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: 2023.05.13 at 06:58:41 PM BST
   6 //
   7
   8
   9 package jalview.xml.binding.jalview;
  10
  11 import java.util.ArrayList;
  12 import java.util.List;
  13 import javax.xml.bind.annotation.XmlAccessType;
  14 import javax.xml.bind.annotation.XmlAccessorType;
  15 import javax.xml.bind.annotation.XmlAttribute;
  16 import javax.xml.bind.annotation.XmlElement;
  17 import javax.xml.bind.annotation.XmlID;
  18 import javax.xml.bind.annotation.XmlSchemaType;
  19 import javax.xml.bind.annotation.XmlType;
  20 import javax.xml.bind.annotation.XmlValue;
  21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
  22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  23 import javax.xml.datatype.XMLGregorianCalendar;
  24
  25
  26 /**
  27  * <p>Java class for JalviewModel complex type.
  28  *
  29  * <p>The following schema fragment specifies the expected content contained within this class.
  30  *
  31  * <pre>
  32  * &lt;complexType name="JalviewModel">
  33  *   &lt;complexContent>
  34  *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  35  *       &lt;sequence>
  36  *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
  37  *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
  38  *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
  39  *         &lt;sequence>
  40  *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  41  *             &lt;complexType>
  42  *               &lt;complexContent>
  43  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  44  *                   &lt;sequence>
  45  *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
  46  *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
  47  *                       &lt;complexType>
  48  *                         &lt;complexContent>
  49  *                           &lt;extension base="{www.jalview.org}pdbentry">
  50  *                             &lt;sequence>
  51  *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
  52  *                                 &lt;complexType>
  53  *                                   &lt;simpleContent>
  54  *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
  55  *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  56  *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  57  *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  58  *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  59  *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  60  *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  61  *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
  62  *                                     &lt;/extension>
  63  *                                   &lt;/simpleContent>
  64  *                                 &lt;/complexType>
  65  *                               &lt;/element>
  66  *                             &lt;/sequence>
  67  *                           &lt;/extension>
  68  *                         &lt;/complexContent>
  69  *                       &lt;/complexType>
  70  *                     &lt;/element>
  71  *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
  72  *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
  73  *                       &lt;complexType>
  74  *                         &lt;complexContent>
  75  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  76  *                             &lt;sequence>
  77  *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
  78  *                                 &lt;complexType>
  79  *                                   &lt;complexContent>
  80  *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  81  *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  82  *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  83  *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  84  *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
  85  *                                     &lt;/restriction>
  86  *                                   &lt;/complexContent>
  87  *                                 &lt;/complexType>
  88  *                               &lt;/element>
  89  *                             &lt;/sequence>
  90  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  91  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  92  *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  93  *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
  94  *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
  95  *                           &lt;/restriction>
  96  *                         &lt;/complexContent>
  97  *                       &lt;/complexType>
  98  *                     &lt;/element>
  99  *                   &lt;/sequence>
 100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                 &lt;/restriction>
 107  *               &lt;/complexContent>
 108  *             &lt;/complexType>
 109  *           &lt;/element>
 110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 111  *             &lt;complexType>
 112  *               &lt;complexContent>
 113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 114  *                   &lt;sequence>
 115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 117  *                   &lt;/sequence>
 118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 137  *                 &lt;/restriction>
 138  *               &lt;/complexContent>
 139  *             &lt;/complexType>
 140  *           &lt;/element>
 141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 142  *             &lt;complexType>
 143  *               &lt;complexContent>
 144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 145  *                   &lt;sequence>
 146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 148  *                       &lt;complexType>
 149  *                         &lt;complexContent>
 150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                           &lt;/restriction>
 154  *                         &lt;/complexContent>
 155  *                       &lt;/complexType>
 156  *                     &lt;/element>
 157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 158  *                       &lt;complexType>
 159  *                         &lt;complexContent>
 160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 164  *                           &lt;/extension>
 165  *                         &lt;/complexContent>
 166  *                       &lt;/complexType>
 167  *                     &lt;/element>
 168  *                     &lt;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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
 214  *                   &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
 215  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 216  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 217  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 218  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 219  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 220  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 221  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 222  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 223  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 224  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 225  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 226  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 227  *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 228  *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 229  *                 &lt;/restriction>
 230  *               &lt;/complexContent>
 231  *             &lt;/complexType>
 232  *           &lt;/element>
 233  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 234  *             &lt;complexType>
 235  *               &lt;complexContent>
 236  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 237  *                   &lt;sequence>
 238  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 239  *                   &lt;/sequence>
 240  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 241  *                 &lt;/restriction>
 242  *               &lt;/complexContent>
 243  *             &lt;/complexType>
 244  *           &lt;/element>
 245  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 246  *             &lt;complexType>
 247  *               &lt;complexContent>
 248  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 249  *                   &lt;sequence minOccurs="0">
 250  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 251  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 252  *                   &lt;/sequence>
 253  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 254  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 255  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 256  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 257  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 258  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 259  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 260  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 261  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 262  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 263  *                   &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 264  *                   &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
 265  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 266  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 267  *                 &lt;/restriction>
 268  *               &lt;/complexContent>
 269  *             &lt;/complexType>
 270  *           &lt;/element>
 271  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 272  *             &lt;complexType>
 273  *               &lt;complexContent>
 274  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 275  *                   &lt;sequence>
 276  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 277  *                       &lt;complexType>
 278  *                         &lt;complexContent>
 279  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 280  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 281  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 282  *                           &lt;/restriction>
 283  *                         &lt;/complexContent>
 284  *                       &lt;/complexType>
 285  *                     &lt;/element>
 286  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 287  *                       &lt;complexType>
 288  *                         &lt;complexContent>
 289  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 290  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 291  *                           &lt;/restriction>
 292  *                         &lt;/complexContent>
 293  *                       &lt;/complexType>
 294  *                     &lt;/element>
 295  *                     &lt;element name="seqPointMin">
 296  *                       &lt;complexType>
 297  *                         &lt;complexContent>
 298  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 299  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 300  *                           &lt;/restriction>
 301  *                         &lt;/complexContent>
 302  *                       &lt;/complexType>
 303  *                     &lt;/element>
 304  *                     &lt;element name="seqPointMax">
 305  *                       &lt;complexType>
 306  *                         &lt;complexContent>
 307  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 308  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 309  *                           &lt;/restriction>
 310  *                         &lt;/complexContent>
 311  *                       &lt;/complexType>
 312  *                     &lt;/element>
 313  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 314  *                   &lt;/sequence>
 315  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 316  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 317  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 318  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 319  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 320  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 321  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 322  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 323  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 324  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 325  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 326  *                 &lt;/restriction>
 327  *               &lt;/complexContent>
 328  *             &lt;/complexType>
 329  *           &lt;/element>
 330  *           &lt;element name="FeatureSettings" minOccurs="0">
 331  *             &lt;complexType>
 332  *               &lt;complexContent>
 333  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 334  *                   &lt;sequence>
 335  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 336  *                       &lt;complexType>
 337  *                         &lt;complexContent>
 338  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 339  *                             &lt;sequence>
 340  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 341  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 342  *                             &lt;/sequence>
 343  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 344  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 345  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 346  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 347  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 348  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 349  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 350  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 351  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 352  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 353  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 354  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 355  *                           &lt;/restriction>
 356  *                         &lt;/complexContent>
 357  *                       &lt;/complexType>
 358  *                     &lt;/element>
 359  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 360  *                       &lt;complexType>
 361  *                         &lt;complexContent>
 362  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 363  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 364  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 365  *                           &lt;/restriction>
 366  *                         &lt;/complexContent>
 367  *                       &lt;/complexType>
 368  *                     &lt;/element>
 369  *                   &lt;/sequence>
 370  *                 &lt;/restriction>
 371  *               &lt;/complexContent>
 372  *             &lt;/complexType>
 373  *           &lt;/element>
 374  *         &lt;/sequence>
 375  *       &lt;/sequence>
 376  *     &lt;/restriction>
 377  *   &lt;/complexContent>
 378  * &lt;/complexType>
 379  * </pre>
 380  *
 381  *
 382  */
 383 @XmlAccessorType(XmlAccessType.FIELD)
 384 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 385     "creationDate",
 386     "version",
 387     "vamsasModel",
 388     "jSeq",
 389     "jGroup",
 390     "viewport",
 391     "userColours",
 392     "tree",
 393     "pcaViewer",
 394     "featureSettings"
 395 })
 396 public class JalviewModel {
 397
 398     @XmlElement(required = true)
 399     @XmlSchemaType(name = "dateTime")
 400     protected XMLGregorianCalendar creationDate;
 401     @XmlElement(required = true)
 402     protected String version;
 403     @XmlElement(required = true)
 404     protected VAMSAS vamsasModel;
 405     @XmlElement(name = "JSeq")
 406     protected List<JalviewModel.JSeq> jSeq;
 407     @XmlElement(name = "JGroup")
 408     protected List<JalviewModel.JGroup> jGroup;
 409     @XmlElement(name = "Viewport")
 410     protected List<JalviewModel.Viewport> viewport;
 411     @XmlElement(name = "UserColours")
 412     protected List<JalviewModel.UserColours> userColours;
 413     protected List<JalviewModel.Tree> tree;
 414     @XmlElement(name = "PcaViewer")
 415     protected List<JalviewModel.PcaViewer> pcaViewer;
 416     @XmlElement(name = "FeatureSettings")
 417     protected JalviewModel.FeatureSettings featureSettings;
 418
 419     /**
 420      * Gets the value of the creationDate property.
 421      *
 422      * @return
 423      *     possible object is
 424      *     {@link XMLGregorianCalendar }
 425      *
 426      */
 427     public XMLGregorianCalendar getCreationDate() {
 428         return creationDate;
 429     }
 430
 431     /**
 432      * Sets the value of the creationDate property.
 433      *
 434      * @param value
 435      *     allowed object is
 436      *     {@link XMLGregorianCalendar }
 437      *
 438      */
 439     public void setCreationDate(XMLGregorianCalendar value) {
 440         this.creationDate = value;
 441     }
 442
 443     /**
 444      * Gets the value of the version property.
 445      *
 446      * @return
 447      *     possible object is
 448      *     {@link String }
 449      *
 450      */
 451     public String getVersion() {
 452         return version;
 453     }
 454
 455     /**
 456      * Sets the value of the version property.
 457      *
 458      * @param value
 459      *     allowed object is
 460      *     {@link String }
 461      *
 462      */
 463     public void setVersion(String value) {
 464         this.version = value;
 465     }
 466
 467     /**
 468      * Gets the value of the vamsasModel property.
 469      *
 470      * @return
 471      *     possible object is
 472      *     {@link VAMSAS }
 473      *
 474      */
 475     public VAMSAS getVamsasModel() {
 476         return vamsasModel;
 477     }
 478
 479     /**
 480      * Sets the value of the vamsasModel property.
 481      *
 482      * @param value
 483      *     allowed object is
 484      *     {@link VAMSAS }
 485      *
 486      */
 487     public void setVamsasModel(VAMSAS value) {
 488         this.vamsasModel = value;
 489     }
 490
 491     /**
 492      * Gets the value of the jSeq property.
 493      *
 494      * <p>
 495      * This accessor method returns a reference to the live list,
 496      * not a snapshot. Therefore any modification you make to the
 497      * returned list will be present inside the JAXB object.
 498      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 499      *
 500      * <p>
 501      * For example, to add a new item, do as follows:
 502      * <pre>
 503      *    getJSeq().add(newItem);
 504      * </pre>
 505      *
 506      *
 507      * <p>
 508      * Objects of the following type(s) are allowed in the list
 509      * {@link JalviewModel.JSeq }
 510      *
 511      *
 512      */
 513     public List<JalviewModel.JSeq> getJSeq() {
 514         if (jSeq == null) {
 515             jSeq = new ArrayList<JalviewModel.JSeq>();
 516         }
 517         return this.jSeq;
 518     }
 519
 520     /**
 521      * Gets the value of the jGroup property.
 522      *
 523      * <p>
 524      * This accessor method returns a reference to the live list,
 525      * not a snapshot. Therefore any modification you make to the
 526      * returned list will be present inside the JAXB object.
 527      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 528      *
 529      * <p>
 530      * For example, to add a new item, do as follows:
 531      * <pre>
 532      *    getJGroup().add(newItem);
 533      * </pre>
 534      *
 535      *
 536      * <p>
 537      * Objects of the following type(s) are allowed in the list
 538      * {@link JalviewModel.JGroup }
 539      *
 540      *
 541      */
 542     public List<JalviewModel.JGroup> getJGroup() {
 543         if (jGroup == null) {
 544             jGroup = new ArrayList<JalviewModel.JGroup>();
 545         }
 546         return this.jGroup;
 547     }
 548
 549     /**
 550      * Gets the value of the viewport property.
 551      *
 552      * <p>
 553      * This accessor method returns a reference to the live list,
 554      * not a snapshot. Therefore any modification you make to the
 555      * returned list will be present inside the JAXB object.
 556      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 557      *
 558      * <p>
 559      * For example, to add a new item, do as follows:
 560      * <pre>
 561      *    getViewport().add(newItem);
 562      * </pre>
 563      *
 564      *
 565      * <p>
 566      * Objects of the following type(s) are allowed in the list
 567      * {@link JalviewModel.Viewport }
 568      *
 569      *
 570      */
 571     public List<JalviewModel.Viewport> getViewport() {
 572         if (viewport == null) {
 573             viewport = new ArrayList<JalviewModel.Viewport>();
 574         }
 575         return this.viewport;
 576     }
 577
 578     /**
 579      * Gets the value of the userColours property.
 580      *
 581      * <p>
 582      * This accessor method returns a reference to the live list,
 583      * not a snapshot. Therefore any modification you make to the
 584      * returned list will be present inside the JAXB object.
 585      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 586      *
 587      * <p>
 588      * For example, to add a new item, do as follows:
 589      * <pre>
 590      *    getUserColours().add(newItem);
 591      * </pre>
 592      *
 593      *
 594      * <p>
 595      * Objects of the following type(s) are allowed in the list
 596      * {@link JalviewModel.UserColours }
 597      *
 598      *
 599      */
 600     public List<JalviewModel.UserColours> getUserColours() {
 601         if (userColours == null) {
 602             userColours = new ArrayList<JalviewModel.UserColours>();
 603         }
 604         return this.userColours;
 605     }
 606
 607     /**
 608      * Gets the value of the tree property.
 609      *
 610      * <p>
 611      * This accessor method returns a reference to the live list,
 612      * not a snapshot. Therefore any modification you make to the
 613      * returned list will be present inside the JAXB object.
 614      * This is why there is not a <CODE>set</CODE> method for the tree property.
 615      *
 616      * <p>
 617      * For example, to add a new item, do as follows:
 618      * <pre>
 619      *    getTree().add(newItem);
 620      * </pre>
 621      *
 622      *
 623      * <p>
 624      * Objects of the following type(s) are allowed in the list
 625      * {@link JalviewModel.Tree }
 626      *
 627      *
 628      */
 629     public List<JalviewModel.Tree> getTree() {
 630         if (tree == null) {
 631             tree = new ArrayList<JalviewModel.Tree>();
 632         }
 633         return this.tree;
 634     }
 635
 636     /**
 637      * Gets the value of the pcaViewer property.
 638      *
 639      * <p>
 640      * This accessor method returns a reference to the live list,
 641      * not a snapshot. Therefore any modification you make to the
 642      * returned list will be present inside the JAXB object.
 643      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 644      *
 645      * <p>
 646      * For example, to add a new item, do as follows:
 647      * <pre>
 648      *    getPcaViewer().add(newItem);
 649      * </pre>
 650      *
 651      *
 652      * <p>
 653      * Objects of the following type(s) are allowed in the list
 654      * {@link JalviewModel.PcaViewer }
 655      *
 656      *
 657      */
 658     public List<JalviewModel.PcaViewer> getPcaViewer() {
 659         if (pcaViewer == null) {
 660             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 661         }
 662         return this.pcaViewer;
 663     }
 664
 665     /**
 666      * Gets the value of the featureSettings property.
 667      *
 668      * @return
 669      *     possible object is
 670      *     {@link JalviewModel.FeatureSettings }
 671      *
 672      */
 673     public JalviewModel.FeatureSettings getFeatureSettings() {
 674         return featureSettings;
 675     }
 676
 677     /**
 678      * Sets the value of the featureSettings property.
 679      *
 680      * @param value
 681      *     allowed object is
 682      *     {@link JalviewModel.FeatureSettings }
 683      *
 684      */
 685     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 686         this.featureSettings = value;
 687     }
 688
 689
 690     /**
 691      * <p>Java class for anonymous complex type.
 692      *
 693      * <p>The following schema fragment specifies the expected content contained within this class.
 694      *
 695      * <pre>
 696      * &lt;complexType>
 697      *   &lt;complexContent>
 698      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 699      *       &lt;sequence>
 700      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 701      *           &lt;complexType>
 702      *             &lt;complexContent>
 703      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 704      *                 &lt;sequence>
 705      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 706      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 707      *                 &lt;/sequence>
 708      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 709      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 710      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 711      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 712      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 713      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 714      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 715      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 716      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 717      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 718      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 719      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 720      *               &lt;/restriction>
 721      *             &lt;/complexContent>
 722      *           &lt;/complexType>
 723      *         &lt;/element>
 724      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 725      *           &lt;complexType>
 726      *             &lt;complexContent>
 727      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 728      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 729      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 730      *               &lt;/restriction>
 731      *             &lt;/complexContent>
 732      *           &lt;/complexType>
 733      *         &lt;/element>
 734      *       &lt;/sequence>
 735      *     &lt;/restriction>
 736      *   &lt;/complexContent>
 737      * &lt;/complexType>
 738      * </pre>
 739      *
 740      *
 741      */
 742     @XmlAccessorType(XmlAccessType.FIELD)
 743     @XmlType(name = "", propOrder = {
 744         "setting",
 745         "group"
 746     })
 747     public static class FeatureSettings {
 748
 749         @XmlElement(namespace = "www.jalview.org")
 750         protected List<JalviewModel.FeatureSettings.Setting> setting;
 751         @XmlElement(namespace = "www.jalview.org")
 752         protected List<JalviewModel.FeatureSettings.Group> group;
 753
 754         /**
 755          * Gets the value of the setting property.
 756          *
 757          * <p>
 758          * This accessor method returns a reference to the live list,
 759          * not a snapshot. Therefore any modification you make to the
 760          * returned list will be present inside the JAXB object.
 761          * This is why there is not a <CODE>set</CODE> method for the setting property.
 762          *
 763          * <p>
 764          * For example, to add a new item, do as follows:
 765          * <pre>
 766          *    getSetting().add(newItem);
 767          * </pre>
 768          *
 769          *
 770          * <p>
 771          * Objects of the following type(s) are allowed in the list
 772          * {@link JalviewModel.FeatureSettings.Setting }
 773          *
 774          *
 775          */
 776         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 777             if (setting == null) {
 778                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 779             }
 780             return this.setting;
 781         }
 782
 783         /**
 784          * Gets the value of the group property.
 785          *
 786          * <p>
 787          * This accessor method returns a reference to the live list,
 788          * not a snapshot. Therefore any modification you make to the
 789          * returned list will be present inside the JAXB object.
 790          * This is why there is not a <CODE>set</CODE> method for the group property.
 791          *
 792          * <p>
 793          * For example, to add a new item, do as follows:
 794          * <pre>
 795          *    getGroup().add(newItem);
 796          * </pre>
 797          *
 798          *
 799          * <p>
 800          * Objects of the following type(s) are allowed in the list
 801          * {@link JalviewModel.FeatureSettings.Group }
 802          *
 803          *
 804          */
 805         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 806             if (group == null) {
 807                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 808             }
 809             return this.group;
 810         }
 811
 812
 813         /**
 814          * <p>Java class for anonymous complex type.
 815          *
 816          * <p>The following schema fragment specifies the expected content contained within this class.
 817          *
 818          * <pre>
 819          * &lt;complexType>
 820          *   &lt;complexContent>
 821          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 822          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 823          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 824          *     &lt;/restriction>
 825          *   &lt;/complexContent>
 826          * &lt;/complexType>
 827          * </pre>
 828          *
 829          *
 830          */
 831         @XmlAccessorType(XmlAccessType.FIELD)
 832         @XmlType(name = "")
 833         public static class Group {
 834
 835             @XmlAttribute(name = "name", required = true)
 836             protected String name;
 837             @XmlAttribute(name = "display", required = true)
 838             protected boolean display;
 839
 840             /**
 841              * Gets the value of the name property.
 842              *
 843              * @return
 844              *     possible object is
 845              *     {@link String }
 846              *
 847              */
 848             public String getName() {
 849                 return name;
 850             }
 851
 852             /**
 853              * Sets the value of the name property.
 854              *
 855              * @param value
 856              *     allowed object is
 857              *     {@link String }
 858              *
 859              */
 860             public void setName(String value) {
 861                 this.name = value;
 862             }
 863
 864             /**
 865              * Gets the value of the display property.
 866              *
 867              */
 868             public boolean isDisplay() {
 869                 return display;
 870             }
 871
 872             /**
 873              * Sets the value of the display property.
 874              *
 875              */
 876             public void setDisplay(boolean value) {
 877                 this.display = value;
 878             }
 879
 880         }
 881
 882
 883         /**
 884          * <p>Java class for anonymous complex type.
 885          *
 886          * <p>The following schema fragment specifies the expected content contained within this class.
 887          *
 888          * <pre>
 889          * &lt;complexType>
 890          *   &lt;complexContent>
 891          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 892          *       &lt;sequence>
 893          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 894          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 895          *       &lt;/sequence>
 896          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 897          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 898          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 899          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 900          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 901          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 902          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 903          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 904          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 905          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 906          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 907          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 908          *     &lt;/restriction>
 909          *   &lt;/complexContent>
 910          * &lt;/complexType>
 911          * </pre>
 912          *
 913          *
 914          */
 915         @XmlAccessorType(XmlAccessType.FIELD)
 916         @XmlType(name = "", propOrder = {
 917             "attributeName",
 918             "matcherSet"
 919         })
 920         public static class Setting {
 921
 922             @XmlElement(namespace = "www.jalview.org")
 923             protected List<String> attributeName;
 924             @XmlElement(namespace = "www.jalview.org")
 925             protected FeatureMatcherSet matcherSet;
 926             @XmlAttribute(name = "type", required = true)
 927             protected String type;
 928             @XmlAttribute(name = "colour", required = true)
 929             protected int colour;
 930             @XmlAttribute(name = "display", required = true)
 931             protected boolean display;
 932             @XmlAttribute(name = "order")
 933             protected Float order;
 934             @XmlAttribute(name = "mincolour")
 935             protected Integer mincolour;
 936             @XmlAttribute(name = "noValueColour")
 937             protected NoValueColour noValueColour;
 938             @XmlAttribute(name = "threshold")
 939             protected Float threshold;
 940             @XmlAttribute(name = "threshstate")
 941             protected Integer threshstate;
 942             @XmlAttribute(name = "max")
 943             protected Float max;
 944             @XmlAttribute(name = "min")
 945             protected Float min;
 946             @XmlAttribute(name = "colourByLabel")
 947             protected Boolean colourByLabel;
 948             @XmlAttribute(name = "autoScale")
 949             protected Boolean autoScale;
 950
 951             /**
 952              * Gets the value of the attributeName property.
 953              *
 954              * <p>
 955              * This accessor method returns a reference to the live list,
 956              * not a snapshot. Therefore any modification you make to the
 957              * returned list will be present inside the JAXB object.
 958              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 959              *
 960              * <p>
 961              * For example, to add a new item, do as follows:
 962              * <pre>
 963              *    getAttributeName().add(newItem);
 964              * </pre>
 965              *
 966              *
 967              * <p>
 968              * Objects of the following type(s) are allowed in the list
 969              * {@link String }
 970              *
 971              *
 972              */
 973             public List<String> getAttributeName() {
 974                 if (attributeName == null) {
 975                     attributeName = new ArrayList<String>();
 976                 }
 977                 return this.attributeName;
 978             }
 979
 980             /**
 981              * Gets the value of the matcherSet property.
 982              *
 983              * @return
 984              *     possible object is
 985              *     {@link FeatureMatcherSet }
 986              *
 987              */
 988             public FeatureMatcherSet getMatcherSet() {
 989                 return matcherSet;
 990             }
 991
 992             /**
 993              * Sets the value of the matcherSet property.
 994              *
 995              * @param value
 996              *     allowed object is
 997              *     {@link FeatureMatcherSet }
 998              *
 999              */
1000             public void setMatcherSet(FeatureMatcherSet value) {
1001                 this.matcherSet = value;
1002             }
1003
1004             /**
1005              * Gets the value of the type property.
1006              *
1007              * @return
1008              *     possible object is
1009              *     {@link String }
1010              *
1011              */
1012             public String getType() {
1013                 return type;
1014             }
1015
1016             /**
1017              * Sets the value of the type property.
1018              *
1019              * @param value
1020              *     allowed object is
1021              *     {@link String }
1022              *
1023              */
1024             public void setType(String value) {
1025                 this.type = value;
1026             }
1027
1028             /**
1029              * Gets the value of the colour property.
1030              *
1031              */
1032             public int getColour() {
1033                 return colour;
1034             }
1035
1036             /**
1037              * Sets the value of the colour property.
1038              *
1039              */
1040             public void setColour(int value) {
1041                 this.colour = value;
1042             }
1043
1044             /**
1045              * Gets the value of the display property.
1046              *
1047              */
1048             public boolean isDisplay() {
1049                 return display;
1050             }
1051
1052             /**
1053              * Sets the value of the display property.
1054              *
1055              */
1056             public void setDisplay(boolean value) {
1057                 this.display = value;
1058             }
1059
1060             /**
1061              * Gets the value of the order property.
1062              *
1063              * @return
1064              *     possible object is
1065              *     {@link Float }
1066              *
1067              */
1068             public Float getOrder() {
1069                 return order;
1070             }
1071
1072             /**
1073              * Sets the value of the order property.
1074              *
1075              * @param value
1076              *     allowed object is
1077              *     {@link Float }
1078              *
1079              */
1080             public void setOrder(Float value) {
1081                 this.order = value;
1082             }
1083
1084             /**
1085              * Gets the value of the mincolour property.
1086              *
1087              * @return
1088              *     possible object is
1089              *     {@link Integer }
1090              *
1091              */
1092             public Integer getMincolour() {
1093                 return mincolour;
1094             }
1095
1096             /**
1097              * Sets the value of the mincolour property.
1098              *
1099              * @param value
1100              *     allowed object is
1101              *     {@link Integer }
1102              *
1103              */
1104             public void setMincolour(Integer value) {
1105                 this.mincolour = value;
1106             }
1107
1108             /**
1109              * Gets the value of the noValueColour property.
1110              *
1111              * @return
1112              *     possible object is
1113              *     {@link NoValueColour }
1114              *
1115              */
1116             public NoValueColour getNoValueColour() {
1117                 if (noValueColour == null) {
1118                     return NoValueColour.MIN;
1119                 } else {
1120                     return noValueColour;
1121                 }
1122             }
1123
1124             /**
1125              * Sets the value of the noValueColour property.
1126              *
1127              * @param value
1128              *     allowed object is
1129              *     {@link NoValueColour }
1130              *
1131              */
1132             public void setNoValueColour(NoValueColour value) {
1133                 this.noValueColour = value;
1134             }
1135
1136             /**
1137              * Gets the value of the threshold property.
1138              *
1139              * @return
1140              *     possible object is
1141              *     {@link Float }
1142              *
1143              */
1144             public Float getThreshold() {
1145                 return threshold;
1146             }
1147
1148             /**
1149              * Sets the value of the threshold property.
1150              *
1151              * @param value
1152              *     allowed object is
1153              *     {@link Float }
1154              *
1155              */
1156             public void setThreshold(Float value) {
1157                 this.threshold = value;
1158             }
1159
1160             /**
1161              * Gets the value of the threshstate property.
1162              *
1163              * @return
1164              *     possible object is
1165              *     {@link Integer }
1166              *
1167              */
1168             public Integer getThreshstate() {
1169                 return threshstate;
1170             }
1171
1172             /**
1173              * Sets the value of the threshstate property.
1174              *
1175              * @param value
1176              *     allowed object is
1177              *     {@link Integer }
1178              *
1179              */
1180             public void setThreshstate(Integer value) {
1181                 this.threshstate = value;
1182             }
1183
1184             /**
1185              * Gets the value of the max property.
1186              *
1187              * @return
1188              *     possible object is
1189              *     {@link Float }
1190              *
1191              */
1192             public Float getMax() {
1193                 return max;
1194             }
1195
1196             /**
1197              * Sets the value of the max property.
1198              *
1199              * @param value
1200              *     allowed object is
1201              *     {@link Float }
1202              *
1203              */
1204             public void setMax(Float value) {
1205                 this.max = value;
1206             }
1207
1208             /**
1209              * Gets the value of the min property.
1210              *
1211              * @return
1212              *     possible object is
1213              *     {@link Float }
1214              *
1215              */
1216             public Float getMin() {
1217                 return min;
1218             }
1219
1220             /**
1221              * Sets the value of the min property.
1222              *
1223              * @param value
1224              *     allowed object is
1225              *     {@link Float }
1226              *
1227              */
1228             public void setMin(Float value) {
1229                 this.min = value;
1230             }
1231
1232             /**
1233              * Gets the value of the colourByLabel property.
1234              *
1235              * @return
1236              *     possible object is
1237              *     {@link Boolean }
1238              *
1239              */
1240             public Boolean isColourByLabel() {
1241                 return colourByLabel;
1242             }
1243
1244             /**
1245              * Sets the value of the colourByLabel property.
1246              *
1247              * @param value
1248              *     allowed object is
1249              *     {@link Boolean }
1250              *
1251              */
1252             public void setColourByLabel(Boolean value) {
1253                 this.colourByLabel = value;
1254             }
1255
1256             /**
1257              * Gets the value of the autoScale property.
1258              *
1259              * @return
1260              *     possible object is
1261              *     {@link Boolean }
1262              *
1263              */
1264             public Boolean isAutoScale() {
1265                 return autoScale;
1266             }
1267
1268             /**
1269              * Sets the value of the autoScale property.
1270              *
1271              * @param value
1272              *     allowed object is
1273              *     {@link Boolean }
1274              *
1275              */
1276             public void setAutoScale(Boolean value) {
1277                 this.autoScale = value;
1278             }
1279
1280         }
1281
1282     }
1283
1284
1285     /**
1286      * <p>Java class for anonymous complex type.
1287      *
1288      * <p>The following schema fragment specifies the expected content contained within this class.
1289      *
1290      * <pre>
1291      * &lt;complexType>
1292      *   &lt;complexContent>
1293      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1294      *       &lt;sequence>
1295      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1296      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1297      *       &lt;/sequence>
1298      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1299      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1300      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1301      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1302      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1303      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1304      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1305      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1306      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1307      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1308      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1309      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1310      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1311      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1312      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1313      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1314      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1315      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1316      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1317      *     &lt;/restriction>
1318      *   &lt;/complexContent>
1319      * &lt;/complexType>
1320      * </pre>
1321      *
1322      *
1323      */
1324     @XmlAccessorType(XmlAccessType.FIELD)
1325     @XmlType(name = "", propOrder = {
1326         "seq",
1327         "annotationColours"
1328     })
1329     public static class JGroup {
1330
1331         @XmlElement(namespace = "www.jalview.org", required = true)
1332         protected List<String> seq;
1333         @XmlElement(namespace = "www.jalview.org")
1334         protected AnnotationColourScheme annotationColours;
1335         @XmlAttribute(name = "start")
1336         protected Integer start;
1337         @XmlAttribute(name = "end")
1338         protected Integer end;
1339         @XmlAttribute(name = "name")
1340         protected String name;
1341         @XmlAttribute(name = "colour")
1342         protected String colour;
1343         @XmlAttribute(name = "consThreshold")
1344         protected Integer consThreshold;
1345         @XmlAttribute(name = "pidThreshold")
1346         protected Integer pidThreshold;
1347         @XmlAttribute(name = "outlineColour")
1348         protected Integer outlineColour;
1349         @XmlAttribute(name = "displayBoxes")
1350         protected Boolean displayBoxes;
1351         @XmlAttribute(name = "displayText")
1352         protected Boolean displayText;
1353         @XmlAttribute(name = "colourText")
1354         protected Boolean colourText;
1355         @XmlAttribute(name = "textCol1")
1356         protected Integer textCol1;
1357         @XmlAttribute(name = "textCol2")
1358         protected Integer textCol2;
1359         @XmlAttribute(name = "textColThreshold")
1360         protected Integer textColThreshold;
1361         @XmlAttribute(name = "showUnconserved")
1362         protected Boolean showUnconserved;
1363         @XmlAttribute(name = "ignoreGapsinConsensus")
1364         protected Boolean ignoreGapsinConsensus;
1365         @XmlAttribute(name = "showConsensusHistogram")
1366         protected Boolean showConsensusHistogram;
1367         @XmlAttribute(name = "showSequenceLogo")
1368         protected Boolean showSequenceLogo;
1369         @XmlAttribute(name = "normaliseSequenceLogo")
1370         protected Boolean normaliseSequenceLogo;
1371         @XmlAttribute(name = "id")
1372         protected String id;
1373
1374         /**
1375          * Gets the value of the seq property.
1376          *
1377          * <p>
1378          * This accessor method returns a reference to the live list,
1379          * not a snapshot. Therefore any modification you make to the
1380          * returned list will be present inside the JAXB object.
1381          * This is why there is not a <CODE>set</CODE> method for the seq property.
1382          *
1383          * <p>
1384          * For example, to add a new item, do as follows:
1385          * <pre>
1386          *    getSeq().add(newItem);
1387          * </pre>
1388          *
1389          *
1390          * <p>
1391          * Objects of the following type(s) are allowed in the list
1392          * {@link String }
1393          *
1394          *
1395          */
1396         public List<String> getSeq() {
1397             if (seq == null) {
1398                 seq = new ArrayList<String>();
1399             }
1400             return this.seq;
1401         }
1402
1403         /**
1404          * Gets the value of the annotationColours property.
1405          *
1406          * @return
1407          *     possible object is
1408          *     {@link AnnotationColourScheme }
1409          *
1410          */
1411         public AnnotationColourScheme getAnnotationColours() {
1412             return annotationColours;
1413         }
1414
1415         /**
1416          * Sets the value of the annotationColours property.
1417          *
1418          * @param value
1419          *     allowed object is
1420          *     {@link AnnotationColourScheme }
1421          *
1422          */
1423         public void setAnnotationColours(AnnotationColourScheme value) {
1424             this.annotationColours = value;
1425         }
1426
1427         /**
1428          * Gets the value of the start property.
1429          *
1430          * @return
1431          *     possible object is
1432          *     {@link Integer }
1433          *
1434          */
1435         public Integer getStart() {
1436             return start;
1437         }
1438
1439         /**
1440          * Sets the value of the start property.
1441          *
1442          * @param value
1443          *     allowed object is
1444          *     {@link Integer }
1445          *
1446          */
1447         public void setStart(Integer value) {
1448             this.start = value;
1449         }
1450
1451         /**
1452          * Gets the value of the end property.
1453          *
1454          * @return
1455          *     possible object is
1456          *     {@link Integer }
1457          *
1458          */
1459         public Integer getEnd() {
1460             return end;
1461         }
1462
1463         /**
1464          * Sets the value of the end property.
1465          *
1466          * @param value
1467          *     allowed object is
1468          *     {@link Integer }
1469          *
1470          */
1471         public void setEnd(Integer value) {
1472             this.end = value;
1473         }
1474
1475         /**
1476          * Gets the value of the name property.
1477          *
1478          * @return
1479          *     possible object is
1480          *     {@link String }
1481          *
1482          */
1483         public String getName() {
1484             return name;
1485         }
1486
1487         /**
1488          * Sets the value of the name property.
1489          *
1490          * @param value
1491          *     allowed object is
1492          *     {@link String }
1493          *
1494          */
1495         public void setName(String value) {
1496             this.name = value;
1497         }
1498
1499         /**
1500          * Gets the value of the colour property.
1501          *
1502          * @return
1503          *     possible object is
1504          *     {@link String }
1505          *
1506          */
1507         public String getColour() {
1508             return colour;
1509         }
1510
1511         /**
1512          * Sets the value of the colour property.
1513          *
1514          * @param value
1515          *     allowed object is
1516          *     {@link String }
1517          *
1518          */
1519         public void setColour(String value) {
1520             this.colour = value;
1521         }
1522
1523         /**
1524          * Gets the value of the consThreshold property.
1525          *
1526          * @return
1527          *     possible object is
1528          *     {@link Integer }
1529          *
1530          */
1531         public Integer getConsThreshold() {
1532             return consThreshold;
1533         }
1534
1535         /**
1536          * Sets the value of the consThreshold property.
1537          *
1538          * @param value
1539          *     allowed object is
1540          *     {@link Integer }
1541          *
1542          */
1543         public void setConsThreshold(Integer value) {
1544             this.consThreshold = value;
1545         }
1546
1547         /**
1548          * Gets the value of the pidThreshold property.
1549          *
1550          * @return
1551          *     possible object is
1552          *     {@link Integer }
1553          *
1554          */
1555         public Integer getPidThreshold() {
1556             return pidThreshold;
1557         }
1558
1559         /**
1560          * Sets the value of the pidThreshold property.
1561          *
1562          * @param value
1563          *     allowed object is
1564          *     {@link Integer }
1565          *
1566          */
1567         public void setPidThreshold(Integer value) {
1568             this.pidThreshold = value;
1569         }
1570
1571         /**
1572          * Gets the value of the outlineColour property.
1573          *
1574          * @return
1575          *     possible object is
1576          *     {@link Integer }
1577          *
1578          */
1579         public Integer getOutlineColour() {
1580             return outlineColour;
1581         }
1582
1583         /**
1584          * Sets the value of the outlineColour property.
1585          *
1586          * @param value
1587          *     allowed object is
1588          *     {@link Integer }
1589          *
1590          */
1591         public void setOutlineColour(Integer value) {
1592             this.outlineColour = value;
1593         }
1594
1595         /**
1596          * Gets the value of the displayBoxes property.
1597          *
1598          * @return
1599          *     possible object is
1600          *     {@link Boolean }
1601          *
1602          */
1603         public Boolean isDisplayBoxes() {
1604             return displayBoxes;
1605         }
1606
1607         /**
1608          * Sets the value of the displayBoxes property.
1609          *
1610          * @param value
1611          *     allowed object is
1612          *     {@link Boolean }
1613          *
1614          */
1615         public void setDisplayBoxes(Boolean value) {
1616             this.displayBoxes = value;
1617         }
1618
1619         /**
1620          * Gets the value of the displayText property.
1621          *
1622          * @return
1623          *     possible object is
1624          *     {@link Boolean }
1625          *
1626          */
1627         public Boolean isDisplayText() {
1628             return displayText;
1629         }
1630
1631         /**
1632          * Sets the value of the displayText property.
1633          *
1634          * @param value
1635          *     allowed object is
1636          *     {@link Boolean }
1637          *
1638          */
1639         public void setDisplayText(Boolean value) {
1640             this.displayText = value;
1641         }
1642
1643         /**
1644          * Gets the value of the colourText property.
1645          *
1646          * @return
1647          *     possible object is
1648          *     {@link Boolean }
1649          *
1650          */
1651         public Boolean isColourText() {
1652             return colourText;
1653         }
1654
1655         /**
1656          * Sets the value of the colourText property.
1657          *
1658          * @param value
1659          *     allowed object is
1660          *     {@link Boolean }
1661          *
1662          */
1663         public void setColourText(Boolean value) {
1664             this.colourText = value;
1665         }
1666
1667         /**
1668          * Gets the value of the textCol1 property.
1669          *
1670          * @return
1671          *     possible object is
1672          *     {@link Integer }
1673          *
1674          */
1675         public Integer getTextCol1() {
1676             return textCol1;
1677         }
1678
1679         /**
1680          * Sets the value of the textCol1 property.
1681          *
1682          * @param value
1683          *     allowed object is
1684          *     {@link Integer }
1685          *
1686          */
1687         public void setTextCol1(Integer value) {
1688             this.textCol1 = value;
1689         }
1690
1691         /**
1692          * Gets the value of the textCol2 property.
1693          *
1694          * @return
1695          *     possible object is
1696          *     {@link Integer }
1697          *
1698          */
1699         public Integer getTextCol2() {
1700             return textCol2;
1701         }
1702
1703         /**
1704          * Sets the value of the textCol2 property.
1705          *
1706          * @param value
1707          *     allowed object is
1708          *     {@link Integer }
1709          *
1710          */
1711         public void setTextCol2(Integer value) {
1712             this.textCol2 = value;
1713         }
1714
1715         /**
1716          * Gets the value of the textColThreshold property.
1717          *
1718          * @return
1719          *     possible object is
1720          *     {@link Integer }
1721          *
1722          */
1723         public Integer getTextColThreshold() {
1724             return textColThreshold;
1725         }
1726
1727         /**
1728          * Sets the value of the textColThreshold property.
1729          *
1730          * @param value
1731          *     allowed object is
1732          *     {@link Integer }
1733          *
1734          */
1735         public void setTextColThreshold(Integer value) {
1736             this.textColThreshold = value;
1737         }
1738
1739         /**
1740          * Gets the value of the showUnconserved property.
1741          *
1742          * @return
1743          *     possible object is
1744          *     {@link Boolean }
1745          *
1746          */
1747         public Boolean isShowUnconserved() {
1748             return showUnconserved;
1749         }
1750
1751         /**
1752          * Sets the value of the showUnconserved property.
1753          *
1754          * @param value
1755          *     allowed object is
1756          *     {@link Boolean }
1757          *
1758          */
1759         public void setShowUnconserved(Boolean value) {
1760             this.showUnconserved = value;
1761         }
1762
1763         /**
1764          * Gets the value of the ignoreGapsinConsensus property.
1765          *
1766          * @return
1767          *     possible object is
1768          *     {@link Boolean }
1769          *
1770          */
1771         public boolean isIgnoreGapsinConsensus() {
1772             if (ignoreGapsinConsensus == null) {
1773                 return true;
1774             } else {
1775                 return ignoreGapsinConsensus;
1776             }
1777         }
1778
1779         /**
1780          * Sets the value of the ignoreGapsinConsensus property.
1781          *
1782          * @param value
1783          *     allowed object is
1784          *     {@link Boolean }
1785          *
1786          */
1787         public void setIgnoreGapsinConsensus(Boolean value) {
1788             this.ignoreGapsinConsensus = value;
1789         }
1790
1791         /**
1792          * Gets the value of the showConsensusHistogram property.
1793          *
1794          * @return
1795          *     possible object is
1796          *     {@link Boolean }
1797          *
1798          */
1799         public boolean isShowConsensusHistogram() {
1800             if (showConsensusHistogram == null) {
1801                 return true;
1802             } else {
1803                 return showConsensusHistogram;
1804             }
1805         }
1806
1807         /**
1808          * Sets the value of the showConsensusHistogram property.
1809          *
1810          * @param value
1811          *     allowed object is
1812          *     {@link Boolean }
1813          *
1814          */
1815         public void setShowConsensusHistogram(Boolean value) {
1816             this.showConsensusHistogram = value;
1817         }
1818
1819         /**
1820          * Gets the value of the showSequenceLogo property.
1821          *
1822          * @return
1823          *     possible object is
1824          *     {@link Boolean }
1825          *
1826          */
1827         public boolean isShowSequenceLogo() {
1828             if (showSequenceLogo == null) {
1829                 return false;
1830             } else {
1831                 return showSequenceLogo;
1832             }
1833         }
1834
1835         /**
1836          * Sets the value of the showSequenceLogo property.
1837          *
1838          * @param value
1839          *     allowed object is
1840          *     {@link Boolean }
1841          *
1842          */
1843         public void setShowSequenceLogo(Boolean value) {
1844             this.showSequenceLogo = value;
1845         }
1846
1847         /**
1848          * Gets the value of the normaliseSequenceLogo property.
1849          *
1850          * @return
1851          *     possible object is
1852          *     {@link Boolean }
1853          *
1854          */
1855         public boolean isNormaliseSequenceLogo() {
1856             if (normaliseSequenceLogo == null) {
1857                 return false;
1858             } else {
1859                 return normaliseSequenceLogo;
1860             }
1861         }
1862
1863         /**
1864          * Sets the value of the normaliseSequenceLogo property.
1865          *
1866          * @param value
1867          *     allowed object is
1868          *     {@link Boolean }
1869          *
1870          */
1871         public void setNormaliseSequenceLogo(Boolean value) {
1872             this.normaliseSequenceLogo = value;
1873         }
1874
1875         /**
1876          * Gets the value of the id property.
1877          *
1878          * @return
1879          *     possible object is
1880          *     {@link String }
1881          *
1882          */
1883         public String getId() {
1884             return id;
1885         }
1886
1887         /**
1888          * Sets the value of the id property.
1889          *
1890          * @param value
1891          *     allowed object is
1892          *     {@link String }
1893          *
1894          */
1895         public void setId(String value) {
1896             this.id = value;
1897         }
1898
1899     }
1900
1901
1902     /**
1903      * <p>Java class for anonymous complex type.
1904      *
1905      * <p>The following schema fragment specifies the expected content contained within this class.
1906      *
1907      * <pre>
1908      * &lt;complexType>
1909      *   &lt;complexContent>
1910      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1911      *       &lt;sequence>
1912      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1913      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1914      *           &lt;complexType>
1915      *             &lt;complexContent>
1916      *               &lt;extension base="{www.jalview.org}pdbentry">
1917      *                 &lt;sequence>
1918      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1919      *                     &lt;complexType>
1920      *                       &lt;simpleContent>
1921      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1922      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1923      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1924      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1925      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1926      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1927      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1928      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1929      *                         &lt;/extension>
1930      *                       &lt;/simpleContent>
1931      *                     &lt;/complexType>
1932      *                   &lt;/element>
1933      *                 &lt;/sequence>
1934      *               &lt;/extension>
1935      *             &lt;/complexContent>
1936      *           &lt;/complexType>
1937      *         &lt;/element>
1938      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1939      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1940      *           &lt;complexType>
1941      *             &lt;complexContent>
1942      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1943      *                 &lt;sequence>
1944      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1945      *                     &lt;complexType>
1946      *                       &lt;complexContent>
1947      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1948      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1949      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1950      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1951      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1952      *                         &lt;/restriction>
1953      *                       &lt;/complexContent>
1954      *                     &lt;/complexType>
1955      *                   &lt;/element>
1956      *                 &lt;/sequence>
1957      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1958      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1959      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1960      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1961      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1962      *               &lt;/restriction>
1963      *             &lt;/complexContent>
1964      *           &lt;/complexType>
1965      *         &lt;/element>
1966      *       &lt;/sequence>
1967      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1968      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1969      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1970      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1971      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1972      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1973      *     &lt;/restriction>
1974      *   &lt;/complexContent>
1975      * &lt;/complexType>
1976      * </pre>
1977      *
1978      *
1979      */
1980     @XmlAccessorType(XmlAccessType.FIELD)
1981     @XmlType(name = "", propOrder = {
1982         "features",
1983         "pdbids",
1984         "hiddenSequences",
1985         "rnaViewer"
1986     })
1987     public static class JSeq {
1988
1989         @XmlElement(namespace = "www.jalview.org")
1990         protected List<Feature> features;
1991         @XmlElement(namespace = "www.jalview.org")
1992         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1993         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1994         protected List<Integer> hiddenSequences;
1995         @XmlElement(namespace = "www.jalview.org")
1996         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1997         @XmlAttribute(name = "colour")
1998         protected Integer colour;
1999         @XmlAttribute(name = "start", required = true)
2000         protected int start;
2001         @XmlAttribute(name = "end", required = true)
2002         protected int end;
2003         @XmlAttribute(name = "id", required = true)
2004         protected String id;
2005         @XmlAttribute(name = "hidden")
2006         protected Boolean hidden;
2007         @XmlAttribute(name = "viewreference")
2008         protected Boolean viewreference;
2009
2010         /**
2011          * Gets the value of the features property.
2012          *
2013          * <p>
2014          * This accessor method returns a reference to the live list,
2015          * not a snapshot. Therefore any modification you make to the
2016          * returned list will be present inside the JAXB object.
2017          * This is why there is not a <CODE>set</CODE> method for the features property.
2018          *
2019          * <p>
2020          * For example, to add a new item, do as follows:
2021          * <pre>
2022          *    getFeatures().add(newItem);
2023          * </pre>
2024          *
2025          *
2026          * <p>
2027          * Objects of the following type(s) are allowed in the list
2028          * {@link Feature }
2029          *
2030          *
2031          */
2032         public List<Feature> getFeatures() {
2033             if (features == null) {
2034                 features = new ArrayList<Feature>();
2035             }
2036             return this.features;
2037         }
2038
2039         /**
2040          * Gets the value of the pdbids property.
2041          *
2042          * <p>
2043          * This accessor method returns a reference to the live list,
2044          * not a snapshot. Therefore any modification you make to the
2045          * returned list will be present inside the JAXB object.
2046          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2047          *
2048          * <p>
2049          * For example, to add a new item, do as follows:
2050          * <pre>
2051          *    getPdbids().add(newItem);
2052          * </pre>
2053          *
2054          *
2055          * <p>
2056          * Objects of the following type(s) are allowed in the list
2057          * {@link JalviewModel.JSeq.Pdbids }
2058          *
2059          *
2060          */
2061         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2062             if (pdbids == null) {
2063                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2064             }
2065             return this.pdbids;
2066         }
2067
2068         /**
2069          * Gets the value of the hiddenSequences property.
2070          *
2071          * <p>
2072          * This accessor method returns a reference to the live list,
2073          * not a snapshot. Therefore any modification you make to the
2074          * returned list will be present inside the JAXB object.
2075          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2076          *
2077          * <p>
2078          * For example, to add a new item, do as follows:
2079          * <pre>
2080          *    getHiddenSequences().add(newItem);
2081          * </pre>
2082          *
2083          *
2084          * <p>
2085          * Objects of the following type(s) are allowed in the list
2086          * {@link Integer }
2087          *
2088          *
2089          */
2090         public List<Integer> getHiddenSequences() {
2091             if (hiddenSequences == null) {
2092                 hiddenSequences = new ArrayList<Integer>();
2093             }
2094             return this.hiddenSequences;
2095         }
2096
2097         /**
2098          * Gets the value of the rnaViewer property.
2099          *
2100          * <p>
2101          * This accessor method returns a reference to the live list,
2102          * not a snapshot. Therefore any modification you make to the
2103          * returned list will be present inside the JAXB object.
2104          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2105          *
2106          * <p>
2107          * For example, to add a new item, do as follows:
2108          * <pre>
2109          *    getRnaViewer().add(newItem);
2110          * </pre>
2111          *
2112          *
2113          * <p>
2114          * Objects of the following type(s) are allowed in the list
2115          * {@link JalviewModel.JSeq.RnaViewer }
2116          *
2117          *
2118          */
2119         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2120             if (rnaViewer == null) {
2121                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2122             }
2123             return this.rnaViewer;
2124         }
2125
2126         /**
2127          * Gets the value of the colour property.
2128          *
2129          * @return
2130          *     possible object is
2131          *     {@link Integer }
2132          *
2133          */
2134         public Integer getColour() {
2135             return colour;
2136         }
2137
2138         /**
2139          * Sets the value of the colour property.
2140          *
2141          * @param value
2142          *     allowed object is
2143          *     {@link Integer }
2144          *
2145          */
2146         public void setColour(Integer value) {
2147             this.colour = value;
2148         }
2149
2150         /**
2151          * Gets the value of the start property.
2152          *
2153          */
2154         public int getStart() {
2155             return start;
2156         }
2157
2158         /**
2159          * Sets the value of the start property.
2160          *
2161          */
2162         public void setStart(int value) {
2163             this.start = value;
2164         }
2165
2166         /**
2167          * Gets the value of the end property.
2168          *
2169          */
2170         public int getEnd() {
2171             return end;
2172         }
2173
2174         /**
2175          * Sets the value of the end property.
2176          *
2177          */
2178         public void setEnd(int value) {
2179             this.end = value;
2180         }
2181
2182         /**
2183          * Gets the value of the id property.
2184          *
2185          * @return
2186          *     possible object is
2187          *     {@link String }
2188          *
2189          */
2190         public String getId() {
2191             return id;
2192         }
2193
2194         /**
2195          * Sets the value of the id property.
2196          *
2197          * @param value
2198          *     allowed object is
2199          *     {@link String }
2200          *
2201          */
2202         public void setId(String value) {
2203             this.id = value;
2204         }
2205
2206         /**
2207          * Gets the value of the hidden property.
2208          *
2209          * @return
2210          *     possible object is
2211          *     {@link Boolean }
2212          *
2213          */
2214         public Boolean isHidden() {
2215             return hidden;
2216         }
2217
2218         /**
2219          * Sets the value of the hidden property.
2220          *
2221          * @param value
2222          *     allowed object is
2223          *     {@link Boolean }
2224          *
2225          */
2226         public void setHidden(Boolean value) {
2227             this.hidden = value;
2228         }
2229
2230         /**
2231          * Gets the value of the viewreference property.
2232          *
2233          * @return
2234          *     possible object is
2235          *     {@link Boolean }
2236          *
2237          */
2238         public Boolean isViewreference() {
2239             return viewreference;
2240         }
2241
2242         /**
2243          * Sets the value of the viewreference property.
2244          *
2245          * @param value
2246          *     allowed object is
2247          *     {@link Boolean }
2248          *
2249          */
2250         public void setViewreference(Boolean value) {
2251             this.viewreference = value;
2252         }
2253
2254
2255         /**
2256          * <p>Java class for anonymous complex type.
2257          *
2258          * <p>The following schema fragment specifies the expected content contained within this class.
2259          *
2260          * <pre>
2261          * &lt;complexType>
2262          *   &lt;complexContent>
2263          *     &lt;extension base="{www.jalview.org}pdbentry">
2264          *       &lt;sequence>
2265          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2266          *           &lt;complexType>
2267          *             &lt;simpleContent>
2268          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2269          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2270          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2271          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2272          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2273          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2274          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2275          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2276          *               &lt;/extension>
2277          *             &lt;/simpleContent>
2278          *           &lt;/complexType>
2279          *         &lt;/element>
2280          *       &lt;/sequence>
2281          *     &lt;/extension>
2282          *   &lt;/complexContent>
2283          * &lt;/complexType>
2284          * </pre>
2285          *
2286          *
2287          */
2288         @XmlAccessorType(XmlAccessType.FIELD)
2289         @XmlType(name = "", propOrder = {
2290             "structureState"
2291         })
2292         public static class Pdbids
2293             extends Pdbentry
2294         {
2295
2296             @XmlElement(namespace = "www.jalview.org")
2297             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2298
2299             /**
2300              * Gets the value of the structureState property.
2301              *
2302              * <p>
2303              * This accessor method returns a reference to the live list,
2304              * not a snapshot. Therefore any modification you make to the
2305              * returned list will be present inside the JAXB object.
2306              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2307              *
2308              * <p>
2309              * For example, to add a new item, do as follows:
2310              * <pre>
2311              *    getStructureState().add(newItem);
2312              * </pre>
2313              *
2314              *
2315              * <p>
2316              * Objects of the following type(s) are allowed in the list
2317              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2318              *
2319              *
2320              */
2321             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2322                 if (structureState == null) {
2323                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2324                 }
2325                 return this.structureState;
2326             }
2327
2328
2329             /**
2330              * <p>Java class for anonymous complex type.
2331              *
2332              * <p>The following schema fragment specifies the expected content contained within this class.
2333              *
2334              * <pre>
2335              * &lt;complexType>
2336              *   &lt;simpleContent>
2337              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2338              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2339              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2340              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2341              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2342              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2343              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2344              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2345              *     &lt;/extension>
2346              *   &lt;/simpleContent>
2347              * &lt;/complexType>
2348              * </pre>
2349              *
2350              *
2351              */
2352             @XmlAccessorType(XmlAccessType.FIELD)
2353             @XmlType(name = "", propOrder = {
2354                 "value"
2355             })
2356             public static class StructureState {
2357
2358                 @XmlValue
2359                 protected String value;
2360                 @XmlAttribute(name = "visible")
2361                 protected Boolean visible;
2362                 @XmlAttribute(name = "viewId")
2363                 protected String viewId;
2364                 @XmlAttribute(name = "alignwithAlignPanel")
2365                 protected Boolean alignwithAlignPanel;
2366                 @XmlAttribute(name = "colourwithAlignPanel")
2367                 protected Boolean colourwithAlignPanel;
2368                 @XmlAttribute(name = "colourByJmol")
2369                 protected Boolean colourByJmol;
2370                 @XmlAttribute(name = "type")
2371                 protected String type;
2372                 @XmlAttribute(name = "width")
2373                 protected Integer width;
2374                 @XmlAttribute(name = "height")
2375                 protected Integer height;
2376                 @XmlAttribute(name = "xpos")
2377                 protected Integer xpos;
2378                 @XmlAttribute(name = "ypos")
2379                 protected Integer ypos;
2380
2381                 /**
2382                  * Gets the value of the value property.
2383                  *
2384                  * @return
2385                  *     possible object is
2386                  *     {@link String }
2387                  *
2388                  */
2389                 public String getValue() {
2390                     return value;
2391                 }
2392
2393                 /**
2394                  * Sets the value of the value property.
2395                  *
2396                  * @param value
2397                  *     allowed object is
2398                  *     {@link String }
2399                  *
2400                  */
2401                 public void setValue(String value) {
2402                     this.value = value;
2403                 }
2404
2405                 /**
2406                  * Gets the value of the visible property.
2407                  *
2408                  * @return
2409                  *     possible object is
2410                  *     {@link Boolean }
2411                  *
2412                  */
2413                 public Boolean isVisible() {
2414                     return visible;
2415                 }
2416
2417                 /**
2418                  * Sets the value of the visible property.
2419                  *
2420                  * @param value
2421                  *     allowed object is
2422                  *     {@link Boolean }
2423                  *
2424                  */
2425                 public void setVisible(Boolean value) {
2426                     this.visible = value;
2427                 }
2428
2429                 /**
2430                  * Gets the value of the viewId property.
2431                  *
2432                  * @return
2433                  *     possible object is
2434                  *     {@link String }
2435                  *
2436                  */
2437                 public String getViewId() {
2438                     return viewId;
2439                 }
2440
2441                 /**
2442                  * Sets the value of the viewId property.
2443                  *
2444                  * @param value
2445                  *     allowed object is
2446                  *     {@link String }
2447                  *
2448                  */
2449                 public void setViewId(String value) {
2450                     this.viewId = value;
2451                 }
2452
2453                 /**
2454                  * Gets the value of the alignwithAlignPanel property.
2455                  *
2456                  * @return
2457                  *     possible object is
2458                  *     {@link Boolean }
2459                  *
2460                  */
2461                 public boolean isAlignwithAlignPanel() {
2462                     if (alignwithAlignPanel == null) {
2463                         return true;
2464                     } else {
2465                         return alignwithAlignPanel;
2466                     }
2467                 }
2468
2469                 /**
2470                  * Sets the value of the alignwithAlignPanel property.
2471                  *
2472                  * @param value
2473                  *     allowed object is
2474                  *     {@link Boolean }
2475                  *
2476                  */
2477                 public void setAlignwithAlignPanel(Boolean value) {
2478                     this.alignwithAlignPanel = value;
2479                 }
2480
2481                 /**
2482                  * Gets the value of the colourwithAlignPanel property.
2483                  *
2484                  * @return
2485                  *     possible object is
2486                  *     {@link Boolean }
2487                  *
2488                  */
2489                 public boolean isColourwithAlignPanel() {
2490                     if (colourwithAlignPanel == null) {
2491                         return false;
2492                     } else {
2493                         return colourwithAlignPanel;
2494                     }
2495                 }
2496
2497                 /**
2498                  * Sets the value of the colourwithAlignPanel property.
2499                  *
2500                  * @param value
2501                  *     allowed object is
2502                  *     {@link Boolean }
2503                  *
2504                  */
2505                 public void setColourwithAlignPanel(Boolean value) {
2506                     this.colourwithAlignPanel = value;
2507                 }
2508
2509                 /**
2510                  * Gets the value of the colourByJmol property.
2511                  *
2512                  * @return
2513                  *     possible object is
2514                  *     {@link Boolean }
2515                  *
2516                  */
2517                 public boolean isColourByJmol() {
2518                     if (colourByJmol == null) {
2519                         return true;
2520                     } else {
2521                         return colourByJmol;
2522                     }
2523                 }
2524
2525                 /**
2526                  * Sets the value of the colourByJmol property.
2527                  *
2528                  * @param value
2529                  *     allowed object is
2530                  *     {@link Boolean }
2531                  *
2532                  */
2533                 public void setColourByJmol(Boolean value) {
2534                     this.colourByJmol = value;
2535                 }
2536
2537                 /**
2538                  * Gets the value of the type property.
2539                  *
2540                  * @return
2541                  *     possible object is
2542                  *     {@link String }
2543                  *
2544                  */
2545                 public String getType() {
2546                     return type;
2547                 }
2548
2549                 /**
2550                  * Sets the value of the type property.
2551                  *
2552                  * @param value
2553                  *     allowed object is
2554                  *     {@link String }
2555                  *
2556                  */
2557                 public void setType(String value) {
2558                     this.type = value;
2559                 }
2560
2561                 /**
2562                  * Gets the value of the width property.
2563                  *
2564                  * @return
2565                  *     possible object is
2566                  *     {@link Integer }
2567                  *
2568                  */
2569                 public Integer getWidth() {
2570                     return width;
2571                 }
2572
2573                 /**
2574                  * Sets the value of the width property.
2575                  *
2576                  * @param value
2577                  *     allowed object is
2578                  *     {@link Integer }
2579                  *
2580                  */
2581                 public void setWidth(Integer value) {
2582                     this.width = value;
2583                 }
2584
2585                 /**
2586                  * Gets the value of the height property.
2587                  *
2588                  * @return
2589                  *     possible object is
2590                  *     {@link Integer }
2591                  *
2592                  */
2593                 public Integer getHeight() {
2594                     return height;
2595                 }
2596
2597                 /**
2598                  * Sets the value of the height property.
2599                  *
2600                  * @param value
2601                  *     allowed object is
2602                  *     {@link Integer }
2603                  *
2604                  */
2605                 public void setHeight(Integer value) {
2606                     this.height = value;
2607                 }
2608
2609                 /**
2610                  * Gets the value of the xpos property.
2611                  *
2612                  * @return
2613                  *     possible object is
2614                  *     {@link Integer }
2615                  *
2616                  */
2617                 public Integer getXpos() {
2618                     return xpos;
2619                 }
2620
2621                 /**
2622                  * Sets the value of the xpos property.
2623                  *
2624                  * @param value
2625                  *     allowed object is
2626                  *     {@link Integer }
2627                  *
2628                  */
2629                 public void setXpos(Integer value) {
2630                     this.xpos = value;
2631                 }
2632
2633                 /**
2634                  * Gets the value of the ypos property.
2635                  *
2636                  * @return
2637                  *     possible object is
2638                  *     {@link Integer }
2639                  *
2640                  */
2641                 public Integer getYpos() {
2642                     return ypos;
2643                 }
2644
2645                 /**
2646                  * Sets the value of the ypos property.
2647                  *
2648                  * @param value
2649                  *     allowed object is
2650                  *     {@link Integer }
2651                  *
2652                  */
2653                 public void setYpos(Integer value) {
2654                     this.ypos = value;
2655                 }
2656
2657             }
2658
2659         }
2660
2661
2662         /**
2663          * <p>Java class for anonymous complex type.
2664          *
2665          * <p>The following schema fragment specifies the expected content contained within this class.
2666          *
2667          * <pre>
2668          * &lt;complexType>
2669          *   &lt;complexContent>
2670          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2671          *       &lt;sequence>
2672          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2673          *           &lt;complexType>
2674          *             &lt;complexContent>
2675          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2676          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2677          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2678          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2679          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2680          *               &lt;/restriction>
2681          *             &lt;/complexContent>
2682          *           &lt;/complexType>
2683          *         &lt;/element>
2684          *       &lt;/sequence>
2685          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2686          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2687          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2688          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2689          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2690          *     &lt;/restriction>
2691          *   &lt;/complexContent>
2692          * &lt;/complexType>
2693          * </pre>
2694          *
2695          *
2696          */
2697         @XmlAccessorType(XmlAccessType.FIELD)
2698         @XmlType(name = "", propOrder = {
2699             "secondaryStructure"
2700         })
2701         public static class RnaViewer {
2702
2703             @XmlElement(namespace = "www.jalview.org", required = true)
2704             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2705             @XmlAttribute(name = "title")
2706             protected String title;
2707             @XmlAttribute(name = "viewId")
2708             protected String viewId;
2709             @XmlAttribute(name = "dividerLocation")
2710             protected Integer dividerLocation;
2711             @XmlAttribute(name = "selectedRna")
2712             protected Integer selectedRna;
2713             @XmlAttribute(name = "width")
2714             protected Integer width;
2715             @XmlAttribute(name = "height")
2716             protected Integer height;
2717             @XmlAttribute(name = "xpos")
2718             protected Integer xpos;
2719             @XmlAttribute(name = "ypos")
2720             protected Integer ypos;
2721
2722             /**
2723              * Gets the value of the secondaryStructure property.
2724              *
2725              * <p>
2726              * This accessor method returns a reference to the live list,
2727              * not a snapshot. Therefore any modification you make to the
2728              * returned list will be present inside the JAXB object.
2729              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2730              *
2731              * <p>
2732              * For example, to add a new item, do as follows:
2733              * <pre>
2734              *    getSecondaryStructure().add(newItem);
2735              * </pre>
2736              *
2737              *
2738              * <p>
2739              * Objects of the following type(s) are allowed in the list
2740              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2741              *
2742              *
2743              */
2744             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2745                 if (secondaryStructure == null) {
2746                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2747                 }
2748                 return this.secondaryStructure;
2749             }
2750
2751             /**
2752              * Gets the value of the title property.
2753              *
2754              * @return
2755              *     possible object is
2756              *     {@link String }
2757              *
2758              */
2759             public String getTitle() {
2760                 return title;
2761             }
2762
2763             /**
2764              * Sets the value of the title property.
2765              *
2766              * @param value
2767              *     allowed object is
2768              *     {@link String }
2769              *
2770              */
2771             public void setTitle(String value) {
2772                 this.title = value;
2773             }
2774
2775             /**
2776              * Gets the value of the viewId property.
2777              *
2778              * @return
2779              *     possible object is
2780              *     {@link String }
2781              *
2782              */
2783             public String getViewId() {
2784                 return viewId;
2785             }
2786
2787             /**
2788              * Sets the value of the viewId property.
2789              *
2790              * @param value
2791              *     allowed object is
2792              *     {@link String }
2793              *
2794              */
2795             public void setViewId(String value) {
2796                 this.viewId = value;
2797             }
2798
2799             /**
2800              * Gets the value of the dividerLocation property.
2801              *
2802              * @return
2803              *     possible object is
2804              *     {@link Integer }
2805              *
2806              */
2807             public Integer getDividerLocation() {
2808                 return dividerLocation;
2809             }
2810
2811             /**
2812              * Sets the value of the dividerLocation property.
2813              *
2814              * @param value
2815              *     allowed object is
2816              *     {@link Integer }
2817              *
2818              */
2819             public void setDividerLocation(Integer value) {
2820                 this.dividerLocation = value;
2821             }
2822
2823             /**
2824              * Gets the value of the selectedRna property.
2825              *
2826              * @return
2827              *     possible object is
2828              *     {@link Integer }
2829              *
2830              */
2831             public Integer getSelectedRna() {
2832                 return selectedRna;
2833             }
2834
2835             /**
2836              * Sets the value of the selectedRna property.
2837              *
2838              * @param value
2839              *     allowed object is
2840              *     {@link Integer }
2841              *
2842              */
2843             public void setSelectedRna(Integer value) {
2844                 this.selectedRna = value;
2845             }
2846
2847             /**
2848              * Gets the value of the width property.
2849              *
2850              * @return
2851              *     possible object is
2852              *     {@link Integer }
2853              *
2854              */
2855             public Integer getWidth() {
2856                 return width;
2857             }
2858
2859             /**
2860              * Sets the value of the width property.
2861              *
2862              * @param value
2863              *     allowed object is
2864              *     {@link Integer }
2865              *
2866              */
2867             public void setWidth(Integer value) {
2868                 this.width = value;
2869             }
2870
2871             /**
2872              * Gets the value of the height property.
2873              *
2874              * @return
2875              *     possible object is
2876              *     {@link Integer }
2877              *
2878              */
2879             public Integer getHeight() {
2880                 return height;
2881             }
2882
2883             /**
2884              * Sets the value of the height property.
2885              *
2886              * @param value
2887              *     allowed object is
2888              *     {@link Integer }
2889              *
2890              */
2891             public void setHeight(Integer value) {
2892                 this.height = value;
2893             }
2894
2895             /**
2896              * Gets the value of the xpos property.
2897              *
2898              * @return
2899              *     possible object is
2900              *     {@link Integer }
2901              *
2902              */
2903             public Integer getXpos() {
2904                 return xpos;
2905             }
2906
2907             /**
2908              * Sets the value of the xpos property.
2909              *
2910              * @param value
2911              *     allowed object is
2912              *     {@link Integer }
2913              *
2914              */
2915             public void setXpos(Integer value) {
2916                 this.xpos = value;
2917             }
2918
2919             /**
2920              * Gets the value of the ypos property.
2921              *
2922              * @return
2923              *     possible object is
2924              *     {@link Integer }
2925              *
2926              */
2927             public Integer getYpos() {
2928                 return ypos;
2929             }
2930
2931             /**
2932              * Sets the value of the ypos property.
2933              *
2934              * @param value
2935              *     allowed object is
2936              *     {@link Integer }
2937              *
2938              */
2939             public void setYpos(Integer value) {
2940                 this.ypos = value;
2941             }
2942
2943
2944             /**
2945              * <p>Java class for anonymous complex type.
2946              *
2947              * <p>The following schema fragment specifies the expected content contained within this class.
2948              *
2949              * <pre>
2950              * &lt;complexType>
2951              *   &lt;complexContent>
2952              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2953              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2954              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2955              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2956              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2957              *     &lt;/restriction>
2958              *   &lt;/complexContent>
2959              * &lt;/complexType>
2960              * </pre>
2961              *
2962              *
2963              */
2964             @XmlAccessorType(XmlAccessType.FIELD)
2965             @XmlType(name = "")
2966             public static class SecondaryStructure {
2967
2968                 @XmlAttribute(name = "title")
2969                 protected String title;
2970                 @XmlAttribute(name = "annotationId", required = true)
2971                 protected String annotationId;
2972                 @XmlAttribute(name = "gapped")
2973                 protected Boolean gapped;
2974                 @XmlAttribute(name = "viewerState")
2975                 protected String viewerState;
2976
2977                 /**
2978                  * Gets the value of the title property.
2979                  *
2980                  * @return
2981                  *     possible object is
2982                  *     {@link String }
2983                  *
2984                  */
2985                 public String getTitle() {
2986                     return title;
2987                 }
2988
2989                 /**
2990                  * Sets the value of the title property.
2991                  *
2992                  * @param value
2993                  *     allowed object is
2994                  *     {@link String }
2995                  *
2996                  */
2997                 public void setTitle(String value) {
2998                     this.title = value;
2999                 }
3000
3001                 /**
3002                  * Gets the value of the annotationId property.
3003                  *
3004                  * @return
3005                  *     possible object is
3006                  *     {@link String }
3007                  *
3008                  */
3009                 public String getAnnotationId() {
3010                     return annotationId;
3011                 }
3012
3013                 /**
3014                  * Sets the value of the annotationId property.
3015                  *
3016                  * @param value
3017                  *     allowed object is
3018                  *     {@link String }
3019                  *
3020                  */
3021                 public void setAnnotationId(String value) {
3022                     this.annotationId = value;
3023                 }
3024
3025                 /**
3026                  * Gets the value of the gapped property.
3027                  *
3028                  * @return
3029                  *     possible object is
3030                  *     {@link Boolean }
3031                  *
3032                  */
3033                 public Boolean isGapped() {
3034                     return gapped;
3035                 }
3036
3037                 /**
3038                  * Sets the value of the gapped property.
3039                  *
3040                  * @param value
3041                  *     allowed object is
3042                  *     {@link Boolean }
3043                  *
3044                  */
3045                 public void setGapped(Boolean value) {
3046                     this.gapped = value;
3047                 }
3048
3049                 /**
3050                  * Gets the value of the viewerState property.
3051                  *
3052                  * @return
3053                  *     possible object is
3054                  *     {@link String }
3055                  *
3056                  */
3057                 public String getViewerState() {
3058                     return viewerState;
3059                 }
3060
3061                 /**
3062                  * Sets the value of the viewerState property.
3063                  *
3064                  * @param value
3065                  *     allowed object is
3066                  *     {@link String }
3067                  *
3068                  */
3069                 public void setViewerState(String value) {
3070                     this.viewerState = value;
3071                 }
3072
3073             }
3074
3075         }
3076
3077     }
3078
3079
3080     /**
3081      * <p>Java class for anonymous complex type.
3082      *
3083      * <p>The following schema fragment specifies the expected content contained within this class.
3084      *
3085      * <pre>
3086      * &lt;complexType>
3087      *   &lt;complexContent>
3088      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3089      *       &lt;sequence>
3090      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3091      *           &lt;complexType>
3092      *             &lt;complexContent>
3093      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3094      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3095      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3096      *               &lt;/restriction>
3097      *             &lt;/complexContent>
3098      *           &lt;/complexType>
3099      *         &lt;/element>
3100      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3101      *           &lt;complexType>
3102      *             &lt;complexContent>
3103      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3104      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3105      *               &lt;/restriction>
3106      *             &lt;/complexContent>
3107      *           &lt;/complexType>
3108      *         &lt;/element>
3109      *         &lt;element name="seqPointMin">
3110      *           &lt;complexType>
3111      *             &lt;complexContent>
3112      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3113      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3114      *               &lt;/restriction>
3115      *             &lt;/complexContent>
3116      *           &lt;/complexType>
3117      *         &lt;/element>
3118      *         &lt;element name="seqPointMax">
3119      *           &lt;complexType>
3120      *             &lt;complexContent>
3121      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3122      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3123      *               &lt;/restriction>
3124      *             &lt;/complexContent>
3125      *           &lt;/complexType>
3126      *         &lt;/element>
3127      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3128      *       &lt;/sequence>
3129      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3130      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3131      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3132      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3133      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3134      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3135      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3136      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3137      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3138      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3139      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3140      *     &lt;/restriction>
3141      *   &lt;/complexContent>
3142      * &lt;/complexType>
3143      * </pre>
3144      *
3145      *
3146      */
3147     @XmlAccessorType(XmlAccessType.FIELD)
3148     @XmlType(name = "", propOrder = {
3149         "sequencePoint",
3150         "axis",
3151         "seqPointMin",
3152         "seqPointMax",
3153         "pcaData"
3154     })
3155     public static class PcaViewer {
3156
3157         @XmlElement(namespace = "www.jalview.org", required = true)
3158         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3159         @XmlElement(namespace = "www.jalview.org", required = true)
3160         protected List<JalviewModel.PcaViewer.Axis> axis;
3161         @XmlElement(namespace = "www.jalview.org", required = true)
3162         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3163         @XmlElement(namespace = "www.jalview.org", required = true)
3164         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3165         @XmlElement(namespace = "www.jalview.org", required = true)
3166         protected PcaDataType pcaData;
3167         @XmlAttribute(name = "title")
3168         protected String title;
3169         @XmlAttribute(name = "scoreModelName")
3170         protected String scoreModelName;
3171         @XmlAttribute(name = "xDim")
3172         protected Integer xDim;
3173         @XmlAttribute(name = "yDim")
3174         protected Integer yDim;
3175         @XmlAttribute(name = "zDim")
3176         protected Integer zDim;
3177         @XmlAttribute(name = "bgColour")
3178         protected Integer bgColour;
3179         @XmlAttribute(name = "scaleFactor")
3180         protected Float scaleFactor;
3181         @XmlAttribute(name = "showLabels")
3182         protected Boolean showLabels;
3183         @XmlAttribute(name = "linkToAllViews")
3184         protected Boolean linkToAllViews;
3185         @XmlAttribute(name = "includeGaps")
3186         protected Boolean includeGaps;
3187         @XmlAttribute(name = "matchGaps")
3188         protected Boolean matchGaps;
3189         @XmlAttribute(name = "includeGappedColumns")
3190         protected Boolean includeGappedColumns;
3191         @XmlAttribute(name = "denominateByShortestLength")
3192         protected Boolean denominateByShortestLength;
3193         @XmlAttribute(name = "width")
3194         protected Integer width;
3195         @XmlAttribute(name = "height")
3196         protected Integer height;
3197         @XmlAttribute(name = "xpos")
3198         protected Integer xpos;
3199         @XmlAttribute(name = "ypos")
3200         protected Integer ypos;
3201
3202         /**
3203          * Gets the value of the sequencePoint property.
3204          *
3205          * <p>
3206          * This accessor method returns a reference to the live list,
3207          * not a snapshot. Therefore any modification you make to the
3208          * returned list will be present inside the JAXB object.
3209          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3210          *
3211          * <p>
3212          * For example, to add a new item, do as follows:
3213          * <pre>
3214          *    getSequencePoint().add(newItem);
3215          * </pre>
3216          *
3217          *
3218          * <p>
3219          * Objects of the following type(s) are allowed in the list
3220          * {@link JalviewModel.PcaViewer.SequencePoint }
3221          *
3222          *
3223          */
3224         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3225             if (sequencePoint == null) {
3226                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3227             }
3228             return this.sequencePoint;
3229         }
3230
3231         /**
3232          * Gets the value of the axis property.
3233          *
3234          * <p>
3235          * This accessor method returns a reference to the live list,
3236          * not a snapshot. Therefore any modification you make to the
3237          * returned list will be present inside the JAXB object.
3238          * This is why there is not a <CODE>set</CODE> method for the axis property.
3239          *
3240          * <p>
3241          * For example, to add a new item, do as follows:
3242          * <pre>
3243          *    getAxis().add(newItem);
3244          * </pre>
3245          *
3246          *
3247          * <p>
3248          * Objects of the following type(s) are allowed in the list
3249          * {@link JalviewModel.PcaViewer.Axis }
3250          *
3251          *
3252          */
3253         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3254             if (axis == null) {
3255                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3256             }
3257             return this.axis;
3258         }
3259
3260         /**
3261          * Gets the value of the seqPointMin property.
3262          *
3263          * @return
3264          *     possible object is
3265          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3266          *
3267          */
3268         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3269             return seqPointMin;
3270         }
3271
3272         /**
3273          * Sets the value of the seqPointMin property.
3274          *
3275          * @param value
3276          *     allowed object is
3277          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3278          *
3279          */
3280         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3281             this.seqPointMin = value;
3282         }
3283
3284         /**
3285          * Gets the value of the seqPointMax property.
3286          *
3287          * @return
3288          *     possible object is
3289          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3290          *
3291          */
3292         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3293             return seqPointMax;
3294         }
3295
3296         /**
3297          * Sets the value of the seqPointMax property.
3298          *
3299          * @param value
3300          *     allowed object is
3301          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3302          *
3303          */
3304         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3305             this.seqPointMax = value;
3306         }
3307
3308         /**
3309          * Gets the value of the pcaData property.
3310          *
3311          * @return
3312          *     possible object is
3313          *     {@link PcaDataType }
3314          *
3315          */
3316         public PcaDataType getPcaData() {
3317             return pcaData;
3318         }
3319
3320         /**
3321          * Sets the value of the pcaData property.
3322          *
3323          * @param value
3324          *     allowed object is
3325          *     {@link PcaDataType }
3326          *
3327          */
3328         public void setPcaData(PcaDataType value) {
3329             this.pcaData = value;
3330         }
3331
3332         /**
3333          * Gets the value of the title property.
3334          *
3335          * @return
3336          *     possible object is
3337          *     {@link String }
3338          *
3339          */
3340         public String getTitle() {
3341             return title;
3342         }
3343
3344         /**
3345          * Sets the value of the title property.
3346          *
3347          * @param value
3348          *     allowed object is
3349          *     {@link String }
3350          *
3351          */
3352         public void setTitle(String value) {
3353             this.title = value;
3354         }
3355
3356         /**
3357          * Gets the value of the scoreModelName property.
3358          *
3359          * @return
3360          *     possible object is
3361          *     {@link String }
3362          *
3363          */
3364         public String getScoreModelName() {
3365             return scoreModelName;
3366         }
3367
3368         /**
3369          * Sets the value of the scoreModelName property.
3370          *
3371          * @param value
3372          *     allowed object is
3373          *     {@link String }
3374          *
3375          */
3376         public void setScoreModelName(String value) {
3377             this.scoreModelName = value;
3378         }
3379
3380         /**
3381          * Gets the value of the xDim property.
3382          *
3383          * @return
3384          *     possible object is
3385          *     {@link Integer }
3386          *
3387          */
3388         public Integer getXDim() {
3389             return xDim;
3390         }
3391
3392         /**
3393          * Sets the value of the xDim property.
3394          *
3395          * @param value
3396          *     allowed object is
3397          *     {@link Integer }
3398          *
3399          */
3400         public void setXDim(Integer value) {
3401             this.xDim = value;
3402         }
3403
3404         /**
3405          * Gets the value of the yDim property.
3406          *
3407          * @return
3408          *     possible object is
3409          *     {@link Integer }
3410          *
3411          */
3412         public Integer getYDim() {
3413             return yDim;
3414         }
3415
3416         /**
3417          * Sets the value of the yDim property.
3418          *
3419          * @param value
3420          *     allowed object is
3421          *     {@link Integer }
3422          *
3423          */
3424         public void setYDim(Integer value) {
3425             this.yDim = value;
3426         }
3427
3428         /**
3429          * Gets the value of the zDim property.
3430          *
3431          * @return
3432          *     possible object is
3433          *     {@link Integer }
3434          *
3435          */
3436         public Integer getZDim() {
3437             return zDim;
3438         }
3439
3440         /**
3441          * Sets the value of the zDim property.
3442          *
3443          * @param value
3444          *     allowed object is
3445          *     {@link Integer }
3446          *
3447          */
3448         public void setZDim(Integer value) {
3449             this.zDim = value;
3450         }
3451
3452         /**
3453          * Gets the value of the bgColour property.
3454          *
3455          * @return
3456          *     possible object is
3457          *     {@link Integer }
3458          *
3459          */
3460         public Integer getBgColour() {
3461             return bgColour;
3462         }
3463
3464         /**
3465          * Sets the value of the bgColour property.
3466          *
3467          * @param value
3468          *     allowed object is
3469          *     {@link Integer }
3470          *
3471          */
3472         public void setBgColour(Integer value) {
3473             this.bgColour = value;
3474         }
3475
3476         /**
3477          * Gets the value of the scaleFactor property.
3478          *
3479          * @return
3480          *     possible object is
3481          *     {@link Float }
3482          *
3483          */
3484         public Float getScaleFactor() {
3485             return scaleFactor;
3486         }
3487
3488         /**
3489          * Sets the value of the scaleFactor property.
3490          *
3491          * @param value
3492          *     allowed object is
3493          *     {@link Float }
3494          *
3495          */
3496         public void setScaleFactor(Float value) {
3497             this.scaleFactor = value;
3498         }
3499
3500         /**
3501          * Gets the value of the showLabels property.
3502          *
3503          * @return
3504          *     possible object is
3505          *     {@link Boolean }
3506          *
3507          */
3508         public Boolean isShowLabels() {
3509             return showLabels;
3510         }
3511
3512         /**
3513          * Sets the value of the showLabels property.
3514          *
3515          * @param value
3516          *     allowed object is
3517          *     {@link Boolean }
3518          *
3519          */
3520         public void setShowLabels(Boolean value) {
3521             this.showLabels = value;
3522         }
3523
3524         /**
3525          * Gets the value of the linkToAllViews property.
3526          *
3527          * @return
3528          *     possible object is
3529          *     {@link Boolean }
3530          *
3531          */
3532         public Boolean isLinkToAllViews() {
3533             return linkToAllViews;
3534         }
3535
3536         /**
3537          * Sets the value of the linkToAllViews property.
3538          *
3539          * @param value
3540          *     allowed object is
3541          *     {@link Boolean }
3542          *
3543          */
3544         public void setLinkToAllViews(Boolean value) {
3545             this.linkToAllViews = value;
3546         }
3547
3548         /**
3549          * Gets the value of the includeGaps property.
3550          *
3551          * @return
3552          *     possible object is
3553          *     {@link Boolean }
3554          *
3555          */
3556         public Boolean isIncludeGaps() {
3557             return includeGaps;
3558         }
3559
3560         /**
3561          * Sets the value of the includeGaps property.
3562          *
3563          * @param value
3564          *     allowed object is
3565          *     {@link Boolean }
3566          *
3567          */
3568         public void setIncludeGaps(Boolean value) {
3569             this.includeGaps = value;
3570         }
3571
3572         /**
3573          * Gets the value of the matchGaps property.
3574          *
3575          * @return
3576          *     possible object is
3577          *     {@link Boolean }
3578          *
3579          */
3580         public Boolean isMatchGaps() {
3581             return matchGaps;
3582         }
3583
3584         /**
3585          * Sets the value of the matchGaps property.
3586          *
3587          * @param value
3588          *     allowed object is
3589          *     {@link Boolean }
3590          *
3591          */
3592         public void setMatchGaps(Boolean value) {
3593             this.matchGaps = value;
3594         }
3595
3596         /**
3597          * Gets the value of the includeGappedColumns property.
3598          *
3599          * @return
3600          *     possible object is
3601          *     {@link Boolean }
3602          *
3603          */
3604         public Boolean isIncludeGappedColumns() {
3605             return includeGappedColumns;
3606         }
3607
3608         /**
3609          * Sets the value of the includeGappedColumns property.
3610          *
3611          * @param value
3612          *     allowed object is
3613          *     {@link Boolean }
3614          *
3615          */
3616         public void setIncludeGappedColumns(Boolean value) {
3617             this.includeGappedColumns = value;
3618         }
3619
3620         /**
3621          * Gets the value of the denominateByShortestLength property.
3622          *
3623          * @return
3624          *     possible object is
3625          *     {@link Boolean }
3626          *
3627          */
3628         public Boolean isDenominateByShortestLength() {
3629             return denominateByShortestLength;
3630         }
3631
3632         /**
3633          * Sets the value of the denominateByShortestLength property.
3634          *
3635          * @param value
3636          *     allowed object is
3637          *     {@link Boolean }
3638          *
3639          */
3640         public void setDenominateByShortestLength(Boolean value) {
3641             this.denominateByShortestLength = value;
3642         }
3643
3644         /**
3645          * Gets the value of the width property.
3646          *
3647          * @return
3648          *     possible object is
3649          *     {@link Integer }
3650          *
3651          */
3652         public Integer getWidth() {
3653             return width;
3654         }
3655
3656         /**
3657          * Sets the value of the width property.
3658          *
3659          * @param value
3660          *     allowed object is
3661          *     {@link Integer }
3662          *
3663          */
3664         public void setWidth(Integer value) {
3665             this.width = value;
3666         }
3667
3668         /**
3669          * Gets the value of the height property.
3670          *
3671          * @return
3672          *     possible object is
3673          *     {@link Integer }
3674          *
3675          */
3676         public Integer getHeight() {
3677             return height;
3678         }
3679
3680         /**
3681          * Sets the value of the height property.
3682          *
3683          * @param value
3684          *     allowed object is
3685          *     {@link Integer }
3686          *
3687          */
3688         public void setHeight(Integer value) {
3689             this.height = value;
3690         }
3691
3692         /**
3693          * Gets the value of the xpos property.
3694          *
3695          * @return
3696          *     possible object is
3697          *     {@link Integer }
3698          *
3699          */
3700         public Integer getXpos() {
3701             return xpos;
3702         }
3703
3704         /**
3705          * Sets the value of the xpos property.
3706          *
3707          * @param value
3708          *     allowed object is
3709          *     {@link Integer }
3710          *
3711          */
3712         public void setXpos(Integer value) {
3713             this.xpos = value;
3714         }
3715
3716         /**
3717          * Gets the value of the ypos property.
3718          *
3719          * @return
3720          *     possible object is
3721          *     {@link Integer }
3722          *
3723          */
3724         public Integer getYpos() {
3725             return ypos;
3726         }
3727
3728         /**
3729          * Sets the value of the ypos property.
3730          *
3731          * @param value
3732          *     allowed object is
3733          *     {@link Integer }
3734          *
3735          */
3736         public void setYpos(Integer value) {
3737             this.ypos = value;
3738         }
3739
3740
3741         /**
3742          * <p>Java class for anonymous complex type.
3743          *
3744          * <p>The following schema fragment specifies the expected content contained within this class.
3745          *
3746          * <pre>
3747          * &lt;complexType>
3748          *   &lt;complexContent>
3749          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3750          *       &lt;attGroup ref="{www.jalview.org}position"/>
3751          *     &lt;/restriction>
3752          *   &lt;/complexContent>
3753          * &lt;/complexType>
3754          * </pre>
3755          *
3756          *
3757          */
3758         @XmlAccessorType(XmlAccessType.FIELD)
3759         @XmlType(name = "")
3760         public static class Axis {
3761
3762             @XmlAttribute(name = "xPos")
3763             protected Float xPos;
3764             @XmlAttribute(name = "yPos")
3765             protected Float yPos;
3766             @XmlAttribute(name = "zPos")
3767             protected Float zPos;
3768
3769             /**
3770              * Gets the value of the xPos property.
3771              *
3772              * @return
3773              *     possible object is
3774              *     {@link Float }
3775              *
3776              */
3777             public Float getXPos() {
3778                 return xPos;
3779             }
3780
3781             /**
3782              * Sets the value of the xPos property.
3783              *
3784              * @param value
3785              *     allowed object is
3786              *     {@link Float }
3787              *
3788              */
3789             public void setXPos(Float value) {
3790                 this.xPos = value;
3791             }
3792
3793             /**
3794              * Gets the value of the yPos property.
3795              *
3796              * @return
3797              *     possible object is
3798              *     {@link Float }
3799              *
3800              */
3801             public Float getYPos() {
3802                 return yPos;
3803             }
3804
3805             /**
3806              * Sets the value of the yPos property.
3807              *
3808              * @param value
3809              *     allowed object is
3810              *     {@link Float }
3811              *
3812              */
3813             public void setYPos(Float value) {
3814                 this.yPos = value;
3815             }
3816
3817             /**
3818              * Gets the value of the zPos property.
3819              *
3820              * @return
3821              *     possible object is
3822              *     {@link Float }
3823              *
3824              */
3825             public Float getZPos() {
3826                 return zPos;
3827             }
3828
3829             /**
3830              * Sets the value of the zPos property.
3831              *
3832              * @param value
3833              *     allowed object is
3834              *     {@link Float }
3835              *
3836              */
3837             public void setZPos(Float value) {
3838                 this.zPos = value;
3839             }
3840
3841         }
3842
3843
3844         /**
3845          * <p>Java class for anonymous complex type.
3846          *
3847          * <p>The following schema fragment specifies the expected content contained within this class.
3848          *
3849          * <pre>
3850          * &lt;complexType>
3851          *   &lt;complexContent>
3852          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3853          *       &lt;attGroup ref="{www.jalview.org}position"/>
3854          *     &lt;/restriction>
3855          *   &lt;/complexContent>
3856          * &lt;/complexType>
3857          * </pre>
3858          *
3859          *
3860          */
3861         @XmlAccessorType(XmlAccessType.FIELD)
3862         @XmlType(name = "")
3863         public static class SeqPointMax {
3864
3865             @XmlAttribute(name = "xPos")
3866             protected Float xPos;
3867             @XmlAttribute(name = "yPos")
3868             protected Float yPos;
3869             @XmlAttribute(name = "zPos")
3870             protected Float zPos;
3871
3872             /**
3873              * Gets the value of the xPos property.
3874              *
3875              * @return
3876              *     possible object is
3877              *     {@link Float }
3878              *
3879              */
3880             public Float getXPos() {
3881                 return xPos;
3882             }
3883
3884             /**
3885              * Sets the value of the xPos property.
3886              *
3887              * @param value
3888              *     allowed object is
3889              *     {@link Float }
3890              *
3891              */
3892             public void setXPos(Float value) {
3893                 this.xPos = value;
3894             }
3895
3896             /**
3897              * Gets the value of the yPos property.
3898              *
3899              * @return
3900              *     possible object is
3901              *     {@link Float }
3902              *
3903              */
3904             public Float getYPos() {
3905                 return yPos;
3906             }
3907
3908             /**
3909              * Sets the value of the yPos property.
3910              *
3911              * @param value
3912              *     allowed object is
3913              *     {@link Float }
3914              *
3915              */
3916             public void setYPos(Float value) {
3917                 this.yPos = value;
3918             }
3919
3920             /**
3921              * Gets the value of the zPos property.
3922              *
3923              * @return
3924              *     possible object is
3925              *     {@link Float }
3926              *
3927              */
3928             public Float getZPos() {
3929                 return zPos;
3930             }
3931
3932             /**
3933              * Sets the value of the zPos property.
3934              *
3935              * @param value
3936              *     allowed object is
3937              *     {@link Float }
3938              *
3939              */
3940             public void setZPos(Float value) {
3941                 this.zPos = value;
3942             }
3943
3944         }
3945
3946
3947         /**
3948          * <p>Java class for anonymous complex type.
3949          *
3950          * <p>The following schema fragment specifies the expected content contained within this class.
3951          *
3952          * <pre>
3953          * &lt;complexType>
3954          *   &lt;complexContent>
3955          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3956          *       &lt;attGroup ref="{www.jalview.org}position"/>
3957          *     &lt;/restriction>
3958          *   &lt;/complexContent>
3959          * &lt;/complexType>
3960          * </pre>
3961          *
3962          *
3963          */
3964         @XmlAccessorType(XmlAccessType.FIELD)
3965         @XmlType(name = "")
3966         public static class SeqPointMin {
3967
3968             @XmlAttribute(name = "xPos")
3969             protected Float xPos;
3970             @XmlAttribute(name = "yPos")
3971             protected Float yPos;
3972             @XmlAttribute(name = "zPos")
3973             protected Float zPos;
3974
3975             /**
3976              * Gets the value of the xPos property.
3977              *
3978              * @return
3979              *     possible object is
3980              *     {@link Float }
3981              *
3982              */
3983             public Float getXPos() {
3984                 return xPos;
3985             }
3986
3987             /**
3988              * Sets the value of the xPos property.
3989              *
3990              * @param value
3991              *     allowed object is
3992              *     {@link Float }
3993              *
3994              */
3995             public void setXPos(Float value) {
3996                 this.xPos = value;
3997             }
3998
3999             /**
4000              * Gets the value of the yPos property.
4001              *
4002              * @return
4003              *     possible object is
4004              *     {@link Float }
4005              *
4006              */
4007             public Float getYPos() {
4008                 return yPos;
4009             }
4010
4011             /**
4012              * Sets the value of the yPos property.
4013              *
4014              * @param value
4015              *     allowed object is
4016              *     {@link Float }
4017              *
4018              */
4019             public void setYPos(Float value) {
4020                 this.yPos = value;
4021             }
4022
4023             /**
4024              * Gets the value of the zPos property.
4025              *
4026              * @return
4027              *     possible object is
4028              *     {@link Float }
4029              *
4030              */
4031             public Float getZPos() {
4032                 return zPos;
4033             }
4034
4035             /**
4036              * Sets the value of the zPos property.
4037              *
4038              * @param value
4039              *     allowed object is
4040              *     {@link Float }
4041              *
4042              */
4043             public void setZPos(Float value) {
4044                 this.zPos = value;
4045             }
4046
4047         }
4048
4049
4050         /**
4051          * <p>Java class for anonymous complex type.
4052          *
4053          * <p>The following schema fragment specifies the expected content contained within this class.
4054          *
4055          * <pre>
4056          * &lt;complexType>
4057          *   &lt;complexContent>
4058          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4059          *       &lt;attGroup ref="{www.jalview.org}position"/>
4060          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4061          *     &lt;/restriction>
4062          *   &lt;/complexContent>
4063          * &lt;/complexType>
4064          * </pre>
4065          *
4066          *
4067          */
4068         @XmlAccessorType(XmlAccessType.FIELD)
4069         @XmlType(name = "")
4070         public static class SequencePoint {
4071
4072             @XmlAttribute(name = "sequenceRef")
4073             protected String sequenceRef;
4074             @XmlAttribute(name = "xPos")
4075             protected Float xPos;
4076             @XmlAttribute(name = "yPos")
4077             protected Float yPos;
4078             @XmlAttribute(name = "zPos")
4079             protected Float zPos;
4080
4081             /**
4082              * Gets the value of the sequenceRef property.
4083              *
4084              * @return
4085              *     possible object is
4086              *     {@link String }
4087              *
4088              */
4089             public String getSequenceRef() {
4090                 return sequenceRef;
4091             }
4092
4093             /**
4094              * Sets the value of the sequenceRef property.
4095              *
4096              * @param value
4097              *     allowed object is
4098              *     {@link String }
4099              *
4100              */
4101             public void setSequenceRef(String value) {
4102                 this.sequenceRef = value;
4103             }
4104
4105             /**
4106              * Gets the value of the xPos property.
4107              *
4108              * @return
4109              *     possible object is
4110              *     {@link Float }
4111              *
4112              */
4113             public Float getXPos() {
4114                 return xPos;
4115             }
4116
4117             /**
4118              * Sets the value of the xPos property.
4119              *
4120              * @param value
4121              *     allowed object is
4122              *     {@link Float }
4123              *
4124              */
4125             public void setXPos(Float value) {
4126                 this.xPos = value;
4127             }
4128
4129             /**
4130              * Gets the value of the yPos property.
4131              *
4132              * @return
4133              *     possible object is
4134              *     {@link Float }
4135              *
4136              */
4137             public Float getYPos() {
4138                 return yPos;
4139             }
4140
4141             /**
4142              * Sets the value of the yPos property.
4143              *
4144              * @param value
4145              *     allowed object is
4146              *     {@link Float }
4147              *
4148              */
4149             public void setYPos(Float value) {
4150                 this.yPos = value;
4151             }
4152
4153             /**
4154              * Gets the value of the zPos property.
4155              *
4156              * @return
4157              *     possible object is
4158              *     {@link Float }
4159              *
4160              */
4161             public Float getZPos() {
4162                 return zPos;
4163             }
4164
4165             /**
4166              * Sets the value of the zPos property.
4167              *
4168              * @param value
4169              *     allowed object is
4170              *     {@link Float }
4171              *
4172              */
4173             public void setZPos(Float value) {
4174                 this.zPos = value;
4175             }
4176
4177         }
4178
4179     }
4180
4181
4182     /**
4183      * <p>Java class for anonymous complex type.
4184      *
4185      * <p>The following schema fragment specifies the expected content contained within this class.
4186      *
4187      * <pre>
4188      * &lt;complexType>
4189      *   &lt;complexContent>
4190      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4191      *       &lt;sequence minOccurs="0">
4192      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4193      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4194      *       &lt;/sequence>
4195      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4196      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4197      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4198      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4199      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4200      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4201      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4202      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4203      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4204      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4205      *       &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4206      *       &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
4207      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4208      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4209      *     &lt;/restriction>
4210      *   &lt;/complexContent>
4211      * &lt;/complexType>
4212      * </pre>
4213      *
4214      *
4215      */
4216     @XmlAccessorType(XmlAccessType.FIELD)
4217     @XmlType(name = "", propOrder = {
4218         "title",
4219         "newick"
4220     })
4221     public static class Tree {
4222
4223         @XmlElement(namespace = "www.jalview.org")
4224         protected String title;
4225         @XmlElement(namespace = "www.jalview.org")
4226         protected String newick;
4227         @XmlAttribute(name = "fontName")
4228         protected String fontName;
4229         @XmlAttribute(name = "fontSize")
4230         protected Integer fontSize;
4231         @XmlAttribute(name = "fontStyle")
4232         protected Integer fontStyle;
4233         @XmlAttribute(name = "threshold")
4234         protected Float threshold;
4235         @XmlAttribute(name = "showBootstrap")
4236         protected Boolean showBootstrap;
4237         @XmlAttribute(name = "showDistances")
4238         protected Boolean showDistances;
4239         @XmlAttribute(name = "markUnlinked")
4240         protected Boolean markUnlinked;
4241         @XmlAttribute(name = "fitToWindow")
4242         protected Boolean fitToWindow;
4243         @XmlAttribute(name = "currentTree")
4244         protected Boolean currentTree;
4245         @XmlAttribute(name = "columnWise")
4246         protected Boolean columnWise;
4247         @XmlAttribute(name = "columnReference")
4248         protected String columnReference;
4249         @XmlAttribute(name = "id")
4250         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4251         @XmlID
4252         @XmlSchemaType(name = "ID")
4253         protected String id;
4254         @XmlAttribute(name = "linkToAllViews")
4255         protected Boolean linkToAllViews;
4256         @XmlAttribute(name = "width")
4257         protected Integer width;
4258         @XmlAttribute(name = "height")
4259         protected Integer height;
4260         @XmlAttribute(name = "xpos")
4261         protected Integer xpos;
4262         @XmlAttribute(name = "ypos")
4263         protected Integer ypos;
4264
4265         /**
4266          * Gets the value of the title property.
4267          *
4268          * @return
4269          *     possible object is
4270          *     {@link String }
4271          *
4272          */
4273         public String getTitle() {
4274             return title;
4275         }
4276
4277         /**
4278          * Sets the value of the title property.
4279          *
4280          * @param value
4281          *     allowed object is
4282          *     {@link String }
4283          *
4284          */
4285         public void setTitle(String value) {
4286             this.title = value;
4287         }
4288
4289         /**
4290          * Gets the value of the newick property.
4291          *
4292          * @return
4293          *     possible object is
4294          *     {@link String }
4295          *
4296          */
4297         public String getNewick() {
4298             return newick;
4299         }
4300
4301         /**
4302          * Sets the value of the newick property.
4303          *
4304          * @param value
4305          *     allowed object is
4306          *     {@link String }
4307          *
4308          */
4309         public void setNewick(String value) {
4310             this.newick = value;
4311         }
4312
4313         /**
4314          * Gets the value of the fontName property.
4315          *
4316          * @return
4317          *     possible object is
4318          *     {@link String }
4319          *
4320          */
4321         public String getFontName() {
4322             return fontName;
4323         }
4324
4325         /**
4326          * Sets the value of the fontName property.
4327          *
4328          * @param value
4329          *     allowed object is
4330          *     {@link String }
4331          *
4332          */
4333         public void setFontName(String value) {
4334             this.fontName = value;
4335         }
4336
4337         /**
4338          * Gets the value of the fontSize property.
4339          *
4340          * @return
4341          *     possible object is
4342          *     {@link Integer }
4343          *
4344          */
4345         public Integer getFontSize() {
4346             return fontSize;
4347         }
4348
4349         /**
4350          * Sets the value of the fontSize property.
4351          *
4352          * @param value
4353          *     allowed object is
4354          *     {@link Integer }
4355          *
4356          */
4357         public void setFontSize(Integer value) {
4358             this.fontSize = value;
4359         }
4360
4361         /**
4362          * Gets the value of the fontStyle property.
4363          *
4364          * @return
4365          *     possible object is
4366          *     {@link Integer }
4367          *
4368          */
4369         public Integer getFontStyle() {
4370             return fontStyle;
4371         }
4372
4373         /**
4374          * Sets the value of the fontStyle property.
4375          *
4376          * @param value
4377          *     allowed object is
4378          *     {@link Integer }
4379          *
4380          */
4381         public void setFontStyle(Integer value) {
4382             this.fontStyle = value;
4383         }
4384
4385         /**
4386          * Gets the value of the threshold property.
4387          *
4388          * @return
4389          *     possible object is
4390          *     {@link Float }
4391          *
4392          */
4393         public Float getThreshold() {
4394             return threshold;
4395         }
4396
4397         /**
4398          * Sets the value of the threshold property.
4399          *
4400          * @param value
4401          *     allowed object is
4402          *     {@link Float }
4403          *
4404          */
4405         public void setThreshold(Float value) {
4406             this.threshold = value;
4407         }
4408
4409         /**
4410          * Gets the value of the showBootstrap property.
4411          *
4412          * @return
4413          *     possible object is
4414          *     {@link Boolean }
4415          *
4416          */
4417         public Boolean isShowBootstrap() {
4418             return showBootstrap;
4419         }
4420
4421         /**
4422          * Sets the value of the showBootstrap property.
4423          *
4424          * @param value
4425          *     allowed object is
4426          *     {@link Boolean }
4427          *
4428          */
4429         public void setShowBootstrap(Boolean value) {
4430             this.showBootstrap = value;
4431         }
4432
4433         /**
4434          * Gets the value of the showDistances property.
4435          *
4436          * @return
4437          *     possible object is
4438          *     {@link Boolean }
4439          *
4440          */
4441         public Boolean isShowDistances() {
4442             return showDistances;
4443         }
4444
4445         /**
4446          * Sets the value of the showDistances property.
4447          *
4448          * @param value
4449          *     allowed object is
4450          *     {@link Boolean }
4451          *
4452          */
4453         public void setShowDistances(Boolean value) {
4454             this.showDistances = value;
4455         }
4456
4457         /**
4458          * Gets the value of the markUnlinked property.
4459          *
4460          * @return
4461          *     possible object is
4462          *     {@link Boolean }
4463          *
4464          */
4465         public Boolean isMarkUnlinked() {
4466             return markUnlinked;
4467         }
4468
4469         /**
4470          * Sets the value of the markUnlinked property.
4471          *
4472          * @param value
4473          *     allowed object is
4474          *     {@link Boolean }
4475          *
4476          */
4477         public void setMarkUnlinked(Boolean value) {
4478             this.markUnlinked = value;
4479         }
4480
4481         /**
4482          * Gets the value of the fitToWindow property.
4483          *
4484          * @return
4485          *     possible object is
4486          *     {@link Boolean }
4487          *
4488          */
4489         public Boolean isFitToWindow() {
4490             return fitToWindow;
4491         }
4492
4493         /**
4494          * Sets the value of the fitToWindow property.
4495          *
4496          * @param value
4497          *     allowed object is
4498          *     {@link Boolean }
4499          *
4500          */
4501         public void setFitToWindow(Boolean value) {
4502             this.fitToWindow = value;
4503         }
4504
4505         /**
4506          * Gets the value of the currentTree property.
4507          *
4508          * @return
4509          *     possible object is
4510          *     {@link Boolean }
4511          *
4512          */
4513         public Boolean isCurrentTree() {
4514             return currentTree;
4515         }
4516
4517         /**
4518          * Sets the value of the currentTree property.
4519          *
4520          * @param value
4521          *     allowed object is
4522          *     {@link Boolean }
4523          *
4524          */
4525         public void setCurrentTree(Boolean value) {
4526             this.currentTree = value;
4527         }
4528
4529         /**
4530          * Gets the value of the columnWise property.
4531          *
4532          * @return
4533          *     possible object is
4534          *     {@link Boolean }
4535          *
4536          */
4537         public boolean isColumnWise() {
4538             if (columnWise == null) {
4539                 return false;
4540             } else {
4541                 return columnWise;
4542             }
4543         }
4544
4545         /**
4546          * Sets the value of the columnWise property.
4547          *
4548          * @param value
4549          *     allowed object is
4550          *     {@link Boolean }
4551          *
4552          */
4553         public void setColumnWise(Boolean value) {
4554             this.columnWise = value;
4555         }
4556
4557         /**
4558          * Gets the value of the columnReference property.
4559          *
4560          * @return
4561          *     possible object is
4562          *     {@link String }
4563          *
4564          */
4565         public String getColumnReference() {
4566             return columnReference;
4567         }
4568
4569         /**
4570          * Sets the value of the columnReference property.
4571          *
4572          * @param value
4573          *     allowed object is
4574          *     {@link String }
4575          *
4576          */
4577         public void setColumnReference(String value) {
4578             this.columnReference = value;
4579         }
4580
4581         /**
4582          * Gets the value of the id property.
4583          *
4584          * @return
4585          *     possible object is
4586          *     {@link String }
4587          *
4588          */
4589         public String getId() {
4590             return id;
4591         }
4592
4593         /**
4594          * Sets the value of the id property.
4595          *
4596          * @param value
4597          *     allowed object is
4598          *     {@link String }
4599          *
4600          */
4601         public void setId(String value) {
4602             this.id = value;
4603         }
4604
4605         /**
4606          * Gets the value of the linkToAllViews property.
4607          *
4608          * @return
4609          *     possible object is
4610          *     {@link Boolean }
4611          *
4612          */
4613         public boolean isLinkToAllViews() {
4614             if (linkToAllViews == null) {
4615                 return false;
4616             } else {
4617                 return linkToAllViews;
4618             }
4619         }
4620
4621         /**
4622          * Sets the value of the linkToAllViews property.
4623          *
4624          * @param value
4625          *     allowed object is
4626          *     {@link Boolean }
4627          *
4628          */
4629         public void setLinkToAllViews(Boolean value) {
4630             this.linkToAllViews = value;
4631         }
4632
4633         /**
4634          * Gets the value of the width property.
4635          *
4636          * @return
4637          *     possible object is
4638          *     {@link Integer }
4639          *
4640          */
4641         public Integer getWidth() {
4642             return width;
4643         }
4644
4645         /**
4646          * Sets the value of the width property.
4647          *
4648          * @param value
4649          *     allowed object is
4650          *     {@link Integer }
4651          *
4652          */
4653         public void setWidth(Integer value) {
4654             this.width = value;
4655         }
4656
4657         /**
4658          * Gets the value of the height property.
4659          *
4660          * @return
4661          *     possible object is
4662          *     {@link Integer }
4663          *
4664          */
4665         public Integer getHeight() {
4666             return height;
4667         }
4668
4669         /**
4670          * Sets the value of the height property.
4671          *
4672          * @param value
4673          *     allowed object is
4674          *     {@link Integer }
4675          *
4676          */
4677         public void setHeight(Integer value) {
4678             this.height = value;
4679         }
4680
4681         /**
4682          * Gets the value of the xpos property.
4683          *
4684          * @return
4685          *     possible object is
4686          *     {@link Integer }
4687          *
4688          */
4689         public Integer getXpos() {
4690             return xpos;
4691         }
4692
4693         /**
4694          * Sets the value of the xpos property.
4695          *
4696          * @param value
4697          *     allowed object is
4698          *     {@link Integer }
4699          *
4700          */
4701         public void setXpos(Integer value) {
4702             this.xpos = value;
4703         }
4704
4705         /**
4706          * Gets the value of the ypos property.
4707          *
4708          * @return
4709          *     possible object is
4710          *     {@link Integer }
4711          *
4712          */
4713         public Integer getYpos() {
4714             return ypos;
4715         }
4716
4717         /**
4718          * Sets the value of the ypos property.
4719          *
4720          * @param value
4721          *     allowed object is
4722          *     {@link Integer }
4723          *
4724          */
4725         public void setYpos(Integer value) {
4726             this.ypos = value;
4727         }
4728
4729     }
4730
4731
4732     /**
4733      * <p>Java class for anonymous complex type.
4734      *
4735      * <p>The following schema fragment specifies the expected content contained within this class.
4736      *
4737      * <pre>
4738      * &lt;complexType>
4739      *   &lt;complexContent>
4740      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4741      *       &lt;sequence>
4742      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4743      *       &lt;/sequence>
4744      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4745      *     &lt;/restriction>
4746      *   &lt;/complexContent>
4747      * &lt;/complexType>
4748      * </pre>
4749      *
4750      *
4751      */
4752     @XmlAccessorType(XmlAccessType.FIELD)
4753     @XmlType(name = "", propOrder = {
4754         "userColourScheme"
4755     })
4756     public static class UserColours {
4757
4758         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4759         protected JalviewUserColours userColourScheme;
4760         @XmlAttribute(name = "id")
4761         protected String id;
4762
4763         /**
4764          * Gets the value of the userColourScheme property.
4765          *
4766          * @return
4767          *     possible object is
4768          *     {@link JalviewUserColours }
4769          *
4770          */
4771         public JalviewUserColours getUserColourScheme() {
4772             return userColourScheme;
4773         }
4774
4775         /**
4776          * Sets the value of the userColourScheme property.
4777          *
4778          * @param value
4779          *     allowed object is
4780          *     {@link JalviewUserColours }
4781          *
4782          */
4783         public void setUserColourScheme(JalviewUserColours value) {
4784             this.userColourScheme = value;
4785         }
4786
4787         /**
4788          * Gets the value of the id property.
4789          *
4790          * @return
4791          *     possible object is
4792          *     {@link String }
4793          *
4794          */
4795         public String getId() {
4796             return id;
4797         }
4798
4799         /**
4800          * Sets the value of the id property.
4801          *
4802          * @param value
4803          *     allowed object is
4804          *     {@link String }
4805          *
4806          */
4807         public void setId(String value) {
4808             this.id = value;
4809         }
4810
4811     }
4812
4813
4814     /**
4815      * <p>Java class for anonymous complex type.
4816      *
4817      * <p>The following schema fragment specifies the expected content contained within this class.
4818      *
4819      * <pre>
4820      * &lt;complexType>
4821      *   &lt;complexContent>
4822      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4823      *       &lt;sequence>
4824      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4825      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4826      *           &lt;complexType>
4827      *             &lt;complexContent>
4828      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4829      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4830      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4831      *               &lt;/restriction>
4832      *             &lt;/complexContent>
4833      *           &lt;/complexType>
4834      *         &lt;/element>
4835      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4836      *           &lt;complexType>
4837      *             &lt;complexContent>
4838      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4839      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4840      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4841      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4842      *               &lt;/extension>
4843      *             &lt;/complexContent>
4844      *           &lt;/complexType>
4845      *         &lt;/element>
4846      *         &lt;element name="overview" minOccurs="0">
4847      *           &lt;complexType>
4848      *             &lt;complexContent>
4849      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4850      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4851      *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4852      *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4853      *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4854      *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4855      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4856      *               &lt;/restriction>
4857      *             &lt;/complexContent>
4858      *           &lt;/complexType>
4859      *         &lt;/element>
4860      *       &lt;/sequence>
4861      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4862      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4863      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4864      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4865      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4866      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4867      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4868      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4869      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4870      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4871      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4872      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4873      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4874      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4875      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4876      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4877      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4878      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4879      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4880      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4881      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4882      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4883      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4884      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4885      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4886      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4887      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4888      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4889      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4890      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4891      *       &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
4892      *       &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
4893      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4894      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4895      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4896      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4897      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4898      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4899      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4900      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4901      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4902      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4903      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4904      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4905      *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4906      *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4907      *     &lt;/restriction>
4908      *   &lt;/complexContent>
4909      * &lt;/complexType>
4910      * </pre>
4911      *
4912      *
4913      */
4914     @XmlAccessorType(XmlAccessType.FIELD)
4915     @XmlType(name = "", propOrder = {
4916         "annotationColours",
4917         "hiddenColumns",
4918         "calcIdParam",
4919         "overview"
4920     })
4921     public static class Viewport {
4922
4923         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4924         protected AnnotationColourScheme annotationColours;
4925         @XmlElement(namespace = "www.jalview.org")
4926         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4927         @XmlElement(namespace = "www.jalview.org")
4928         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4929         @XmlElement(namespace = "www.jalview.org")
4930         protected JalviewModel.Viewport.Overview overview;
4931         @XmlAttribute(name = "conservationSelected")
4932         protected Boolean conservationSelected;
4933         @XmlAttribute(name = "pidSelected")
4934         protected Boolean pidSelected;
4935         @XmlAttribute(name = "bgColour")
4936         protected String bgColour;
4937         @XmlAttribute(name = "consThreshold")
4938         protected Integer consThreshold;
4939         @XmlAttribute(name = "pidThreshold")
4940         protected Integer pidThreshold;
4941         @XmlAttribute(name = "title")
4942         protected String title;
4943         @XmlAttribute(name = "showFullId")
4944         protected Boolean showFullId;
4945         @XmlAttribute(name = "rightAlignIds")
4946         protected Boolean rightAlignIds;
4947         @XmlAttribute(name = "showText")
4948         protected Boolean showText;
4949         @XmlAttribute(name = "showColourText")
4950         protected Boolean showColourText;
4951         @XmlAttribute(name = "showUnconserved")
4952         protected Boolean showUnconserved;
4953         @XmlAttribute(name = "showBoxes")
4954         protected Boolean showBoxes;
4955         @XmlAttribute(name = "wrapAlignment")
4956         protected Boolean wrapAlignment;
4957         @XmlAttribute(name = "renderGaps")
4958         protected Boolean renderGaps;
4959         @XmlAttribute(name = "showSequenceFeatures")
4960         protected Boolean showSequenceFeatures;
4961         @XmlAttribute(name = "showNPfeatureTooltip")
4962         protected Boolean showNPfeatureTooltip;
4963         @XmlAttribute(name = "showDbRefTooltip")
4964         protected Boolean showDbRefTooltip;
4965         @XmlAttribute(name = "followHighlight")
4966         protected Boolean followHighlight;
4967         @XmlAttribute(name = "followSelection")
4968         protected Boolean followSelection;
4969         @XmlAttribute(name = "showAnnotation")
4970         protected Boolean showAnnotation;
4971         @XmlAttribute(name = "centreColumnLabels")
4972         protected Boolean centreColumnLabels;
4973         @XmlAttribute(name = "showGroupConservation")
4974         protected Boolean showGroupConservation;
4975         @XmlAttribute(name = "showGroupConsensus")
4976         protected Boolean showGroupConsensus;
4977         @XmlAttribute(name = "showConsensusHistogram")
4978         protected Boolean showConsensusHistogram;
4979         @XmlAttribute(name = "showSequenceLogo")
4980         protected Boolean showSequenceLogo;
4981         @XmlAttribute(name = "normaliseSequenceLogo")
4982         protected Boolean normaliseSequenceLogo;
4983         @XmlAttribute(name = "ignoreGapsinConsensus")
4984         protected Boolean ignoreGapsinConsensus;
4985         @XmlAttribute(name = "startRes")
4986         protected Integer startRes;
4987         @XmlAttribute(name = "startSeq")
4988         protected Integer startSeq;
4989         @XmlAttribute(name = "charWidth")
4990         protected Integer charWidth;
4991         @XmlAttribute(name = "charHeight")
4992         protected Integer charHeight;
4993         @XmlAttribute(name = "fontName")
4994         protected String fontName;
4995         @XmlAttribute(name = "fontSize")
4996         protected Integer fontSize;
4997         @XmlAttribute(name = "fontStyle")
4998         protected Integer fontStyle;
4999         @XmlAttribute(name = "scaleProteinAsCdna")
5000         protected Boolean scaleProteinAsCdna;
5001         @XmlAttribute(name = "viewName")
5002         protected String viewName;
5003         @XmlAttribute(name = "sequenceSetId")
5004         protected String sequenceSetId;
5005         @XmlAttribute(name = "gatheredViews")
5006         protected Boolean gatheredViews;
5007         @XmlAttribute(name = "textCol1")
5008         protected Integer textCol1;
5009         @XmlAttribute(name = "textCol2")
5010         protected Integer textCol2;
5011         @XmlAttribute(name = "textColThreshold")
5012         protected Integer textColThreshold;
5013         @XmlAttribute(name = "id")
5014         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5015         @XmlID
5016         @XmlSchemaType(name = "ID")
5017         protected String id;
5018         @XmlAttribute(name = "complementId")
5019         protected String complementId;
5020         @XmlAttribute(name = "showComplementFeatures")
5021         protected Boolean showComplementFeatures;
5022         @XmlAttribute(name = "showComplementFeaturesOnTop")
5023         protected Boolean showComplementFeaturesOnTop;
5024         @XmlAttribute(name = "width")
5025         protected Integer width;
5026         @XmlAttribute(name = "height")
5027         protected Integer height;
5028         @XmlAttribute(name = "xpos")
5029         protected Integer xpos;
5030         @XmlAttribute(name = "ypos")
5031         protected Integer ypos;
5032
5033         /**
5034          * Gets the value of the annotationColours property.
5035          *
5036          * @return
5037          *     possible object is
5038          *     {@link AnnotationColourScheme }
5039          *
5040          */
5041         public AnnotationColourScheme getAnnotationColours() {
5042             return annotationColours;
5043         }
5044
5045         /**
5046          * Sets the value of the annotationColours property.
5047          *
5048          * @param value
5049          *     allowed object is
5050          *     {@link AnnotationColourScheme }
5051          *
5052          */
5053         public void setAnnotationColours(AnnotationColourScheme value) {
5054             this.annotationColours = value;
5055         }
5056
5057         /**
5058          * Gets the value of the hiddenColumns property.
5059          *
5060          * <p>
5061          * This accessor method returns a reference to the live list,
5062          * not a snapshot. Therefore any modification you make to the
5063          * returned list will be present inside the JAXB object.
5064          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
5065          *
5066          * <p>
5067          * For example, to add a new item, do as follows:
5068          * <pre>
5069          *    getHiddenColumns().add(newItem);
5070          * </pre>
5071          *
5072          *
5073          * <p>
5074          * Objects of the following type(s) are allowed in the list
5075          * {@link JalviewModel.Viewport.HiddenColumns }
5076          *
5077          *
5078          */
5079         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5080             if (hiddenColumns == null) {
5081                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5082             }
5083             return this.hiddenColumns;
5084         }
5085
5086         /**
5087          * Gets the value of the calcIdParam property.
5088          *
5089          * <p>
5090          * This accessor method returns a reference to the live list,
5091          * not a snapshot. Therefore any modification you make to the
5092          * returned list will be present inside the JAXB object.
5093          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5094          *
5095          * <p>
5096          * For example, to add a new item, do as follows:
5097          * <pre>
5098          *    getCalcIdParam().add(newItem);
5099          * </pre>
5100          *
5101          *
5102          * <p>
5103          * Objects of the following type(s) are allowed in the list
5104          * {@link JalviewModel.Viewport.CalcIdParam }
5105          *
5106          *
5107          */
5108         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5109             if (calcIdParam == null) {
5110                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5111             }
5112             return this.calcIdParam;
5113         }
5114
5115         /**
5116          * Gets the value of the overview property.
5117          *
5118          * @return
5119          *     possible object is
5120          *     {@link JalviewModel.Viewport.Overview }
5121          *
5122          */
5123         public JalviewModel.Viewport.Overview getOverview() {
5124             return overview;
5125         }
5126
5127         /**
5128          * Sets the value of the overview property.
5129          *
5130          * @param value
5131          *     allowed object is
5132          *     {@link JalviewModel.Viewport.Overview }
5133          *
5134          */
5135         public void setOverview(JalviewModel.Viewport.Overview value) {
5136             this.overview = value;
5137         }
5138
5139         /**
5140          * Gets the value of the conservationSelected property.
5141          *
5142          * @return
5143          *     possible object is
5144          *     {@link Boolean }
5145          *
5146          */
5147         public Boolean isConservationSelected() {
5148             return conservationSelected;
5149         }
5150
5151         /**
5152          * Sets the value of the conservationSelected property.
5153          *
5154          * @param value
5155          *     allowed object is
5156          *     {@link Boolean }
5157          *
5158          */
5159         public void setConservationSelected(Boolean value) {
5160             this.conservationSelected = value;
5161         }
5162
5163         /**
5164          * Gets the value of the pidSelected property.
5165          *
5166          * @return
5167          *     possible object is
5168          *     {@link Boolean }
5169          *
5170          */
5171         public Boolean isPidSelected() {
5172             return pidSelected;
5173         }
5174
5175         /**
5176          * Sets the value of the pidSelected property.
5177          *
5178          * @param value
5179          *     allowed object is
5180          *     {@link Boolean }
5181          *
5182          */
5183         public void setPidSelected(Boolean value) {
5184             this.pidSelected = value;
5185         }
5186
5187         /**
5188          * Gets the value of the bgColour property.
5189          *
5190          * @return
5191          *     possible object is
5192          *     {@link String }
5193          *
5194          */
5195         public String getBgColour() {
5196             return bgColour;
5197         }
5198
5199         /**
5200          * Sets the value of the bgColour property.
5201          *
5202          * @param value
5203          *     allowed object is
5204          *     {@link String }
5205          *
5206          */
5207         public void setBgColour(String value) {
5208             this.bgColour = value;
5209         }
5210
5211         /**
5212          * Gets the value of the consThreshold property.
5213          *
5214          * @return
5215          *     possible object is
5216          *     {@link Integer }
5217          *
5218          */
5219         public Integer getConsThreshold() {
5220             return consThreshold;
5221         }
5222
5223         /**
5224          * Sets the value of the consThreshold property.
5225          *
5226          * @param value
5227          *     allowed object is
5228          *     {@link Integer }
5229          *
5230          */
5231         public void setConsThreshold(Integer value) {
5232             this.consThreshold = value;
5233         }
5234
5235         /**
5236          * Gets the value of the pidThreshold property.
5237          *
5238          * @return
5239          *     possible object is
5240          *     {@link Integer }
5241          *
5242          */
5243         public Integer getPidThreshold() {
5244             return pidThreshold;
5245         }
5246
5247         /**
5248          * Sets the value of the pidThreshold property.
5249          *
5250          * @param value
5251          *     allowed object is
5252          *     {@link Integer }
5253          *
5254          */
5255         public void setPidThreshold(Integer value) {
5256             this.pidThreshold = value;
5257         }
5258
5259         /**
5260          * Gets the value of the title property.
5261          *
5262          * @return
5263          *     possible object is
5264          *     {@link String }
5265          *
5266          */
5267         public String getTitle() {
5268             return title;
5269         }
5270
5271         /**
5272          * Sets the value of the title property.
5273          *
5274          * @param value
5275          *     allowed object is
5276          *     {@link String }
5277          *
5278          */
5279         public void setTitle(String value) {
5280             this.title = value;
5281         }
5282
5283         /**
5284          * Gets the value of the showFullId property.
5285          *
5286          * @return
5287          *     possible object is
5288          *     {@link Boolean }
5289          *
5290          */
5291         public Boolean isShowFullId() {
5292             return showFullId;
5293         }
5294
5295         /**
5296          * Sets the value of the showFullId property.
5297          *
5298          * @param value
5299          *     allowed object is
5300          *     {@link Boolean }
5301          *
5302          */
5303         public void setShowFullId(Boolean value) {
5304             this.showFullId = value;
5305         }
5306
5307         /**
5308          * Gets the value of the rightAlignIds property.
5309          *
5310          * @return
5311          *     possible object is
5312          *     {@link Boolean }
5313          *
5314          */
5315         public Boolean isRightAlignIds() {
5316             return rightAlignIds;
5317         }
5318
5319         /**
5320          * Sets the value of the rightAlignIds property.
5321          *
5322          * @param value
5323          *     allowed object is
5324          *     {@link Boolean }
5325          *
5326          */
5327         public void setRightAlignIds(Boolean value) {
5328             this.rightAlignIds = value;
5329         }
5330
5331         /**
5332          * Gets the value of the showText property.
5333          *
5334          * @return
5335          *     possible object is
5336          *     {@link Boolean }
5337          *
5338          */
5339         public Boolean isShowText() {
5340             return showText;
5341         }
5342
5343         /**
5344          * Sets the value of the showText property.
5345          *
5346          * @param value
5347          *     allowed object is
5348          *     {@link Boolean }
5349          *
5350          */
5351         public void setShowText(Boolean value) {
5352             this.showText = value;
5353         }
5354
5355         /**
5356          * Gets the value of the showColourText property.
5357          *
5358          * @return
5359          *     possible object is
5360          *     {@link Boolean }
5361          *
5362          */
5363         public Boolean isShowColourText() {
5364             return showColourText;
5365         }
5366
5367         /**
5368          * Sets the value of the showColourText property.
5369          *
5370          * @param value
5371          *     allowed object is
5372          *     {@link Boolean }
5373          *
5374          */
5375         public void setShowColourText(Boolean value) {
5376             this.showColourText = value;
5377         }
5378
5379         /**
5380          * Gets the value of the showUnconserved property.
5381          *
5382          * @return
5383          *     possible object is
5384          *     {@link Boolean }
5385          *
5386          */
5387         public boolean isShowUnconserved() {
5388             if (showUnconserved == null) {
5389                 return false;
5390             } else {
5391                 return showUnconserved;
5392             }
5393         }
5394
5395         /**
5396          * Sets the value of the showUnconserved property.
5397          *
5398          * @param value
5399          *     allowed object is
5400          *     {@link Boolean }
5401          *
5402          */
5403         public void setShowUnconserved(Boolean value) {
5404             this.showUnconserved = value;
5405         }
5406
5407         /**
5408          * Gets the value of the showBoxes property.
5409          *
5410          * @return
5411          *     possible object is
5412          *     {@link Boolean }
5413          *
5414          */
5415         public Boolean isShowBoxes() {
5416             return showBoxes;
5417         }
5418
5419         /**
5420          * Sets the value of the showBoxes property.
5421          *
5422          * @param value
5423          *     allowed object is
5424          *     {@link Boolean }
5425          *
5426          */
5427         public void setShowBoxes(Boolean value) {
5428             this.showBoxes = value;
5429         }
5430
5431         /**
5432          * Gets the value of the wrapAlignment property.
5433          *
5434          * @return
5435          *     possible object is
5436          *     {@link Boolean }
5437          *
5438          */
5439         public Boolean isWrapAlignment() {
5440             return wrapAlignment;
5441         }
5442
5443         /**
5444          * Sets the value of the wrapAlignment property.
5445          *
5446          * @param value
5447          *     allowed object is
5448          *     {@link Boolean }
5449          *
5450          */
5451         public void setWrapAlignment(Boolean value) {
5452             this.wrapAlignment = value;
5453         }
5454
5455         /**
5456          * Gets the value of the renderGaps property.
5457          *
5458          * @return
5459          *     possible object is
5460          *     {@link Boolean }
5461          *
5462          */
5463         public Boolean isRenderGaps() {
5464             return renderGaps;
5465         }
5466
5467         /**
5468          * Sets the value of the renderGaps property.
5469          *
5470          * @param value
5471          *     allowed object is
5472          *     {@link Boolean }
5473          *
5474          */
5475         public void setRenderGaps(Boolean value) {
5476             this.renderGaps = value;
5477         }
5478
5479         /**
5480          * Gets the value of the showSequenceFeatures property.
5481          *
5482          * @return
5483          *     possible object is
5484          *     {@link Boolean }
5485          *
5486          */
5487         public Boolean isShowSequenceFeatures() {
5488             return showSequenceFeatures;
5489         }
5490
5491         /**
5492          * Sets the value of the showSequenceFeatures property.
5493          *
5494          * @param value
5495          *     allowed object is
5496          *     {@link Boolean }
5497          *
5498          */
5499         public void setShowSequenceFeatures(Boolean value) {
5500             this.showSequenceFeatures = value;
5501         }
5502
5503         /**
5504          * Gets the value of the showNPfeatureTooltip property.
5505          *
5506          * @return
5507          *     possible object is
5508          *     {@link Boolean }
5509          *
5510          */
5511         public Boolean isShowNPfeatureTooltip() {
5512             return showNPfeatureTooltip;
5513         }
5514
5515         /**
5516          * Sets the value of the showNPfeatureTooltip property.
5517          *
5518          * @param value
5519          *     allowed object is
5520          *     {@link Boolean }
5521          *
5522          */
5523         public void setShowNPfeatureTooltip(Boolean value) {
5524             this.showNPfeatureTooltip = value;
5525         }
5526
5527         /**
5528          * Gets the value of the showDbRefTooltip property.
5529          *
5530          * @return
5531          *     possible object is
5532          *     {@link Boolean }
5533          *
5534          */
5535         public Boolean isShowDbRefTooltip() {
5536             return showDbRefTooltip;
5537         }
5538
5539         /**
5540          * Sets the value of the showDbRefTooltip property.
5541          *
5542          * @param value
5543          *     allowed object is
5544          *     {@link Boolean }
5545          *
5546          */
5547         public void setShowDbRefTooltip(Boolean value) {
5548             this.showDbRefTooltip = value;
5549         }
5550
5551         /**
5552          * Gets the value of the followHighlight property.
5553          *
5554          * @return
5555          *     possible object is
5556          *     {@link Boolean }
5557          *
5558          */
5559         public boolean isFollowHighlight() {
5560             if (followHighlight == null) {
5561                 return true;
5562             } else {
5563                 return followHighlight;
5564             }
5565         }
5566
5567         /**
5568          * Sets the value of the followHighlight property.
5569          *
5570          * @param value
5571          *     allowed object is
5572          *     {@link Boolean }
5573          *
5574          */
5575         public void setFollowHighlight(Boolean value) {
5576             this.followHighlight = value;
5577         }
5578
5579         /**
5580          * Gets the value of the followSelection property.
5581          *
5582          * @return
5583          *     possible object is
5584          *     {@link Boolean }
5585          *
5586          */
5587         public boolean isFollowSelection() {
5588             if (followSelection == null) {
5589                 return true;
5590             } else {
5591                 return followSelection;
5592             }
5593         }
5594
5595         /**
5596          * Sets the value of the followSelection property.
5597          *
5598          * @param value
5599          *     allowed object is
5600          *     {@link Boolean }
5601          *
5602          */
5603         public void setFollowSelection(Boolean value) {
5604             this.followSelection = value;
5605         }
5606
5607         /**
5608          * Gets the value of the showAnnotation property.
5609          *
5610          * @return
5611          *     possible object is
5612          *     {@link Boolean }
5613          *
5614          */
5615         public Boolean isShowAnnotation() {
5616             return showAnnotation;
5617         }
5618
5619         /**
5620          * Sets the value of the showAnnotation property.
5621          *
5622          * @param value
5623          *     allowed object is
5624          *     {@link Boolean }
5625          *
5626          */
5627         public void setShowAnnotation(Boolean value) {
5628             this.showAnnotation = value;
5629         }
5630
5631         /**
5632          * Gets the value of the centreColumnLabels property.
5633          *
5634          * @return
5635          *     possible object is
5636          *     {@link Boolean }
5637          *
5638          */
5639         public boolean isCentreColumnLabels() {
5640             if (centreColumnLabels == null) {
5641                 return false;
5642             } else {
5643                 return centreColumnLabels;
5644             }
5645         }
5646
5647         /**
5648          * Sets the value of the centreColumnLabels property.
5649          *
5650          * @param value
5651          *     allowed object is
5652          *     {@link Boolean }
5653          *
5654          */
5655         public void setCentreColumnLabels(Boolean value) {
5656             this.centreColumnLabels = value;
5657         }
5658
5659         /**
5660          * Gets the value of the showGroupConservation property.
5661          *
5662          * @return
5663          *     possible object is
5664          *     {@link Boolean }
5665          *
5666          */
5667         public boolean isShowGroupConservation() {
5668             if (showGroupConservation == null) {
5669                 return false;
5670             } else {
5671                 return showGroupConservation;
5672             }
5673         }
5674
5675         /**
5676          * Sets the value of the showGroupConservation property.
5677          *
5678          * @param value
5679          *     allowed object is
5680          *     {@link Boolean }
5681          *
5682          */
5683         public void setShowGroupConservation(Boolean value) {
5684             this.showGroupConservation = value;
5685         }
5686
5687         /**
5688          * Gets the value of the showGroupConsensus property.
5689          *
5690          * @return
5691          *     possible object is
5692          *     {@link Boolean }
5693          *
5694          */
5695         public boolean isShowGroupConsensus() {
5696             if (showGroupConsensus == null) {
5697                 return false;
5698             } else {
5699                 return showGroupConsensus;
5700             }
5701         }
5702
5703         /**
5704          * Sets the value of the showGroupConsensus property.
5705          *
5706          * @param value
5707          *     allowed object is
5708          *     {@link Boolean }
5709          *
5710          */
5711         public void setShowGroupConsensus(Boolean value) {
5712             this.showGroupConsensus = value;
5713         }
5714
5715         /**
5716          * Gets the value of the showConsensusHistogram property.
5717          *
5718          * @return
5719          *     possible object is
5720          *     {@link Boolean }
5721          *
5722          */
5723         public boolean isShowConsensusHistogram() {
5724             if (showConsensusHistogram == null) {
5725                 return true;
5726             } else {
5727                 return showConsensusHistogram;
5728             }
5729         }
5730
5731         /**
5732          * Sets the value of the showConsensusHistogram property.
5733          *
5734          * @param value
5735          *     allowed object is
5736          *     {@link Boolean }
5737          *
5738          */
5739         public void setShowConsensusHistogram(Boolean value) {
5740             this.showConsensusHistogram = value;
5741         }
5742
5743         /**
5744          * Gets the value of the showSequenceLogo property.
5745          *
5746          * @return
5747          *     possible object is
5748          *     {@link Boolean }
5749          *
5750          */
5751         public boolean isShowSequenceLogo() {
5752             if (showSequenceLogo == null) {
5753                 return false;
5754             } else {
5755                 return showSequenceLogo;
5756             }
5757         }
5758
5759         /**
5760          * Sets the value of the showSequenceLogo property.
5761          *
5762          * @param value
5763          *     allowed object is
5764          *     {@link Boolean }
5765          *
5766          */
5767         public void setShowSequenceLogo(Boolean value) {
5768             this.showSequenceLogo = value;
5769         }
5770
5771         /**
5772          * Gets the value of the normaliseSequenceLogo property.
5773          *
5774          * @return
5775          *     possible object is
5776          *     {@link Boolean }
5777          *
5778          */
5779         public boolean isNormaliseSequenceLogo() {
5780             if (normaliseSequenceLogo == null) {
5781                 return false;
5782             } else {
5783                 return normaliseSequenceLogo;
5784             }
5785         }
5786
5787         /**
5788          * Sets the value of the normaliseSequenceLogo property.
5789          *
5790          * @param value
5791          *     allowed object is
5792          *     {@link Boolean }
5793          *
5794          */
5795         public void setNormaliseSequenceLogo(Boolean value) {
5796             this.normaliseSequenceLogo = value;
5797         }
5798
5799         /**
5800          * Gets the value of the ignoreGapsinConsensus property.
5801          *
5802          * @return
5803          *     possible object is
5804          *     {@link Boolean }
5805          *
5806          */
5807         public boolean isIgnoreGapsinConsensus() {
5808             if (ignoreGapsinConsensus == null) {
5809                 return true;
5810             } else {
5811                 return ignoreGapsinConsensus;
5812             }
5813         }
5814
5815         /**
5816          * Sets the value of the ignoreGapsinConsensus property.
5817          *
5818          * @param value
5819          *     allowed object is
5820          *     {@link Boolean }
5821          *
5822          */
5823         public void setIgnoreGapsinConsensus(Boolean value) {
5824             this.ignoreGapsinConsensus = value;
5825         }
5826
5827         /**
5828          * Gets the value of the startRes property.
5829          *
5830          * @return
5831          *     possible object is
5832          *     {@link Integer }
5833          *
5834          */
5835         public Integer getStartRes() {
5836             return startRes;
5837         }
5838
5839         /**
5840          * Sets the value of the startRes property.
5841          *
5842          * @param value
5843          *     allowed object is
5844          *     {@link Integer }
5845          *
5846          */
5847         public void setStartRes(Integer value) {
5848             this.startRes = value;
5849         }
5850
5851         /**
5852          * Gets the value of the startSeq property.
5853          *
5854          * @return
5855          *     possible object is
5856          *     {@link Integer }
5857          *
5858          */
5859         public Integer getStartSeq() {
5860             return startSeq;
5861         }
5862
5863         /**
5864          * Sets the value of the startSeq property.
5865          *
5866          * @param value
5867          *     allowed object is
5868          *     {@link Integer }
5869          *
5870          */
5871         public void setStartSeq(Integer value) {
5872             this.startSeq = value;
5873         }
5874
5875         /**
5876          * Gets the value of the charWidth property.
5877          *
5878          * @return
5879          *     possible object is
5880          *     {@link Integer }
5881          *
5882          */
5883         public Integer getCharWidth() {
5884             return charWidth;
5885         }
5886
5887         /**
5888          * Sets the value of the charWidth property.
5889          *
5890          * @param value
5891          *     allowed object is
5892          *     {@link Integer }
5893          *
5894          */
5895         public void setCharWidth(Integer value) {
5896             this.charWidth = value;
5897         }
5898
5899         /**
5900          * Gets the value of the charHeight property.
5901          *
5902          * @return
5903          *     possible object is
5904          *     {@link Integer }
5905          *
5906          */
5907         public Integer getCharHeight() {
5908             return charHeight;
5909         }
5910
5911         /**
5912          * Sets the value of the charHeight property.
5913          *
5914          * @param value
5915          *     allowed object is
5916          *     {@link Integer }
5917          *
5918          */
5919         public void setCharHeight(Integer value) {
5920             this.charHeight = value;
5921         }
5922
5923         /**
5924          * Gets the value of the fontName property.
5925          *
5926          * @return
5927          *     possible object is
5928          *     {@link String }
5929          *
5930          */
5931         public String getFontName() {
5932             return fontName;
5933         }
5934
5935         /**
5936          * Sets the value of the fontName property.
5937          *
5938          * @param value
5939          *     allowed object is
5940          *     {@link String }
5941          *
5942          */
5943         public void setFontName(String value) {
5944             this.fontName = value;
5945         }
5946
5947         /**
5948          * Gets the value of the fontSize property.
5949          *
5950          * @return
5951          *     possible object is
5952          *     {@link Integer }
5953          *
5954          */
5955         public Integer getFontSize() {
5956             return fontSize;
5957         }
5958
5959         /**
5960          * Sets the value of the fontSize property.
5961          *
5962          * @param value
5963          *     allowed object is
5964          *     {@link Integer }
5965          *
5966          */
5967         public void setFontSize(Integer value) {
5968             this.fontSize = value;
5969         }
5970
5971         /**
5972          * Gets the value of the fontStyle property.
5973          *
5974          * @return
5975          *     possible object is
5976          *     {@link Integer }
5977          *
5978          */
5979         public Integer getFontStyle() {
5980             return fontStyle;
5981         }
5982
5983         /**
5984          * Sets the value of the fontStyle property.
5985          *
5986          * @param value
5987          *     allowed object is
5988          *     {@link Integer }
5989          *
5990          */
5991         public void setFontStyle(Integer value) {
5992             this.fontStyle = value;
5993         }
5994
5995         /**
5996          * Gets the value of the scaleProteinAsCdna property.
5997          *
5998          * @return
5999          *     possible object is
6000          *     {@link Boolean }
6001          *
6002          */
6003         public boolean isScaleProteinAsCdna() {
6004             if (scaleProteinAsCdna == null) {
6005                 return true;
6006             } else {
6007                 return scaleProteinAsCdna;
6008             }
6009         }
6010
6011         /**
6012          * Sets the value of the scaleProteinAsCdna property.
6013          *
6014          * @param value
6015          *     allowed object is
6016          *     {@link Boolean }
6017          *
6018          */
6019         public void setScaleProteinAsCdna(Boolean value) {
6020             this.scaleProteinAsCdna = value;
6021         }
6022
6023         /**
6024          * Gets the value of the viewName property.
6025          *
6026          * @return
6027          *     possible object is
6028          *     {@link String }
6029          *
6030          */
6031         public String getViewName() {
6032             return viewName;
6033         }
6034
6035         /**
6036          * Sets the value of the viewName property.
6037          *
6038          * @param value
6039          *     allowed object is
6040          *     {@link String }
6041          *
6042          */
6043         public void setViewName(String value) {
6044             this.viewName = value;
6045         }
6046
6047         /**
6048          * Gets the value of the sequenceSetId property.
6049          *
6050          * @return
6051          *     possible object is
6052          *     {@link String }
6053          *
6054          */
6055         public String getSequenceSetId() {
6056             return sequenceSetId;
6057         }
6058
6059         /**
6060          * Sets the value of the sequenceSetId property.
6061          *
6062          * @param value
6063          *     allowed object is
6064          *     {@link String }
6065          *
6066          */
6067         public void setSequenceSetId(String value) {
6068             this.sequenceSetId = value;
6069         }
6070
6071         /**
6072          * Gets the value of the gatheredViews property.
6073          *
6074          * @return
6075          *     possible object is
6076          *     {@link Boolean }
6077          *
6078          */
6079         public Boolean isGatheredViews() {
6080             return gatheredViews;
6081         }
6082
6083         /**
6084          * Sets the value of the gatheredViews property.
6085          *
6086          * @param value
6087          *     allowed object is
6088          *     {@link Boolean }
6089          *
6090          */
6091         public void setGatheredViews(Boolean value) {
6092             this.gatheredViews = value;
6093         }
6094
6095         /**
6096          * Gets the value of the textCol1 property.
6097          *
6098          * @return
6099          *     possible object is
6100          *     {@link Integer }
6101          *
6102          */
6103         public Integer getTextCol1() {
6104             return textCol1;
6105         }
6106
6107         /**
6108          * Sets the value of the textCol1 property.
6109          *
6110          * @param value
6111          *     allowed object is
6112          *     {@link Integer }
6113          *
6114          */
6115         public void setTextCol1(Integer value) {
6116             this.textCol1 = value;
6117         }
6118
6119         /**
6120          * Gets the value of the textCol2 property.
6121          *
6122          * @return
6123          *     possible object is
6124          *     {@link Integer }
6125          *
6126          */
6127         public Integer getTextCol2() {
6128             return textCol2;
6129         }
6130
6131         /**
6132          * Sets the value of the textCol2 property.
6133          *
6134          * @param value
6135          *     allowed object is
6136          *     {@link Integer }
6137          *
6138          */
6139         public void setTextCol2(Integer value) {
6140             this.textCol2 = value;
6141         }
6142
6143         /**
6144          * Gets the value of the textColThreshold property.
6145          *
6146          * @return
6147          *     possible object is
6148          *     {@link Integer }
6149          *
6150          */
6151         public Integer getTextColThreshold() {
6152             return textColThreshold;
6153         }
6154
6155         /**
6156          * Sets the value of the textColThreshold property.
6157          *
6158          * @param value
6159          *     allowed object is
6160          *     {@link Integer }
6161          *
6162          */
6163         public void setTextColThreshold(Integer value) {
6164             this.textColThreshold = value;
6165         }
6166
6167         /**
6168          * Gets the value of the id property.
6169          *
6170          * @return
6171          *     possible object is
6172          *     {@link String }
6173          *
6174          */
6175         public String getId() {
6176             return id;
6177         }
6178
6179         /**
6180          * Sets the value of the id property.
6181          *
6182          * @param value
6183          *     allowed object is
6184          *     {@link String }
6185          *
6186          */
6187         public void setId(String value) {
6188             this.id = value;
6189         }
6190
6191         /**
6192          * Gets the value of the complementId property.
6193          *
6194          * @return
6195          *     possible object is
6196          *     {@link String }
6197          *
6198          */
6199         public String getComplementId() {
6200             return complementId;
6201         }
6202
6203         /**
6204          * Sets the value of the complementId property.
6205          *
6206          * @param value
6207          *     allowed object is
6208          *     {@link String }
6209          *
6210          */
6211         public void setComplementId(String value) {
6212             this.complementId = value;
6213         }
6214
6215         /**
6216          * Gets the value of the showComplementFeatures property.
6217          *
6218          * @return
6219          *     possible object is
6220          *     {@link Boolean }
6221          *
6222          */
6223         public boolean isShowComplementFeatures() {
6224             if (showComplementFeatures == null) {
6225                 return false;
6226             } else {
6227                 return showComplementFeatures;
6228             }
6229         }
6230
6231         /**
6232          * Sets the value of the showComplementFeatures property.
6233          *
6234          * @param value
6235          *     allowed object is
6236          *     {@link Boolean }
6237          *
6238          */
6239         public void setShowComplementFeatures(Boolean value) {
6240             this.showComplementFeatures = value;
6241         }
6242
6243         /**
6244          * Gets the value of the showComplementFeaturesOnTop property.
6245          *
6246          * @return
6247          *     possible object is
6248          *     {@link Boolean }
6249          *
6250          */
6251         public boolean isShowComplementFeaturesOnTop() {
6252             if (showComplementFeaturesOnTop == null) {
6253                 return false;
6254             } else {
6255                 return showComplementFeaturesOnTop;
6256             }
6257         }
6258
6259         /**
6260          * Sets the value of the showComplementFeaturesOnTop property.
6261          *
6262          * @param value
6263          *     allowed object is
6264          *     {@link Boolean }
6265          *
6266          */
6267         public void setShowComplementFeaturesOnTop(Boolean value) {
6268             this.showComplementFeaturesOnTop = value;
6269         }
6270
6271         /**
6272          * Gets the value of the width property.
6273          *
6274          * @return
6275          *     possible object is
6276          *     {@link Integer }
6277          *
6278          */
6279         public Integer getWidth() {
6280             return width;
6281         }
6282
6283         /**
6284          * Sets the value of the width property.
6285          *
6286          * @param value
6287          *     allowed object is
6288          *     {@link Integer }
6289          *
6290          */
6291         public void setWidth(Integer value) {
6292             this.width = value;
6293         }
6294
6295         /**
6296          * Gets the value of the height property.
6297          *
6298          * @return
6299          *     possible object is
6300          *     {@link Integer }
6301          *
6302          */
6303         public Integer getHeight() {
6304             return height;
6305         }
6306
6307         /**
6308          * Sets the value of the height property.
6309          *
6310          * @param value
6311          *     allowed object is
6312          *     {@link Integer }
6313          *
6314          */
6315         public void setHeight(Integer value) {
6316             this.height = value;
6317         }
6318
6319         /**
6320          * Gets the value of the xpos property.
6321          *
6322          * @return
6323          *     possible object is
6324          *     {@link Integer }
6325          *
6326          */
6327         public Integer getXpos() {
6328             return xpos;
6329         }
6330
6331         /**
6332          * Sets the value of the xpos property.
6333          *
6334          * @param value
6335          *     allowed object is
6336          *     {@link Integer }
6337          *
6338          */
6339         public void setXpos(Integer value) {
6340             this.xpos = value;
6341         }
6342
6343         /**
6344          * Gets the value of the ypos property.
6345          *
6346          * @return
6347          *     possible object is
6348          *     {@link Integer }
6349          *
6350          */
6351         public Integer getYpos() {
6352             return ypos;
6353         }
6354
6355         /**
6356          * Sets the value of the ypos property.
6357          *
6358          * @param value
6359          *     allowed object is
6360          *     {@link Integer }
6361          *
6362          */
6363         public void setYpos(Integer value) {
6364             this.ypos = value;
6365         }
6366
6367
6368         /**
6369          * <p>Java class for anonymous complex type.
6370          *
6371          * <p>The following schema fragment specifies the expected content contained within this class.
6372          *
6373          * <pre>
6374          * &lt;complexType>
6375          *   &lt;complexContent>
6376          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6377          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6378          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6379          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6380          *     &lt;/extension>
6381          *   &lt;/complexContent>
6382          * &lt;/complexType>
6383          * </pre>
6384          *
6385          *
6386          */
6387         @XmlAccessorType(XmlAccessType.FIELD)
6388         @XmlType(name = "")
6389         public static class CalcIdParam
6390             extends WebServiceParameterSet
6391         {
6392
6393             @XmlAttribute(name = "calcId", required = true)
6394             protected String calcId;
6395             @XmlAttribute(name = "needsUpdate")
6396             protected Boolean needsUpdate;
6397             @XmlAttribute(name = "autoUpdate", required = true)
6398             protected boolean autoUpdate;
6399
6400             /**
6401              * Gets the value of the calcId property.
6402              *
6403              * @return
6404              *     possible object is
6405              *     {@link String }
6406              *
6407              */
6408             public String getCalcId() {
6409                 return calcId;
6410             }
6411
6412             /**
6413              * Sets the value of the calcId property.
6414              *
6415              * @param value
6416              *     allowed object is
6417              *     {@link String }
6418              *
6419              */
6420             public void setCalcId(String value) {
6421                 this.calcId = value;
6422             }
6423
6424             /**
6425              * Gets the value of the needsUpdate property.
6426              *
6427              * @return
6428              *     possible object is
6429              *     {@link Boolean }
6430              *
6431              */
6432             public boolean isNeedsUpdate() {
6433                 if (needsUpdate == null) {
6434                     return false;
6435                 } else {
6436                     return needsUpdate;
6437                 }
6438             }
6439
6440             /**
6441              * Sets the value of the needsUpdate property.
6442              *
6443              * @param value
6444              *     allowed object is
6445              *     {@link Boolean }
6446              *
6447              */
6448             public void setNeedsUpdate(Boolean value) {
6449                 this.needsUpdate = value;
6450             }
6451
6452             /**
6453              * Gets the value of the autoUpdate property.
6454              *
6455              */
6456             public boolean isAutoUpdate() {
6457                 return autoUpdate;
6458             }
6459
6460             /**
6461              * Sets the value of the autoUpdate property.
6462              *
6463              */
6464             public void setAutoUpdate(boolean value) {
6465                 this.autoUpdate = value;
6466             }
6467
6468         }
6469
6470
6471         /**
6472          * <p>Java class for anonymous complex type.
6473          *
6474          * <p>The following schema fragment specifies the expected content contained within this class.
6475          *
6476          * <pre>
6477          * &lt;complexType>
6478          *   &lt;complexContent>
6479          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6480          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6481          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6482          *     &lt;/restriction>
6483          *   &lt;/complexContent>
6484          * &lt;/complexType>
6485          * </pre>
6486          *
6487          *
6488          */
6489         @XmlAccessorType(XmlAccessType.FIELD)
6490         @XmlType(name = "")
6491         public static class HiddenColumns {
6492
6493             @XmlAttribute(name = "start")
6494             protected Integer start;
6495             @XmlAttribute(name = "end")
6496             protected Integer end;
6497
6498             /**
6499              * Gets the value of the start property.
6500              *
6501              * @return
6502              *     possible object is
6503              *     {@link Integer }
6504              *
6505              */
6506             public Integer getStart() {
6507                 return start;
6508             }
6509
6510             /**
6511              * Sets the value of the start property.
6512              *
6513              * @param value
6514              *     allowed object is
6515              *     {@link Integer }
6516              *
6517              */
6518             public void setStart(Integer value) {
6519                 this.start = value;
6520             }
6521
6522             /**
6523              * Gets the value of the end property.
6524              *
6525              * @return
6526              *     possible object is
6527              *     {@link Integer }
6528              *
6529              */
6530             public Integer getEnd() {
6531                 return end;
6532             }
6533
6534             /**
6535              * Sets the value of the end property.
6536              *
6537              * @param value
6538              *     allowed object is
6539              *     {@link Integer }
6540              *
6541              */
6542             public void setEnd(Integer value) {
6543                 this.end = value;
6544             }
6545
6546         }
6547
6548
6549         /**
6550          * <p>Java class for anonymous complex type.
6551          *
6552          * <p>The following schema fragment specifies the expected content contained within this class.
6553          *
6554          * <pre>
6555          * &lt;complexType>
6556          *   &lt;complexContent>
6557          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6558          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
6559          *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6560          *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6561          *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6562          *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6563          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6564          *     &lt;/restriction>
6565          *   &lt;/complexContent>
6566          * &lt;/complexType>
6567          * </pre>
6568          *
6569          *
6570          */
6571         @XmlAccessorType(XmlAccessType.FIELD)
6572         @XmlType(name = "")
6573         public static class Overview {
6574
6575             @XmlAttribute(name = "showHidden")
6576             protected Boolean showHidden;
6577             @XmlAttribute(name = "residueColour")
6578             protected Integer residueColour;
6579             @XmlAttribute(name = "gapColour")
6580             protected Integer gapColour;
6581             @XmlAttribute(name = "hiddenColour")
6582             protected Integer hiddenColour;
6583             @XmlAttribute(name = "title")
6584             protected String title;
6585             @XmlAttribute(name = "width")
6586             protected Integer width;
6587             @XmlAttribute(name = "height")
6588             protected Integer height;
6589             @XmlAttribute(name = "xpos")
6590             protected Integer xpos;
6591             @XmlAttribute(name = "ypos")
6592             protected Integer ypos;
6593
6594             /**
6595              * Gets the value of the showHidden property.
6596              *
6597              * @return
6598              *     possible object is
6599              *     {@link Boolean }
6600              *
6601              */
6602             public Boolean isShowHidden() {
6603                 return showHidden;
6604             }
6605
6606             /**
6607              * Sets the value of the showHidden property.
6608              *
6609              * @param value
6610              *     allowed object is
6611              *     {@link Boolean }
6612              *
6613              */
6614             public void setShowHidden(Boolean value) {
6615                 this.showHidden = value;
6616             }
6617
6618             /**
6619              * Gets the value of the residueColour property.
6620              *
6621              * @return
6622              *     possible object is
6623              *     {@link Integer }
6624              *
6625              */
6626             public Integer getResidueColour() {
6627                 return residueColour;
6628             }
6629
6630             /**
6631              * Sets the value of the residueColour property.
6632              *
6633              * @param value
6634              *     allowed object is
6635              *     {@link Integer }
6636              *
6637              */
6638             public void setResidueColour(Integer value) {
6639                 this.residueColour = value;
6640             }
6641
6642             /**
6643              * Gets the value of the gapColour property.
6644              *
6645              * @return
6646              *     possible object is
6647              *     {@link Integer }
6648              *
6649              */
6650             public Integer getGapColour() {
6651                 return gapColour;
6652             }
6653
6654             /**
6655              * Sets the value of the gapColour property.
6656              *
6657              * @param value
6658              *     allowed object is
6659              *     {@link Integer }
6660              *
6661              */
6662             public void setGapColour(Integer value) {
6663                 this.gapColour = value;
6664             }
6665
6666             /**
6667              * Gets the value of the hiddenColour property.
6668              *
6669              * @return
6670              *     possible object is
6671              *     {@link Integer }
6672              *
6673              */
6674             public Integer getHiddenColour() {
6675                 return hiddenColour;
6676             }
6677
6678             /**
6679              * Sets the value of the hiddenColour property.
6680              *
6681              * @param value
6682              *     allowed object is
6683              *     {@link Integer }
6684              *
6685              */
6686             public void setHiddenColour(Integer value) {
6687                 this.hiddenColour = value;
6688             }
6689
6690             /**
6691              * Gets the value of the title property.
6692              *
6693              * @return
6694              *     possible object is
6695              *     {@link String }
6696              *
6697              */
6698             public String getTitle() {
6699                 return title;
6700             }
6701
6702             /**
6703              * Sets the value of the title property.
6704              *
6705              * @param value
6706              *     allowed object is
6707              *     {@link String }
6708              *
6709              */
6710             public void setTitle(String value) {
6711                 this.title = value;
6712             }
6713
6714             /**
6715              * Gets the value of the width property.
6716              *
6717              * @return
6718              *     possible object is
6719              *     {@link Integer }
6720              *
6721              */
6722             public Integer getWidth() {
6723                 return width;
6724             }
6725
6726             /**
6727              * Sets the value of the width property.
6728              *
6729              * @param value
6730              *     allowed object is
6731              *     {@link Integer }
6732              *
6733              */
6734             public void setWidth(Integer value) {
6735                 this.width = value;
6736             }
6737
6738             /**
6739              * Gets the value of the height property.
6740              *
6741              * @return
6742              *     possible object is
6743              *     {@link Integer }
6744              *
6745              */
6746             public Integer getHeight() {
6747                 return height;
6748             }
6749
6750             /**
6751              * Sets the value of the height property.
6752              *
6753              * @param value
6754              *     allowed object is
6755              *     {@link Integer }
6756              *
6757              */
6758             public void setHeight(Integer value) {
6759                 this.height = value;
6760             }
6761
6762             /**
6763              * Gets the value of the xpos property.
6764              *
6765              * @return
6766              *     possible object is
6767              *     {@link Integer }
6768              *
6769              */
6770             public Integer getXpos() {
6771                 return xpos;
6772             }
6773
6774             /**
6775              * Sets the value of the xpos property.
6776              *
6777              * @param value
6778              *     allowed object is
6779              *     {@link Integer }
6780              *
6781              */
6782             public void setXpos(Integer value) {
6783                 this.xpos = value;
6784             }
6785
6786             /**
6787              * Gets the value of the ypos property.
6788              *
6789              * @return
6790              *     possible object is
6791              *     {@link Integer }
6792              *
6793              */
6794             public Integer getYpos() {
6795                 return ypos;
6796             }
6797
6798             /**
6799              * Sets the value of the ypos property.
6800              *
6801              * @param value
6802              *     allowed object is
6803              *     {@link Integer }
6804              *
6805              */
6806             public void setYpos(Integer value) {
6807                 this.ypos = value;
6808             }
6809
6810         }
6811
6812     }
6813
6814 }