourByLabel property.
1242              *
1243              * @param value
1244              *     allowed object is
1245              *     {@link Boolean }
1246              *
1247              */
1248             public void setColourByLabel(Boolean value) {
1249                 this.colourByLabel = value;
1250             }
1251
1252             /**
1253              * Gets the value of the autoScale property.
1254              *
1255              * @return
1256              *     possible object is
1257              *     {@link Boolean }
1258              *
1259              */
1260             public Boolean isAutoScale() {
1261                 return autoScale;
1262             }
1263
1264             /**
1265              * Sets the value of the autoScale property.
1266              *
1267              * @param value
1268              *     allowed object is
1269              *     {@link Boolean }
1270              *
1271              */
1272             public void setAutoScale(Boolean value) {
1273                 this.autoScale = value;
1274             }
1275
1276         }
1277
1278     }
1279
1280
1281     /**
1282      * <p>Java class for anonymous complex type.
1283      *
1284      * <p>The following schema fragment specifies the expected content contained within this class.
1285      *
1286      * <pre>
1287      * &lt;complexType>
1288      *   &lt;complexContent>
1289      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1290      *       &lt;sequence>
1291      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1292      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1293      *       &lt;/sequence>
1294      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1295      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1296      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1297      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1298      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1299      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1300      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1301      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1302      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1303      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1304      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1305      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1306      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1307      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1308      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1309      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1310      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1311      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1312      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1313      *     &lt;/restriction>
1314      *   &lt;/complexContent>
1315      * &lt;/complexType>
1316      * </pre>
1317      *
1318      *
1319      */
1320     @XmlAccessorType(XmlAccessType.FIELD)
1321     @XmlType(name = "", propOrder = {
1322         "seq",
1323         "annotationColours"
1324     })
1325     public static class JGroup {
1326
1327         @XmlElement(namespace = "www.jalview.org", required = true)
1328         protected List<String> seq;
1329         @XmlElement(namespace = "www.jalview.org")
1330         protected AnnotationColourScheme annotationColours;
1331         @XmlAttribute(name = "start")
1332         protected Integer start;
1333         @XmlAttribute(name = "end")
1334         protected Integer end;
1335         @XmlAttribute(name = "name")
1336         protected String name;
1337         @XmlAttribute(name = "colour")
1338         protected String colour;
1339         @XmlAttribute(name = "consThreshold")
1340         protected Integer consThreshold;
1341         @XmlAttribute(name = "pidThreshold")
1342         protected Integer pidThreshold;
1343         @XmlAttribute(name = "outlineColour")
1344         protected Integer outlineColour;
1345         @XmlAttribute(name = "displayBoxes")
1346         protected Boolean displayBoxes;
1347         @XmlAttribute(name = "displayText")
1348         protected Boolean displayText;
1349         @XmlAttribute(name = "colourText")
1350         protected Boolean colourText;
1351         @XmlAttribute(name = "textCol1")
1352         protected Integer textCol1;
1353         @XmlAttribute(name = "textCol2")
1354         protected Integer textCol2;
1355         @XmlAttribute(name = "textColThreshold")
1356         protected Integer textColThreshold;
1357         @XmlAttribute(name = "showUnconserved")
1358         protected Boolean showUnconserved;
1359         @XmlAttribute(name = "ignoreGapsinConsensus")
1360         protected Boolean ignoreGapsinConsensus;
1361         @XmlAttribute(name = "showConsensusHistogram")
1362         protected Boolean showConsensusHistogram;
1363         @XmlAttribute(name = "showSequenceLogo")
1364         protected Boolean showSequenceLogo;
1365         @XmlAttribute(name = "normaliseSequenceLogo")
1366         protected Boolean normaliseSequenceLogo;
1367         @XmlAttribute(name = "id")
1368         protected String id;
1369
1370         /**
1371          * Gets the value of the seq property.
1372          *
1373          * <p>
1374          * This accessor method returns a reference to the live list,
1375          * not a snapshot. Therefore any modification you make to the
1376          * returned list will be present inside the JAXB object.
1377          * This is why there is not a <CODE>set</CODE> method for the seq property.
1378          *
1379          * <p>
1380          * For example, to add a new item, do as follows:
1381          * <pre>
1382          *    getSeq().add(newItem);
1383          * </pre>
1384          *
1385          *
1386          * <p>
1387          * Objects of the following type(s) are allowed in the list
1388          * {@link String }
1389          *
1390          *
1391          */
1392         public List<String> getSeq() {
1393             if (seq == null) {
1394                 seq = new ArrayList<String>();
1395             }
1396             return this.seq;
1397         }
1398
1399         /**
1400          * Gets the value of the annotationColours property.
1401          *
1402          * @return
1403          *     possible object is
1404          *     {@link AnnotationColourScheme }
1405          *
1406          */
1407         public AnnotationColourScheme getAnnotationColours() {
1408             return annotationColours;
1409         }
1410
1411         /**
1412          * Sets the value of the annotationColours property.
1413          *
1414          * @param value
1415          *     allowed object is
1416          *     {@link AnnotationColourScheme }
1417          *
1418          */
1419         public void setAnnotationColours(AnnotationColourScheme value) {
1420             this.annotationColours = value;
1421         }
1422
1423         /**
1424          * Gets the value of the start property.
1425          *
1426          * @return
1427          *     possible object is
1428          *     {@link Integer }
1429          *
1430          */
1431         public Integer getStart() {
1432             return start;
1433         }
1434
1435         /**
1436          * Sets the value of the start property.
1437          *
1438          * @param value
1439          *     allowed object is
1440          *     {@link Integer }
1441          *
1442          */
1443         public void setStart(Integer value) {
1444             this.start = value;
1445         }
1446
1447         /**
1448          * Gets the value of the end property.
1449          *
1450          * @return
1451          *     possible object is
1452          *     {@link Integer }
1453          *
1454          */
1455         public Integer getEnd() {
1456             return end;
1457         }
1458
1459         /**
1460          * Sets the value of the end property.
1461          *
1462          * @param value
1463          *     allowed object is
1464          *     {@link Integer }
1465          *
1466          */
1467         public void setEnd(Integer value) {
1468             this.end = value;
1469         }
1470
1471         /**
1472          * Gets the value of the name property.
1473          *
1474          * @return
1475          *     possible object is
1476          *     {@link String }
1477          *
1478          */
1479         public String getName() {
1480             return name;
1481         }
1482
1483         /**
1484          * Sets the value of the name property.
1485          *
1486          * @param value
1487          *     allowed object is
1488          *     {@link String }
1489          *
1490          */
1491         public void setName(String value) {
1492             this.name = value;
1493         }
1494
1495         /**
1496          * Gets the value of the colour property.
1497          *
1498          * @return
1499          *     possible object is
1500          *     {@link String }
1501          *
1502          */
1503         public String getColour() {
1504             return colour;
1505         }
1506
1507         /**
1508          * Sets the value of the colour property.
1509          *
1510          * @param value
1511          *     allowed object is
1512          *     {@link String }
1513          *
1514          */
1515         public void setColour(String value) {
1516             this.colour = value;
1517         }
1518
1519         /**
1520          * Gets the value of the consThreshold property.
1521          *
1522          * @return
1523          *     possible object is
1524          *     {@link Integer }
1525          *
1526          */
1527         public Integer getConsThreshold() {
1528             return consThreshold;
1529         }
1530
1531         /**
1532          * Sets the value of the consThreshold property.
1533          *
1534          * @param value
1535          *     allowed object is
1536          *     {@link Integer }
1537          *
1538          */
1539         public void setConsThreshold(Integer value) {
1540             this.consThreshold = value;
1541         }
1542
1543         /**
1544          * Gets the value of the pidThreshold property.
1545          *
1546          * @return
1547          *     possible object is
1548          *     {@link Integer }
1549          *
1550          */
1551         public Integer getPidThreshold() {
1552             return pidThreshold;
1553         }
1554
1555         /**
1556          * Sets the value of the pidThreshold property.
1557          *
1558          * @param value
1559          *     allowed object is
1560          *     {@link Integer }
1561          *
1562          */
1563         public void setPidThreshold(Integer value) {
1564             this.pidThreshold = value;
1565         }
1566
1567         /**
1568          * Gets the value of the outlineColour property.
1569          *
1570          * @return
1571          *     possible object is
1572          *     {@link Integer }
1573          *
1574          */
1575         public Integer getOutlineColour() {
1576             return outlineColour;
1577         }
1578
1579         /**
1580          * Sets the value of the outlineColour property.
1581          *
1582          * @param value
1583          *     allowed object is
1584          *     {@link Integer }
1585          *
1586          */
1587         public void setOutlineColour(Integer value) {
1588             this.outlineColour = value;
1589         }
1590
1591         /**
1592          * Gets the value of the displayBoxes property.
1593          *
1594          * @return
1595          *     possible object is
1596          *     {@link Boolean }
1597          *
1598          */
1599         public Boolean isDisplayBoxes() {
1600             return displayBoxes;
1601         }
1602
1603         /**
1604          * Sets the value of the displayBoxes property.
1605          *
1606          * @param value
1607          *     allowed object is
1608          *     {@link Boolean }
1609          *
1610          */
1611         public void setDisplayBoxes(Boolean value) {
1612             this.displayBoxes = value;
1613         }
1614
1615         /**
1616          * Gets the value of the displayText property.
1617          *
1618          * @return
1619          *     possible object is
1620          *     {@link Boolean }
1621          *
1622          */
1623         public Boolean isDisplayText() {
1624             return displayText;
1625         }
1626
1627         /**
1628          * Sets the value of the displayText property.
1629          *
1630          * @param value
1631          *     allowed object is
1632          *     {@link Boolean }
1633          *
1634          */
1635         public void setDisplayText(Boolean value) {
1636             this.displayText = value;
1637         }
1638
1639         /**
1640          * Gets the value of the colourText property.
1641          *
1642          * @return
1643          *     possible object is
1644          *     {@link Boolean }
1645          *
1646          */
1647         public Boolean isColourText() {
1648             return colourText;
1649         }
1650
1651         /**
1652          * Sets the value of the colourText property.
1653          *
1654          * @param value
1655          *     allowed object is
1656          *     {@link Boolean }
1657          *
1658          */
1659         public void setColourText(Boolean value) {
1660             this.colourText = value;
1661         }
1662
1663         /**
1664          * Gets the value of the textCol1 property.
1665          *
1666          * @return
1667          *     possible object is
1668          *     {@link Integer }
1669          *
1670          */
1671         public Integer getTextCol1() {
1672             return textCol1;
1673         }
1674
1675         /**
1676          * Sets the value of the textCol1 property.
1677          *
1678          * @param value
1679          *     allowed object is
1680          *     {@link Integer }
1681          *
1682          */
1683         public void setTextCol1(Integer value) {
1684             this.textCol1 = value;
1685         }
1686
1687         /**
1688          * Gets the value of the textCol2 property.
1689          *
1690          * @return
1691          *     possible object is
1692          *     {@link Integer }
1693          *
1694          */
1695         public Integer getTextCol2() {
1696             return textCol2;
1697         }
1698
1699         /**
1700          * Sets the value of the textCol2 property.
1701          *
1702          * @param value
1703          *     allowed object is
1704          *     {@link Integer }
1705          *
1706          */
1707         public void setTextCol2(Integer value) {
1708             this.textCol2 = value;
1709         }
1710
1711         /**
1712          * Gets the value of the textColThreshold property.
1713          *
1714          * @return
1715          *     possible object is
1716          *     {@link Integer }
1717          *
1718          */
1719         public Integer getTextColThreshold() {
1720             return textColThreshold;
1721         }
1722
1723         /**
1724          * Sets the value of the textColThreshold property.
1725          *
1726          * @param value
1727          *     allowed object is
1728          *     {@link Integer }
1729          *
1730          */
1731         public void setTextColThreshold(Integer value) {
1732             this.textColThreshold = value;
1733         }
1734
1735         /**
1736          * Gets the value of the showUnconserved property.
1737          *
1738          * @return
1739          *     possible object is
1740          *     {@link Boolean }
1741          *
1742          */
1743         public Boolean isShowUnconserved() {
1744             return showUnconserved;
1745         }
1746
1747         /**
1748          * Sets the value of the showUnconserved property.
1749          *
1750          * @param value
1751          *     allowed object is
1752          *     {@link Boolean }
1753          *
1754          */
1755         public void setShowUnconserved(Boolean value) {
1756             this.showUnconserved = value;
1757         }
1758
1759         /**
1760          * Gets the value of the ignoreGapsinConsensus property.
1761          *
1762          * @return
1763          *     possible object is
1764          *     {@link Boolean }
1765          *
1766          */
1767         public boolean isIgnoreGapsinConsensus() {
1768             if (ignoreGapsinConsensus == null) {
1769                 return true;
1770             } else {
1771                 return ignoreGapsinConsensus;
1772             }
1773         }
1774
1775         /**
1776          * Sets the value of the ignoreGapsinConsensus property.
1777          *
1778          * @param value
1779          *     allowed object is
1780          *     {@link Boolean }
1781          *
1782          */
1783         public void setIgnoreGapsinConsensus(Boolean value) {
1784             this.ignoreGapsinConsensus = value;
1785         }
1786
1787         /**
1788          * Gets the value of the showConsensusHistogram property.
1789          *
1790          * @return
1791          *     possible object is
1792          *     {@link Boolean }
1793          *
1794          */
1795         public boolean isShowConsensusHistogram() {
1796             if (showConsensusHistogram == null) {
1797                 return true;
1798             } else {
1799                 return showConsensusHistogram;
1800             }
1801         }
1802
1803         /**
1804          * Sets the value of the showConsensusHistogram property.
1805          *
1806          * @param value
1807          *     allowed object is
1808          *     {@link Boolean }
1809          *
1810          */
1811         public void setShowConsensusHistogram(Boolean value) {
1812             this.showConsensusHistogram = value;
1813         }
1814
1815         /**
1816          * Gets the value of the showSequenceLogo property.
1817          *
1818          * @return
1819          *     possible object is
1820          *     {@link Boolean }
1821          *
1822          */
1823         public boolean isShowSequenceLogo() {
1824             if (showSequenceLogo == null) {
1825                 return false;
1826             } else {
1827                 return showSequenceLogo;
1828             }
1829         }
1830
1831         /**
1832          * Sets the value of the showSequenceLogo property.
1833          *
1834          * @param value
1835          *     allowed object is
1836          *     {@link Boolean }
1837          *
1838          */
1839         public void setShowSequenceLogo(Boolean value) {
1840             this.showSequenceLogo = value;
1841         }
1842
1843         /**
1844          * Gets the value of the normaliseSequenceLogo property.
1845          *
1846          * @return
1847          *     possible object is
1848          *     {@link Boolean }
1849          *
1850          */
1851         public boolean isNormaliseSequenceLogo() {
1852             if (normaliseSequenceLogo == null) {
1853                 return false;
1854             } else {
1855                 return normaliseSequenceLogo;
1856             }
1857         }
1858
1859         /**
1860          * Sets the value of the normaliseSequenceLogo property.
1861          *
1862          * @param value
1863          *     allowed object is
1864          *     {@link Boolean }
1865          *
1866          */
1867         public void setNormaliseSequenceLogo(Boolean value) {
1868             this.normaliseSequenceLogo = value;
1869         }
1870
1871         /**
1872          * Gets the value of the id property.
1873          *
1874          * @return
1875          *     possible object is
1876          *     {@link String }
1877          *
1878          */
1879         public String getId() {
1880             return id;
1881         }
1882
1883         /**
1884          * Sets the value of the id property.
1885          *
1886          * @param value
1887          *     allowed object is
1888          *     {@link String }
1889          *
1890          */
1891         public void setId(String value) {
1892             this.id = value;
1893         }
1894
1895     }
1896
1897
1898     /**
1899      * <p>Java class for anonymous complex type.
1900      *
1901      * <p>The following schema fragment specifies the expected content contained within this class.
1902      *
1903      * <pre>
1904      * &lt;complexType>
1905      *   &lt;complexContent>
1906      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1907      *       &lt;sequence>
1908      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1909      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1910      *           &lt;complexType>
1911      *             &lt;complexContent>
1912      *               &lt;extension base="{www.jalview.org}pdbentry">
1913      *                 &lt;sequence>
1914      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1915      *                     &lt;complexType>
1916      *                       &lt;simpleContent>
1917      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1918      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1919      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1920      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1921      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1922      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1923      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1924      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1925      *                         &lt;/extension>
1926      *                       &lt;/simpleContent>
1927      *                     &lt;/complexType>
1928      *                   &lt;/element>
1929      *                 &lt;/sequence>
1930      *               &lt;/extension>
1931      *             &lt;/complexContent>
1932      *           &lt;/complexType>
1933      *         &lt;/element>
1934      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1935      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1936      *           &lt;complexType>
1937      *             &lt;complexContent>
1938      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1939      *                 &lt;sequence>
1940      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1941      *                     &lt;complexType>
1942      *                       &lt;complexContent>
1943      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1944      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1945      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1946      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1947      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1948      *                         &lt;/restriction>
1949      *                       &lt;/complexContent>
1950      *                     &lt;/complexType>
1951      *                   &lt;/element>
1952      *                 &lt;/sequence>
1953      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1954      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1955      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1956      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1957      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1958      *               &lt;/restriction>
1959      *             &lt;/complexContent>
1960      *           &lt;/complexType>
1961      *         &lt;/element>
1962      *       &lt;/sequence>
1963      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1964      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1965      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1966      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1967      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1968      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1969      *     &lt;/restriction>
1970      *   &lt;/complexContent>
1971      * &lt;/complexType>
1972      * </pre>
1973      *
1974      *
1975      */
1976     @XmlAccessorType(XmlAccessType.FIELD)
1977     @XmlType(name = "", propOrder = {
1978         "features",
1979         "pdbids",
1980         "hiddenSequences",
1981         "rnaViewer"
1982     })
1983     public static class JSeq {
1984
1985         @XmlElement(namespace = "www.jalview.org")
1986         protected List<Feature> features;
1987         @XmlElement(namespace = "www.jalview.org")
1988         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1989         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1990         protected List<Integer> hiddenSequences;
1991         @XmlElement(namespace = "www.jalview.org")
1992         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1993         @XmlAttribute(name = "colour")
1994         protected Integer colour;
1995         @XmlAttribute(name = "start", required = true)
1996         protected int start;
1997         @XmlAttribute(name = "end", required = true)
1998         protected int end;
1999         @XmlAttribute(name = "id", required = true)
2000         protected String id;
2001         @XmlAttribute(name = "hidden")
2002         protected Boolean hidden;
2003         @XmlAttribute(name = "viewreference")
2004         protected Boolean viewreference;
2005
2006         /**
2007          * Gets the value of the features property.
2008          *
2009          * <p>
2010          * This accessor method returns a reference to the live list,
2011          * not a snapshot. Therefore any modification you make to the
2012          * returned list will be present inside the JAXB object.
2013          * This is why there is not a <CODE>set</CODE> method for the features property.
2014          *
2015          * <p>
2016          * For example, to add a new item, do as follows:
2017          * <pre>
2018          *    getFeatures().add(newItem);
2019          * </pre>
2020          *
2021          *
2022          * <p>
2023          * Objects of the following type(s) are allowed in the list
2024          * {@link Feature }
2025          *
2026          *
2027          */
2028         public List<Feature> getFeatures() {
2029             if (features == null) {
2030                 features = new ArrayList<Feature>();
2031             }
2032             return this.features;
2033         }
2034
2035         /**
2036          * Gets the value of the pdbids property.
2037          *
2038          * <p>
2039          * This accessor method returns a reference to the live list,
2040          * not a snapshot. Therefore any modification you make to the
2041          * returned list will be present inside the JAXB object.
2042          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2043          *
2044          * <p>
2045          * For example, to add a new item, do as follows:
2046          * <pre>
2047          *    getPdbids().add(newItem);
2048          * </pre>
2049          *
2050          *
2051          * <p>
2052          * Objects of the following type(s) are allowed in the list
2053          * {@link JalviewModel.JSeq.Pdbids }
2054          *
2055          *
2056          */
2057         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2058             if (pdbids == null) {
2059                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2060             }
2061             return this.pdbids;
2062         }
2063
2064         /**
2065          * Gets the value of the hiddenSequences property.
2066          *
2067          * <p>
2068          * This accessor method returns a reference to the live list,
2069          * not a snapshot. Therefore any modification you make to the
2070          * returned list will be present inside the JAXB object.
2071          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2072          *
2073          * <p>
2074          * For example, to add a new item, do as follows:
2075          * <pre>
2076          *    getHiddenSequences().add(newItem);
2077          * </pre>
2078          *
2079          *
2080          * <p>
2081          * Objects of the following type(s) are allowed in the list
2082          * {@link Integer }
2083          *
2084          *
2085          */
2086         public List<Integer> getHiddenSequences() {
2087             if (hiddenSequences == null) {
2088                 hiddenSequences = new ArrayList<Integer>();
2089             }
2090             return this.hiddenSequences;
2091         }
2092
2093         /**
2094          * Gets the value of the rnaViewer property.
2095          *
2096          * <p>
2097          * This accessor method returns a reference to the live list,
2098          * not a snapshot. Therefore any modification you make to the
2099          * returned list will be present inside the JAXB object.
2100          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2101          *
2102          * <p>
2103          * For example, to add a new item, do as follows:
2104          * <pre>
2105          *    getRnaViewer().add(newItem);
2106          * </pre>
2107          *
2108          *
2109          * <p>
2110          * Objects of the following type(s) are allowed in the list
2111          * {@link JalviewModel.JSeq.RnaViewer }
2112          *
2113          *
2114          */
2115         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2116             if (rnaViewer == null) {
2117                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2118             }
2119             return this.rnaViewer;
2120         }
2121
2122         /**
2123          * Gets the value of the colour property.
2124          *
2125          * @return
2126          *     possible object is
2127          *     {@link Integer }
2128          *
2129          */
2130         public Integer getColour() {
2131             return colour;
2132         }
2133
2134         /**
2135          * Sets the value of the colour property.
2136          *
2137          * @param value
2138          *     allowed object is
2139          *     {@link Integer }
2140          *
2141          */
2142         public void setColour(Integer value) {
2143             this.colour = value;
2144         }
2145
2146         /**
2147          * Gets the value of the start property.
2148          *
2149          */
2150         public int getStart() {
2151             return start;
2152         }
2153
2154         /**
2155          * Sets the value of the start property.
2156          *
2157          */
2158         public void setStart(int value) {
2159             this.start = value;
2160         }
2161
2162         /**
2163          * Gets the value of the end property.
2164          *
2165          */
2166         public int getEnd() {
2167             return end;
2168         }
2169
2170         /**
2171          * Sets the value of the end property.
2172          *
2173          */
2174         public void setEnd(int value) {
2175             this.end = value;
2176         }
2177
2178         /**
2179          * Gets the value of the id property.
2180          *
2181          * @return
2182          *     possible object is
2183          *     {@link String }
2184          *
2185          */
2186         public String getId() {
2187             return id;
2188         }
2189
2190         /**
2191          * Sets the value of the id property.
2192          *
2193          * @param value
2194          *     allowed object is
2195          *     {@link String }
2196          *
2197          */
2198         public void setId(String value) {
2199             this.id = value;
2200         }
2201
2202         /**
2203          * Gets the value of the hidden property.
2204          *
2205          * @return
2206          *     possible object is
2207          *     {@link Boolean }
2208          *
2209          */
2210         public Boolean isHidden() {
2211             return hidden;
2212         }
2213
2214         /**
2215          * Sets the value of the hidden property.
2216          *
2217          * @param value
2218          *     allowed object is
2219          *     {@link Boolean }
2220          *
2221          */
2222         public void setHidden(Boolean value) {
2223             this.hidden = value;
2224         }
2225
2226         /**
2227          * Gets the value of the viewreference property.
2228          *
2229          * @return
2230          *     possible object is
2231          *     {@link Boolean }
2232          *
2233          */
2234         public Boolean isViewreference() {
2235             return viewreference;
2236         }
2237
2238         /**
2239          * Sets the value of the viewreference property.
2240          *
2241          * @param value
2242          *     allowed object is
2243          *     {@link Boolean }
2244          *
2245          */
2246         public void setViewreference(Boolean value) {
2247             this.viewreference = value;
2248         }
2249
2250
2251         /**
2252          * <p>Java class for anonymous complex type.
2253          *
2254          * <p>The following schema fragment specifies the expected content contained within this class.
2255          *
2256          * <pre>
2257          * &lt;complexType>
2258          *   &lt;complexContent>
2259          *     &lt;extension base="{www.jalview.org}pdbentry">
2260          *       &lt;sequence>
2261          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2262          *           &lt;complexType>
2263          *             &lt;simpleContent>
2264          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2265          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2266          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2267          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2268          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2269          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2270          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2271          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2272          *               &lt;/extension>
2273          *             &lt;/simpleContent>
2274          *           &lt;/complexType>
2275          *         &lt;/element>
2276          *       &lt;/sequence>
2277          *     &lt;/extension>
2278          *   &lt;/complexContent>
2279          * &lt;/complexType>
2280          * </pre>
2281          *
2282          *
2283          */
2284         @XmlAccessorType(XmlAccessType.FIELD)
2285         @XmlType(name = "", propOrder = {
2286             "structureState"
2287         })
2288         public static class Pdbids
2289             extends Pdbentry
2290         {
2291
2292             @XmlElement(namespace = "www.jalview.org")
2293             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2294
2295             /**
2296              * Gets the value of the structureState property.
2297              *
2298              * <p>
2299              * This accessor method returns a reference to the live list,
2300              * not a snapshot. Therefore any modification you make to the
2301              * returned list will be present inside the JAXB object.
2302              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2303              *
2304              * <p>
2305              * For example, to add a new item, do as follows:
2306              * <pre>
2307              *    getStructureState().add(newItem);
2308              * </pre>
2309              *
2310              *
2311              * <p>
2312              * Objects of the following type(s) are allowed in the list
2313              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2314              *
2315              *
2316              */
2317             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2318                 if (structureState == null) {
2319                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2320                 }
2321                 return this.structureState;
2322             }
2323
2324
2325             /**
2326              * <p>Java class for anonymous complex type.
2327              *
2328              * <p>The following schema fragment specifies the expected content contained within this class.
2329              *
2330              * <pre>
2331              * &lt;complexType>
2332              *   &lt;simpleContent>
2333              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2334              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2335              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2336              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2337              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2338              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2339              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2340              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2341              *     &lt;/extension>
2342              *   &lt;/simpleContent>
2343              * &lt;/complexType>
2344              * </pre>
2345              *
2346              *
2347              */
2348             @XmlAccessorType(XmlAccessType.FIELD)
2349             @XmlType(name = "", propOrder = {
2350                 "value"
2351             })
2352             public static class StructureState {
2353
2354                 @XmlValue
2355                 protected String value;
2356                 @XmlAttribute(name = "visible")
2357                 protected Boolean visible;
2358                 @XmlAttribute(name = "viewId")
2359                 protected String viewId;
2360                 @XmlAttribute(name = "alignwithAlignPanel")
2361                 protected Boolean alignwithAlignPanel;
2362                 @XmlAttribute(name = "colourwithAlignPanel")
2363                 protected Boolean colourwithAlignPanel;
2364                 @XmlAttribute(name = "colourByJmol")
2365                 protected Boolean colourByJmol;
2366                 @XmlAttribute(name = "type")
2367                 protected String type;
2368                 @XmlAttribute(name = "width")
2369                 protected Integer width;
2370                 @XmlAttribute(name = "height")
2371                 protected Integer height;
2372                 @XmlAttribute(name = "xpos")
2373                 protected Integer xpos;
2374                 @XmlAttribute(name = "ypos")
2375                 protected Integer ypos;
2376
2377                 /**
2378                  * Gets the value of the value property.
2379                  *
2380                  * @return
2381                  *     possible object is
2382                  *     {@link String }
2383                  *
2384                  */
2385                 public String getValue() {
2386                     return value;
2387                 }
2388
2389                 /**
2390                  * Sets the value of the value property.
2391                  *
2392                  * @param value
2393                  *     allowed object is
2394                  *     {@link String }
2395                  *
2396                  */
2397                 public void setValue(String value) {
2398                     this.value = value;
2399                 }
2400
2401                 /**
2402                  * Gets the value of the visible property.
2403                  *
2404                  * @return
2405                  *     possible object is
2406                  *     {@link Boolean }
2407                  *
2408                  */
2409                 public Boolean isVisible() {
2410                     return visible;
2411                 }
2412
2413                 /**
2414                  * Sets the value of the visible property.
2415                  *
2416                  * @param value
2417                  *     allowed object is
2418                  *     {@link Boolean }
2419                  *
2420                  */
2421                 public void setVisible(Boolean value) {
2422                     this.visible = value;
2423                 }
2424
2425                 /**
2426                  * Gets the value of the viewId property.
2427                  *
2428                  * @return
2429                  *     possible object is
2430                  *     {@link String }
2431                  *
2432                  */
2433                 public String getViewId() {
2434                     return viewId;
2435                 }
2436
2437                 /**
2438                  * Sets the value of the viewId property.
2439                  *
2440                  * @param value
2441                  *     allowed object is
2442                  *     {@link String }
2443                  *
2444                  */
2445                 public void setViewId(String value) {
2446                     this.viewId = value;
2447                 }
2448
2449                 /**
2450                  * Gets the value of the alignwithAlignPanel property.
2451                  *
2452                  * @return
2453                  *     possible object is
2454                  *     {@link Boolean }
2455                  *
2456                  */
2457                 public boolean isAlignwithAlignPanel() {
2458                     if (alignwithAlignPanel == null) {
2459                         return true;
2460                     } else {
2461                         return alignwithAlignPanel;
2462                     }
2463                 }
2464
2465                 /**
2466                  * Sets the value of the alignwithAlignPanel property.
2467                  *
2468                  * @param value
2469                  *     allowed object is
2470                  *     {@link Boolean }
2471                  *
2472                  */
2473                 public void setAlignwithAlignPanel(Boolean value) {
2474                     this.alignwithAlignPanel = value;
2475                 }
2476
2477                 /**
2478                  * Gets the value of the colourwithAlignPanel property.
2479                  *
2480                  * @return
2481                  *     possible object is
2482                  *     {@link Boolean }
2483                  *
2484                  */
2485                 public boolean isColourwithAlignPanel() {
2486                     if (colourwithAlignPanel == null) {
2487                         return false;
2488                     } else {
2489                         return colourwithAlignPanel;
2490                     }
2491                 }
2492
2493                 /**
2494                  * Sets the value of the colourwithAlignPanel property.
2495                  *
2496                  * @param value
2497                  *     allowed object is
2498                  *     {@link Boolean }
2499                  *
2500                  */
2501                 public void setColourwithAlignPanel(Boolean value) {
2502                     this.colourwithAlignPanel = value;
2503                 }
2504
2505                 /**
2506                  * Gets the value of the colourByJmol property.
2507                  *
2508                  * @return
2509                  *     possible object is
2510                  *     {@link Boolean }
2511                  *
2512                  */
2513                 public boolean isColourByJmol() {
2514                     if (colourByJmol == null) {
2515                         return true;
2516                     } else {
2517                         return colourByJmol;
2518                     }
2519                 }
2520
2521                 /**
2522                  * Sets the value of the colourByJmol property.
2523                  *
2524                  * @param value
2525                  *     allowed object is
2526                  *     {@link Boolean }
2527                  *
2528                  */
2529                 public void setColourByJmol(Boolean value) {
2530                     this.colourByJmol = value;
2531                 }
2532
2533                 /**
2534                  * Gets the value of the type property.
2535                  *
2536                  * @return
2537                  *     possible object is
2538                  *     {@link String }
2539                  *
2540                  */
2541                 public String getType() {
2542                     return type;
2543                 }
2544
2545                 /**
2546                  * Sets the value of the type property.
2547                  *
2548                  * @param value
2549                  *     allowed object is
2550                  *     {@link String }
2551                  *
2552                  */
2553                 public void setType(String value) {
2554                     this.type = value;
2555                 }
2556
2557                 /**
2558                  * Gets the value of the width property.
2559                  *
2560                  * @return
2561                  *     possible object is
2562                  *     {@link Integer }
2563                  *
2564                  */
2565                 public Integer getWidth() {
2566                     return width;
2567                 }
2568
2569                 /**
2570                  * Sets the value of the width property.
2571                  *
2572                  * @param value
2573                  *     allowed object is
2574                  *     {@link Integer }
2575                  *
2576                  */
2577                 public void setWidth(Integer value) {
2578                     this.width = value;
2579                 }
2580
2581                 /**
2582                  * Gets the value of the height property.
2583                  *
2584                  * @return
2585                  *     possible object is
2586                  *     {@link Integer }
2587                  *
2588                  */
2589                 public Integer getHeight() {
2590                     return height;
2591                 }
2592
2593                 /**
2594                  * Sets the value of the height property.
2595                  *
2596                  * @param value
2597                  *     allowed object is
2598                  *     {@link Integer }
2599                  *
2600                  */
2601                 public void setHeight(Integer value) {
2602                     this.height = value;
2603                 }
2604
2605                 /**
2606                  * Gets the value of the xpos property.
2607                  *
2608                  * @return
2609                  *     possible object is
2610                  *     {@link Integer }
2611                  *
2612                  */
2613                 public Integer getXpos() {
2614                     return xpos;
2615                 }
2616
2617                 /**
2618                  * Sets the value of the xpos property.
2619                  *
2620                  * @param value
2621                  *     allowed object is
2622                  *     {@link Integer }
2623                  *
2624                  */
2625                 public void setXpos(Integer value) {
2626                     this.xpos = value;
2627                 }
2628
2629                 /**
2630                  * Gets the value of the ypos property.
2631                  *
2632                  * @return
2633                  *     possible object is
2634                  *     {@link Integer }
2635                  *
2636                  */
2637                 public Integer getYpos() {
2638                     return ypos;
2639                 }
2640
2641                 /**
2642                  * Sets the value of the ypos property.
2643                  *
2644                  * @param value
2645                  *     allowed object is
2646                  *     {@link Integer }
2647                  *
2648                  */
2649                 public void setYpos(Integer value) {
2650                     this.ypos = value;
2651                 }
2652
2653             }
2654
2655         }
2656
2657
2658         /**
2659          * <p>Java class for anonymous complex type.
2660          *
2661          * <p>The following schema fragment specifies the expected content contained within this class.
2662          *
2663          * <pre>
2664          * &lt;complexType>
2665          *   &lt;complexContent>
2666          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2667          *       &lt;sequence>
2668          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2669          *           &lt;complexType>
2670          *             &lt;complexContent>
2671          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2672          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2673          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2674          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2675          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2676          *               &lt;/restriction>
2677          *             &lt;/complexContent>
2678          *           &lt;/complexType>
2679          *         &lt;/element>
2680          *       &lt;/sequence>
2681          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2682          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2683          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2684          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2685          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2686          *     &lt;/restriction>
2687          *   &lt;/complexContent>
2688          * &lt;/complexType>
2689          * </pre>
2690          *
2691          *
2692          */
2693         @XmlAccessorType(XmlAccessType.FIELD)
2694         @XmlType(name = "", propOrder = {
2695             "secondaryStructure"
2696         })
2697         public static class RnaViewer {
2698
2699             @XmlElement(namespace = "www.jalview.org", required = true)
2700             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2701             @XmlAttribute(name = "title")
2702             protected String title;
2703             @XmlAttribute(name = "viewId")
2704             protected String viewId;
2705             @XmlAttribute(name = "dividerLocation")
2706             protected Integer dividerLocation;
2707             @XmlAttribute(name = "selectedRna")
2708             protected Integer selectedRna;
2709             @XmlAttribute(name = "width")
2710             protected Integer width;
2711             @XmlAttribute(name = "height")
2712             protected Integer height;
2713             @XmlAttribute(name = "xpos")
2714             protected Integer xpos;
2715             @XmlAttribute(name = "ypos")
2716             protected Integer ypos;
2717
2718             /**
2719              * Gets the value of the secondaryStructure property.
2720              *
2721              * <p>
2722              * This accessor method returns a reference to the live list,
2723              * not a snapshot. Therefore any modification you make to the
2724              * returned list will be present inside the JAXB object.
2725              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2726              *
2727              * <p>
2728              * For example, to add a new item, do as follows:
2729              * <pre>
2730              *    getSecondaryStructure().add(newItem);
2731              * </pre>
2732              *
2733              *
2734              * <p>
2735              * Objects of the following type(s) are allowed in the list
2736              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2737              *
2738              *
2739              */
2740             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2741                 if (secondaryStructure == null) {
2742                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2743                 }
2744                 return this.secondaryStructure;
2745             }
2746
2747             /**
2748              * Gets the value of the title property.
2749              *
2750              * @return
2751              *     possible object is
2752              *     {@link String }
2753              *
2754              */
2755             public String getTitle() {
2756                 return title;
2757             }
2758
2759             /**
2760              * Sets the value of the title property.
2761              *
2762              * @param value
2763              *     allowed object is
2764              *     {@link String }
2765              *
2766              */
2767             public void setTitle(String value) {
2768                 this.title = value;
2769             }
2770
2771             /**
2772              * Gets the value of the viewId property.
2773              *
2774              * @return
2775              *     possible object is
2776              *     {@link String }
2777              *
2778              */
2779             public String getViewId() {
2780                 return viewId;
2781             }
2782
2783             /**
2784              * Sets the value of the viewId property.
2785              *
2786              * @param value
2787              *     allowed object is
2788              *     {@link String }
2789              *
2790              */
2791             public void setViewId(String value) {
2792                 this.viewId = value;
2793             }
2794
2795             /**
2796              * Gets the value of the dividerLocation property.
2797              *
2798              * @return
2799              *     possible object is
2800              *     {@link Integer }
2801              *
2802              */
2803             public Integer getDividerLocation() {
2804                 return dividerLocation;
2805             }
2806
2807             /**
2808              * Sets the value of the dividerLocation property.
2809              *
2810              * @param value
2811              *     allowed object is
2812              *     {@link Integer }
2813              *
2814              */
2815             public void setDividerLocation(Integer value) {
2816                 this.dividerLocation = value;
2817             }
2818
2819             /**
2820              * Gets the value of the selectedRna property.
2821              *
2822              * @return
2823              *     possible object is
2824              *     {@link Integer }
2825              *
2826              */
2827             public Integer getSelectedRna() {
2828                 return selectedRna;
2829             }
2830
2831             /**
2832              * Sets the value of the selectedRna property.
2833              *
2834              * @param value
2835              *     allowed object is
2836              *     {@link Integer }
2837              *
2838              */
2839             public void setSelectedRna(Integer value) {
2840                 this.selectedRna = value;
2841             }
2842
2843             /**
2844              * Gets the value of the width property.
2845              *
2846              * @return
2847              *     possible object is
2848              *     {@link Integer }
2849              *
2850              */
2851             public Integer getWidth() {
2852                 return width;
2853             }
2854
2855             /**
2856              * Sets the value of the width property.
2857              *
2858              * @param value
2859              *     allowed object is
2860              *     {@link Integer }
2861              *
2862              */
2863             public void setWidth(Integer value) {
2864                 this.width = value;
2865             }
2866
2867             /**
2868              * Gets the value of the height property.
2869              *
2870              * @return
2871              *     possible object is
2872              *     {@link Integer }
2873              *
2874              */
2875             public Integer getHeight() {
2876                 return height;
2877             }
2878
2879             /**
2880              * Sets the value of the height property.
2881              *
2882              * @param value
2883              *     allowed object is
2884              *     {@link Integer }
2885              *
2886              */
2887             public void setHeight(Integer value) {
2888                 this.height = value;
2889             }
2890
2891             /**
2892              * Gets the value of the xpos property.
2893              *
2894              * @return
2895              *     possible object is
2896              *     {@link Integer }
2897              *
2898              */
2899             public Integer getXpos() {
2900                 return xpos;
2901             }
2902
2903             /**
2904              * Sets the value of the xpos property.
2905              *
2906              * @param value
2907              *     allowed object is
2908              *     {@link Integer }
2909              *
2910              */
2911             public void setXpos(Integer value) {
2912                 this.xpos = value;
2913             }
2914
2915             /**
2916              * Gets the value of the ypos property.
2917              *
2918              * @return
2919              *     possible object is
2920              *     {@link Integer }
2921              *
2922              */
2923             public Integer getYpos() {
2924                 return ypos;
2925             }
2926
2927             /**
2928              * Sets the value of the ypos property.
2929              *
2930              * @param value
2931              *     allowed object is
2932              *     {@link Integer }
2933              *
2934              */
2935             public void setYpos(Integer value) {
2936                 this.ypos = value;
2937             }
2938
2939
2940             /**
2941              * <p>Java class for anonymous complex type.
2942              *
2943              * <p>The following schema fragment specifies the expected content contained within this class.
2944              *
2945              * <pre>
2946              * &lt;complexType>
2947              *   &lt;complexContent>
2948              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2949              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2950              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2951              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2952              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2953              *     &lt;/restriction>
2954              *   &lt;/complexContent>
2955              * &lt;/complexType>
2956              * </pre>
2957              *
2958              *
2959              */
2960             @XmlAccessorType(XmlAccessType.FIELD)
2961             @XmlType(name = "")
2962             public static class SecondaryStructure {
2963
2964                 @XmlAttribute(name = "title")
2965                 protected String title;
2966                 @XmlAttribute(name = "annotationId", required = true)
2967                 protected String annotationId;
2968                 @XmlAttribute(name = "gapped")
2969                 protected Boolean gapped;
2970                 @XmlAttribute(name = "viewerState")
2971                 protected String viewerState;
2972
2973                 /**
2974                  * Gets the value of the title property.
2975                  *
2976                  * @return
2977                  *     possible object is
2978                  *     {@link String }
2979                  *
2980                  */
2981                 public String getTitle() {
2982                     return title;
2983                 }
2984
2985                 /**
2986                  * Sets the value of the title property.
2987                  *
2988                  * @param value
2989                  *     allowed object is
2990                  *     {@link String }
2991                  *
2992                  */
2993                 public void setTitle(String value) {
2994                     this.title = value;
2995                 }
2996
2997                 /**
2998                  * Gets the value of the annotationId property.
2999                  *
3000                  * @return
3001                  *     possible object is
3002                  *     {@link String }
3003                  *
3004                  */
3005                 public String getAnnotationId() {
3006                     return annotationId;
3007                 }
3008
3009                 /**
3010                  * Sets the value of the annotationId property.
3011                  *
3012                  * @param value
3013                  *     allowed object is
3014                  *     {@link String }
3015                  *
3016                  */
3017                 public void setAnnotationId(String value) {
3018                     this.annotationId = value;
3019                 }
3020
3021                 /**
3022                  * Gets the value of the gapped property.
3023                  *
3024                  * @return
3025                  *     possible object is
3026                  *     {@link Boolean }
3027                  *
3028                  */
3029                 public Boolean isGapped() {
3030                     return gapped;
3031                 }
3032
3033                 /**
3034                  * Sets the value of the gapped property.
3035                  *
3036                  * @param value
3037                  *     allowed object is
3038                  *     {@link Boolean }
3039                  *
3040                  */
3041                 public void setGapped(Boolean value) {
3042                     this.gapped = value;
3043                 }
3044
3045                 /**
3046                  * Gets the value of the viewerState property.
3047                  *
3048                  * @return
3049                  *     possible object is
3050                  *     {@link String }
3051                  *
3052                  */
3053                 public String getViewerState() {
3054                     return viewerState;
3055                 }
3056
3057                 /**
3058                  * Sets the value of the viewerState property.
3059                  *
3060                  * @param value
3061                  *     allowed object is
3062                  *     {@link String }
3063                  *
3064                  */
3065                 public void setViewerState(String value) {
3066                     this.viewerState = value;
3067                 }
3068
3069             }
3070
3071         }
3072
3073     }
3074
3075
3076     /**
3077      * <p>Java class for anonymous complex type.
3078      *
3079      * <p>The following schema fragment specifies the expected content contained within this class.
3080      *
3081      * <pre>
3082      * &lt;complexType>
3083      *   &lt;complexContent>
3084      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3085      *       &lt;sequence>
3086      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3087      *           &lt;complexType>
3088      *             &lt;complexContent>
3089      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3090      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3091      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3092      *               &lt;/restriction>
3093      *             &lt;/complexContent>
3094      *           &lt;/complexType>
3095      *         &lt;/element>
3096      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3097      *           &lt;complexType>
3098      *             &lt;complexContent>
3099      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3100      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3101      *               &lt;/restriction>
3102      *             &lt;/complexContent>
3103      *           &lt;/complexType>
3104      *         &lt;/element>
3105      *         &lt;element name="seqPointMin">
3106      *           &lt;complexType>
3107      *             &lt;complexContent>
3108      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3109      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3110      *               &lt;/restriction>
3111      *             &lt;/complexContent>
3112      *           &lt;/complexType>
3113      *         &lt;/element>
3114      *         &lt;element name="seqPointMax">
3115      *           &lt;complexType>
3116      *             &lt;complexContent>
3117      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3118      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3119      *               &lt;/restriction>
3120      *             &lt;/complexContent>
3121      *           &lt;/complexType>
3122      *         &lt;/element>
3123      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3124      *       &lt;/sequence>
3125      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3126      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3127      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3128      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3129      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3130      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3131      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3132      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3133      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3134      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3135      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3136      *     &lt;/restriction>
3137      *   &lt;/complexContent>
3138      * &lt;/complexType>
3139      * </pre>
3140      *
3141      *
3142      */
3143     @XmlAccessorType(XmlAccessType.FIELD)
3144     @XmlType(name = "", propOrder = {
3145         "sequencePoint",
3146         "axis",
3147         "seqPointMin",
3148         "seqPointMax",
3149         "pcaData"
3150     })
3151     public static class PcaViewer {
3152
3153         @XmlElement(namespace = "www.jalview.org", required = true)
3154         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3155         @XmlElement(namespace = "www.jalview.org", required = true)
3156         protected List<JalviewModel.PcaViewer.Axis> axis;
3157         @XmlElement(namespace = "www.jalview.org", required = true)
3158         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3159         @XmlElement(namespace = "www.jalview.org", required = true)
3160         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3161         @XmlElement(namespace = "www.jalview.org", required = true)
3162         protected PcaDataType pcaData;
3163         @XmlAttribute(name = "title")
3164         protected String title;
3165         @XmlAttribute(name = "scoreModelName")
3166         protected String scoreModelName;
3167         @XmlAttribute(name = "xDim")
3168         protected Integer xDim;
3169         @XmlAttribute(name = "yDim")
3170         protected Integer yDim;
3171         @XmlAttribute(name = "zDim")
3172         protected Integer zDim;
3173         @XmlAttribute(name = "bgColour")
3174         protected Integer bgColour;
3175         @XmlAttribute(name = "scaleFactor")
3176         protected Float scaleFactor;
3177         @XmlAttribute(name = "showLabels")
3178         protected Boolean showLabels;
3179         @XmlAttribute(name = "linkToAllViews")
3180         protected Boolean linkToAllViews;
3181         @XmlAttribute(name = "includeGaps")
3182         protected Boolean includeGaps;
3183         @XmlAttribute(name = "matchGaps")
3184         protected Boolean matchGaps;
3185         @XmlAttribute(name = "includeGappedColumns")
3186         protected Boolean includeGappedColumns;
3187         @XmlAttribute(name = "denominateByShortestLength")
3188         protected Boolean denominateByShortestLength;
3189         @XmlAttribute(name = "width")
3190         protected Integer width;
3191         @XmlAttribute(name = "height")
3192         protected Integer height;
3193         @XmlAttribute(name = "xpos")
3194         protected Integer xpos;
3195         @XmlAttribute(name = "ypos")
3196         protected Integer ypos;
3197
3198         /**
3199          * Gets the value of the sequencePoint property.
3200          *
3201          * <p>
3202          * This accessor method returns a reference to the live list,
3203          * not a snapshot. Therefore any modification you make to the
3204          * returned list will be present inside the JAXB object.
3205          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3206          *
3207          * <p>
3208          * For example, to add a new item, do as follows:
3209          * <pre>
3210          *    getSequencePoint().add(newItem);
3211          * </pre>
3212          *
3213          *
3214          * <p>
3215          * Objects of the following type(s) are allowed in the list
3216          * {@link JalviewModel.PcaViewer.SequencePoint }
3217          *
3218          *
3219          */
3220         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3221             if (sequencePoint == null) {
3222                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3223             }
3224             return this.sequencePoint;
3225         }
3226
3227         /**
3228          * Gets the value of the axis property.
3229          *
3230          * <p>
3231          * This accessor method returns a reference to the live list,
3232          * not a snapshot. Therefore any modification you make to the
3233          * returned list will be present inside the JAXB object.
3234          * This is why there is not a <CODE>set</CODE> method for the axis property.
3235          *
3236          * <p>
3237          * For example, to add a new item, do as follows:
3238          * <pre>
3239          *    getAxis().add(newItem);
3240          * </pre>
3241          *
3242          *
3243          * <p>
3244          * Objects of the following type(s) are allowed in the list
3245          * {@link JalviewModel.PcaViewer.Axis }
3246          *
3247          *
3248          */
3249         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3250             if (axis == null) {
3251                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3252             }
3253             return this.axis;
3254         }
3255
3256         /**
3257          * Gets the value of the seqPointMin property.
3258          *
3259          * @return
3260          *     possible object is
3261          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3262          *
3263          */
3264         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3265             return seqPointMin;
3266         }
3267
3268         /**
3269          * Sets the value of the seqPointMin property.
3270          *
3271          * @param value
3272          *     allowed object is
3273          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3274          *
3275          */
3276         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3277             this.seqPointMin = value;
3278         }
3279
3280         /**
3281          * Gets the value of the seqPointMax property.
3282          *
3283          * @return
3284          *     possible object is
3285          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3286          *
3287          */
3288         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3289             return seqPointMax;
3290         }
3291
3292         /**
3293          * Sets the value of the seqPointMax property.
3294          *
3295          * @param value
3296          *     allowed object is
3297          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3298          *
3299          */
3300         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3301             this.seqPointMax = value;
3302         }
3303
3304         /**
3305          * Gets the value of the pcaData property.
3306          *
3307          * @return
3308          *     possible object is
3309          *     {@link PcaDataType }
3310          *
3311          */
3312         public PcaDataType getPcaData() {
3313             return pcaData;
3314         }
3315
3316         /**
3317          * Sets the value of the pcaData property.
3318          *
3319          * @param value
3320          *     allowed object is
3321          *     {@link PcaDataType }
3322          *
3323          */
3324         public void setPcaData(PcaDataType value) {
3325             this.pcaData = value;
3326         }
3327
3328         /**
3329          * Gets the value of the title property.
3330          *
3331          * @return
3332          *     possible object is
3333          *     {@link String }
3334          *
3335          */
3336         public String getTitle() {
3337             return title;
3338         }
3339
3340         /**
3341          * Sets the value of the title property.
3342          *
3343          * @param value
3344          *     allowed object is
3345          *     {@link String }
3346          *
3347          */
3348         public void setTitle(String value) {
3349             this.title = value;
3350         }
3351
3352         /**
3353          * Gets the value of the scoreModelName property.
3354          *
3355          * @return
3356          *     possible object is
3357          *     {@link String }
3358          *
3359          */
3360         public String getScoreModelName() {
3361             return scoreModelName;
3362         }
3363
3364         /**
3365          * Sets the value of the scoreModelName property.
3366          *
3367          * @param value
3368          *     allowed object is
3369          *     {@link String }
3370          *
3371          */
3372         public void setScoreModelName(String value) {
3373             this.scoreModelName = value;
3374         }
3375
3376         /**
3377          * Gets the value of the xDim property.
3378          *
3379          * @return
3380          *     possible object is
3381          *     {@link Integer }
3382          *
3383          */
3384         public Integer getXDim() {
3385             return xDim;
3386         }
3387
3388         /**
3389          * Sets the value of the xDim property.
3390          *
3391          * @param value
3392          *     allowed object is
3393          *     {@link Integer }
3394          *
3395          */
3396         public void setXDim(Integer value) {
3397             this.xDim = value;
3398         }
3399
3400         /**
3401          * Gets the value of the yDim property.
3402          *
3403          * @return
3404          *     possible object is
3405          *     {@link Integer }
3406          *
3407          */
3408         public Integer getYDim() {
3409             return yDim;
3410         }
3411
3412         /**
3413          * Sets the value of the yDim property.
3414          *
3415          * @param value
3416          *     allowed object is
3417          *     {@link Integer }
3418          *
3419          */
3420         public void setYDim(Integer value) {
3421             this.yDim = value;
3422         }
3423
3424         /**
3425          * Gets the value of the zDim property.
3426          *
3427          * @return
3428          *     possible object is
3429          *     {@link Integer }
3430          *
3431          */
3432         public Integer getZDim() {
3433             return zDim;
3434         }
3435
3436         /**
3437          * Sets the value of the zDim property.
3438          *
3439          * @param value
3440          *     allowed object is
3441          *     {@link Integer }
3442          *
3443          */
3444         public void setZDim(Integer value) {
3445             this.zDim = value;
3446         }
3447
3448         /**
3449          * Gets the value of the bgColour property.
3450          *
3451          * @return
3452          *     possible object is
3453          *     {@link Integer }
3454          *
3455          */
3456         public Integer getBgColour() {
3457             return bgColour;
3458         }
3459
3460         /**
3461          * Sets the value of the bgColour property.
3462          *
3463          * @param value
3464          *     allowed object is
3465          *     {@link Integer }
3466          *
3467          */
3468         public void setBgColour(Integer value) {
3469             this.bgColour = value;
3470         }
3471
3472         /**
3473          * Gets the value of the scaleFactor property.
3474          *
3475          * @return
3476          *     possible object is
3477          *     {@link Float }
3478          *
3479          */
3480         public Float getScaleFactor() {
3481             return scaleFactor;
3482         }
3483
3484         /**
3485          * Sets the value of the scaleFactor property.
3486          *
3487          * @param value
3488          *     allowed object is
3489          *     {@link Float }
3490          *
3491          */
3492         public void setScaleFactor(Float value) {
3493             this.scaleFactor = value;
3494         }
3495
3496         /**
3497          * Gets the value of the showLabels property.
3498          *
3499          * @return
3500          *     possible object is
3501          *     {@link Boolean }
3502          *
3503          */
3504         public Boolean isShowLabels() {
3505             return showLabels;
3506         }
3507
3508         /**
3509          * Sets the value of the showLabels property.
3510          *
3511          * @param value
3512          *     allowed object is
3513          *     {@link Boolean }
3514          *
3515          */
3516         public void setShowLabels(Boolean value) {
3517             this.showLabels = value;
3518         }
3519
3520         /**
3521          * Gets the value of the linkToAllViews property.
3522          *
3523          * @return
3524          *     possible object is
3525          *     {@link Boolean }
3526          *
3527          */
3528         public Boolean isLinkToAllViews() {
3529             return linkToAllViews;
3530         }
3531
3532         /**
3533          * Sets the value of the linkToAllViews property.
3534          *
3535          * @param value
3536          *     allowed object is
3537          *     {@link Boolean }
3538          *
3539          */
3540         public void setLinkToAllViews(Boolean value) {
3541             this.linkToAllViews = value;
3542         }
3543
3544         /**
3545          * Gets the value of the includeGaps property.
3546          *
3547          * @return
3548          *     possible object is
3549          *     {@link Boolean }
3550          *
3551          */
3552         public Boolean isIncludeGaps() {
3553             return includeGaps;
3554         }
3555
3556         /**
3557          * Sets the value of the includeGaps property.
3558          *
3559          * @param value
3560          *     allowed object is
3561          *     {@link Boolean }
3562          *
3563          */
3564         public void setIncludeGaps(Boolean value) {
3565             this.includeGaps = value;
3566         }
3567
3568         /**
3569          * Gets the value of the matchGaps property.
3570          *
3571          * @return
3572          *     possible object is
3573          *     {@link Boolean }
3574          *
3575          */
3576         public Boolean isMatchGaps() {
3577             return matchGaps;
3578         }
3579
3580         /**
3581          * Sets the value of the matchGaps property.
3582          *
3583          * @param value
3584          *     allowed object is
3585          *     {@link Boolean }
3586          *
3587          */
3588         public void setMatchGaps(Boolean value) {
3589             this.matchGaps = value;
3590         }
3591
3592         /**
3593          * Gets the value of the includeGappedColumns property.
3594          *
3595          * @return
3596          *     possible object is
3597          *     {@link Boolean }
3598          *
3599          */
3600         public Boolean isIncludeGappedColumns() {
3601             return includeGappedColumns;
3602         }
3603
3604         /**
3605          * Sets the value of the includeGappedColumns property.
3606          *
3607          * @param value
3608          *     allowed object is
3609          *     {@link Boolean }
3610          *
3611          */
3612         public void setIncludeGappedColumns(Boolean value) {
3613             this.includeGappedColumns = value;
3614         }
3615
3616         /**
3617          * Gets the value of the denominateByShortestLength property.
3618          *
3619          * @return
3620          *     possible object is
3621          *     {@link Boolean }
3622          *
3623          */
3624         public Boolean isDenominateByShortestLength() {
3625             return denominateByShortestLength;
3626         }
3627
3628         /**
3629          * Sets the value of the denominateByShortestLength property.
3630          *
3631          * @param value
3632          *     allowed object is
3633          *     {@link Boolean }
3634          *
3635          */
3636         public void setDenominateByShortestLength(Boolean value) {
3637             this.denominateByShortestLength = value;
3638         }
3639
3640         /**
3641          * Gets the value of the width property.
3642          *
3643          * @return
3644          *     possible object is
3645          *     {@link Integer }
3646          *
3647          */
3648         public Integer getWidth() {
3649             return width;
3650         }
3651
3652         /**
3653          * Sets the value of the width property.
3654          *
3655          * @param value
3656          *     allowed object is
3657          *     {@link Integer }
3658          *
3659          */
3660         public void setWidth(Integer value) {
3661             this.width = value;
3662         }
3663
3664         /**
3665          * Gets the value of the height property.
3666          *
3667          * @return
3668          *     possible object is
3669          *     {@link Integer }
3670          *
3671          */
3672         public Integer getHeight() {
3673             return height;
3674         }
3675
3676         /**
3677          * Sets the value of the height property.
3678          *
3679          * @param value
3680          *     allowed object is
3681          *     {@link Integer }
3682          *
3683          */
3684         public void setHeight(Integer value) {
3685             this.height = value;
3686         }
3687
3688         /**
3689          * Gets the value of the xpos property.
3690          *
3691          * @return
3692          *     possible object is
3693          *     {@link Integer }
3694          *
3695          */
3696         public Integer getXpos() {
3697             return xpos;
3698         }
3699
3700         /**
3701          * Sets the value of the xpos property.
3702          *
3703          * @param value
3704          *     allowed object is
3705          *     {@link Integer }
3706          *
3707          */
3708         public void setXpos(Integer value) {
3709             this.xpos = value;
3710         }
3711
3712         /**
3713          * Gets the value of the ypos property.
3714          *
3715          * @return
3716          *     possible object is
3717          *     {@link Integer }
3718          *
3719          */
3720         public Integer getYpos() {
3721             return ypos;
3722         }
3723
3724         /**
3725          * Sets the value of the ypos property.
3726          *
3727          * @param value
3728          *     allowed object is
3729          *     {@link Integer }
3730          *
3731          */
3732         public void setYpos(Integer value) {
3733             this.ypos = value;
3734         }
3735
3736
3737         /**
3738          * <p>Java class for anonymous complex type.
3739          *
3740          * <p>The following schema fragment specifies the expected content contained within this class.
3741          *
3742          * <pre>
3743          * &lt;complexType>
3744          *   &lt;complexContent>
3745          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3746          *       &lt;attGroup ref="{www.jalview.org}position"/>
3747          *     &lt;/restriction>
3748          *   &lt;/complexContent>
3749          * &lt;/complexType>
3750          * </pre>
3751          *
3752          *
3753          */
3754         @XmlAccessorType(XmlAccessType.FIELD)
3755         @XmlType(name = "")
3756         public static class Axis {
3757
3758             @XmlAttribute(name = "xPos")
3759             protected Float xPos;
3760             @XmlAttribute(name = "yPos")
3761             protected Float yPos;
3762             @XmlAttribute(name = "zPos")
3763             protected Float zPos;
3764
3765             /**
3766              * Gets the value of the xPos property.
3767              *
3768              * @return
3769              *     possible object is
3770              *     {@link Float }
3771              *
3772              */
3773             public Float getXPos() {
3774                 return xPos;
3775             }
3776
3777             /**
3778              * Sets the value of the xPos property.
3779              *
3780              * @param value
3781              *     allowed object is
3782              *     {@link Float }
3783              *
3784              */
3785             public void setXPos(Float value) {
3786                 this.xPos = value;
3787             }
3788
3789             /**
3790              * Gets the value of the yPos property.
3791              *
3792              * @return
3793              *     possible object is
3794              *     {@link Float }
3795              *
3796              */
3797             public Float getYPos() {
3798                 return yPos;
3799             }
3800
3801             /**
3802              * Sets the value of the yPos property.
3803              *
3804              * @param value
3805              *     allowed object is
3806              *     {@link Float }
3807              *
3808              */
3809             public void setYPos(Float value) {
3810                 this.yPos = value;
3811             }
3812
3813             /**
3814              * Gets the value of the zPos property.
3815              *
3816              * @return
3817              *     possible object is
3818              *     {@link Float }
3819              *
3820              */
3821             public Float getZPos() {
3822                 return zPos;
3823             }
3824
3825             /**
3826              * Sets the value of the zPos property.
3827              *
3828              * @param value
3829              *     allowed object is
3830              *     {@link Float }
3831              *
3832              */
3833             public void setZPos(Float value) {
3834                 this.zPos = value;
3835             }
3836
3837         }
3838
3839
3840         /**
3841          * <p>Java class for anonymous complex type.
3842          *
3843          * <p>The following schema fragment specifies the expected content contained within this class.
3844          *
3845          * <pre>
3846          * &lt;complexType>
3847          *   &lt;complexContent>
3848          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3849          *       &lt;attGroup ref="{www.jalview.org}position"/>
3850          *     &lt;/restriction>
3851          *   &lt;/complexContent>
3852          * &lt;/complexType>
3853          * </pre>
3854          *
3855          *
3856          */
3857         @XmlAccessorType(XmlAccessType.FIELD)
3858         @XmlType(name = "")
3859         public static class SeqPointMax {
3860
3861             @XmlAttribute(name = "xPos")
3862             protected Float xPos;
3863             @XmlAttribute(name = "yPos")
3864             protected Float yPos;
3865             @XmlAttribute(name = "zPos")
3866             protected Float zPos;
3867
3868             /**
3869              * Gets the value of the xPos property.
3870              *
3871              * @return
3872              *     possible object is
3873              *     {@link Float }
3874              *
3875              */
3876             public Float getXPos() {
3877                 return xPos;
3878             }
3879
3880             /**
3881              * Sets the value of the xPos property.
3882              *
3883              * @param value
3884              *     allowed object is
3885              *     {@link Float }
3886              *
3887              */
3888             public void setXPos(Float value) {
3889                 this.xPos = value;
3890             }
3891
3892             /**
3893              * Gets the value of the yPos property.
3894              *
3895              * @return
3896              *     possible object is
3897              *     {@link Float }
3898              *
3899              */
3900             public Float getYPos() {
3901                 return yPos;
3902             }
3903
3904             /**
3905              * Sets the value of the yPos property.
3906              *
3907              * @param value
3908              *     allowed object is
3909              *     {@link Float }
3910              *
3911              */
3912             public void setYPos(Float value) {
3913                 this.yPos = value;
3914             }
3915
3916             /**
3917              * Gets the value of the zPos property.
3918              *
3919              * @return
3920              *     possible object is
3921              *     {@link Float }
3922              *
3923              */
3924             public Float getZPos() {
3925                 return zPos;
3926             }
3927
3928             /**
3929              * Sets the value of the zPos property.
3930              *
3931              * @param value
3932              *     allowed object is
3933              *     {@link Float }
3934              *
3935              */
3936             public void setZPos(Float value) {
3937                 this.zPos = value;
3938             }
3939
3940         }
3941
3942
3943         /**
3944          * <p>Java class for anonymous complex type.
3945          *
3946          * <p>The following schema fragment specifies the expected content contained within this class.
3947          *
3948          * <pre>
3949          * &lt;complexType>
3950          *   &lt;complexContent>
3951          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3952          *       &lt;attGroup ref="{www.jalview.org}position"/>
3953          *     &lt;/restriction>
3954          *   &lt;/complexContent>
3955          * &lt;/complexType>
3956          * </pre>
3957          *
3958          *
3959          */
3960         @XmlAccessorType(XmlAccessType.FIELD)
3961         @XmlType(name = "")
3962         public static class SeqPointMin {
3963
3964             @XmlAttribute(name = "xPos")
3965             protected Float xPos;
3966             @XmlAttribute(name = "yPos")
3967             protected Float yPos;
3968             @XmlAttribute(name = "zPos")
3969             protected Float zPos;
3970
3971             /**
3972              * Gets the value of the xPos property.
3973              *
3974              * @return
3975              *     possible object is
3976              *     {@link Float }
3977              *
3978              */
3979             public Float getXPos() {
3980                 return xPos;
3981             }
3982
3983             /**
3984              * Sets the value of the xPos property.
3985              *
3986              * @param value
3987              *     allowed object is
3988              *     {@link Float }
3989              *
3990              */
3991             public void setXPos(Float value) {
3992                 this.xPos = value;
3993             }
3994
3995             /**
3996              * Gets the value of the yPos property.
3997              *
3998              * @return
3999              *     possible object is
4000              *     {@link Float }
4001              *
4002              */
4003             public Float getYPos() {
4004                 return yPos;
4005             }
4006
4007             /**
4008              * Sets the value of the yPos property.
4009              *
4010              * @param value
4011              *     allowed object is
4012              *     {@link Float }
4013              *
4014              */
4015             public void setYPos(Float value) {
4016                 this.yPos = value;
4017             }
4018
4019             /**
4020              * Gets the value of the zPos property.
4021              *
4022              * @return
4023              *     possible object is
4024              *     {@link Float }
4025              *
4026              */
4027             public Float getZPos() {
4028                 return zPos;
4029             }
4030
4031             /**
4032              * Sets the value of the zPos property.
4033              *
4034              * @param value
4035              *     allowed object is
4036              *     {@link Float }
4037              *
4038              */
4039             public void setZPos(Float value) {
4040                 this.zPos = value;
4041             }
4042
4043         }
4044
4045
4046         /**
4047          * <p>Java class for anonymous complex type.
4048          *
4049          * <p>The following schema fragment specifies the expected content contained within this class.
4050          *
4051          * <pre>
4052          * &lt;complexType>
4053          *   &lt;complexContent>
4054          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4055          *       &lt;attGroup ref="{www.jalview.org}position"/>
4056          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4057          *     &lt;/restriction>
4058          *   &lt;/complexContent>
4059          * &lt;/complexType>
4060          * </pre>
4061          *
4062          *
4063          */
4064         @XmlAccessorType(XmlAccessType.FIELD)
4065         @XmlType(name = "")
4066         public static class SequencePoint {
4067
4068             @XmlAttribute(name = "sequenceRef")
4069             protected String sequenceRef;
4070             @XmlAttribute(name = "xPos")
4071             protected Float xPos;
4072             @XmlAttribute(name = "yPos")
4073             protected Float yPos;
4074             @XmlAttribute(name = "zPos")
4075             protected Float zPos;
4076
4077             /**
4078              * Gets the value of the sequenceRef property.
4079              *
4080              * @return
4081              *     possible object is
4082              *     {@link String }
4083              *
4084              */
4085             public String getSequenceRef() {
4086                 return sequenceRef;
4087             }
4088
4089             /**
4090              * Sets the value of the sequenceRef property.
4091              *
4092              * @param value
4093              *     allowed object is
4094              *     {@link String }
4095              *
4096              */
4097             public void setSequenceRef(String value) {
4098                 this.sequenceRef = value;
4099             }
4100
4101             /**
4102              * Gets the value of the xPos property.
4103              *
4104              * @return
4105              *     possible object is
4106              *     {@link Float }
4107              *
4108              */
4109             public Float getXPos() {
4110                 return xPos;
4111             }
4112
4113             /**
4114              * Sets the value of the xPos property.
4115              *
4116              * @param value
4117              *     allowed object is
4118              *     {@link Float }
4119              *
4120              */
4121             public void setXPos(Float value) {
4122                 this.xPos = value;
4123             }
4124
4125             /**
4126              * Gets the value of the yPos property.
4127              *
4128              * @return
4129              *     possible object is
4130              *     {@link Float }
4131              *
4132              */
4133             public Float getYPos() {
4134                 return yPos;
4135             }
4136
4137             /**
4138              * Sets the value of the yPos property.
4139              *
4140              * @param value
4141              *     allowed object is
4142              *     {@link Float }
4143              *
4144              */
4145             public void setYPos(Float value) {
4146                 this.yPos = value;
4147             }
4148
4149             /**
4150              * Gets the value of the zPos property.
4151              *
4152              * @return
4153              *     possible object is
4154              *     {@link Float }
4155              *
4156              */
4157             public Float getZPos() {
4158                 return zPos;
4159             }
4160
4161             /**
4162              * Sets the value of the zPos property.
4163              *
4164              * @param value
4165              *     allowed object is
4166              *     {@link Float }
4167              *
4168              */
4169             public void setZPos(Float value) {
4170                 this.zPos = value;
4171             }
4172
4173         }
4174
4175     }
4176
4177
4178     /**
4179      * <p>Java class for anonymous complex type.
4180      *
4181      * <p>The following schema fragment specifies the expected content contained within this class.
4182      *
4183      * <pre>
4184      * &lt;complexType>
4185      *   &lt;complexContent>
4186      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4187      *       &lt;sequence minOccurs="0">
4188      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4189      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4190      *       &lt;/sequence>
4191      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4192      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4193      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4194      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4195      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4196      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4197      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4198      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4199      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4200      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4201      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4202      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4203      *     &lt;/restriction>
4204      *   &lt;/complexContent>
4205      * &lt;/complexType>
4206      * </pre>
4207      *
4208      *
4209      */
4210     @XmlAccessorType(XmlAccessType.FIELD)
4211     @XmlType(name = "", propOrder = {
4212         "title",
4213         "newick"
4214     })
4215     public static class Tree {
4216
4217         @XmlElement(namespace = "www.jalview.org")
4218         protected String title;
4219         @XmlElement(namespace = "www.jalview.org")
4220         protected String newick;
4221         @XmlAttribute(name = "fontName")
4222         protected String fontName;
4223         @XmlAttribute(name = "fontSize")
4224         protected Integer fontSize;
4225         @XmlAttribute(name = "fontStyle")
4226         protected Integer fontStyle;
4227         @XmlAttribute(name = "threshold")
4228         protected Float threshold;
4229         @XmlAttribute(name = "showBootstrap")
4230         protected Boolean showBootstrap;
4231         @XmlAttribute(name = "showDistances")
4232         protected Boolean showDistances;
4233         @XmlAttribute(name = "markUnlinked")
4234         protected Boolean markUnlinked;
4235         @XmlAttribute(name = "fitToWindow")
4236         protected Boolean fitToWindow;
4237         @XmlAttribute(name = "currentTree")
4238         protected Boolean currentTree;
4239         @XmlAttribute(name = "id")
4240         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4241         @XmlID
4242         @XmlSchemaType(name = "ID")
4243         protected String id;
4244         @XmlAttribute(name = "linkToAllViews")
4245         protected Boolean linkToAllViews;
4246         @XmlAttribute(name = "width")
4247         protected Integer width;
4248         @XmlAttribute(name = "height")
4249         protected Integer height;
4250         @XmlAttribute(name = "xpos")
4251         protected Integer xpos;
4252         @XmlAttribute(name = "ypos")
4253         protected Integer ypos;
4254
4255         /**
4256          * Gets the value of the title property.
4257          *
4258          * @return
4259          *     possible object is
4260          *     {@link String }
4261          *
4262          */
4263         public String getTitle() {
4264             return title;
4265         }
4266
4267         /**
4268          * Sets the value of the title property.
4269          *
4270          * @param value
4271          *     allowed object is
4272          *     {@link String }
4273          *
4274          */
4275         public void setTitle(String value) {
4276             this.title = value;
4277         }
4278
4279         /**
4280          * Gets the value of the newick property.
4281          *
4282          * @return
4283          *     possible object is
4284          *     {@link String }
4285          *
4286          */
4287         public String getNewick() {
4288             return newick;
4289         }
4290
4291         /**
4292          * Sets the value of the newick property.
4293          *
4294          * @param value
4295          *     allowed object is
4296          *     {@link String }
4297          *
4298          */
4299         public void setNewick(String value) {
4300             this.newick = value;
4301         }
4302
4303         /**
4304          * Gets the value of the fontName property.
4305          *
4306          * @return
4307          *     possible object is
4308          *     {@link String }
4309          *
4310          */
4311         public String getFontName() {
4312             return fontName;
4313         }
4314
4315         /**
4316          * Sets the value of the fontName property.
4317          *
4318          * @param value
4319          *     allowed object is
4320          *     {@link String }
4321          *
4322          */
4323         public void setFontName(String value) {
4324             this.fontName = value;
4325         }
4326
4327         /**
4328          * Gets the value of the fontSize property.
4329          *
4330          * @return
4331          *     possible object is
4332          *     {@link Integer }
4333          *
4334          */
4335         public Integer getFontSize() {
4336             return fontSize;
4337         }
4338
4339         /**
4340          * Sets the value of the fontSize property.
4341          *
4342          * @param value
4343          *     allowed object is
4344          *     {@link Integer }
4345          *
4346          */
4347         public void setFontSize(Integer value) {
4348             this.fontSize = value;
4349         }
4350
4351         /**
4352          * Gets the value of the fontStyle property.
4353          *
4354          * @return
4355          *     possible object is
4356          *     {@link Integer }
4357          *
4358          */
4359         public Integer getFontStyle() {
4360             return fontStyle;
4361         }
4362
4363         /**
4364          * Sets the value of the fontStyle property.
4365          *
4366          * @param value
4367          *     allowed object is
4368          *     {@link Integer }
4369          *
4370          */
4371         public void setFontStyle(Integer value) {
4372             this.fontStyle = value;
4373         }
4374
4375         /**
4376          * Gets the value of the threshold property.
4377          *
4378          * @return
4379          *     possible object is
4380          *     {@link Float }
4381          *
4382          */
4383         public Float getThreshold() {
4384             return threshold;
4385         }
4386
4387         /**
4388          * Sets the value of the threshold property.
4389          *
4390          * @param value
4391          *     allowed object is
4392          *     {@link Float }
4393          *
4394          */
4395         public void setThreshold(Float value) {
4396             this.threshold = value;
4397         }
4398
4399         /**
4400          * Gets the value of the showBootstrap property.
4401          *
4402          * @return
4403          *     possible object is
4404          *     {@link Boolean }
4405          *
4406          */
4407         public Boolean isShowBootstrap() {
4408             return showBootstrap;
4409         }
4410
4411         /**
4412          * Sets the value of the showBootstrap property.
4413          *
4414          * @param value
4415          *     allowed object is
4416          *     {@link Boolean }
4417          *
4418          */
4419         public void setShowBootstrap(Boolean value) {
4420             this.showBootstrap = value;
4421         }
4422
4423         /**
4424          * Gets the value of the showDistances property.
4425          *
4426          * @return
4427          *     possible object is
4428          *     {@link Boolean }
4429          *
4430          */
4431         public Boolean isShowDistances() {
4432             return showDistances;
4433         }
4434
4435         /**
4436          * Sets the value of the showDistances property.
4437          *
4438          * @param value
4439          *     allowed object is
4440          *     {@link Boolean }
4441          *
4442          */
4443         public void setShowDistances(Boolean value) {
4444             this.showDistances = value;
4445         }
4446
4447         /**
4448          * Gets the value of the markUnlinked property.
4449          *
4450          * @return
4451          *     possible object is
4452          *     {@link Boolean }
4453          *
4454          */
4455         public Boolean isMarkUnlinked() {
4456             return markUnlinked;
4457         }
4458
4459         /**
4460          * Sets the value of the markUnlinked property.
4461          *
4462          * @param value
4463          *     allowed object is
4464          *     {@link Boolean }
4465          *
4466          */
4467         public void setMarkUnlinked(Boolean value) {
4468             this.markUnlinked = value;
4469         }
4470
4471         /**
4472          * Gets the value of the fitToWindow property.
4473          *
4474          * @return
4475          *     possible object is
4476          *     {@link Boolean }
4477          *
4478          */
4479         public Boolean isFitToWindow() {
4480             return fitToWindow;
4481         }
4482
4483         /**
4484          * Sets the value of the fitToWindow property.
4485          *
4486          * @param value
4487          *     allowed object is
4488          *     {@link Boolean }
4489          *
4490          */
4491         public void setFitToWindow(Boolean value) {
4492             this.fitToWindow = value;
4493         }
4494
4495         /**
4496          * Gets the value of the currentTree property.
4497          *
4498          * @return
4499          *     possible object is
4500          *     {@link Boolean }
4501          *
4502          */
4503         public Boolean isCurrentTree() {
4504             return currentTree;
4505         }
4506
4507         /**
4508          * Sets the value of the currentTree property.
4509          *
4510          * @param value
4511          *     allowed object is
4512          *     {@link Boolean }
4513          *
4514          */
4515         public void setCurrentTree(Boolean value) {
4516             this.currentTree = value;
4517         }
4518
4519         /**
4520          * Gets the value of the id property.
4521          *
4522          * @return
4523          *     possible object is
4524          *     {@link String }
4525          *
4526          */
4527         public String getId() {
4528             return id;
4529         }
4530
4531         /**
4532          * Sets the value of the id property.
4533          *
4534          * @param value
4535          *     allowed object is
4536          *     {@link String }
4537          *
4538          */
4539         public void setId(String value) {
4540             this.id = value;
4541         }
4542
4543         /**
4544          * Gets the value of the linkToAllViews property.
4545          *
4546          * @return
4547          *     possible object is
4548          *     {@link Boolean }
4549          *
4550          */
4551         public boolean isLinkToAllViews() {
4552             if (linkToAllViews == null) {
4553                 return false;
4554             } else {
4555                 return linkToAllViews;
4556             }
4557         }
4558
4559         /**
4560          * Sets the value of the linkToAllViews property.
4561          *
4562          * @param value
4563          *     allowed object is
4564          *     {@link Boolean }
4565          *
4566          */
4567         public void setLinkToAllViews(Boolean value) {
4568             this.linkToAllViews = value;
4569         }
4570
4571         /**
4572          * Gets the value of the width property.
4573          *
4574          * @return
4575          *     possible object is
4576          *     {@link Integer }
4577          *
4578          */
4579         public Integer getWidth() {
4580             return width;
4581         }
4582
4583         /**
4584          * Sets the value of the width property.
4585          *
4586          * @param value
4587          *     allowed object is
4588          *     {@link Integer }
4589          *
4590          */
4591         public void setWidth(Integer value) {
4592             this.width = value;
4593         }
4594
4595         /**
4596          * Gets the value of the height property.
4597          *
4598          * @return
4599          *     possible object is
4600          *     {@link Integer }
4601          *
4602          */
4603         public Integer getHeight() {
4604             return height;
4605         }
4606
4607         /**
4608          * Sets the value of the height property.
4609          *
4610          * @param value
4611          *     allowed object is
4612          *     {@link Integer }
4613          *
4614          */
4615         public void setHeight(Integer value) {
4616             this.height = value;
4617         }
4618
4619         /**
4620          * Gets the value of the xpos property.
4621          *
4622          * @return
4623          *     possible object is
4624          *     {@link Integer }
4625          *
4626          */
4627         public Integer getXpos() {
4628             return xpos;
4629         }
4630
4631         /**
4632          * Sets the value of the xpos property.
4633          *
4634          * @param value
4635          *     allowed object is
4636          *     {@link Integer }
4637          *
4638          */
4639         public void setXpos(Integer value) {
4640             this.xpos = value;
4641         }
4642
4643         /**
4644          * Gets the value of the ypos property.
4645          *
4646          * @return
4647          *     possible object is
4648          *     {@link Integer }
4649          *
4650          */
4651         public Integer getYpos() {
4652             return ypos;
4653         }
4654
4655         /**
4656          * Sets the value of the ypos property.
4657          *
4658          * @param value
4659          *     allowed object is
4660          *     {@link Integer }
4661          *
4662          */
4663         public void setYpos(Integer value) {
4664             this.ypos = value;
4665         }
4666
4667     }
4668
4669
4670     /**
4671      * <p>Java class for anonymous complex type.
4672      *
4673      * <p>The following schema fragment specifies the expected content contained within this class.
4674      *
4675      * <pre>
4676      * &lt;complexType>
4677      *   &lt;complexContent>
4678      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4679      *       &lt;sequence>
4680      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4681      *       &lt;/sequence>
4682      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4683      *     &lt;/restriction>
4684      *   &lt;/complexContent>
4685      * &lt;/complexType>
4686      * </pre>
4687      *
4688      *
4689      */
4690     @XmlAccessorType(XmlAccessType.FIELD)
4691     @XmlType(name = "", propOrder = {
4692         "userColourScheme"
4693     })
4694     public static class UserColours {
4695
4696         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4697         protected JalviewUserColours userColourScheme;
4698         @XmlAttribute(name = "id")
4699         protected String id;
4700
4701         /**
4702          * Gets the value of the userColourScheme property.
4703          *
4704          * @return
4705          *     possible object is
4706          *     {@link JalviewUserColours }
4707          *
4708          */
4709         public JalviewUserColours getUserColourScheme() {
4710             return userColourScheme;
4711         }
4712
4713         /**
4714          * Sets the value of the userColourScheme property.
4715          *
4716          * @param value
4717          *     allowed object is
4718          *     {@link JalviewUserColours }
4719          *
4720          */
4721         public void setUserColourScheme(JalviewUserColours value) {
4722             this.userColourScheme = value;
4723         }
4724
4725         /**
4726          * Gets the value of the id property.
4727          *
4728          * @return
4729          *     possible object is
4730          *     {@link String }
4731          *
4732          */
4733         public String getId() {
4734             return id;
4735         }
4736
4737         /**
4738          * Sets the value of the id property.
4739          *
4740          * @param value
4741          *     allowed object is
4742          *     {@link String }
4743          *
4744          */
4745         public void setId(String value) {
4746             this.id = value;
4747         }
4748
4749     }
4750
4751
4752     /**
4753      * <p>Java class for anonymous complex type.
4754      *
4755      * <p>The following schema fragment specifies the expected content contained within this class.
4756      *
4757      * <pre>
4758      * &lt;complexType>
4759      *   &lt;complexContent>
4760      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4761      *       &lt;sequence>
4762      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4763      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4764      *           &lt;complexType>
4765      *             &lt;complexContent>
4766      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4767      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4768      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4769      *               &lt;/restriction>
4770      *             &lt;/complexContent>
4771      *           &lt;/complexType>
4772      *         &lt;/element>
4773      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4774      *           &lt;complexType>
4775      *             &lt;complexContent>
4776      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4777      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4778      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4779      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4780      *               &lt;/extension>
4781      *             &lt;/complexContent>
4782      *           &lt;/complexType>
4783      *         &lt;/element>
4784      *         &lt;element name="overview" minOccurs="0">
4785      *           &lt;complexType>
4786      *             &lt;complexContent>
4787      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4788      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4789      *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4790      *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4791      *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4792      *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4793      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4794      *               &lt;/restriction>
4795      *             &lt;/complexContent>
4796      *           &lt;/complexType>
4797      *         &lt;/element>
4798      *       &lt;/sequence>
4799      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4800      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4801      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4802      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4803      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4804      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4805      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4806      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4807      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4811      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4817      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4818      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4819      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4820      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4821      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4822      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4824      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4825      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4826      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4827      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4828      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4829      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4830      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4831      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4832      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4833      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4834      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4835      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4836      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4837      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4838      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4839      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4840      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4841      *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4842      *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4843      *     &lt;/restriction>
4844      *   &lt;/complexContent>
4845      * &lt;/complexType>
4846      * </pre>
4847      *
4848      *
4849      */
4850     @XmlAccessorType(XmlAccessType.FIELD)
4851     @XmlType(name = "", propOrder = {
4852         "annotationColours",
4853         "hiddenColumns",
4854         "calcIdParam",
4855         "overview"
4856     })
4857     public static class Viewport {
4858
4859         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4860         protected AnnotationColourScheme annotationColours;
4861         @XmlElement(namespace = "www.jalview.org")
4862         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4863         @XmlElement(namespace = "www.jalview.org")
4864         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4865         @XmlElement(namespace = "www.jalview.org")
4866         protected JalviewModel.Viewport.Overview overview;
4867         @XmlAttribute(name = "conservationSelected")
4868         protected Boolean conservationSelected;
4869         @XmlAttribute(name = "pidSelected")
4870         protected Boolean pidSelected;
4871         @XmlAttribute(name = "bgColour")
4872         protected String bgColour;
4873         @XmlAttribute(name = "consThreshold")
4874         protected Integer consThreshold;
4875         @XmlAttribute(name = "pidThreshold")
4876         protected Integer pidThreshold;
4877         @XmlAttribute(name = "title")
4878         protected String title;
4879         @XmlAttribute(name = "showFullId")
4880         protected Boolean showFullId;
4881         @XmlAttribute(name = "rightAlignIds")
4882         protected Boolean rightAlignIds;
4883         @XmlAttribute(name = "showText")
4884         protected Boolean showText;
4885         @XmlAttribute(name = "showColourText")
4886         protected Boolean showColourText;
4887         @XmlAttribute(name = "showUnconserved")
4888         protected Boolean showUnconserved;
4889         @XmlAttribute(name = "showBoxes")
4890         protected Boolean showBoxes;
4891         @XmlAttribute(name = "wrapAlignment")
4892         protected Boolean wrapAlignment;
4893         @XmlAttribute(name = "renderGaps")
4894         protected Boolean renderGaps;
4895         @XmlAttribute(name = "showSequenceFeatures")
4896         protected Boolean showSequenceFeatures;
4897         @XmlAttribute(name = "showNPfeatureTooltip")
4898         protected Boolean showNPfeatureTooltip;
4899         @XmlAttribute(name = "showDbRefTooltip")
4900         protected Boolean showDbRefTooltip;
4901         @XmlAttribute(name = "followHighlight")
4902         protected Boolean followHighlight;
4903         @XmlAttribute(name = "followSelection")
4904         protected Boolean followSelection;
4905         @XmlAttribute(name = "showAnnotation")
4906         protected Boolean showAnnotation;
4907         @XmlAttribute(name = "centreColumnLabels")
4908         protected Boolean centreColumnLabels;
4909         @XmlAttribute(name = "showGroupConservation")
4910         protected Boolean showGroupConservation;
4911         @XmlAttribute(name = "showGroupConsensus")
4912         protected Boolean showGroupConsensus;
4913         @XmlAttribute(name = "showConsensusHistogram")
4914         protected Boolean showConsensusHistogram;
4915         @XmlAttribute(name = "showSequenceLogo")
4916         protected Boolean showSequenceLogo;
4917         @XmlAttribute(name = "normaliseSequenceLogo")
4918         protected Boolean normaliseSequenceLogo;
4919         @XmlAttribute(name = "ignoreGapsinConsensus")
4920         protected Boolean ignoreGapsinConsensus;
4921         @XmlAttribute(name = "startRes")
4922         protected Integer startRes;
4923         @XmlAttribute(name = "startSeq")
4924         protected Integer startSeq;
4925         @XmlAttribute(name = "fontName")
4926         protected String fontName;
4927         @XmlAttribute(name = "fontSize")
4928         protected Integer fontSize;
4929         @XmlAttribute(name = "fontStyle")
4930         protected Integer fontStyle;
4931         @XmlAttribute(name = "scaleProteinAsCdna")
4932         protected Boolean scaleProteinAsCdna;
4933         @XmlAttribute(name = "viewName")
4934         protected String viewName;
4935         @XmlAttribute(name = "sequenceSetId")
4936         protected String sequenceSetId;
4937         @XmlAttribute(name = "gatheredViews")
4938         protected Boolean gatheredViews;
4939         @XmlAttribute(name = "textCol1")
4940         protected Integer textCol1;
4941         @XmlAttribute(name = "textCol2")
4942         protected Integer textCol2;
4943         @XmlAttribute(name = "textColThreshold")
4944         protected Integer textColThreshold;
4945         @XmlAttribute(name = "id")
4946         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4947         @XmlID
4948         @XmlSchemaType(name = "ID")
4949         protected String id;
4950         @XmlAttribute(name = "complementId")
4951         protected String complementId;
4952         @XmlAttribute(name = "showComplementFeatures")
4953         protected Boolean showComplementFeatures;
4954         @XmlAttribute(name = "showComplementFeaturesOnTop")
4955         protected Boolean showComplementFeaturesOnTop;
4956         @XmlAttribute(name = "width")
4957         protected Integer width;
4958         @XmlAttribute(name = "height")
4959         protected Integer height;
4960         @XmlAttribute(name = "xpos")
4961         protected Integer xpos;
4962         @XmlAttribute(name = "ypos")
4963         protected Integer ypos;
4964
4965         /**
4966          * Gets the value of the annotationColours property.
4967          *
4968          * @return
4969          *     possible object is
4970          *     {@link AnnotationColourScheme }
4971          *
4972          */
4973         public AnnotationColourScheme getAnnotationColours() {
4974             return annotationColours;
4975         }
4976
4977         /**
4978          * Sets the value of the annotationColours property.
4979          *
4980          * @param value
4981          *     allowed object is
4982          *     {@link AnnotationColourScheme }
4983          *
4984          */
4985         public void setAnnotationColours(AnnotationColourScheme value) {
4986             this.annotationColours = value;
4987         }
4988
4989         /**
4990          * Gets the value of the hiddenColumns property.
4991          *
4992          * <p>
4993          * This accessor method returns a reference to the live list,
4994          * not a snapshot. Therefore any modification you make to the
4995          * returned list will be present inside the JAXB object.
4996          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4997          *
4998          * <p>
4999          * For example, to add a new item, do as follows:
5000          * <pre>
5001          *    getHiddenColumns().add(newItem);
5002          * </pre>
5003          *
5004          *
5005          * <p>
5006          * Objects of the following type(s) are allowed in the list
5007          * {@link JalviewModel.Viewport.HiddenColumns }
5008          *
5009          *
5010          */
5011         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5012             if (hiddenColumns == null) {
5013                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5014             }
5015             return this.hiddenColumns;
5016         }
5017
5018         /**
5019          * Gets the value of the calcIdParam property.
5020          *
5021          * <p>
5022          * This accessor method returns a reference to the live list,
5023          * not a snapshot. Therefore any modification you make to the
5024          * returned list will be present inside the JAXB object.
5025          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5026          *
5027          * <p>
5028          * For example, to add a new item, do as follows:
5029          * <pre>
5030          *    getCalcIdParam().add(newItem);
5031          * </pre>
5032          *
5033          *
5034          * <p>
5035          * Objects of the following type(s) are allowed in the list
5036          * {@link JalviewModel.Viewport.CalcIdParam }
5037          *
5038          *
5039          */
5040         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5041             if (calcIdParam == null) {
5042                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5043             }
5044             return this.calcIdParam;
5045         }
5046
5047         /**
5048          * Gets the value of the overview property.
5049          *
5050          * @return
5051          *     possible object is
5052          *     {@link JalviewModel.Viewport.Overview }
5053          *
5054          */
5055         public JalviewModel.Viewport.Overview getOverview() {
5056             return overview;
5057         }
5058
5059         /**
5060          * Sets the value of the overview property.
5061          *
5062          * @param value
5063          *     allowed object is
5064          *     {@link JalviewModel.Viewport.Overview }
5065          *
5066          */
5067         public void setOverview(JalviewModel.Viewport.Overview value) {
5068             this.overview = value;
5069         }
5070
5071         /**
5072          * Gets the value of the conservationSelected property.
5073          *
5074          * @return
5075          *     possible object is
5076          *     {@link Boolean }
5077          *
5078          */
5079         public Boolean isConservationSelected() {
5080             return conservationSelected;
5081         }
5082
5083         /**
5084          * Sets the value of the conservationSelected property.
5085          *
5086          * @param value
5087          *     allowed object is
5088          *     {@link Boolean }
5089          *
5090          */
5091         public void setConservationSelected(Boolean value) {
5092             this.conservationSelected = value;
5093         }
5094
5095         /**
5096          * Gets the value of the pidSelected property.
5097          *
5098          * @return
5099          *     possible object is
5100          *     {@link Boolean }
5101          *
5102          */
5103         public Boolean isPidSelected() {
5104             return pidSelected;
5105         }
5106
5107         /**
5108          * Sets the value of the pidSelected property.
5109          *
5110          * @param value
5111          *     allowed object is
5112          *     {@link Boolean }
5113          *
5114          */
5115         public void setPidSelected(Boolean value) {
5116             this.pidSelected = value;
5117         }
5118
5119         /**
5120          * Gets the value of the bgColour property.
5121          *
5122          * @return
5123          *     possible object is
5124          *     {@link String }
5125          *
5126          */
5127         public String getBgColour() {
5128             return bgColour;
5129         }
5130
5131         /**
5132          * Sets the value of the bgColour property.
5133          *
5134          * @param value
5135          *     allowed object is
5136          *     {@link String }
5137          *
5138          */
5139         public void setBgColour(String value) {
5140             this.bgColour = value;
5141         }
5142
5143         /**
5144          * Gets the value of the consThreshold property.
5145          *
5146          * @return
5147          *     possible object is
5148          *     {@link Integer }
5149          *
5150          */
5151         public Integer getConsThreshold() {
5152             return consThreshold;
5153         }
5154
5155         /**
5156          * Sets the value of the consThreshold property.
5157          *
5158          * @param value
5159          *     allowed object is
5160          *     {@link Integer }
5161          *
5162          */
5163         public void setConsThreshold(Integer value) {
5164             this.consThreshold = value;
5165         }
5166
5167         /**
5168          * Gets the value of the pidThreshold property.
5169          *
5170          * @return
5171          *     possible object is
5172          *     {@link Integer }
5173          *
5174          */
5175         public Integer getPidThreshold() {
5176             return pidThreshold;
5177         }
5178
5179         /**
5180          * Sets the value of the pidThreshold property.
5181          *
5182          * @param value
5183          *     allowed object is
5184          *     {@link Integer }
5185          *
5186          */
5187         public void setPidThreshold(Integer value) {
5188             this.pidThreshold = value;
5189         }
5190
5191         /**
5192          * Gets the value of the title property.
5193          *
5194          * @return
5195          *     possible object is
5196          *     {@link String }
5197          *
5198          */
5199         public String getTitle() {
5200             return title;
5201         }
5202
5203         /**
5204          * Sets the value of the title property.
5205          *
5206          * @param value
5207          *     allowed object is
5208          *     {@link String }
5209          *
5210          */
5211         public void setTitle(String value) {
5212             this.title = value;
5213         }
5214
5215         /**
5216          * Gets the value of the showFullId property.
5217          *
5218          * @return
5219          *     possible object is
5220          *     {@link Boolean }
5221          *
5222          */
5223         public Boolean isShowFullId() {
5224             return showFullId;
5225         }
5226
5227         /**
5228          * Sets the value of the showFullId property.
5229          *
5230          * @param value
5231          *     allowed object is
5232          *     {@link Boolean }
5233          *
5234          */
5235         public void setShowFullId(Boolean value) {
5236             this.showFullId = value;
5237         }
5238
5239         /**
5240          * Gets the value of the rightAlignIds property.
5241          *
5242          * @return
5243          *     possible object is
5244          *     {@link Boolean }
5245          *
5246          */
5247         public Boolean isRightAlignIds() {
5248             return rightAlignIds;
5249         }
5250
5251         /**
5252          * Sets the value of the rightAlignIds property.
5253          *
5254          * @param value
5255          *     allowed object is
5256          *     {@link Boolean }
5257          *
5258          */
5259         public void setRightAlignIds(Boolean value) {
5260             this.rightAlignIds = value;
5261         }
5262
5263         /**
5264          * Gets the value of the showText property.
5265          *
5266          * @return
5267          *     possible object is
5268          *     {@link Boolean }
5269          *
5270          */
5271         public Boolean isShowText() {
5272             return showText;
5273         }
5274
5275         /**
5276          * Sets the value of the showText property.
5277          *
5278          * @param value
5279          *     allowed object is
5280          *     {@link Boolean }
5281          *
5282          */
5283         public void setShowText(Boolean value) {
5284             this.showText = value;
5285         }
5286
5287         /**
5288          * Gets the value of the showColourText property.
5289          *
5290          * @return
5291          *     possible object is
5292          *     {@link Boolean }
5293          *
5294          */
5295         public Boolean isShowColourText() {
5296             return showColourText;
5297         }
5298
5299         /**
5300          * Sets the value of the showColourText property.
5301          *
5302          * @param value
5303          *     allowed object is
5304          *     {@link Boolean }
5305          *
5306          */
5307         public void setShowColourText(Boolean value) {
5308             this.showColourText = value;
5309         }
5310
5311         /**
5312          * Gets the value of the showUnconserved property.
5313          *
5314          * @return
5315          *     possible object is
5316          *     {@link Boolean }
5317          *
5318          */
5319         public boolean isShowUnconserved() {
5320             if (showUnconserved == null) {
5321                 return false;
5322             } else {
5323                 return showUnconserved;
5324             }
5325         }
5326
5327         /**
5328          * Sets the value of the showUnconserved property.
5329          *
5330          * @param value
5331          *     allowed object is
5332          *     {@link Boolean }
5333          *
5334          */
5335         public void setShowUnconserved(Boolean value) {
5336             this.showUnconserved = value;
5337         }
5338
5339         /**
5340          * Gets the value of the showBoxes property.
5341          *
5342          * @return
5343          *     possible object is
5344          *     {@link Boolean }
5345          *
5346          */
5347         public Boolean isShowBoxes() {
5348             return showBoxes;
5349         }
5350
5351         /**
5352          * Sets the value of the showBoxes property.
5353          *
5354          * @param value
5355          *     allowed object is
5356          *     {@link Boolean }
5357          *
5358          */
5359         public void setShowBoxes(Boolean value) {
5360             this.showBoxes = value;
5361         }
5362
5363         /**
5364          * Gets the value of the wrapAlignment property.
5365          *
5366          * @return
5367          *     possible object is
5368          *     {@link Boolean }
5369          *
5370          */
5371         public Boolean isWrapAlignment() {
5372             return wrapAlignment;
5373         }
5374
5375         /**
5376          * Sets the value of the wrapAlignment property.
5377          *
5378          * @param value
5379          *     allowed object is
5380          *     {@link Boolean }
5381          *
5382          */
5383         public void setWrapAlignment(Boolean value) {
5384             this.wrapAlignment = value;
5385         }
5386
5387         /**
5388          * Gets the value of the renderGaps property.
5389          *
5390          * @return
5391          *     possible object is
5392          *     {@link Boolean }
5393          *
5394          */
5395         public Boolean isRenderGaps() {
5396             return renderGaps;
5397         }
5398
5399         /**
5400          * Sets the value of the renderGaps property.
5401          *
5402          * @param value
5403          *     allowed object is
5404          *     {@link Boolean }
5405          *
5406          */
5407         public void setRenderGaps(Boolean value) {
5408             this.renderGaps = value;
5409         }
5410
5411         /**
5412          * Gets the value of the showSequenceFeatures property.
5413          *
5414          * @return
5415          *     possible object is
5416          *     {@link Boolean }
5417          *
5418          */
5419         public Boolean isShowSequenceFeatures() {
5420             return showSequenceFeatures;
5421         }
5422
5423         /**
5424          * Sets the value of the showSequenceFeatures property.
5425          *
5426          * @param value
5427          *     allowed object is
5428          *     {@link Boolean }
5429          *
5430          */
5431         public void setShowSequenceFeatures(Boolean value) {
5432             this.showSequenceFeatures = value;
5433         }
5434
5435         /**
5436          * Gets the value of the showNPfeatureTooltip property.
5437          *
5438          * @return
5439          *     possible object is
5440          *     {@link Boolean }
5441          *
5442          */
5443         public Boolean isShowNPfeatureTooltip() {
5444             return showNPfeatureTooltip;
5445         }
5446
5447         /**
5448          * Sets the value of the showNPfeatureTooltip property.
5449          *
5450          * @param value
5451          *     allowed object is
5452          *     {@link Boolean }
5453          *
5454          */
5455         public void setShowNPfeatureTooltip(Boolean value) {
5456             this.showNPfeatureTooltip = value;
5457         }
5458
5459         /**
5460          * Gets the value of the showDbRefTooltip property.
5461          *
5462          * @return
5463          *     possible object is
5464          *     {@link Boolean }
5465          *
5466          */
5467         public Boolean isShowDbRefTooltip() {
5468             return showDbRefTooltip;
5469         }
5470
5471         /**
5472          * Sets the value of the showDbRefTooltip property.
5473          *
5474          * @param value
5475          *     allowed object is
5476          *     {@link Boolean }
5477          *
5478          */
5479         public void setShowDbRefTooltip(Boolean value) {
5480             this.showDbRefTooltip = value;
5481         }
5482
5483         /**
5484          * Gets the value of the followHighlight property.
5485          *
5486          * @return
5487          *     possible object is
5488          *     {@link Boolean }
5489          *
5490          */
5491         public boolean isFollowHighlight() {
5492             if (followHighlight == null) {
5493                 return true;
5494             } else {
5495                 return followHighlight;
5496             }
5497         }
5498
5499         /**
5500          * Sets the value of the followHighlight property.
5501          *
5502          * @param value
5503          *     allowed object is
5504          *     {@link Boolean }
5505          *
5506          */
5507         public void setFollowHighlight(Boolean value) {
5508             this.followHighlight = value;
5509         }
5510
5511         /**
5512          * Gets the value of the followSelection property.
5513          *
5514          * @return
5515          *     possible object is
5516          *     {@link Boolean }
5517          *
5518          */
5519         public boolean isFollowSelection() {
5520             if (followSelection == null) {
5521                 return true;
5522             } else {
5523                 return followSelection;
5524             }
5525         }
5526
5527         /**
5528          * Sets the value of the followSelection property.
5529          *
5530          * @param value
5531          *     allowed object is
5532          *     {@link Boolean }
5533          *
5534          */
5535         public void setFollowSelection(Boolean value) {
5536             this.followSelection = value;
5537         }
5538
5539         /**
5540          * Gets the value of the showAnnotation property.
5541          *
5542          * @return
5543          *     possible object is
5544          *     {@link Boolean }
5545          *
5546          */
5547         public Boolean isShowAnnotation() {
5548             return showAnnotation;
5549         }
5550
5551         /**
5552          * Sets the value of the showAnnotation property.
5553          *
5554          * @param value
5555          *     allowed object is
5556          *     {@link Boolean }
5557          *
5558          */
5559         public void setShowAnnotation(Boolean value) {
5560             this.showAnnotation = value;
5561         }
5562
5563         /**
5564          * Gets the value of the centreColumnLabels property.
5565          *
5566          * @return
5567          *     possible object is
5568          *     {@link Boolean }
5569          *
5570          */
5571         public boolean isCentreColumnLabels() {
5572             if (centreColumnLabels == null) {
5573                 return false;
5574             } else {
5575                 return centreColumnLabels;
5576             }
5577         }
5578
5579         /**
5580          * Sets the value of the centreColumnLabels property.
5581          *
5582          * @param value
5583          *     allowed object is
5584          *     {@link Boolean }
5585          *
5586          */
5587         public void setCentreColumnLabels(Boolean value) {
5588             this.centreColumnLabels = value;
5589         }
5590
5591         /**
5592          * Gets the value of the showGroupConservation property.
5593          *
5594          * @return
5595          *     possible object is
5596          *     {@link Boolean }
5597          *
5598          */
5599         public boolean isShowGroupConservation() {
5600             if (showGroupConservation == null) {
5601                 return false;
5602             } else {
5603                 return showGroupConservation;
5604             }
5605         }
5606
5607         /**
5608          * Sets the value of the showGroupConservation property.
5609          *
5610          * @param value
5611          *     allowed object is
5612          *     {@link Boolean }
5613          *
5614          */
5615         public void setShowGroupConservation(Boolean value) {
5616             this.showGroupConservation = value;
5617         }
5618
5619         /**
5620          * Gets the value of the showGroupConsensus property.
5621          *
5622          * @return
5623          *     possible object is
5624          *     {@link Boolean }
5625          *
5626          */
5627         public boolean isShowGroupConsensus() {
5628             if (showGroupConsensus == null) {
5629                 return false;
5630             } else {
5631                 return showGroupConsensus;
5632             }
5633         }
5634
5635         /**
5636          * Sets the value of the showGroupConsensus property.
5637          *
5638          * @param value
5639          *     allowed object is
5640          *     {@link Boolean }
5641          *
5642          */
5643         public void setShowGroupConsensus(Boolean value) {
5644             this.showGroupConsensus = value;
5645         }
5646
5647         /**
5648          * Gets the value of the showConsensusHistogram property.
5649          *
5650          * @return
5651          *     possible object is
5652          *     {@link Boolean }
5653          *
5654          */
5655         public boolean isShowConsensusHistogram() {
5656             if (showConsensusHistogram == null) {
5657                 return true;
5658             } else {
5659                 return showConsensusHistogram;
5660             }
5661         }
5662
5663         /**
5664          * Sets the value of the showConsensusHistogram property.
5665          *
5666          * @param value
5667          *     allowed object is
5668          *     {@link Boolean }
5669          *
5670          */
5671         public void setShowConsensusHistogram(Boolean value) {
5672             this.showConsensusHistogram = value;
5673         }
5674
5675         /**
5676          * Gets the value of the showSequenceLogo property.
5677          *
5678          * @return
5679          *     possible object is
5680          *     {@link Boolean }
5681          *
5682          */
5683         public boolean isShowSequenceLogo() {
5684             if (showSequenceLogo == null) {
5685                 return false;
5686             } else {
5687                 return showSequenceLogo;
5688             }
5689         }
5690
5691         /**
5692          * Sets the value of the showSequenceLogo property.
5693          *
5694          * @param value
5695          *     allowed object is
5696          *     {@link Boolean }
5697          *
5698          */
5699         public void setShowSequenceLogo(Boolean value) {
5700             this.showSequenceLogo = value;
5701         }
5702
5703         /**
5704          * Gets the value of the normaliseSequenceLogo property.
5705          *
5706          * @return
5707          *     possible object is
5708          *     {@link Boolean }
5709          *
5710          */
5711         public boolean isNormaliseSequenceLogo() {
5712             if (normaliseSequenceLogo == null) {
5713                 return false;
5714             } else {
5715                 return normaliseSequenceLogo;
5716             }
5717         }
5718
5719         /**
5720          * Sets the value of the normaliseSequenceLogo property.
5721          *
5722          * @param value
5723          *     allowed object is
5724          *     {@link Boolean }
5725          *
5726          */
5727         public void setNormaliseSequenceLogo(Boolean value) {
5728             this.normaliseSequenceLogo = value;
5729         }
5730
5731         /**
5732          * Gets the value of the ignoreGapsinConsensus property.
5733          *
5734          * @return
5735          *     possible object is
5736          *     {@link Boolean }
5737          *
5738          */
5739         public boolean isIgnoreGapsinConsensus() {
5740             if (ignoreGapsinConsensus == null) {
5741                 return true;
5742             } else {
5743                 return ignoreGapsinConsensus;
5744             }
5745         }
5746
5747         /**
5748          * Sets the value of the ignoreGapsinConsensus property.
5749          *
5750          * @param value
5751          *     allowed object is
5752          *     {@link Boolean }
5753          *
5754          */
5755         public void setIgnoreGapsinConsensus(Boolean value) {
5756             this.ignoreGapsinConsensus = value;
5757         }
5758
5759         /**
5760          * Gets the value of the startRes property.
5761          *
5762          * @return
5763          *     possible object is
5764          *     {@link Integer }
5765          *
5766          */
5767         public Integer getStartRes() {
5768             return startRes;
5769         }
5770
5771         /**
5772          * Sets the value of the startRes property.
5773          *
5774          * @param value
5775          *     allowed object is
5776          *     {@link Integer }
5777          *
5778          */
5779         public void setStartRes(Integer value) {
5780             this.startRes = value;
5781         }
5782
5783         /**
5784          * Gets the value of the startSeq property.
5785          *
5786          * @return
5787          *     possible object is
5788          *     {@link Integer }
5789          *
5790          */
5791         public Integer getStartSeq() {
5792             return startSeq;
5793         }
5794
5795         /**
5796          * Sets the value of the startSeq property.
5797          *
5798          * @param value
5799          *     allowed object is
5800          *     {@link Integer }
5801          *
5802          */
5803         public void setStartSeq(Integer value) {
5804             this.startSeq = value;
5805         }
5806
5807         /**
5808          * Gets the value of the fontName property.
5809          *
5810          * @return
5811          *     possible object is
5812          *     {@link String }
5813          *
5814          */
5815         public String getFontName() {
5816             return fontName;
5817         }
5818
5819         /**
5820          * Sets the value of the fontName property.
5821          *
5822          * @param value
5823          *     allowed object is
5824          *     {@link String }
5825          *
5826          */
5827         public void setFontName(String value) {
5828             this.fontName = value;
5829         }
5830
5831         /**
5832          * Gets the value of the fontSize property.
5833          *
5834          * @return
5835          *     possible object is
5836          *     {@link Integer }
5837          *
5838          */
5839         public Integer getFontSize() {
5840             return fontSize;
5841         }
5842
5843         /**
5844          * Sets the value of the fontSize property.
5845          *
5846          * @param value
5847          *     allowed object is
5848          *     {@link Integer }
5849          *
5850          */
5851         public void setFontSize(Integer value) {
5852             this.fontSize = value;
5853         }
5854
5855         /**
5856          * Gets the value of the fontStyle property.
5857          *
5858          * @return
5859          *     possible object is
5860          *     {@link Integer }
5861          *
5862          */
5863         public Integer getFontStyle() {
5864             return fontStyle;
5865         }
5866
5867         /**
5868          * Sets the value of the fontStyle property.
5869          *
5870          * @param value
5871          *     allowed object is
5872          *     {@link Integer }
5873          *
5874          */
5875         public void setFontStyle(Integer value) {
5876             this.fontStyle = value;
5877         }
5878
5879         /**
5880          * Gets the value of the scaleProteinAsCdna property.
5881          *
5882          * @return
5883          *     possible object is
5884          *     {@link Boolean }
5885          *
5886          */
5887         public boolean isScaleProteinAsCdna() {
5888             if (scaleProteinAsCdna == null) {
5889                 return true;
5890             } else {
5891                 return scaleProteinAsCdna;
5892             }
5893         }
5894
5895         /**
5896          * Sets the value of the scaleProteinAsCdna property.
5897          *
5898          * @param value
5899          *     allowed object is
5900          *     {@link Boolean }
5901          *
5902          */
5903         public void setScaleProteinAsCdna(Boolean value) {
5904             this.scaleProteinAsCdna = value;
5905         }
5906
5907         /**
5908          * Gets the value of the viewName property.
5909          *
5910          * @return
5911          *     possible object is
5912          *     {@link String }
5913          *
5914          */
5915         public String getViewName() {
5916             return viewName;
5917         }
5918
5919         /**
5920          * Sets the value of the viewName property.
5921          *
5922          * @param value
5923          *     allowed object is
5924          *     {@link String }
5925          *
5926          */
5927         public void setViewName(String value) {
5928             this.viewName = value;
5929         }
5930
5931         /**
5932          * Gets the value of the sequenceSetId property.
5933          *
5934          * @return
5935          *     possible object is
5936          *     {@link String }
5937          *
5938          */
5939         public String getSequenceSetId() {
5940             return sequenceSetId;
5941         }
5942
5943         /**
5944          * Sets the value of the sequenceSetId property.
5945          *
5946          * @param value
5947          *     allowed object is
5948          *     {@link String }
5949          *
5950          */
5951         public void setSequenceSetId(String value) {
5952             this.sequenceSetId = value;
5953         }
5954
5955         /**
5956          * Gets the value of the gatheredViews property.
5957          *
5958          * @return
5959          *     possible object is
5960          *     {@link Boolean }
5961          *
5962          */
5963         public Boolean isGatheredViews() {
5964             return gatheredViews;
5965         }
5966
5967         /**
5968          * Sets the value of the gatheredViews property.
5969          *
5970          * @param value
5971          *     allowed object is
5972          *     {@link Boolean }
5973          *
5974          */
5975         public void setGatheredViews(Boolean value) {
5976             this.gatheredViews = value;
5977         }
5978
5979         /**
5980          * Gets the value of the textCol1 property.
5981          *
5982          * @return
5983          *     possible object is
5984          *     {@link Integer }
5985          *
5986          */
5987         public Integer getTextCol1() {
5988             return textCol1;
5989         }
5990
5991         /**
5992          * Sets the value of the textCol1 property.
5993          *
5994          * @param value
5995          *     allowed object is
5996          *     {@link Integer }
5997          *
5998          */
5999         public void setTextCol1(Integer value) {
6000             this.textCol1 = value;
6001         }
6002
6003         /**
6004          * Gets the value of the textCol2 property.
6005          *
6006          * @return
6007          *     possible object is
6008          *     {@link Integer }
6009          *
6010          */
6011         public Integer getTextCol2() {
6012             return textCol2;
6013         }
6014
6015         /**
6016          * Sets the value of the textCol2 property.
6017          *
6018          * @param value
6019          *     allowed object is
6020          *     {@link Integer }
6021          *
6022          */
6023         public void setTextCol2(Integer value) {
6024             this.textCol2 = value;
6025         }
6026
6027         /**
6028          * Gets the value of the textColThreshold property.
6029          *
6030          * @return
6031          *     possible object is
6032          *     {@link Integer }
6033          *
6034          */
6035         public Integer getTextColThreshold() {
6036             return textColThreshold;
6037         }
6038
6039         /**
6040          * Sets the value of the textColThreshold property.
6041          *
6042          * @param value
6043          *     allowed object is
6044          *     {@link Integer }
6045          *
6046          */
6047         public void setTextColThreshold(Integer value) {
6048             this.textColThreshold = value;
6049         }
6050
6051         /**
6052          * Gets the value of the id property.
6053          *
6054          * @return
6055          *     possible object is
6056          *     {@link String }
6057          *
6058          */
6059         public String getId() {
6060             return id;
6061         }
6062
6063         /**
6064          * Sets the value of the id property.
6065          *
6066          * @param value
6067          *     allowed object is
6068          *     {@link String }
6069          *
6070          */
6071         public void setId(String value) {
6072             this.id = value;
6073         }
6074
6075         /**
6076          * Gets the value of the complementId property.
6077          *
6078          * @return
6079          *     possible object is
6080          *     {@link String }
6081          *
6082          */
6083         public String getComplementId() {
6084             return complementId;
6085         }
6086
6087         /**
6088          * Sets the value of the complementId property.
6089          *
6090          * @param value
6091          *     allowed object is
6092          *     {@link String }
6093          *
6094          */
6095         public void setComplementId(String value) {
6096             this.complementId = value;
6097         }
6098
6099         /**
6100          * Gets the value of the showComplementFeatures property.
6101          *
6102          * @return
6103          *     possible object is
6104          *     {@link Boolean }
6105          *
6106          */
6107         public boolean isShowComplementFeatures() {
6108             if (showComplementFeatures == null) {
6109                 return false;
6110             } else {
6111                 return showComplementFeatures;
6112             }
6113         }
6114
6115         /**
6116          * Sets the value of the showComplementFeatures property.
6117          *
6118          * @param value
6119          *     allowed object is
6120          *     {@link Boolean }
6121          *
6122          */
6123         public void setShowComplementFeatures(Boolean value) {
6124             this.showComplementFeatures = value;
6125         }
6126
6127         /**
6128          * Gets the value of the showComplementFeaturesOnTop property.
6129          *
6130          * @return
6131          *     possible object is
6132          *     {@link Boolean }
6133          *
6134          */
6135         public boolean isShowComplementFeaturesOnTop() {
6136             if (showComplementFeaturesOnTop == null) {
6137                 return false;
6138             } else {
6139                 return showComplementFeaturesOnTop;
6140             }
6141         }
6142
6143         /**
6144          * Sets the value of the showComplementFeaturesOnTop property.
6145          *
6146          * @param value
6147          *     allowed object is
6148          *     {@link Boolean }
6149          *
6150          */
6151         public void setShowComplementFeaturesOnTop(Boolean value) {
6152             this.showComplementFeaturesOnTop = value;
6153         }
6154
6155         /**
6156          * Gets the value of the width property.
6157          *
6158          * @return
6159          *     possible object is
6160          *     {@link Integer }
6161          *
6162          */
6163         public Integer getWidth() {
6164             return width;
6165         }
6166
6167         /**
6168          * Sets the value of the width property.
6169          *
6170          * @param value
6171          *     allowed object is
6172          *     {@link Integer }
6173          *
6174          */
6175         public void setWidth(Integer value) {
6176             this.width = value;
6177         }
6178
6179         /**
6180          * Gets the value of the height property.
6181          *
6182          * @return
6183          *     possible object is
6184          *     {@link Integer }
6185          *
6186          */
6187         public Integer getHeight() {
6188             return height;
6189         }
6190
6191         /**
6192          * Sets the value of the height property.
6193          *
6194          * @param value
6195          *     allowed object is
6196          *     {@link Integer }
6197          *
6198          */
6199         public void setHeight(Integer value) {
6200             this.height = value;
6201         }
6202
6203         /**
6204          * Gets the value of the xpos property.
6205          *
6206          * @return
6207          *     possible object is
6208          *     {@link Integer }
6209          *
6210          */
6211         public Integer getXpos() {
6212             return xpos;
6213         }
6214
6215         /**
6216          * Sets the value of the xpos property.
6217          *
6218          * @param value
6219          *     allowed object is
6220          *     {@link Integer }
6221          *
6222          */
6223         public void setXpos(Integer value) {
6224             this.xpos = value;
6225         }
6226
6227         /**
6228          * Gets the value of the ypos property.
6229          *
6230          * @return
6231          *     possible object is
6232          *     {@link Integer }
6233          *
6234          */
6235         public Integer getYpos() {
6236             return ypos;
6237         }
6238
6239         /**
6240          * Sets the value of the ypos property.
6241          *
6242          * @param value
6243          *     allowed object is
6244          *     {@link Integer }
6245          *
6246          */
6247         public void setYpos(Integer value) {
6248             this.ypos = value;
6249         }
6250
6251
6252         /**
6253          * <p>Java class for anonymous complex type.
6254          *
6255          * <p>The following schema fragment specifies the expected content contained within this class.
6256          *
6257          * <pre>
6258          * &lt;complexType>
6259          *   &lt;complexContent>
6260          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6261          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6262          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6263          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6264          *     &lt;/extension>
6265          *   &lt;/complexContent>
6266          * &lt;/complexType>
6267          * </pre>
6268          *
6269          *
6270          */
6271         @XmlAccessorType(XmlAccessType.FIELD)
6272         @XmlType(name = "")
6273         public static class CalcIdParam
6274             extends WebServiceParameterSet
6275         {
6276
6277             @XmlAttribute(name = "calcId", required = true)
6278             protected String calcId;
6279             @XmlAttribute(name = "needsUpdate")
6280             protected Boolean needsUpdate;
6281             @XmlAttribute(name = "autoUpdate", required = true)
6282             protected boolean autoUpdate;
6283
6284             /**
6285              * Gets the value of the calcId property.
6286              *
6287              * @return
6288              *     possible object is
6289              *     {@link String }
6290              *
6291              */
6292             public String getCalcId() {
6293                 return calcId;
6294             }
6295
6296             /**
6297              * Sets the value of the calcId property.
6298              *
6299              * @param value
6300              *     allowed object is
6301              *     {@link String }
6302              *
6303              */
6304             public void setCalcId(String value) {
6305                 this.calcId = value;
6306             }
6307
6308             /**
6309              * Gets the value of the needsUpdate property.
6310              *
6311              * @return
6312              *     possible object is
6313              *     {@link Boolean }
6314              *
6315              */
6316             public boolean isNeedsUpdate() {
6317                 if (needsUpdate == null) {
6318                     return false;
6319                 } else {
6320                     return needsUpdate;
6321                 }
6322             }
6323
6324             /**
6325              * Sets the value of the needsUpdate property.
6326              *
6327              * @param value
6328              *     allowed object is
6329              *     {@link Boolean }
6330              *
6331              */
6332             public void setNeedsUpdate(Boolean value) {
6333                 this.needsUpdate = value;
6334             }
6335
6336             /**
6337              * Gets the value of the autoUpdate property.
6338              *
6339              */
6340             public boolean isAutoUpdate() {
6341                 return autoUpdate;
6342             }
6343
6344             /**
6345              * Sets the value of the autoUpdate property.
6346              *
6347              */
6348             public void setAutoUpdate(boolean value) {
6349                 this.autoUpdate = value;
6350             }
6351
6352         }
6353
6354
6355         /**
6356          * <p>Java class for anonymous complex type.
6357          *
6358          * <p>The following schema fragment specifies the expected content contained within this class.
6359          *
6360          * <pre>
6361          * &lt;complexType>
6362          *   &lt;complexContent>
6363          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6364          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6365          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6366          *     &lt;/restriction>
6367          *   &lt;/complexContent>
6368          * &lt;/complexType>
6369          * </pre>
6370          *
6371          *
6372          */
6373         @XmlAccessorType(XmlAccessType.FIELD)
6374         @XmlType(name = "")
6375         public static class HiddenColumns {
6376
6377             @XmlAttribute(name = "start")
6378             protected Integer start;
6379             @XmlAttribute(name = "end")
6380             protected Integer end;
6381
6382             /**
6383              * Gets the value of the start property.
6384              *
6385              * @return
6386              *     possible object is
6387              *     {@link Integer }
6388              *
6389              */
6390             public Integer getStart() {
6391                 return start;
6392             }
6393
6394             /**
6395              * Sets the value of the start property.
6396              *
6397              * @param value
6398              *     allowed object is
6399              *     {@link Integer }
6400              *
6401              */
6402             public void setStart(Integer value) {
6403                 this.start = value;
6404             }
6405
6406             /**
6407              * Gets the value of the end property.
6408              *
6409              * @return
6410              *     possible object is
6411              *     {@link Integer }
6412              *
6413              */
6414             public Integer getEnd() {
6415                 return end;
6416             }
6417
6418             /**
6419              * Sets the value of the end property.
6420              *
6421              * @param value
6422              *     allowed object is
6423              *     {@link Integer }
6424              *
6425              */
6426             public void setEnd(Integer value) {
6427                 this.end = value;
6428             }
6429
6430         }
6431
6432
6433         /**
6434          * <p>Java class for anonymous complex type.
6435          *
6436          * <p>The following schema fragment specifies the expected content contained within this class.
6437          *
6438          * <pre>
6439          * &lt;complexType>
6440          *   &lt;complexContent>
6441          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6442          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
6443          *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6444          *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6445          *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6446          *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6447          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6448          *     &lt;/restriction>
6449          *   &lt;/complexContent>
6450          * &lt;/complexType>
6451          * </pre>
6452          *
6453          *
6454          */
6455         @XmlAccessorType(XmlAccessType.FIELD)
6456         @XmlType(name = "")
6457         public static class Overview {
6458
6459             @XmlAttribute(name = "showHidden")
6460             protected Boolean showHidden;
6461             @XmlAttribute(name = "residueColour")
6462             protected Integer residueColour;
6463             @XmlAttribute(name = "gapColour")
6464             protected Integer gapColour;
6465             @XmlAttribute(name = "hiddenColour")
6466             protected Integer hiddenColour;
6467             @XmlAttribute(name = "title")
6468             protected String title;
6469             @XmlAttribute(name = "width")
6470             protected Integer width;
6471             @XmlAttribute(name = "height")
6472             protected Integer height;
6473             @XmlAttribute(name = "xpos")
6474             protected Integer xpos;
6475             @XmlAttribute(name = "ypos")
6476             protected Integer ypos;
6477
6478             /**
6479              * Gets the value of the showHidden property.
6480              *
6481              * @return
6482              *     possible object is
6483              *     {@link Boolean }
6484              *
6485              */
6486             public Boolean isShowHidden() {
6487                 return showHidden;
6488             }
6489
6490             /**
6491              * Sets the value of the showHidden property.
6492              *
6493              * @param value
6494              *     allowed object is
6495              *     {@link Boolean }
6496              *
6497              */
6498             public void setShowHidden(Boolean value) {
6499                 this.showHidden = value;
6500             }
6501
6502             /**
6503              * Gets the value of the residueColour property.
6504              *
6505              * @return
6506              *     possible object is
6507              *     {@link Integer }
6508              *
6509              */
6510             public Integer getResidueColour() {
6511                 return residueColour;
6512             }
6513
6514             /**
6515              * Sets the value of the residueColour property.
6516              *
6517              * @param value
6518              *     allowed object is
6519              *     {@link Integer }
6520              *
6521              */
6522             public void setResidueColour(Integer value) {
6523                 this.residueColour = value;
6524             }
6525
6526             /**
6527              * Gets the value of the gapColour property.
6528              *
6529              * @return
6530              *     possible object is
6531              *     {@link Integer }
6532              *
6533              */
6534             public Integer getGapColour() {
6535                 return gapColour;
6536             }
6537
6538             /**
6539              * Sets the value of the gapColour property.
6540              *
6541              * @param value
6542              *     allowed object is
6543              *     {@link Integer }
6544              *
6545              */
6546             public void setGapColour(Integer value) {
6547                 this.gapColour = value;
6548             }
6549
6550             /**
6551              * Gets the value of the hiddenColour property.
6552              *
6553              * @return
6554              *     possible object is
6555              *     {@link Integer }
6556              *
6557              */
6558             public Integer getHiddenColour() {
6559                 return hiddenColour;
6560             }
6561
6562             /**
6563              * Sets the value of the hiddenColour property.
6564              *
6565              * @param value
6566              *     allowed object is
6567              *     {@link Integer }
6568              *
6569              */
6570             public void setHiddenColour(Integer value) {
6571                 this.hiddenColour = value;
6572             }
6573
6574             /**
6575              * Gets the value of the title property.
6576              *
6577              * @return
6578              *     possible object is
6579              *     {@link String }
6580              *
6581              */
6582             public String getTitle() {
6583                 return title;
6584             }
6585
6586             /**
6587              * Sets the value of the title property.
6588              *
6589              * @param value
6590              *     allowed object is
6591              *     {@link String }
6592              *
6593              */
6594             public void setTitle(String value) {
6595                 this.title = value;
6596             }
6597
6598             /**
6599              * Gets the value of the width property.
6600              *
6601              * @return
6602              *     possible object is
6603              *     {@link Integer }
6604              *
6605              */
6606             public Integer getWidth() {
6607                 return width;
6608             }
6609
6610             /**
6611              * Sets the value of the width property.
6612              *
6613              * @param value
6614              *     allowed object is
6615              *     {@link Integer }
6616              *
6617              */
6618             public void setWidth(Integer value) {
6619                 this.width = value;
6620             }
6621
6622             /**
6623              * Gets the value of the height property.
6624              *
6625              * @return
6626              *     possible object is
6627              *     {@link Integer }
6628              *
6629              */
6630             public Integer getHeight() {
6631                 return height;
6632             }
6633
6634             /**
6635              * Sets the value of the height property.
6636              *
6637              * @param value
6638              *     allowed object is
6639              *     {@link Integer }
6640              *
6641              */
6642             public void setHeight(Integer value) {
6643                 this.height = value;
6644             }
6645
6646             /**
6647              * Gets the value of the xpos property.
6648              *
6649              * @return
6650              *     possible object is
6651              *     {@link Integer }
6652              *
6653              */
6654             public Integer getXpos() {
6655                 return xpos;
6656             }
6657
6658             /**
6659              * Sets the value of the xpos property.
6660              *
6661              * @param value
6662              *     allowed object is
6663              *     {@link Integer }
6664              *
6665              */
6666             public void setXpos(Integer value) {
6667                 this.xpos = value;
6668             }
6669
6670             /**
6671              * Gets the value of the ypos property.
6672              *
6673              * @return
6674              *     possible object is
6675              *     {@link Integer }
6676              *
6677              */
6678             public Integer getYpos() {
6679                 return ypos;
6680             }
6681
6682             /**
6683              * Sets the value of the ypos property.
6684              *
6685              * @param value
6686              *     allowed object is
6687              *     {@link Integer }
6688              *
6689              */
6690             public void setYpos(Integer value) {
6691                 this.ypos = value;
6692             }
6693
6694         }
6695
6696     }
6697
6698 }