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: 2018.09.28 at 12:18:54 PM BST
   6 //
   7
   8
   9 package jalview.xml.binding.jalview;
  10
  11 import java.util.ArrayList;
  12 import java.util.List;
  13 import javax.xml.bind.annotation.XmlAccessType;
  14 import javax.xml.bind.annotation.XmlAccessorType;
  15 import javax.xml.bind.annotation.XmlAttribute;
  16 import javax.xml.bind.annotation.XmlElement;
  17 import javax.xml.bind.annotation.XmlID;
  18 import javax.xml.bind.annotation.XmlSchemaType;
  19 import javax.xml.bind.annotation.XmlType;
  20 import javax.xml.bind.annotation.XmlValue;
  21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
  22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  23 import javax.xml.datatype.XMLGregorianCalendar;
  24
  25
  26 /**
  27  * <p>Java class for JalviewModel complex type.
  28  *
  29  * <p>The following schema fragment specifies the expected content contained within this class.
  30  *
  31  * <pre>
  32  * &lt;complexType name="JalviewModel">
  33  *   &lt;complexContent>
  34  *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  35  *       &lt;sequence>
  36  *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
  37  *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
  38  *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
  39  *         &lt;sequence>
  40  *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  41  *             &lt;complexType>
  42  *               &lt;complexContent>
  43  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  44  *                   &lt;sequence>
  45  *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
  46  *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
  47  *                       &lt;complexType>
  48  *                         &lt;complexContent>
  49  *                           &lt;extension base="{www.jalview.org}pdbentry">
  50  *                             &lt;sequence>
  51  *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
  52  *                                 &lt;complexType>
  53  *                                   &lt;simpleContent>
  54  *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
  55  *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  56  *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  57  *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  58  *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  59  *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  60  *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  61  *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
  62  *                                     &lt;/extension>
  63  *                                   &lt;/simpleContent>
  64  *                                 &lt;/complexType>
  65  *                               &lt;/element>
  66  *                             &lt;/sequence>
  67  *                           &lt;/extension>
  68  *                         &lt;/complexContent>
  69  *                       &lt;/complexType>
  70  *                     &lt;/element>
  71  *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
  72  *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
  73  *                       &lt;complexType>
  74  *                         &lt;complexContent>
  75  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  76  *                             &lt;sequence>
  77  *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
  78  *                                 &lt;complexType>
  79  *                                   &lt;complexContent>
  80  *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  81  *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  82  *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  83  *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  84  *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
  85  *                                     &lt;/restriction>
  86  *                                   &lt;/complexContent>
  87  *                                 &lt;/complexType>
  88  *                               &lt;/element>
  89  *                             &lt;/sequence>
  90  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  91  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  92  *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  93  *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
  94  *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
  95  *                           &lt;/restriction>
  96  *                         &lt;/complexContent>
  97  *                       &lt;/complexType>
  98  *                     &lt;/element>
  99  *                   &lt;/sequence>
 100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                 &lt;/restriction>
 107  *               &lt;/complexContent>
 108  *             &lt;/complexType>
 109  *           &lt;/element>
 110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 111  *             &lt;complexType>
 112  *               &lt;complexContent>
 113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 114  *                   &lt;sequence>
 115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 117  *                   &lt;/sequence>
 118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 137  *                 &lt;/restriction>
 138  *               &lt;/complexContent>
 139  *             &lt;/complexType>
 140  *           &lt;/element>
 141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 142  *             &lt;complexType>
 143  *               &lt;complexContent>
 144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 145  *                   &lt;sequence>
 146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 148  *                       &lt;complexType>
 149  *                         &lt;complexContent>
 150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                           &lt;/restriction>
 154  *                         &lt;/complexContent>
 155  *                       &lt;/complexType>
 156  *                     &lt;/element>
 157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 158  *                       &lt;complexType>
 159  *                         &lt;complexContent>
 160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 164  *                           &lt;/extension>
 165  *                         &lt;/complexContent>
 166  *                       &lt;/complexType>
 167  *                     &lt;/element>
 168  *                   &lt;/sequence>
 169  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 170  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 171  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 172  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 173  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 174  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 175  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 176  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 177  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 178  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 179  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 180  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 181  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 182  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 183  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 184  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 185  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 186  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 187  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 188  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 189  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 190  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 191  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 192  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 193  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 194  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 195  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 196  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 197  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 198  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 199  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 200  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 201  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 202  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 203  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 204  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 205  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 206  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 207  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 208  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 209  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 210  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 211  *                 &lt;/restriction>
 212  *               &lt;/complexContent>
 213  *             &lt;/complexType>
 214  *           &lt;/element>
 215  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 216  *             &lt;complexType>
 217  *               &lt;complexContent>
 218  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 219  *                   &lt;sequence>
 220  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 221  *                   &lt;/sequence>
 222  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 223  *                 &lt;/restriction>
 224  *               &lt;/complexContent>
 225  *             &lt;/complexType>
 226  *           &lt;/element>
 227  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 228  *             &lt;complexType>
 229  *               &lt;complexContent>
 230  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 231  *                   &lt;sequence minOccurs="0">
 232  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 233  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 234  *                   &lt;/sequence>
 235  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 236  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 237  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 238  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 239  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 240  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 241  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 242  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 243  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 244  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 245  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 246  *                 &lt;/restriction>
 247  *               &lt;/complexContent>
 248  *             &lt;/complexType>
 249  *           &lt;/element>
 250  *           &lt;element name="FeatureSettings" minOccurs="0">
 251  *             &lt;complexType>
 252  *               &lt;complexContent>
 253  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 254  *                   &lt;sequence>
 255  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 256  *                       &lt;complexType>
 257  *                         &lt;complexContent>
 258  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 259  *                             &lt;sequence>
 260  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 261  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 262  *                             &lt;/sequence>
 263  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 264  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 265  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 266  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 267  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 268  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 269  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 270  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 271  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 272  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 273  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 274  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 275  *                           &lt;/restriction>
 276  *                         &lt;/complexContent>
 277  *                       &lt;/complexType>
 278  *                     &lt;/element>
 279  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 280  *                       &lt;complexType>
 281  *                         &lt;complexContent>
 282  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 283  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 284  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 285  *                           &lt;/restriction>
 286  *                         &lt;/complexContent>
 287  *                       &lt;/complexType>
 288  *                     &lt;/element>
 289  *                   &lt;/sequence>
 290  *                 &lt;/restriction>
 291  *               &lt;/complexContent>
 292  *             &lt;/complexType>
 293  *           &lt;/element>
 294  *         &lt;/sequence>
 295  *       &lt;/sequence>
 296  *     &lt;/restriction>
 297  *   &lt;/complexContent>
 298  * &lt;/complexType>
 299  * </pre>
 300  *
 301  *
 302  */
 303 @XmlAccessorType(XmlAccessType.FIELD)
 304 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 305     "creationDate",
 306     "version",
 307     "vamsasModel",
 308     "jSeq",
 309     "jGroup",
 310     "viewport",
 311     "userColours",
 312     "tree",
 313     "featureSettings"
 314 })
 315 public class JalviewModel {
 316
 317     @XmlElement(required = true)
 318     @XmlSchemaType(name = "dateTime")
 319     protected XMLGregorianCalendar creationDate;
 320     @XmlElement(required = true)
 321     protected String version;
 322     @XmlElement(required = true)
 323     protected VAMSAS vamsasModel;
 324     @XmlElement(name = "JSeq")
 325     protected List<JalviewModel.JSeq> jSeq;
 326     @XmlElement(name = "JGroup")
 327     protected List<JalviewModel.JGroup> jGroup;
 328     @XmlElement(name = "Viewport")
 329     protected List<JalviewModel.Viewport> viewport;
 330     @XmlElement(name = "UserColours")
 331     protected List<JalviewModel.UserColours> userColours;
 332     protected List<JalviewModel.Tree> tree;
 333     @XmlElement(name = "FeatureSettings")
 334     protected JalviewModel.FeatureSettings featureSettings;
 335
 336     /**
 337      * Gets the value of the creationDate property.
 338      *
 339      * @return
 340      *     possible object is
 341      *     {@link XMLGregorianCalendar }
 342      *
 343      */
 344     public XMLGregorianCalendar getCreationDate() {
 345         return creationDate;
 346     }
 347
 348     /**
 349      * Sets the value of the creationDate property.
 350      *
 351      * @param value
 352      *     allowed object is
 353      *     {@link XMLGregorianCalendar }
 354      *
 355      */
 356     public void setCreationDate(XMLGregorianCalendar value) {
 357         this.creationDate = value;
 358     }
 359
 360     /**
 361      * Gets the value of the version property.
 362      *
 363      * @return
 364      *     possible object is
 365      *     {@link String }
 366      *
 367      */
 368     public String getVersion() {
 369         return version;
 370     }
 371
 372     /**
 373      * Sets the value of the version property.
 374      *
 375      * @param value
 376      *     allowed object is
 377      *     {@link String }
 378      *
 379      */
 380     public void setVersion(String value) {
 381         this.version = value;
 382     }
 383
 384     /**
 385      * Gets the value of the vamsasModel property.
 386      *
 387      * @return
 388      *     possible object is
 389      *     {@link VAMSAS }
 390      *
 391      */
 392     public VAMSAS getVamsasModel() {
 393         return vamsasModel;
 394     }
 395
 396     /**
 397      * Sets the value of the vamsasModel property.
 398      *
 399      * @param value
 400      *     allowed object is
 401      *     {@link VAMSAS }
 402      *
 403      */
 404     public void setVamsasModel(VAMSAS value) {
 405         this.vamsasModel = value;
 406     }
 407
 408     /**
 409      * Gets the value of the jSeq property.
 410      *
 411      * <p>
 412      * This accessor method returns a reference to the live list,
 413      * not a snapshot. Therefore any modification you make to the
 414      * returned list will be present inside the JAXB object.
 415      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 416      *
 417      * <p>
 418      * For example, to add a new item, do as follows:
 419      * <pre>
 420      *    getJSeq().add(newItem);
 421      * </pre>
 422      *
 423      *
 424      * <p>
 425      * Objects of the following type(s) are allowed in the list
 426      * {@link JalviewModel.JSeq }
 427      *
 428      *
 429      */
 430     public List<JalviewModel.JSeq> getJSeq() {
 431         if (jSeq == null) {
 432             jSeq = new ArrayList<JalviewModel.JSeq>();
 433         }
 434         return this.jSeq;
 435     }
 436
 437     /**
 438      * Gets the value of the jGroup property.
 439      *
 440      * <p>
 441      * This accessor method returns a reference to the live list,
 442      * not a snapshot. Therefore any modification you make to the
 443      * returned list will be present inside the JAXB object.
 444      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 445      *
 446      * <p>
 447      * For example, to add a new item, do as follows:
 448      * <pre>
 449      *    getJGroup().add(newItem);
 450      * </pre>
 451      *
 452      *
 453      * <p>
 454      * Objects of the following type(s) are allowed in the list
 455      * {@link JalviewModel.JGroup }
 456      *
 457      *
 458      */
 459     public List<JalviewModel.JGroup> getJGroup() {
 460         if (jGroup == null) {
 461             jGroup = new ArrayList<JalviewModel.JGroup>();
 462         }
 463         return this.jGroup;
 464     }
 465
 466     /**
 467      * Gets the value of the viewport property.
 468      *
 469      * <p>
 470      * This accessor method returns a reference to the live list,
 471      * not a snapshot. Therefore any modification you make to the
 472      * returned list will be present inside the JAXB object.
 473      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 474      *
 475      * <p>
 476      * For example, to add a new item, do as follows:
 477      * <pre>
 478      *    getViewport().add(newItem);
 479      * </pre>
 480      *
 481      *
 482      * <p>
 483      * Objects of the following type(s) are allowed in the list
 484      * {@link JalviewModel.Viewport }
 485      *
 486      *
 487      */
 488     public List<JalviewModel.Viewport> getViewport() {
 489         if (viewport == null) {
 490             viewport = new ArrayList<JalviewModel.Viewport>();
 491         }
 492         return this.viewport;
 493     }
 494
 495     /**
 496      * Gets the value of the userColours property.
 497      *
 498      * <p>
 499      * This accessor method returns a reference to the live list,
 500      * not a snapshot. Therefore any modification you make to the
 501      * returned list will be present inside the JAXB object.
 502      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 503      *
 504      * <p>
 505      * For example, to add a new item, do as follows:
 506      * <pre>
 507      *    getUserColours().add(newItem);
 508      * </pre>
 509      *
 510      *
 511      * <p>
 512      * Objects of the following type(s) are allowed in the list
 513      * {@link JalviewModel.UserColours }
 514      *
 515      *
 516      */
 517     public List<JalviewModel.UserColours> getUserColours() {
 518         if (userColours == null) {
 519             userColours = new ArrayList<JalviewModel.UserColours>();
 520         }
 521         return this.userColours;
 522     }
 523
 524     /**
 525      * Gets the value of the tree property.
 526      *
 527      * <p>
 528      * This accessor method returns a reference to the live list,
 529      * not a snapshot. Therefore any modification you make to the
 530      * returned list will be present inside the JAXB object.
 531      * This is why there is not a <CODE>set</CODE> method for the tree property.
 532      *
 533      * <p>
 534      * For example, to add a new item, do as follows:
 535      * <pre>
 536      *    getTree().add(newItem);
 537      * </pre>
 538      *
 539      *
 540      * <p>
 541      * Objects of the following type(s) are allowed in the list
 542      * {@link JalviewModel.Tree }
 543      *
 544      *
 545      */
 546     public List<JalviewModel.Tree> getTree() {
 547         if (tree == null) {
 548             tree = new ArrayList<JalviewModel.Tree>();
 549         }
 550         return this.tree;
 551     }
 552
 553     /**
 554      * Gets the value of the featureSettings property.
 555      *
 556      * @return
 557      *     possible object is
 558      *     {@link JalviewModel.FeatureSettings }
 559      *
 560      */
 561     public JalviewModel.FeatureSettings getFeatureSettings() {
 562         return featureSettings;
 563     }
 564
 565     /**
 566      * Sets the value of the featureSettings property.
 567      *
 568      * @param value
 569      *     allowed object is
 570      *     {@link JalviewModel.FeatureSettings }
 571      *
 572      */
 573     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 574         this.featureSettings = value;
 575     }
 576
 577
 578     /**
 579      * <p>Java class for anonymous complex type.
 580      *
 581      * <p>The following schema fragment specifies the expected content contained within this class.
 582      *
 583      * <pre>
 584      * &lt;complexType>
 585      *   &lt;complexContent>
 586      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 587      *       &lt;sequence>
 588      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 589      *           &lt;complexType>
 590      *             &lt;complexContent>
 591      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 592      *                 &lt;sequence>
 593      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 594      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 595      *                 &lt;/sequence>
 596      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 597      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 598      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 599      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 600      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 601      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 602      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 603      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 604      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 605      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 606      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 607      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 608      *               &lt;/restriction>
 609      *             &lt;/complexContent>
 610      *           &lt;/complexType>
 611      *         &lt;/element>
 612      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 613      *           &lt;complexType>
 614      *             &lt;complexContent>
 615      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 616      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 617      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 618      *               &lt;/restriction>
 619      *             &lt;/complexContent>
 620      *           &lt;/complexType>
 621      *         &lt;/element>
 622      *       &lt;/sequence>
 623      *     &lt;/restriction>
 624      *   &lt;/complexContent>
 625      * &lt;/complexType>
 626      * </pre>
 627      *
 628      *
 629      */
 630     @XmlAccessorType(XmlAccessType.FIELD)
 631     @XmlType(name = "", propOrder = {
 632         "setting",
 633         "group"
 634     })
 635     public static class FeatureSettings {
 636
 637         @XmlElement(namespace = "www.jalview.org")
 638         protected List<JalviewModel.FeatureSettings.Setting> setting;
 639         @XmlElement(namespace = "www.jalview.org")
 640         protected List<JalviewModel.FeatureSettings.Group> group;
 641
 642         /**
 643          * Gets the value of the setting property.
 644          *
 645          * <p>
 646          * This accessor method returns a reference to the live list,
 647          * not a snapshot. Therefore any modification you make to the
 648          * returned list will be present inside the JAXB object.
 649          * This is why there is not a <CODE>set</CODE> method for the setting property.
 650          *
 651          * <p>
 652          * For example, to add a new item, do as follows:
 653          * <pre>
 654          *    getSetting().add(newItem);
 655          * </pre>
 656          *
 657          *
 658          * <p>
 659          * Objects of the following type(s) are allowed in the list
 660          * {@link JalviewModel.FeatureSettings.Setting }
 661          *
 662          *
 663          */
 664         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 665             if (setting == null) {
 666                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 667             }
 668             return this.setting;
 669         }
 670
 671         /**
 672          * Gets the value of the group property.
 673          *
 674          * <p>
 675          * This accessor method returns a reference to the live list,
 676          * not a snapshot. Therefore any modification you make to the
 677          * returned list will be present inside the JAXB object.
 678          * This is why there is not a <CODE>set</CODE> method for the group property.
 679          *
 680          * <p>
 681          * For example, to add a new item, do as follows:
 682          * <pre>
 683          *    getGroup().add(newItem);
 684          * </pre>
 685          *
 686          *
 687          * <p>
 688          * Objects of the following type(s) are allowed in the list
 689          * {@link JalviewModel.FeatureSettings.Group }
 690          *
 691          *
 692          */
 693         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 694             if (group == null) {
 695                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 696             }
 697             return this.group;
 698         }
 699
 700
 701         /**
 702          * <p>Java class for anonymous complex type.
 703          *
 704          * <p>The following schema fragment specifies the expected content contained within this class.
 705          *
 706          * <pre>
 707          * &lt;complexType>
 708          *   &lt;complexContent>
 709          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 710          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 711          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 712          *     &lt;/restriction>
 713          *   &lt;/complexContent>
 714          * &lt;/complexType>
 715          * </pre>
 716          *
 717          *
 718          */
 719         @XmlAccessorType(XmlAccessType.FIELD)
 720         @XmlType(name = "")
 721         public static class Group {
 722
 723             @XmlAttribute(name = "name", required = true)
 724             protected String name;
 725             @XmlAttribute(name = "display", required = true)
 726             protected boolean display;
 727
 728             /**
 729              * Gets the value of the name property.
 730              *
 731              * @return
 732              *     possible object is
 733              *     {@link String }
 734              *
 735              */
 736             public String getName() {
 737                 return name;
 738             }
 739
 740             /**
 741              * Sets the value of the name property.
 742              *
 743              * @param value
 744              *     allowed object is
 745              *     {@link String }
 746              *
 747              */
 748             public void setName(String value) {
 749                 this.name = value;
 750             }
 751
 752             /**
 753              * Gets the value of the display property.
 754              *
 755              */
 756             public boolean isDisplay() {
 757                 return display;
 758             }
 759
 760             /**
 761              * Sets the value of the display property.
 762              *
 763              */
 764             public void setDisplay(boolean value) {
 765                 this.display = value;
 766             }
 767
 768         }
 769
 770
 771         /**
 772          * <p>Java class for anonymous complex type.
 773          *
 774          * <p>The following schema fragment specifies the expected content contained within this class.
 775          *
 776          * <pre>
 777          * &lt;complexType>
 778          *   &lt;complexContent>
 779          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 780          *       &lt;sequence>
 781          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 782          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 783          *       &lt;/sequence>
 784          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 785          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 786          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 787          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 788          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 789          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 790          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 791          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 792          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 793          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 794          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 795          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 796          *     &lt;/restriction>
 797          *   &lt;/complexContent>
 798          * &lt;/complexType>
 799          * </pre>
 800          *
 801          *
 802          */
 803         @XmlAccessorType(XmlAccessType.FIELD)
 804         @XmlType(name = "", propOrder = {
 805             "attributeName",
 806             "matcherSet"
 807         })
 808         public static class Setting {
 809
 810             @XmlElement(namespace = "www.jalview.org")
 811             protected List<String> attributeName;
 812             @XmlElement(namespace = "www.jalview.org")
 813             protected FeatureMatcherSet matcherSet;
 814             @XmlAttribute(name = "type", required = true)
 815             protected String type;
 816             @XmlAttribute(name = "colour", required = true)
 817             protected int colour;
 818             @XmlAttribute(name = "display", required = true)
 819             protected boolean display;
 820             @XmlAttribute(name = "order")
 821             protected Float order;
 822             @XmlAttribute(name = "mincolour")
 823             protected Integer mincolour;
 824             @XmlAttribute(name = "noValueColour")
 825             protected NoValueColour noValueColour;
 826             @XmlAttribute(name = "threshold")
 827             protected Float threshold;
 828             @XmlAttribute(name = "threshstate")
 829             protected Integer threshstate;
 830             @XmlAttribute(name = "max")
 831             protected Float max;
 832             @XmlAttribute(name = "min")
 833             protected Float min;
 834             @XmlAttribute(name = "colourByLabel")
 835             protected Boolean colourByLabel;
 836             @XmlAttribute(name = "autoScale")
 837             protected Boolean autoScale;
 838
 839             /**
 840              * Gets the value of the attributeName property.
 841              *
 842              * <p>
 843              * This accessor method returns a reference to the live list,
 844              * not a snapshot. Therefore any modification you make to the
 845              * returned list will be present inside the JAXB object.
 846              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 847              *
 848              * <p>
 849              * For example, to add a new item, do as follows:
 850              * <pre>
 851              *    getAttributeName().add(newItem);
 852              * </pre>
 853              *
 854              *
 855              * <p>
 856              * Objects of the following type(s) are allowed in the list
 857              * {@link String }
 858              *
 859              *
 860              */
 861             public List<String> getAttributeName() {
 862                 if (attributeName == null) {
 863                     attributeName = new ArrayList<String>();
 864                 }
 865                 return this.attributeName;
 866             }
 867
 868             /**
 869              * Gets the value of the matcherSet property.
 870              *
 871              * @return
 872              *     possible object is
 873              *     {@link FeatureMatcherSet }
 874              *
 875              */
 876             public FeatureMatcherSet getMatcherSet() {
 877                 return matcherSet;
 878             }
 879
 880             /**
 881              * Sets the value of the matcherSet property.
 882              *
 883              * @param value
 884              *     allowed object is
 885              *     {@link FeatureMatcherSet }
 886              *
 887              */
 888             public void setMatcherSet(FeatureMatcherSet value) {
 889                 this.matcherSet = value;
 890             }
 891
 892             /**
 893              * Gets the value of the type property.
 894              *
 895              * @return
 896              *     possible object is
 897              *     {@link String }
 898              *
 899              */
 900             public String getType() {
 901                 return type;
 902             }
 903
 904             /**
 905              * Sets the value of the type property.
 906              *
 907              * @param value
 908              *     allowed object is
 909              *     {@link String }
 910              *
 911              */
 912             public void setType(String value) {
 913                 this.type = value;
 914             }
 915
 916             /**
 917              * Gets the value of the colour property.
 918              *
 919              */
 920             public int getColour() {
 921                 return colour;
 922             }
 923
 924             /**
 925              * Sets the value of the colour property.
 926              *
 927              */
 928             public void setColour(int value) {
 929                 this.colour = value;
 930             }
 931
 932             /**
 933              * Gets the value of the display property.
 934              *
 935              */
 936             public boolean isDisplay() {
 937                 return display;
 938             }
 939
 940             /**
 941              * Sets the value of the display property.
 942              *
 943              */
 944             public void setDisplay(boolean value) {
 945                 this.display = value;
 946             }
 947
 948             /**
 949              * Gets the value of the order property.
 950              *
 951              * @return
 952              *     possible object is
 953              *     {@link Float }
 954              *
 955              */
 956             public Float getOrder() {
 957                 return order;
 958             }
 959
 960             /**
 961              * Sets the value of the order property.
 962              *
 963              * @param value
 964              *     allowed object is
 965              *     {@link Float }
 966              *
 967              */
 968             public void setOrder(Float value) {
 969                 this.order = value;
 970             }
 971
 972             /**
 973              * Gets the value of the mincolour property.
 974              *
 975              * @return
 976              *     possible object is
 977              *     {@link Integer }
 978              *
 979              */
 980             public Integer getMincolour() {
 981                 return mincolour;
 982             }
 983
 984             /**
 985              * Sets the value of the mincolour property.
 986              *
 987              * @param value
 988              *     allowed object is
 989              *     {@link Integer }
 990              *
 991              */
 992             public void setMincolour(Integer value) {
 993                 this.mincolour = value;
 994             }
 995
 996             /**
 997              * Gets the value of the noValueColour property.
 998              *
 999              * @return
1000              *     possible object is
1001              *     {@link NoValueColour }
1002              *
1003              */
1004             public NoValueColour getNoValueColour() {
1005                 if (noValueColour == null) {
1006                     return NoValueColour.MIN;
1007                 } else {
1008                     return noValueColour;
1009                 }
1010             }
1011
1012             /**
1013              * Sets the value of the noValueColour property.
1014              *
1015              * @param value
1016              *     allowed object is
1017              *     {@link NoValueColour }
1018              *
1019              */
1020             public void setNoValueColour(NoValueColour value) {
1021                 this.noValueColour = value;
1022             }
1023
1024             /**
1025              * Gets the value of the threshold property.
1026              *
1027              * @return
1028              *     possible object is
1029              *     {@link Float }
1030              *
1031              */
1032             public Float getThreshold() {
1033                 return threshold;
1034             }
1035
1036             /**
1037              * Sets the value of the threshold property.
1038              *
1039              * @param value
1040              *     allowed object is
1041              *     {@link Float }
1042              *
1043              */
1044             public void setThreshold(Float value) {
1045                 this.threshold = value;
1046             }
1047
1048             /**
1049              * Gets the value of the threshstate property.
1050              *
1051              * @return
1052              *     possible object is
1053              *     {@link Integer }
1054              *
1055              */
1056             public Integer getThreshstate() {
1057                 return threshstate;
1058             }
1059
1060             /**
1061              * Sets the value of the threshstate property.
1062              *
1063              * @param value
1064              *     allowed object is
1065              *     {@link Integer }
1066              *
1067              */
1068             public void setThreshstate(Integer value) {
1069                 this.threshstate = value;
1070             }
1071
1072             /**
1073              * Gets the value of the max property.
1074              *
1075              * @return
1076              *     possible object is
1077              *     {@link Float }
1078              *
1079              */
1080             public Float getMax() {
1081                 return max;
1082             }
1083
1084             /**
1085              * Sets the value of the max property.
1086              *
1087              * @param value
1088              *     allowed object is
1089              *     {@link Float }
1090              *
1091              */
1092             public void setMax(Float value) {
1093                 this.max = value;
1094             }
1095
1096             /**
1097              * Gets the value of the min property.
1098              *
1099              * @return
1100              *     possible object is
1101              *     {@link Float }
1102              *
1103              */
1104             public Float getMin() {
1105                 return min;
1106             }
1107
1108             /**
1109              * Sets the value of the min property.
1110              *
1111              * @param value
1112              *     allowed object is
1113              *     {@link Float }
1114              *
1115              */
1116             public void setMin(Float value) {
1117                 this.min = value;
1118             }
1119
1120             /**
1121              * Gets the value of the colourByLabel property.
1122              *
1123              * @return
1124              *     possible object is
1125              *     {@link Boolean }
1126              *
1127              */
1128             public Boolean isColourByLabel() {
1129                 return colourByLabel;
1130             }
1131
1132             /**
1133              * Sets the value of the colourByLabel property.
1134              *
1135              * @param value
1136              *     allowed object is
1137              *     {@link Boolean }
1138              *
1139              */
1140             public void setColourByLabel(Boolean value) {
1141                 this.colourByLabel = value;
1142             }
1143
1144             /**
1145              * Gets the value of the autoScale property.
1146              *
1147              * @return
1148              *     possible object is
1149              *     {@link Boolean }
1150              *
1151              */
1152             public Boolean isAutoScale() {
1153                 return autoScale;
1154             }
1155
1156             /**
1157              * Sets the value of the autoScale property.
1158              *
1159              * @param value
1160              *     allowed object is
1161              *     {@link Boolean }
1162              *
1163              */
1164             public void setAutoScale(Boolean value) {
1165                 this.autoScale = value;
1166             }
1167
1168         }
1169
1170     }
1171
1172
1173     /**
1174      * <p>Java class for anonymous complex type.
1175      *
1176      * <p>The following schema fragment specifies the expected content contained within this class.
1177      *
1178      * <pre>
1179      * &lt;complexType>
1180      *   &lt;complexContent>
1181      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1182      *       &lt;sequence>
1183      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1184      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1185      *       &lt;/sequence>
1186      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1187      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1188      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1189      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1190      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1191      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1192      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1193      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1194      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1195      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1196      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1197      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1198      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1199      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1200      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1201      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1202      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1203      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1204      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1205      *     &lt;/restriction>
1206      *   &lt;/complexContent>
1207      * &lt;/complexType>
1208      * </pre>
1209      *
1210      *
1211      */
1212     @XmlAccessorType(XmlAccessType.FIELD)
1213     @XmlType(name = "", propOrder = {
1214         "seq",
1215         "annotationColours"
1216     })
1217     public static class JGroup {
1218
1219         @XmlElement(namespace = "www.jalview.org", required = true)
1220         protected List<String> seq;
1221         @XmlElement(namespace = "www.jalview.org")
1222         protected AnnotationColourScheme annotationColours;
1223         @XmlAttribute(name = "start")
1224         protected Integer start;
1225         @XmlAttribute(name = "end")
1226         protected Integer end;
1227         @XmlAttribute(name = "name")
1228         protected String name;
1229         @XmlAttribute(name = "colour")
1230         protected String colour;
1231         @XmlAttribute(name = "consThreshold")
1232         protected Integer consThreshold;
1233         @XmlAttribute(name = "pidThreshold")
1234         protected Integer pidThreshold;
1235         @XmlAttribute(name = "outlineColour")
1236         protected Integer outlineColour;
1237         @XmlAttribute(name = "displayBoxes")
1238         protected Boolean displayBoxes;
1239         @XmlAttribute(name = "displayText")
1240         protected Boolean displayText;
1241         @XmlAttribute(name = "colourText")
1242         protected Boolean colourText;
1243         @XmlAttribute(name = "textCol1")
1244         protected Integer textCol1;
1245         @XmlAttribute(name = "textCol2")
1246         protected Integer textCol2;
1247         @XmlAttribute(name = "textColThreshold")
1248         protected Integer textColThreshold;
1249         @XmlAttribute(name = "showUnconserved")
1250         protected Boolean showUnconserved;
1251         @XmlAttribute(name = "ignoreGapsinConsensus")
1252         protected Boolean ignoreGapsinConsensus;
1253         @XmlAttribute(name = "showConsensusHistogram")
1254         protected Boolean showConsensusHistogram;
1255         @XmlAttribute(name = "showSequenceLogo")
1256         protected Boolean showSequenceLogo;
1257         @XmlAttribute(name = "normaliseSequenceLogo")
1258         protected Boolean normaliseSequenceLogo;
1259         @XmlAttribute(name = "id")
1260         protected String id;
1261
1262         /**
1263          * Gets the value of the seq property.
1264          *
1265          * <p>
1266          * This accessor method returns a reference to the live list,
1267          * not a snapshot. Therefore any modification you make to the
1268          * returned list will be present inside the JAXB object.
1269          * This is why there is not a <CODE>set</CODE> method for the seq property.
1270          *
1271          * <p>
1272          * For example, to add a new item, do as follows:
1273          * <pre>
1274          *    getSeq().add(newItem);
1275          * </pre>
1276          *
1277          *
1278          * <p>
1279          * Objects of the following type(s) are allowed in the list
1280          * {@link String }
1281          *
1282          *
1283          */
1284         public List<String> getSeq() {
1285             if (seq == null) {
1286                 seq = new ArrayList<String>();
1287             }
1288             return this.seq;
1289         }
1290
1291         /**
1292          * Gets the value of the annotationColours property.
1293          *
1294          * @return
1295          *     possible object is
1296          *     {@link AnnotationColourScheme }
1297          *
1298          */
1299         public AnnotationColourScheme getAnnotationColours() {
1300             return annotationColours;
1301         }
1302
1303         /**
1304          * Sets the value of the annotationColours property.
1305          *
1306          * @param value
1307          *     allowed object is
1308          *     {@link AnnotationColourScheme }
1309          *
1310          */
1311         public void setAnnotationColours(AnnotationColourScheme value) {
1312             this.annotationColours = value;
1313         }
1314
1315         /**
1316          * Gets the value of the start property.
1317          *
1318          * @return
1319          *     possible object is
1320          *     {@link Integer }
1321          *
1322          */
1323         public Integer getStart() {
1324             return start;
1325         }
1326
1327         /**
1328          * Sets the value of the start property.
1329          *
1330          * @param value
1331          *     allowed object is
1332          *     {@link Integer }
1333          *
1334          */
1335         public void setStart(Integer value) {
1336             this.start = value;
1337         }
1338
1339         /**
1340          * Gets the value of the end property.
1341          *
1342          * @return
1343          *     possible object is
1344          *     {@link Integer }
1345          *
1346          */
1347         public Integer getEnd() {
1348             return end;
1349         }
1350
1351         /**
1352          * Sets the value of the end property.
1353          *
1354          * @param value
1355          *     allowed object is
1356          *     {@link Integer }
1357          *
1358          */
1359         public void setEnd(Integer value) {
1360             this.end = value;
1361         }
1362
1363         /**
1364          * Gets the value of the name property.
1365          *
1366          * @return
1367          *     possible object is
1368          *     {@link String }
1369          *
1370          */
1371         public String getName() {
1372             return name;
1373         }
1374
1375         /**
1376          * Sets the value of the name property.
1377          *
1378          * @param value
1379          *     allowed object is
1380          *     {@link String }
1381          *
1382          */
1383         public void setName(String value) {
1384             this.name = value;
1385         }
1386
1387         /**
1388          * Gets the value of the colour property.
1389          *
1390          * @return
1391          *     possible object is
1392          *     {@link String }
1393          *
1394          */
1395         public String getColour() {
1396             return colour;
1397         }
1398
1399         /**
1400          * Sets the value of the colour property.
1401          *
1402          * @param value
1403          *     allowed object is
1404          *     {@link String }
1405          *
1406          */
1407         public void setColour(String value) {
1408             this.colour = value;
1409         }
1410
1411         /**
1412          * Gets the value of the consThreshold property.
1413          *
1414          * @return
1415          *     possible object is
1416          *     {@link Integer }
1417          *
1418          */
1419         public Integer getConsThreshold() {
1420             return consThreshold;
1421         }
1422
1423         /**
1424          * Sets the value of the consThreshold property.
1425          *
1426          * @param value
1427          *     allowed object is
1428          *     {@link Integer }
1429          *
1430          */
1431         public void setConsThreshold(Integer value) {
1432             this.consThreshold = value;
1433         }
1434
1435         /**
1436          * Gets the value of the pidThreshold property.
1437          *
1438          * @return
1439          *     possible object is
1440          *     {@link Integer }
1441          *
1442          */
1443         public Integer getPidThreshold() {
1444             return pidThreshold;
1445         }
1446
1447         /**
1448          * Sets the value of the pidThreshold property.
1449          *
1450          * @param value
1451          *     allowed object is
1452          *     {@link Integer }
1453          *
1454          */
1455         public void setPidThreshold(Integer value) {
1456             this.pidThreshold = value;
1457         }
1458
1459         /**
1460          * Gets the value of the outlineColour property.
1461          *
1462          * @return
1463          *     possible object is
1464          *     {@link Integer }
1465          *
1466          */
1467         public Integer getOutlineColour() {
1468             return outlineColour;
1469         }
1470
1471         /**
1472          * Sets the value of the outlineColour property.
1473          *
1474          * @param value
1475          *     allowed object is
1476          *     {@link Integer }
1477          *
1478          */
1479         public void setOutlineColour(Integer value) {
1480             this.outlineColour = value;
1481         }
1482
1483         /**
1484          * Gets the value of the displayBoxes property.
1485          *
1486          * @return
1487          *     possible object is
1488          *     {@link Boolean }
1489          *
1490          */
1491         public Boolean isDisplayBoxes() {
1492             return displayBoxes;
1493         }
1494
1495         /**
1496          * Sets the value of the displayBoxes property.
1497          *
1498          * @param value
1499          *     allowed object is
1500          *     {@link Boolean }
1501          *
1502          */
1503         public void setDisplayBoxes(Boolean value) {
1504             this.displayBoxes = value;
1505         }
1506
1507         /**
1508          * Gets the value of the displayText property.
1509          *
1510          * @return
1511          *     possible object is
1512          *     {@link Boolean }
1513          *
1514          */
1515         public Boolean isDisplayText() {
1516             return displayText;
1517         }
1518
1519         /**
1520          * Sets the value of the displayText property.
1521          *
1522          * @param value
1523          *     allowed object is
1524          *     {@link Boolean }
1525          *
1526          */
1527         public void setDisplayText(Boolean value) {
1528             this.displayText = value;
1529         }
1530
1531         /**
1532          * Gets the value of the colourText property.
1533          *
1534          * @return
1535          *     possible object is
1536          *     {@link Boolean }
1537          *
1538          */
1539         public Boolean isColourText() {
1540             return colourText;
1541         }
1542
1543         /**
1544          * Sets the value of the colourText property.
1545          *
1546          * @param value
1547          *     allowed object is
1548          *     {@link Boolean }
1549          *
1550          */
1551         public void setColourText(Boolean value) {
1552             this.colourText = value;
1553         }
1554
1555         /**
1556          * Gets the value of the textCol1 property.
1557          *
1558          * @return
1559          *     possible object is
1560          *     {@link Integer }
1561          *
1562          */
1563         public Integer getTextCol1() {
1564             return textCol1;
1565         }
1566
1567         /**
1568          * Sets the value of the textCol1 property.
1569          *
1570          * @param value
1571          *     allowed object is
1572          *     {@link Integer }
1573          *
1574          */
1575         public void setTextCol1(Integer value) {
1576             this.textCol1 = value;
1577         }
1578
1579         /**
1580          * Gets the value of the textCol2 property.
1581          *
1582          * @return
1583          *     possible object is
1584          *     {@link Integer }
1585          *
1586          */
1587         public Integer getTextCol2() {
1588             return textCol2;
1589         }
1590
1591         /**
1592          * Sets the value of the textCol2 property.
1593          *
1594          * @param value
1595          *     allowed object is
1596          *     {@link Integer }
1597          *
1598          */
1599         public void setTextCol2(Integer value) {
1600             this.textCol2 = value;
1601         }
1602
1603         /**
1604          * Gets the value of the textColThreshold property.
1605          *
1606          * @return
1607          *     possible object is
1608          *     {@link Integer }
1609          *
1610          */
1611         public Integer getTextColThreshold() {
1612             return textColThreshold;
1613         }
1614
1615         /**
1616          * Sets the value of the textColThreshold property.
1617          *
1618          * @param value
1619          *     allowed object is
1620          *     {@link Integer }
1621          *
1622          */
1623         public void setTextColThreshold(Integer value) {
1624             this.textColThreshold = value;
1625         }
1626
1627         /**
1628          * Gets the value of the showUnconserved property.
1629          *
1630          * @return
1631          *     possible object is
1632          *     {@link Boolean }
1633          *
1634          */
1635         public Boolean isShowUnconserved() {
1636             return showUnconserved;
1637         }
1638
1639         /**
1640          * Sets the value of the showUnconserved property.
1641          *
1642          * @param value
1643          *     allowed object is
1644          *     {@link Boolean }
1645          *
1646          */
1647         public void setShowUnconserved(Boolean value) {
1648             this.showUnconserved = value;
1649         }
1650
1651         /**
1652          * Gets the value of the ignoreGapsinConsensus property.
1653          *
1654          * @return
1655          *     possible object is
1656          *     {@link Boolean }
1657          *
1658          */
1659         public boolean isIgnoreGapsinConsensus() {
1660             if (ignoreGapsinConsensus == null) {
1661                 return true;
1662             } else {
1663                 return ignoreGapsinConsensus;
1664             }
1665         }
1666
1667         /**
1668          * Sets the value of the ignoreGapsinConsensus property.
1669          *
1670          * @param value
1671          *     allowed object is
1672          *     {@link Boolean }
1673          *
1674          */
1675         public void setIgnoreGapsinConsensus(Boolean value) {
1676             this.ignoreGapsinConsensus = value;
1677         }
1678
1679         /**
1680          * Gets the value of the showConsensusHistogram property.
1681          *
1682          * @return
1683          *     possible object is
1684          *     {@link Boolean }
1685          *
1686          */
1687         public boolean isShowConsensusHistogram() {
1688             if (showConsensusHistogram == null) {
1689                 return true;
1690             } else {
1691                 return showConsensusHistogram;
1692             }
1693         }
1694
1695         /**
1696          * Sets the value of the showConsensusHistogram property.
1697          *
1698          * @param value
1699          *     allowed object is
1700          *     {@link Boolean }
1701          *
1702          */
1703         public void setShowConsensusHistogram(Boolean value) {
1704             this.showConsensusHistogram = value;
1705         }
1706
1707         /**
1708          * Gets the value of the showSequenceLogo property.
1709          *
1710          * @return
1711          *     possible object is
1712          *     {@link Boolean }
1713          *
1714          */
1715         public boolean isShowSequenceLogo() {
1716             if (showSequenceLogo == null) {
1717                 return false;
1718             } else {
1719                 return showSequenceLogo;
1720             }
1721         }
1722
1723         /**
1724          * Sets the value of the showSequenceLogo property.
1725          *
1726          * @param value
1727          *     allowed object is
1728          *     {@link Boolean }
1729          *
1730          */
1731         public void setShowSequenceLogo(Boolean value) {
1732             this.showSequenceLogo = value;
1733         }
1734
1735         /**
1736          * Gets the value of the normaliseSequenceLogo property.
1737          *
1738          * @return
1739          *     possible object is
1740          *     {@link Boolean }
1741          *
1742          */
1743         public boolean isNormaliseSequenceLogo() {
1744             if (normaliseSequenceLogo == null) {
1745                 return false;
1746             } else {
1747                 return normaliseSequenceLogo;
1748             }
1749         }
1750
1751         /**
1752          * Sets the value of the normaliseSequenceLogo property.
1753          *
1754          * @param value
1755          *     allowed object is
1756          *     {@link Boolean }
1757          *
1758          */
1759         public void setNormaliseSequenceLogo(Boolean value) {
1760             this.normaliseSequenceLogo = value;
1761         }
1762
1763         /**
1764          * Gets the value of the id property.
1765          *
1766          * @return
1767          *     possible object is
1768          *     {@link String }
1769          *
1770          */
1771         public String getId() {
1772             return id;
1773         }
1774
1775         /**
1776          * Sets the value of the id property.
1777          *
1778          * @param value
1779          *     allowed object is
1780          *     {@link String }
1781          *
1782          */
1783         public void setId(String value) {
1784             this.id = value;
1785         }
1786
1787     }
1788
1789
1790     /**
1791      * <p>Java class for anonymous complex type.
1792      *
1793      * <p>The following schema fragment specifies the expected content contained within this class.
1794      *
1795      * <pre>
1796      * &lt;complexType>
1797      *   &lt;complexContent>
1798      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1799      *       &lt;sequence>
1800      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1801      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1802      *           &lt;complexType>
1803      *             &lt;complexContent>
1804      *               &lt;extension base="{www.jalview.org}pdbentry">
1805      *                 &lt;sequence>
1806      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1807      *                     &lt;complexType>
1808      *                       &lt;simpleContent>
1809      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1810      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1811      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1812      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1813      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1814      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1815      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1816      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1817      *                         &lt;/extension>
1818      *                       &lt;/simpleContent>
1819      *                     &lt;/complexType>
1820      *                   &lt;/element>
1821      *                 &lt;/sequence>
1822      *               &lt;/extension>
1823      *             &lt;/complexContent>
1824      *           &lt;/complexType>
1825      *         &lt;/element>
1826      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1827      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1828      *           &lt;complexType>
1829      *             &lt;complexContent>
1830      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1831      *                 &lt;sequence>
1832      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1833      *                     &lt;complexType>
1834      *                       &lt;complexContent>
1835      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1836      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1837      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1838      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1839      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1840      *                         &lt;/restriction>
1841      *                       &lt;/complexContent>
1842      *                     &lt;/complexType>
1843      *                   &lt;/element>
1844      *                 &lt;/sequence>
1845      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1846      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1847      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1848      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1849      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1850      *               &lt;/restriction>
1851      *             &lt;/complexContent>
1852      *           &lt;/complexType>
1853      *         &lt;/element>
1854      *       &lt;/sequence>
1855      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1856      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1857      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1858      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1859      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1860      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1861      *     &lt;/restriction>
1862      *   &lt;/complexContent>
1863      * &lt;/complexType>
1864      * </pre>
1865      *
1866      *
1867      */
1868     @XmlAccessorType(XmlAccessType.FIELD)
1869     @XmlType(name = "", propOrder = {
1870         "features",
1871         "pdbids",
1872         "hiddenSequences",
1873         "rnaViewer"
1874     })
1875     public static class JSeq {
1876
1877         @XmlElement(namespace = "www.jalview.org")
1878         protected List<Feature> features;
1879         @XmlElement(namespace = "www.jalview.org")
1880         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1881         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1882         protected List<Integer> hiddenSequences;
1883         @XmlElement(namespace = "www.jalview.org")
1884         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1885         @XmlAttribute(name = "colour")
1886         protected Integer colour;
1887         @XmlAttribute(name = "start", required = true)
1888         protected int start;
1889         @XmlAttribute(name = "end", required = true)
1890         protected int end;
1891         @XmlAttribute(name = "id", required = true)
1892         protected String id;
1893         @XmlAttribute(name = "hidden")
1894         protected Boolean hidden;
1895         @XmlAttribute(name = "viewreference")
1896         protected Boolean viewreference;
1897
1898         /**
1899          * Gets the value of the features property.
1900          *
1901          * <p>
1902          * This accessor method returns a reference to the live list,
1903          * not a snapshot. Therefore any modification you make to the
1904          * returned list will be present inside the JAXB object.
1905          * This is why there is not a <CODE>set</CODE> method for the features property.
1906          *
1907          * <p>
1908          * For example, to add a new item, do as follows:
1909          * <pre>
1910          *    getFeatures().add(newItem);
1911          * </pre>
1912          *
1913          *
1914          * <p>
1915          * Objects of the following type(s) are allowed in the list
1916          * {@link Feature }
1917          *
1918          *
1919          */
1920         public List<Feature> getFeatures() {
1921             if (features == null) {
1922                 features = new ArrayList<Feature>();
1923             }
1924             return this.features;
1925         }
1926
1927         /**
1928          * Gets the value of the pdbids property.
1929          *
1930          * <p>
1931          * This accessor method returns a reference to the live list,
1932          * not a snapshot. Therefore any modification you make to the
1933          * returned list will be present inside the JAXB object.
1934          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
1935          *
1936          * <p>
1937          * For example, to add a new item, do as follows:
1938          * <pre>
1939          *    getPdbids().add(newItem);
1940          * </pre>
1941          *
1942          *
1943          * <p>
1944          * Objects of the following type(s) are allowed in the list
1945          * {@link JalviewModel.JSeq.Pdbids }
1946          *
1947          *
1948          */
1949         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
1950             if (pdbids == null) {
1951                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
1952             }
1953             return this.pdbids;
1954         }
1955
1956         /**
1957          * Gets the value of the hiddenSequences property.
1958          *
1959          * <p>
1960          * This accessor method returns a reference to the live list,
1961          * not a snapshot. Therefore any modification you make to the
1962          * returned list will be present inside the JAXB object.
1963          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
1964          *
1965          * <p>
1966          * For example, to add a new item, do as follows:
1967          * <pre>
1968          *    getHiddenSequences().add(newItem);
1969          * </pre>
1970          *
1971          *
1972          * <p>
1973          * Objects of the following type(s) are allowed in the list
1974          * {@link Integer }
1975          *
1976          *
1977          */
1978         public List<Integer> getHiddenSequences() {
1979             if (hiddenSequences == null) {
1980                 hiddenSequences = new ArrayList<Integer>();
1981             }
1982             return this.hiddenSequences;
1983         }
1984
1985         /**
1986          * Gets the value of the rnaViewer property.
1987          *
1988          * <p>
1989          * This accessor method returns a reference to the live list,
1990          * not a snapshot. Therefore any modification you make to the
1991          * returned list will be present inside the JAXB object.
1992          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
1993          *
1994          * <p>
1995          * For example, to add a new item, do as follows:
1996          * <pre>
1997          *    getRnaViewer().add(newItem);
1998          * </pre>
1999          *
2000          *
2001          * <p>
2002          * Objects of the following type(s) are allowed in the list
2003          * {@link JalviewModel.JSeq.RnaViewer }
2004          *
2005          *
2006          */
2007         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2008             if (rnaViewer == null) {
2009                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2010             }
2011             return this.rnaViewer;
2012         }
2013
2014         /**
2015          * Gets the value of the colour property.
2016          *
2017          * @return
2018          *     possible object is
2019          *     {@link Integer }
2020          *
2021          */
2022         public Integer getColour() {
2023             return colour;
2024         }
2025
2026         /**
2027          * Sets the value of the colour property.
2028          *
2029          * @param value
2030          *     allowed object is
2031          *     {@link Integer }
2032          *
2033          */
2034         public void setColour(Integer value) {
2035             this.colour = value;
2036         }
2037
2038         /**
2039          * Gets the value of the start property.
2040          *
2041          */
2042         public int getStart() {
2043             return start;
2044         }
2045
2046         /**
2047          * Sets the value of the start property.
2048          *
2049          */
2050         public void setStart(int value) {
2051             this.start = value;
2052         }
2053
2054         /**
2055          * Gets the value of the end property.
2056          *
2057          */
2058         public int getEnd() {
2059             return end;
2060         }
2061
2062         /**
2063          * Sets the value of the end property.
2064          *
2065          */
2066         public void setEnd(int value) {
2067             this.end = value;
2068         }
2069
2070         /**
2071          * Gets the value of the id property.
2072          *
2073          * @return
2074          *     possible object is
2075          *     {@link String }
2076          *
2077          */
2078         public String getId() {
2079             return id;
2080         }
2081
2082         /**
2083          * Sets the value of the id property.
2084          *
2085          * @param value
2086          *     allowed object is
2087          *     {@link String }
2088          *
2089          */
2090         public void setId(String value) {
2091             this.id = value;
2092         }
2093
2094         /**
2095          * Gets the value of the hidden property.
2096          *
2097          * @return
2098          *     possible object is
2099          *     {@link Boolean }
2100          *
2101          */
2102         public Boolean isHidden() {
2103             return hidden;
2104         }
2105
2106         /**
2107          * Sets the value of the hidden property.
2108          *
2109          * @param value
2110          *     allowed object is
2111          *     {@link Boolean }
2112          *
2113          */
2114         public void setHidden(Boolean value) {
2115             this.hidden = value;
2116         }
2117
2118         /**
2119          * Gets the value of the viewreference property.
2120          *
2121          * @return
2122          *     possible object is
2123          *     {@link Boolean }
2124          *
2125          */
2126         public Boolean isViewreference() {
2127             return viewreference;
2128         }
2129
2130         /**
2131          * Sets the value of the viewreference property.
2132          *
2133          * @param value
2134          *     allowed object is
2135          *     {@link Boolean }
2136          *
2137          */
2138         public void setViewreference(Boolean value) {
2139             this.viewreference = value;
2140         }
2141
2142
2143         /**
2144          * <p>Java class for anonymous complex type.
2145          *
2146          * <p>The following schema fragment specifies the expected content contained within this class.
2147          *
2148          * <pre>
2149          * &lt;complexType>
2150          *   &lt;complexContent>
2151          *     &lt;extension base="{www.jalview.org}pdbentry">
2152          *       &lt;sequence>
2153          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2154          *           &lt;complexType>
2155          *             &lt;simpleContent>
2156          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2157          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2158          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2159          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2160          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2161          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2162          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2163          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2164          *               &lt;/extension>
2165          *             &lt;/simpleContent>
2166          *           &lt;/complexType>
2167          *         &lt;/element>
2168          *       &lt;/sequence>
2169          *     &lt;/extension>
2170          *   &lt;/complexContent>
2171          * &lt;/complexType>
2172          * </pre>
2173          *
2174          *
2175          */
2176         @XmlAccessorType(XmlAccessType.FIELD)
2177         @XmlType(name = "", propOrder = {
2178             "structureState"
2179         })
2180         public static class Pdbids
2181             extends Pdbentry
2182         {
2183
2184             @XmlElement(namespace = "www.jalview.org")
2185             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2186
2187             /**
2188              * Gets the value of the structureState property.
2189              *
2190              * <p>
2191              * This accessor method returns a reference to the live list,
2192              * not a snapshot. Therefore any modification you make to the
2193              * returned list will be present inside the JAXB object.
2194              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2195              *
2196              * <p>
2197              * For example, to add a new item, do as follows:
2198              * <pre>
2199              *    getStructureState().add(newItem);
2200              * </pre>
2201              *
2202              *
2203              * <p>
2204              * Objects of the following type(s) are allowed in the list
2205              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2206              *
2207              *
2208              */
2209             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2210                 if (structureState == null) {
2211                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2212                 }
2213                 return this.structureState;
2214             }
2215
2216
2217             /**
2218              * <p>Java class for anonymous complex type.
2219              *
2220              * <p>The following schema fragment specifies the expected content contained within this class.
2221              *
2222              * <pre>
2223              * &lt;complexType>
2224              *   &lt;simpleContent>
2225              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2226              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2227              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2228              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2229              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2230              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2231              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2232              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2233              *     &lt;/extension>
2234              *   &lt;/simpleContent>
2235              * &lt;/complexType>
2236              * </pre>
2237              *
2238              *
2239              */
2240             @XmlAccessorType(XmlAccessType.FIELD)
2241             @XmlType(name = "", propOrder = {
2242                 "value"
2243             })
2244             public static class StructureState {
2245
2246                 @XmlValue
2247                 protected String value;
2248                 @XmlAttribute(name = "visible")
2249                 protected Boolean visible;
2250                 @XmlAttribute(name = "viewId")
2251                 protected String viewId;
2252                 @XmlAttribute(name = "alignwithAlignPanel")
2253                 protected Boolean alignwithAlignPanel;
2254                 @XmlAttribute(name = "colourwithAlignPanel")
2255                 protected Boolean colourwithAlignPanel;
2256                 @XmlAttribute(name = "colourByJmol")
2257                 protected Boolean colourByJmol;
2258                 @XmlAttribute(name = "type")
2259                 protected String type;
2260                 @XmlAttribute(name = "width")
2261                 protected Integer width;
2262                 @XmlAttribute(name = "height")
2263                 protected Integer height;
2264                 @XmlAttribute(name = "xpos")
2265                 protected Integer xpos;
2266                 @XmlAttribute(name = "ypos")
2267                 protected Integer ypos;
2268
2269                 /**
2270                  * Gets the value of the value property.
2271                  *
2272                  * @return
2273                  *     possible object is
2274                  *     {@link String }
2275                  *
2276                  */
2277                 public String getValue() {
2278                     return value;
2279                 }
2280
2281                 /**
2282                  * Sets the value of the value property.
2283                  *
2284                  * @param value
2285                  *     allowed object is
2286                  *     {@link String }
2287                  *
2288                  */
2289                 public void setValue(String value) {
2290                     this.value = value;
2291                 }
2292
2293                 /**
2294                  * Gets the value of the visible property.
2295                  *
2296                  * @return
2297                  *     possible object is
2298                  *     {@link Boolean }
2299                  *
2300                  */
2301                 public Boolean isVisible() {
2302                     return visible;
2303                 }
2304
2305                 /**
2306                  * Sets the value of the visible property.
2307                  *
2308                  * @param value
2309                  *     allowed object is
2310                  *     {@link Boolean }
2311                  *
2312                  */
2313                 public void setVisible(Boolean value) {
2314                     this.visible = value;
2315                 }
2316
2317                 /**
2318                  * Gets the value of the viewId property.
2319                  *
2320                  * @return
2321                  *     possible object is
2322                  *     {@link String }
2323                  *
2324                  */
2325                 public String getViewId() {
2326                     return viewId;
2327                 }
2328
2329                 /**
2330                  * Sets the value of the viewId property.
2331                  *
2332                  * @param value
2333                  *     allowed object is
2334                  *     {@link String }
2335                  *
2336                  */
2337                 public void setViewId(String value) {
2338                     this.viewId = value;
2339                 }
2340
2341                 /**
2342                  * Gets the value of the alignwithAlignPanel property.
2343                  *
2344                  * @return
2345                  *     possible object is
2346                  *     {@link Boolean }
2347                  *
2348                  */
2349                 public boolean isAlignwithAlignPanel() {
2350                     if (alignwithAlignPanel == null) {
2351                         return true;
2352                     } else {
2353                         return alignwithAlignPanel;
2354                     }
2355                 }
2356
2357                 /**
2358                  * Sets the value of the alignwithAlignPanel property.
2359                  *
2360                  * @param value
2361                  *     allowed object is
2362                  *     {@link Boolean }
2363                  *
2364                  */
2365                 public void setAlignwithAlignPanel(Boolean value) {
2366                     this.alignwithAlignPanel = value;
2367                 }
2368
2369                 /**
2370                  * Gets the value of the colourwithAlignPanel property.
2371                  *
2372                  * @return
2373                  *     possible object is
2374                  *     {@link Boolean }
2375                  *
2376                  */
2377                 public boolean isColourwithAlignPanel() {
2378                     if (colourwithAlignPanel == null) {
2379                         return false;
2380                     } else {
2381                         return colourwithAlignPanel;
2382                     }
2383                 }
2384
2385                 /**
2386                  * Sets the value of the colourwithAlignPanel property.
2387                  *
2388                  * @param value
2389                  *     allowed object is
2390                  *     {@link Boolean }
2391                  *
2392                  */
2393                 public void setColourwithAlignPanel(Boolean value) {
2394                     this.colourwithAlignPanel = value;
2395                 }
2396
2397                 /**
2398                  * Gets the value of the colourByJmol property.
2399                  *
2400                  * @return
2401                  *     possible object is
2402                  *     {@link Boolean }
2403                  *
2404                  */
2405                 public boolean isColourByJmol() {
2406                     if (colourByJmol == null) {
2407                         return true;
2408                     } else {
2409                         return colourByJmol;
2410                     }
2411                 }
2412
2413                 /**
2414                  * Sets the value of the colourByJmol property.
2415                  *
2416                  * @param value
2417                  *     allowed object is
2418                  *     {@link Boolean }
2419                  *
2420                  */
2421                 public void setColourByJmol(Boolean value) {
2422                     this.colourByJmol = value;
2423                 }
2424
2425                 /**
2426                  * Gets the value of the type property.
2427                  *
2428                  * @return
2429                  *     possible object is
2430                  *     {@link String }
2431                  *
2432                  */
2433                 public String getType() {
2434                     return type;
2435                 }
2436
2437                 /**
2438                  * Sets the value of the type property.
2439                  *
2440                  * @param value
2441                  *     allowed object is
2442                  *     {@link String }
2443                  *
2444                  */
2445                 public void setType(String value) {
2446                     this.type = value;
2447                 }
2448
2449                 /**
2450                  * Gets the value of the width property.
2451                  *
2452                  * @return
2453                  *     possible object is
2454                  *     {@link Integer }
2455                  *
2456                  */
2457                 public Integer getWidth() {
2458                     return width;
2459                 }
2460
2461                 /**
2462                  * Sets the value of the width property.
2463                  *
2464                  * @param value
2465                  *     allowed object is
2466                  *     {@link Integer }
2467                  *
2468                  */
2469                 public void setWidth(Integer value) {
2470                     this.width = value;
2471                 }
2472
2473                 /**
2474                  * Gets the value of the height property.
2475                  *
2476                  * @return
2477                  *     possible object is
2478                  *     {@link Integer }
2479                  *
2480                  */
2481                 public Integer getHeight() {
2482                     return height;
2483                 }
2484
2485                 /**
2486                  * Sets the value of the height property.
2487                  *
2488                  * @param value
2489                  *     allowed object is
2490                  *     {@link Integer }
2491                  *
2492                  */
2493                 public void setHeight(Integer value) {
2494                     this.height = value;
2495                 }
2496
2497                 /**
2498                  * Gets the value of the xpos property.
2499                  *
2500                  * @return
2501                  *     possible object is
2502                  *     {@link Integer }
2503                  *
2504                  */
2505                 public Integer getXpos() {
2506                     return xpos;
2507                 }
2508
2509                 /**
2510                  * Sets the value of the xpos property.
2511                  *
2512                  * @param value
2513                  *     allowed object is
2514                  *     {@link Integer }
2515                  *
2516                  */
2517                 public void setXpos(Integer value) {
2518                     this.xpos = value;
2519                 }
2520
2521                 /**
2522                  * Gets the value of the ypos property.
2523                  *
2524                  * @return
2525                  *     possible object is
2526                  *     {@link Integer }
2527                  *
2528                  */
2529                 public Integer getYpos() {
2530                     return ypos;
2531                 }
2532
2533                 /**
2534                  * Sets the value of the ypos property.
2535                  *
2536                  * @param value
2537                  *     allowed object is
2538                  *     {@link Integer }
2539                  *
2540                  */
2541                 public void setYpos(Integer value) {
2542                     this.ypos = value;
2543                 }
2544
2545             }
2546
2547         }
2548
2549
2550         /**
2551          * <p>Java class for anonymous complex type.
2552          *
2553          * <p>The following schema fragment specifies the expected content contained within this class.
2554          *
2555          * <pre>
2556          * &lt;complexType>
2557          *   &lt;complexContent>
2558          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2559          *       &lt;sequence>
2560          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2561          *           &lt;complexType>
2562          *             &lt;complexContent>
2563          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2564          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2565          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2566          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2567          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2568          *               &lt;/restriction>
2569          *             &lt;/complexContent>
2570          *           &lt;/complexType>
2571          *         &lt;/element>
2572          *       &lt;/sequence>
2573          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2574          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2575          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2576          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2577          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2578          *     &lt;/restriction>
2579          *   &lt;/complexContent>
2580          * &lt;/complexType>
2581          * </pre>
2582          *
2583          *
2584          */
2585         @XmlAccessorType(XmlAccessType.FIELD)
2586         @XmlType(name = "", propOrder = {
2587             "secondaryStructure"
2588         })
2589         public static class RnaViewer {
2590
2591             @XmlElement(namespace = "www.jalview.org", required = true)
2592             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2593             @XmlAttribute(name = "title")
2594             protected String title;
2595             @XmlAttribute(name = "viewId")
2596             protected String viewId;
2597             @XmlAttribute(name = "dividerLocation")
2598             protected Integer dividerLocation;
2599             @XmlAttribute(name = "selectedRna")
2600             protected Integer selectedRna;
2601             @XmlAttribute(name = "width")
2602             protected Integer width;
2603             @XmlAttribute(name = "height")
2604             protected Integer height;
2605             @XmlAttribute(name = "xpos")
2606             protected Integer xpos;
2607             @XmlAttribute(name = "ypos")
2608             protected Integer ypos;
2609
2610             /**
2611              * Gets the value of the secondaryStructure property.
2612              *
2613              * <p>
2614              * This accessor method returns a reference to the live list,
2615              * not a snapshot. Therefore any modification you make to the
2616              * returned list will be present inside the JAXB object.
2617              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2618              *
2619              * <p>
2620              * For example, to add a new item, do as follows:
2621              * <pre>
2622              *    getSecondaryStructure().add(newItem);
2623              * </pre>
2624              *
2625              *
2626              * <p>
2627              * Objects of the following type(s) are allowed in the list
2628              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2629              *
2630              *
2631              */
2632             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2633                 if (secondaryStructure == null) {
2634                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2635                 }
2636                 return this.secondaryStructure;
2637             }
2638
2639             /**
2640              * Gets the value of the title property.
2641              *
2642              * @return
2643              *     possible object is
2644              *     {@link String }
2645              *
2646              */
2647             public String getTitle() {
2648                 return title;
2649             }
2650
2651             /**
2652              * Sets the value of the title property.
2653              *
2654              * @param value
2655              *     allowed object is
2656              *     {@link String }
2657              *
2658              */
2659             public void setTitle(String value) {
2660                 this.title = value;
2661             }
2662
2663             /**
2664              * Gets the value of the viewId property.
2665              *
2666              * @return
2667              *     possible object is
2668              *     {@link String }
2669              *
2670              */
2671             public String getViewId() {
2672                 return viewId;
2673             }
2674
2675             /**
2676              * Sets the value of the viewId property.
2677              *
2678              * @param value
2679              *     allowed object is
2680              *     {@link String }
2681              *
2682              */
2683             public void setViewId(String value) {
2684                 this.viewId = value;
2685             }
2686
2687             /**
2688              * Gets the value of the dividerLocation property.
2689              *
2690              * @return
2691              *     possible object is
2692              *     {@link Integer }
2693              *
2694              */
2695             public Integer getDividerLocation() {
2696                 return dividerLocation;
2697             }
2698
2699             /**
2700              * Sets the value of the dividerLocation property.
2701              *
2702              * @param value
2703              *     allowed object is
2704              *     {@link Integer }
2705              *
2706              */
2707             public void setDividerLocation(Integer value) {
2708                 this.dividerLocation = value;
2709             }
2710
2711             /**
2712              * Gets the value of the selectedRna property.
2713              *
2714              * @return
2715              *     possible object is
2716              *     {@link Integer }
2717              *
2718              */
2719             public Integer getSelectedRna() {
2720                 return selectedRna;
2721             }
2722
2723             /**
2724              * Sets the value of the selectedRna property.
2725              *
2726              * @param value
2727              *     allowed object is
2728              *     {@link Integer }
2729              *
2730              */
2731             public void setSelectedRna(Integer value) {
2732                 this.selectedRna = value;
2733             }
2734
2735             /**
2736              * Gets the value of the width property.
2737              *
2738              * @return
2739              *     possible object is
2740              *     {@link Integer }
2741              *
2742              */
2743             public Integer getWidth() {
2744                 return width;
2745             }
2746
2747             /**
2748              * Sets the value of the width property.
2749              *
2750              * @param value
2751              *     allowed object is
2752              *     {@link Integer }
2753              *
2754              */
2755             public void setWidth(Integer value) {
2756                 this.width = value;
2757             }
2758
2759             /**
2760              * Gets the value of the height property.
2761              *
2762              * @return
2763              *     possible object is
2764              *     {@link Integer }
2765              *
2766              */
2767             public Integer getHeight() {
2768                 return height;
2769             }
2770
2771             /**
2772              * Sets the value of the height property.
2773              *
2774              * @param value
2775              *     allowed object is
2776              *     {@link Integer }
2777              *
2778              */
2779             public void setHeight(Integer value) {
2780                 this.height = value;
2781             }
2782
2783             /**
2784              * Gets the value of the xpos property.
2785              *
2786              * @return
2787              *     possible object is
2788              *     {@link Integer }
2789              *
2790              */
2791             public Integer getXpos() {
2792                 return xpos;
2793             }
2794
2795             /**
2796              * Sets the value of the xpos property.
2797              *
2798              * @param value
2799              *     allowed object is
2800              *     {@link Integer }
2801              *
2802              */
2803             public void setXpos(Integer value) {
2804                 this.xpos = value;
2805             }
2806
2807             /**
2808              * Gets the value of the ypos property.
2809              *
2810              * @return
2811              *     possible object is
2812              *     {@link Integer }
2813              *
2814              */
2815             public Integer getYpos() {
2816                 return ypos;
2817             }
2818
2819             /**
2820              * Sets the value of the ypos property.
2821              *
2822              * @param value
2823              *     allowed object is
2824              *     {@link Integer }
2825              *
2826              */
2827             public void setYpos(Integer value) {
2828                 this.ypos = value;
2829             }
2830
2831
2832             /**
2833              * <p>Java class for anonymous complex type.
2834              *
2835              * <p>The following schema fragment specifies the expected content contained within this class.
2836              *
2837              * <pre>
2838              * &lt;complexType>
2839              *   &lt;complexContent>
2840              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2841              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2842              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2843              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2844              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2845              *     &lt;/restriction>
2846              *   &lt;/complexContent>
2847              * &lt;/complexType>
2848              * </pre>
2849              *
2850              *
2851              */
2852             @XmlAccessorType(XmlAccessType.FIELD)
2853             @XmlType(name = "")
2854             public static class SecondaryStructure {
2855
2856                 @XmlAttribute(name = "title")
2857                 protected String title;
2858                 @XmlAttribute(name = "annotationId", required = true)
2859                 protected String annotationId;
2860                 @XmlAttribute(name = "gapped")
2861                 protected Boolean gapped;
2862                 @XmlAttribute(name = "viewerState")
2863                 protected String viewerState;
2864
2865                 /**
2866                  * Gets the value of the title property.
2867                  *
2868                  * @return
2869                  *     possible object is
2870                  *     {@link String }
2871                  *
2872                  */
2873                 public String getTitle() {
2874                     return title;
2875                 }
2876
2877                 /**
2878                  * Sets the value of the title property.
2879                  *
2880                  * @param value
2881                  *     allowed object is
2882                  *     {@link String }
2883                  *
2884                  */
2885                 public void setTitle(String value) {
2886                     this.title = value;
2887                 }
2888
2889                 /**
2890                  * Gets the value of the annotationId property.
2891                  *
2892                  * @return
2893                  *     possible object is
2894                  *     {@link String }
2895                  *
2896                  */
2897                 public String getAnnotationId() {
2898                     return annotationId;
2899                 }
2900
2901                 /**
2902                  * Sets the value of the annotationId property.
2903                  *
2904                  * @param value
2905                  *     allowed object is
2906                  *     {@link String }
2907                  *
2908                  */
2909                 public void setAnnotationId(String value) {
2910                     this.annotationId = value;
2911                 }
2912
2913                 /**
2914                  * Gets the value of the gapped property.
2915                  *
2916                  * @return
2917                  *     possible object is
2918                  *     {@link Boolean }
2919                  *
2920                  */
2921                 public Boolean isGapped() {
2922                     return gapped;
2923                 }
2924
2925                 /**
2926                  * Sets the value of the gapped property.
2927                  *
2928                  * @param value
2929                  *     allowed object is
2930                  *     {@link Boolean }
2931                  *
2932                  */
2933                 public void setGapped(Boolean value) {
2934                     this.gapped = value;
2935                 }
2936
2937                 /**
2938                  * Gets the value of the viewerState property.
2939                  *
2940                  * @return
2941                  *     possible object is
2942                  *     {@link String }
2943                  *
2944                  */
2945                 public String getViewerState() {
2946                     return viewerState;
2947                 }
2948
2949                 /**
2950                  * Sets the value of the viewerState property.
2951                  *
2952                  * @param value
2953                  *     allowed object is
2954                  *     {@link String }
2955                  *
2956                  */
2957                 public void setViewerState(String value) {
2958                     this.viewerState = value;
2959                 }
2960
2961             }
2962
2963         }
2964
2965     }
2966
2967
2968     /**
2969      * <p>Java class for anonymous complex type.
2970      *
2971      * <p>The following schema fragment specifies the expected content contained within this class.
2972      *
2973      * <pre>
2974      * &lt;complexType>
2975      *   &lt;complexContent>
2976      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2977      *       &lt;sequence minOccurs="0">
2978      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
2979      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
2980      *       &lt;/sequence>
2981      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2982      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
2983      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
2984      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
2985      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
2986      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2987      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2988      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2989      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2990      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2991      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
2992      *     &lt;/restriction>
2993      *   &lt;/complexContent>
2994      * &lt;/complexType>
2995      * </pre>
2996      *
2997      *
2998      */
2999     @XmlAccessorType(XmlAccessType.FIELD)
3000     @XmlType(name = "", propOrder = {
3001         "title",
3002         "newick"
3003     })
3004     public static class Tree {
3005
3006         @XmlElement(namespace = "www.jalview.org")
3007         protected String title;
3008         @XmlElement(namespace = "www.jalview.org")
3009         protected String newick;
3010         @XmlAttribute(name = "fontName")
3011         protected String fontName;
3012         @XmlAttribute(name = "fontSize")
3013         protected Integer fontSize;
3014         @XmlAttribute(name = "fontStyle")
3015         protected Integer fontStyle;
3016         @XmlAttribute(name = "threshold")
3017         protected Float threshold;
3018         @XmlAttribute(name = "showBootstrap")
3019         protected Boolean showBootstrap;
3020         @XmlAttribute(name = "showDistances")
3021         protected Boolean showDistances;
3022         @XmlAttribute(name = "markUnlinked")
3023         protected Boolean markUnlinked;
3024         @XmlAttribute(name = "fitToWindow")
3025         protected Boolean fitToWindow;
3026         @XmlAttribute(name = "currentTree")
3027         protected Boolean currentTree;
3028         @XmlAttribute(name = "id")
3029         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
3030         @XmlID
3031         @XmlSchemaType(name = "ID")
3032         protected String id;
3033         @XmlAttribute(name = "width")
3034         protected Integer width;
3035         @XmlAttribute(name = "height")
3036         protected Integer height;
3037         @XmlAttribute(name = "xpos")
3038         protected Integer xpos;
3039         @XmlAttribute(name = "ypos")
3040         protected Integer ypos;
3041
3042         /**
3043          * Gets the value of the title property.
3044          *
3045          * @return
3046          *     possible object is
3047          *     {@link String }
3048          *
3049          */
3050         public String getTitle() {
3051             return title;
3052         }
3053
3054         /**
3055          * Sets the value of the title property.
3056          *
3057          * @param value
3058          *     allowed object is
3059          *     {@link String }
3060          *
3061          */
3062         public void setTitle(String value) {
3063             this.title = value;
3064         }
3065
3066         /**
3067          * Gets the value of the newick property.
3068          *
3069          * @return
3070          *     possible object is
3071          *     {@link String }
3072          *
3073          */
3074         public String getNewick() {
3075             return newick;
3076         }
3077
3078         /**
3079          * Sets the value of the newick property.
3080          *
3081          * @param value
3082          *     allowed object is
3083          *     {@link String }
3084          *
3085          */
3086         public void setNewick(String value) {
3087             this.newick = value;
3088         }
3089
3090         /**
3091          * Gets the value of the fontName property.
3092          *
3093          * @return
3094          *     possible object is
3095          *     {@link String }
3096          *
3097          */
3098         public String getFontName() {
3099             return fontName;
3100         }
3101
3102         /**
3103          * Sets the value of the fontName property.
3104          *
3105          * @param value
3106          *     allowed object is
3107          *     {@link String }
3108          *
3109          */
3110         public void setFontName(String value) {
3111             this.fontName = value;
3112         }
3113
3114         /**
3115          * Gets the value of the fontSize property.
3116          *
3117          * @return
3118          *     possible object is
3119          *     {@link Integer }
3120          *
3121          */
3122         public Integer getFontSize() {
3123             return fontSize;
3124         }
3125
3126         /**
3127          * Sets the value of the fontSize property.
3128          *
3129          * @param value
3130          *     allowed object is
3131          *     {@link Integer }
3132          *
3133          */
3134         public void setFontSize(Integer value) {
3135             this.fontSize = value;
3136         }
3137
3138         /**
3139          * Gets the value of the fontStyle property.
3140          *
3141          * @return
3142          *     possible object is
3143          *     {@link Integer }
3144          *
3145          */
3146         public Integer getFontStyle() {
3147             return fontStyle;
3148         }
3149
3150         /**
3151          * Sets the value of the fontStyle property.
3152          *
3153          * @param value
3154          *     allowed object is
3155          *     {@link Integer }
3156          *
3157          */
3158         public void setFontStyle(Integer value) {
3159             this.fontStyle = value;
3160         }
3161
3162         /**
3163          * Gets the value of the threshold property.
3164          *
3165          * @return
3166          *     possible object is
3167          *     {@link Float }
3168          *
3169          */
3170         public Float getThreshold() {
3171             return threshold;
3172         }
3173
3174         /**
3175          * Sets the value of the threshold property.
3176          *
3177          * @param value
3178          *     allowed object is
3179          *     {@link Float }
3180          *
3181          */
3182         public void setThreshold(Float value) {
3183             this.threshold = value;
3184         }
3185
3186         /**
3187          * Gets the value of the showBootstrap property.
3188          *
3189          * @return
3190          *     possible object is
3191          *     {@link Boolean }
3192          *
3193          */
3194         public Boolean isShowBootstrap() {
3195             return showBootstrap;
3196         }
3197
3198         /**
3199          * Sets the value of the showBootstrap property.
3200          *
3201          * @param value
3202          *     allowed object is
3203          *     {@link Boolean }
3204          *
3205          */
3206         public void setShowBootstrap(Boolean value) {
3207             this.showBootstrap = value;
3208         }
3209
3210         /**
3211          * Gets the value of the showDistances property.
3212          *
3213          * @return
3214          *     possible object is
3215          *     {@link Boolean }
3216          *
3217          */
3218         public Boolean isShowDistances() {
3219             return showDistances;
3220         }
3221
3222         /**
3223          * Sets the value of the showDistances property.
3224          *
3225          * @param value
3226          *     allowed object is
3227          *     {@link Boolean }
3228          *
3229          */
3230         public void setShowDistances(Boolean value) {
3231             this.showDistances = value;
3232         }
3233
3234         /**
3235          * Gets the value of the markUnlinked property.
3236          *
3237          * @return
3238          *     possible object is
3239          *     {@link Boolean }
3240          *
3241          */
3242         public Boolean isMarkUnlinked() {
3243             return markUnlinked;
3244         }
3245
3246         /**
3247          * Sets the value of the markUnlinked property.
3248          *
3249          * @param value
3250          *     allowed object is
3251          *     {@link Boolean }
3252          *
3253          */
3254         public void setMarkUnlinked(Boolean value) {
3255             this.markUnlinked = value;
3256         }
3257
3258         /**
3259          * Gets the value of the fitToWindow property.
3260          *
3261          * @return
3262          *     possible object is
3263          *     {@link Boolean }
3264          *
3265          */
3266         public Boolean isFitToWindow() {
3267             return fitToWindow;
3268         }
3269
3270         /**
3271          * Sets the value of the fitToWindow property.
3272          *
3273          * @param value
3274          *     allowed object is
3275          *     {@link Boolean }
3276          *
3277          */
3278         public void setFitToWindow(Boolean value) {
3279             this.fitToWindow = value;
3280         }
3281
3282         /**
3283          * Gets the value of the currentTree property.
3284          *
3285          * @return
3286          *     possible object is
3287          *     {@link Boolean }
3288          *
3289          */
3290         public Boolean isCurrentTree() {
3291             return currentTree;
3292         }
3293
3294         /**
3295          * Sets the value of the currentTree property.
3296          *
3297          * @param value
3298          *     allowed object is
3299          *     {@link Boolean }
3300          *
3301          */
3302         public void setCurrentTree(Boolean value) {
3303             this.currentTree = value;
3304         }
3305
3306         /**
3307          * Gets the value of the id property.
3308          *
3309          * @return
3310          *     possible object is
3311          *     {@link String }
3312          *
3313          */
3314         public String getId() {
3315             return id;
3316         }
3317
3318         /**
3319          * Sets the value of the id property.
3320          *
3321          * @param value
3322          *     allowed object is
3323          *     {@link String }
3324          *
3325          */
3326         public void setId(String value) {
3327             this.id = value;
3328         }
3329
3330         /**
3331          * Gets the value of the width property.
3332          *
3333          * @return
3334          *     possible object is
3335          *     {@link Integer }
3336          *
3337          */
3338         public Integer getWidth() {
3339             return width;
3340         }
3341
3342         /**
3343          * Sets the value of the width property.
3344          *
3345          * @param value
3346          *     allowed object is
3347          *     {@link Integer }
3348          *
3349          */
3350         public void setWidth(Integer value) {
3351             this.width = value;
3352         }
3353
3354         /**
3355          * Gets the value of the height property.
3356          *
3357          * @return
3358          *     possible object is
3359          *     {@link Integer }
3360          *
3361          */
3362         public Integer getHeight() {
3363             return height;
3364         }
3365
3366         /**
3367          * Sets the value of the height property.
3368          *
3369          * @param value
3370          *     allowed object is
3371          *     {@link Integer }
3372          *
3373          */
3374         public void setHeight(Integer value) {
3375             this.height = value;
3376         }
3377
3378         /**
3379          * Gets the value of the xpos property.
3380          *
3381          * @return
3382          *     possible object is
3383          *     {@link Integer }
3384          *
3385          */
3386         public Integer getXpos() {
3387             return xpos;
3388         }
3389
3390         /**
3391          * Sets the value of the xpos property.
3392          *
3393          * @param value
3394          *     allowed object is
3395          *     {@link Integer }
3396          *
3397          */
3398         public void setXpos(Integer value) {
3399             this.xpos = value;
3400         }
3401
3402         /**
3403          * Gets the value of the ypos property.
3404          *
3405          * @return
3406          *     possible object is
3407          *     {@link Integer }
3408          *
3409          */
3410         public Integer getYpos() {
3411             return ypos;
3412         }
3413
3414         /**
3415          * Sets the value of the ypos property.
3416          *
3417          * @param value
3418          *     allowed object is
3419          *     {@link Integer }
3420          *
3421          */
3422         public void setYpos(Integer value) {
3423             this.ypos = value;
3424         }
3425
3426     }
3427
3428
3429     /**
3430      * <p>Java class for anonymous complex type.
3431      *
3432      * <p>The following schema fragment specifies the expected content contained within this class.
3433      *
3434      * <pre>
3435      * &lt;complexType>
3436      *   &lt;complexContent>
3437      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3438      *       &lt;sequence>
3439      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
3440      *       &lt;/sequence>
3441      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
3442      *     &lt;/restriction>
3443      *   &lt;/complexContent>
3444      * &lt;/complexType>
3445      * </pre>
3446      *
3447      *
3448      */
3449     @XmlAccessorType(XmlAccessType.FIELD)
3450     @XmlType(name = "", propOrder = {
3451         "userColourScheme"
3452     })
3453     public static class UserColours {
3454
3455         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
3456         protected JalviewUserColours userColourScheme;
3457         @XmlAttribute(name = "id")
3458         protected String id;
3459
3460         /**
3461          * Gets the value of the userColourScheme property.
3462          *
3463          * @return
3464          *     possible object is
3465          *     {@link JalviewUserColours }
3466          *
3467          */
3468         public JalviewUserColours getUserColourScheme() {
3469             return userColourScheme;
3470         }
3471
3472         /**
3473          * Sets the value of the userColourScheme property.
3474          *
3475          * @param value
3476          *     allowed object is
3477          *     {@link JalviewUserColours }
3478          *
3479          */
3480         public void setUserColourScheme(JalviewUserColours value) {
3481             this.userColourScheme = value;
3482         }
3483
3484         /**
3485          * Gets the value of the id property.
3486          *
3487          * @return
3488          *     possible object is
3489          *     {@link String }
3490          *
3491          */
3492         public String getId() {
3493             return id;
3494         }
3495
3496         /**
3497          * Sets the value of the id property.
3498          *
3499          * @param value
3500          *     allowed object is
3501          *     {@link String }
3502          *
3503          */
3504         public void setId(String value) {
3505             this.id = value;
3506         }
3507
3508     }
3509
3510
3511     /**
3512      * <p>Java class for anonymous complex type.
3513      *
3514      * <p>The following schema fragment specifies the expected content contained within this class.
3515      *
3516      * <pre>
3517      * &lt;complexType>
3518      *   &lt;complexContent>
3519      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3520      *       &lt;sequence>
3521      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
3522      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
3523      *           &lt;complexType>
3524      *             &lt;complexContent>
3525      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3526      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
3527      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
3528      *               &lt;/restriction>
3529      *             &lt;/complexContent>
3530      *           &lt;/complexType>
3531      *         &lt;/element>
3532      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
3533      *           &lt;complexType>
3534      *             &lt;complexContent>
3535      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
3536      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
3537      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3538      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3539      *               &lt;/extension>
3540      *             &lt;/complexContent>
3541      *           &lt;/complexType>
3542      *         &lt;/element>
3543      *       &lt;/sequence>
3544      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3545      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3546      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3547      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
3548      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
3549      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
3550      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3551      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3552      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3553      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3554      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3555      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3556      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3557      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3558      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3559      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3560      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3561      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3562      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3563      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3564      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3565      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3566      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3567      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3568      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3569      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3570      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3571      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3572      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
3573      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
3574      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
3575      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
3576      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
3577      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3578      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
3579      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
3580      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3581      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
3582      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
3583      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
3584      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
3585      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
3586      *     &lt;/restriction>
3587      *   &lt;/complexContent>
3588      * &lt;/complexType>
3589      * </pre>
3590      *
3591      *
3592      */
3593     @XmlAccessorType(XmlAccessType.FIELD)
3594     @XmlType(name = "", propOrder = {
3595         "annotationColours",
3596         "hiddenColumns",
3597         "calcIdParam"
3598     })
3599     public static class Viewport {
3600
3601         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
3602         protected AnnotationColourScheme annotationColours;
3603         @XmlElement(namespace = "www.jalview.org")
3604         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
3605         @XmlElement(namespace = "www.jalview.org")
3606         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
3607         @XmlAttribute(name = "conservationSelected")
3608         protected Boolean conservationSelected;
3609         @XmlAttribute(name = "pidSelected")
3610         protected Boolean pidSelected;
3611         @XmlAttribute(name = "bgColour")
3612         protected String bgColour;
3613         @XmlAttribute(name = "consThreshold")
3614         protected Integer consThreshold;
3615         @XmlAttribute(name = "pidThreshold")
3616         protected Integer pidThreshold;
3617         @XmlAttribute(name = "title")
3618         protected String title;
3619         @XmlAttribute(name = "showFullId")
3620         protected Boolean showFullId;
3621         @XmlAttribute(name = "rightAlignIds")
3622         protected Boolean rightAlignIds;
3623         @XmlAttribute(name = "showText")
3624         protected Boolean showText;
3625         @XmlAttribute(name = "showColourText")
3626         protected Boolean showColourText;
3627         @XmlAttribute(name = "showUnconserved")
3628         protected Boolean showUnconserved;
3629         @XmlAttribute(name = "showBoxes")
3630         protected Boolean showBoxes;
3631         @XmlAttribute(name = "wrapAlignment")
3632         protected Boolean wrapAlignment;
3633         @XmlAttribute(name = "renderGaps")
3634         protected Boolean renderGaps;
3635         @XmlAttribute(name = "showSequenceFeatures")
3636         protected Boolean showSequenceFeatures;
3637         @XmlAttribute(name = "showNPfeatureTooltip")
3638         protected Boolean showNPfeatureTooltip;
3639         @XmlAttribute(name = "showDbRefTooltip")
3640         protected Boolean showDbRefTooltip;
3641         @XmlAttribute(name = "followHighlight")
3642         protected Boolean followHighlight;
3643         @XmlAttribute(name = "followSelection")
3644         protected Boolean followSelection;
3645         @XmlAttribute(name = "showAnnotation")
3646         protected Boolean showAnnotation;
3647         @XmlAttribute(name = "centreColumnLabels")
3648         protected Boolean centreColumnLabels;
3649         @XmlAttribute(name = "showGroupConservation")
3650         protected Boolean showGroupConservation;
3651         @XmlAttribute(name = "showGroupConsensus")
3652         protected Boolean showGroupConsensus;
3653         @XmlAttribute(name = "showConsensusHistogram")
3654         protected Boolean showConsensusHistogram;
3655         @XmlAttribute(name = "showSequenceLogo")
3656         protected Boolean showSequenceLogo;
3657         @XmlAttribute(name = "normaliseSequenceLogo")
3658         protected Boolean normaliseSequenceLogo;
3659         @XmlAttribute(name = "ignoreGapsinConsensus")
3660         protected Boolean ignoreGapsinConsensus;
3661         @XmlAttribute(name = "startRes")
3662         protected Integer startRes;
3663         @XmlAttribute(name = "startSeq")
3664         protected Integer startSeq;
3665         @XmlAttribute(name = "fontName")
3666         protected String fontName;
3667         @XmlAttribute(name = "fontSize")
3668         protected Integer fontSize;
3669         @XmlAttribute(name = "fontStyle")
3670         protected Integer fontStyle;
3671         @XmlAttribute(name = "scaleProteinAsCdna")
3672         protected Boolean scaleProteinAsCdna;
3673         @XmlAttribute(name = "viewName")
3674         protected String viewName;
3675         @XmlAttribute(name = "sequenceSetId")
3676         protected String sequenceSetId;
3677         @XmlAttribute(name = "gatheredViews")
3678         protected Boolean gatheredViews;
3679         @XmlAttribute(name = "textCol1")
3680         protected Integer textCol1;
3681         @XmlAttribute(name = "textCol2")
3682         protected Integer textCol2;
3683         @XmlAttribute(name = "textColThreshold")
3684         protected Integer textColThreshold;
3685         @XmlAttribute(name = "id")
3686         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
3687         @XmlID
3688         @XmlSchemaType(name = "ID")
3689         protected String id;
3690         @XmlAttribute(name = "complementId")
3691         protected String complementId;
3692         @XmlAttribute(name = "width")
3693         protected Integer width;
3694         @XmlAttribute(name = "height")
3695         protected Integer height;
3696         @XmlAttribute(name = "xpos")
3697         protected Integer xpos;
3698         @XmlAttribute(name = "ypos")
3699         protected Integer ypos;
3700
3701         /**
3702          * Gets the value of the annotationColours property.
3703          *
3704          * @return
3705          *     possible object is
3706          *     {@link AnnotationColourScheme }
3707          *
3708          */
3709         public AnnotationColourScheme getAnnotationColours() {
3710             return annotationColours;
3711         }
3712
3713         /**
3714          * Sets the value of the annotationColours property.
3715          *
3716          * @param value
3717          *     allowed object is
3718          *     {@link AnnotationColourScheme }
3719          *
3720          */
3721         public void setAnnotationColours(AnnotationColourScheme value) {
3722             this.annotationColours = value;
3723         }
3724
3725         /**
3726          * Gets the value of the hiddenColumns property.
3727          *
3728          * <p>
3729          * This accessor method returns a reference to the live list,
3730          * not a snapshot. Therefore any modification you make to the
3731          * returned list will be present inside the JAXB object.
3732          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
3733          *
3734          * <p>
3735          * For example, to add a new item, do as follows:
3736          * <pre>
3737          *    getHiddenColumns().add(newItem);
3738          * </pre>
3739          *
3740          *
3741          * <p>
3742          * Objects of the following type(s) are allowed in the list
3743          * {@link JalviewModel.Viewport.HiddenColumns }
3744          *
3745          *
3746          */
3747         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
3748             if (hiddenColumns == null) {
3749                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
3750             }
3751             return this.hiddenColumns;
3752         }
3753
3754         /**
3755          * Gets the value of the calcIdParam property.
3756          *
3757          * <p>
3758          * This accessor method returns a reference to the live list,
3759          * not a snapshot. Therefore any modification you make to the
3760          * returned list will be present inside the JAXB object.
3761          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
3762          *
3763          * <p>
3764          * For example, to add a new item, do as follows:
3765          * <pre>
3766          *    getCalcIdParam().add(newItem);
3767          * </pre>
3768          *
3769          *
3770          * <p>
3771          * Objects of the following type(s) are allowed in the list
3772          * {@link JalviewModel.Viewport.CalcIdParam }
3773          *
3774          *
3775          */
3776         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
3777             if (calcIdParam == null) {
3778                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
3779             }
3780             return this.calcIdParam;
3781         }
3782
3783         /**
3784          * Gets the value of the conservationSelected property.
3785          *
3786          * @return
3787          *     possible object is
3788          *     {@link Boolean }
3789          *
3790          */
3791         public Boolean isConservationSelected() {
3792             return conservationSelected;
3793         }
3794
3795         /**
3796          * Sets the value of the conservationSelected property.
3797          *
3798          * @param value
3799          *     allowed object is
3800          *     {@link Boolean }
3801          *
3802          */
3803         public void setConservationSelected(Boolean value) {
3804             this.conservationSelected = value;
3805         }
3806
3807         /**
3808          * Gets the value of the pidSelected property.
3809          *
3810          * @return
3811          *     possible object is
3812          *     {@link Boolean }
3813          *
3814          */
3815         public Boolean isPidSelected() {
3816             return pidSelected;
3817         }
3818
3819         /**
3820          * Sets the value of the pidSelected property.
3821          *
3822          * @param value
3823          *     allowed object is
3824          *     {@link Boolean }
3825          *
3826          */
3827         public void setPidSelected(Boolean value) {
3828             this.pidSelected = value;
3829         }
3830
3831         /**
3832          * Gets the value of the bgColour property.
3833          *
3834          * @return
3835          *     possible object is
3836          *     {@link String }
3837          *
3838          */
3839         public String getBgColour() {
3840             return bgColour;
3841         }
3842
3843         /**
3844          * Sets the value of the bgColour property.
3845          *
3846          * @param value
3847          *     allowed object is
3848          *     {@link String }
3849          *
3850          */
3851         public void setBgColour(String value) {
3852             this.bgColour = value;
3853         }
3854
3855         /**
3856          * Gets the value of the consThreshold property.
3857          *
3858          * @return
3859          *     possible object is
3860          *     {@link Integer }
3861          *
3862          */
3863         public Integer getConsThreshold() {
3864             return consThreshold;
3865         }
3866
3867         /**
3868          * Sets the value of the consThreshold property.
3869          *
3870          * @param value
3871          *     allowed object is
3872          *     {@link Integer }
3873          *
3874          */
3875         public void setConsThreshold(Integer value) {
3876             this.consThreshold = value;
3877         }
3878
3879         /**
3880          * Gets the value of the pidThreshold property.
3881          *
3882          * @return
3883          *     possible object is
3884          *     {@link Integer }
3885          *
3886          */
3887         public Integer getPidThreshold() {
3888             return pidThreshold;
3889         }
3890
3891         /**
3892          * Sets the value of the pidThreshold property.
3893          *
3894          * @param value
3895          *     allowed object is
3896          *     {@link Integer }
3897          *
3898          */
3899         public void setPidThreshold(Integer value) {
3900             this.pidThreshold = value;
3901         }
3902
3903         /**
3904          * Gets the value of the title property.
3905          *
3906          * @return
3907          *     possible object is
3908          *     {@link String }
3909          *
3910          */
3911         public String getTitle() {
3912             return title;
3913         }
3914
3915         /**
3916          * Sets the value of the title property.
3917          *
3918          * @param value
3919          *     allowed object is
3920          *     {@link String }
3921          *
3922          */
3923         public void setTitle(String value) {
3924             this.title = value;
3925         }
3926
3927         /**
3928          * Gets the value of the showFullId property.
3929          *
3930          * @return
3931          *     possible object is
3932          *     {@link Boolean }
3933          *
3934          */
3935         public Boolean isShowFullId() {
3936             return showFullId;
3937         }
3938
3939         /**
3940          * Sets the value of the showFullId property.
3941          *
3942          * @param value
3943          *     allowed object is
3944          *     {@link Boolean }
3945          *
3946          */
3947         public void setShowFullId(Boolean value) {
3948             this.showFullId = value;
3949         }
3950
3951         /**
3952          * Gets the value of the rightAlignIds property.
3953          *
3954          * @return
3955          *     possible object is
3956          *     {@link Boolean }
3957          *
3958          */
3959         public Boolean isRightAlignIds() {
3960             return rightAlignIds;
3961         }
3962
3963         /**
3964          * Sets the value of the rightAlignIds property.
3965          *
3966          * @param value
3967          *     allowed object is
3968          *     {@link Boolean }
3969          *
3970          */
3971         public void setRightAlignIds(Boolean value) {
3972             this.rightAlignIds = value;
3973         }
3974
3975         /**
3976          * Gets the value of the showText property.
3977          *
3978          * @return
3979          *     possible object is
3980          *     {@link Boolean }
3981          *
3982          */
3983         public Boolean isShowText() {
3984             return showText;
3985         }
3986
3987         /**
3988          * Sets the value of the showText property.
3989          *
3990          * @param value
3991          *     allowed object is
3992          *     {@link Boolean }
3993          *
3994          */
3995         public void setShowText(Boolean value) {
3996             this.showText = value;
3997         }
3998
3999         /**
4000          * Gets the value of the showColourText property.
4001          *
4002          * @return
4003          *     possible object is
4004          *     {@link Boolean }
4005          *
4006          */
4007         public Boolean isShowColourText() {
4008             return showColourText;
4009         }
4010
4011         /**
4012          * Sets the value of the showColourText property.
4013          *
4014          * @param value
4015          *     allowed object is
4016          *     {@link Boolean }
4017          *
4018          */
4019         public void setShowColourText(Boolean value) {
4020             this.showColourText = value;
4021         }
4022
4023         /**
4024          * Gets the value of the showUnconserved property.
4025          *
4026          * @return
4027          *     possible object is
4028          *     {@link Boolean }
4029          *
4030          */
4031         public boolean isShowUnconserved() {
4032             if (showUnconserved == null) {
4033                 return false;
4034             } else {
4035                 return showUnconserved;
4036             }
4037         }
4038
4039         /**
4040          * Sets the value of the showUnconserved property.
4041          *
4042          * @param value
4043          *     allowed object is
4044          *     {@link Boolean }
4045          *
4046          */
4047         public void setShowUnconserved(Boolean value) {
4048             this.showUnconserved = value;
4049         }
4050
4051         /**
4052          * Gets the value of the showBoxes property.
4053          *
4054          * @return
4055          *     possible object is
4056          *     {@link Boolean }
4057          *
4058          */
4059         public Boolean isShowBoxes() {
4060             return showBoxes;
4061         }
4062
4063         /**
4064          * Sets the value of the showBoxes property.
4065          *
4066          * @param value
4067          *     allowed object is
4068          *     {@link Boolean }
4069          *
4070          */
4071         public void setShowBoxes(Boolean value) {
4072             this.showBoxes = value;
4073         }
4074
4075         /**
4076          * Gets the value of the wrapAlignment property.
4077          *
4078          * @return
4079          *     possible object is
4080          *     {@link Boolean }
4081          *
4082          */
4083         public Boolean isWrapAlignment() {
4084             return wrapAlignment;
4085         }
4086
4087         /**
4088          * Sets the value of the wrapAlignment property.
4089          *
4090          * @param value
4091          *     allowed object is
4092          *     {@link Boolean }
4093          *
4094          */
4095         public void setWrapAlignment(Boolean value) {
4096             this.wrapAlignment = value;
4097         }
4098
4099         /**
4100          * Gets the value of the renderGaps property.
4101          *
4102          * @return
4103          *     possible object is
4104          *     {@link Boolean }
4105          *
4106          */
4107         public Boolean isRenderGaps() {
4108             return renderGaps;
4109         }
4110
4111         /**
4112          * Sets the value of the renderGaps property.
4113          *
4114          * @param value
4115          *     allowed object is
4116          *     {@link Boolean }
4117          *
4118          */
4119         public void setRenderGaps(Boolean value) {
4120             this.renderGaps = value;
4121         }
4122
4123         /**
4124          * Gets the value of the showSequenceFeatures property.
4125          *
4126          * @return
4127          *     possible object is
4128          *     {@link Boolean }
4129          *
4130          */
4131         public Boolean isShowSequenceFeatures() {
4132             return showSequenceFeatures;
4133         }
4134
4135         /**
4136          * Sets the value of the showSequenceFeatures property.
4137          *
4138          * @param value
4139          *     allowed object is
4140          *     {@link Boolean }
4141          *
4142          */
4143         public void setShowSequenceFeatures(Boolean value) {
4144             this.showSequenceFeatures = value;
4145         }
4146
4147         /**
4148          * Gets the value of the showNPfeatureTooltip property.
4149          *
4150          * @return
4151          *     possible object is
4152          *     {@link Boolean }
4153          *
4154          */
4155         public Boolean isShowNPfeatureTooltip() {
4156             return showNPfeatureTooltip;
4157         }
4158
4159         /**
4160          * Sets the value of the showNPfeatureTooltip property.
4161          *
4162          * @param value
4163          *     allowed object is
4164          *     {@link Boolean }
4165          *
4166          */
4167         public void setShowNPfeatureTooltip(Boolean value) {
4168             this.showNPfeatureTooltip = value;
4169         }
4170
4171         /**
4172          * Gets the value of the showDbRefTooltip property.
4173          *
4174          * @return
4175          *     possible object is
4176          *     {@link Boolean }
4177          *
4178          */
4179         public Boolean isShowDbRefTooltip() {
4180             return showDbRefTooltip;
4181         }
4182
4183         /**
4184          * Sets the value of the showDbRefTooltip property.
4185          *
4186          * @param value
4187          *     allowed object is
4188          *     {@link Boolean }
4189          *
4190          */
4191         public void setShowDbRefTooltip(Boolean value) {
4192             this.showDbRefTooltip = value;
4193         }
4194
4195         /**
4196          * Gets the value of the followHighlight property.
4197          *
4198          * @return
4199          *     possible object is
4200          *     {@link Boolean }
4201          *
4202          */
4203         public boolean isFollowHighlight() {
4204             if (followHighlight == null) {
4205                 return true;
4206             } else {
4207                 return followHighlight;
4208             }
4209         }
4210
4211         /**
4212          * Sets the value of the followHighlight property.
4213          *
4214          * @param value
4215          *     allowed object is
4216          *     {@link Boolean }
4217          *
4218          */
4219         public void setFollowHighlight(Boolean value) {
4220             this.followHighlight = value;
4221         }
4222
4223         /**
4224          * Gets the value of the followSelection property.
4225          *
4226          * @return
4227          *     possible object is
4228          *     {@link Boolean }
4229          *
4230          */
4231         public boolean isFollowSelection() {
4232             if (followSelection == null) {
4233                 return true;
4234             } else {
4235                 return followSelection;
4236             }
4237         }
4238
4239         /**
4240          * Sets the value of the followSelection property.
4241          *
4242          * @param value
4243          *     allowed object is
4244          *     {@link Boolean }
4245          *
4246          */
4247         public void setFollowSelection(Boolean value) {
4248             this.followSelection = value;
4249         }
4250
4251         /**
4252          * Gets the value of the showAnnotation property.
4253          *
4254          * @return
4255          *     possible object is
4256          *     {@link Boolean }
4257          *
4258          */
4259         public Boolean isShowAnnotation() {
4260             return showAnnotation;
4261         }
4262
4263         /**
4264          * Sets the value of the showAnnotation property.
4265          *
4266          * @param value
4267          *     allowed object is
4268          *     {@link Boolean }
4269          *
4270          */
4271         public void setShowAnnotation(Boolean value) {
4272             this.showAnnotation = value;
4273         }
4274
4275         /**
4276          * Gets the value of the centreColumnLabels property.
4277          *
4278          * @return
4279          *     possible object is
4280          *     {@link Boolean }
4281          *
4282          */
4283         public boolean isCentreColumnLabels() {
4284             if (centreColumnLabels == null) {
4285                 return false;
4286             } else {
4287                 return centreColumnLabels;
4288             }
4289         }
4290
4291         /**
4292          * Sets the value of the centreColumnLabels property.
4293          *
4294          * @param value
4295          *     allowed object is
4296          *     {@link Boolean }
4297          *
4298          */
4299         public void setCentreColumnLabels(Boolean value) {
4300             this.centreColumnLabels = value;
4301         }
4302
4303         /**
4304          * Gets the value of the showGroupConservation property.
4305          *
4306          * @return
4307          *     possible object is
4308          *     {@link Boolean }
4309          *
4310          */
4311         public boolean isShowGroupConservation() {
4312             if (showGroupConservation == null) {
4313                 return false;
4314             } else {
4315                 return showGroupConservation;
4316             }
4317         }
4318
4319         /**
4320          * Sets the value of the showGroupConservation property.
4321          *
4322          * @param value
4323          *     allowed object is
4324          *     {@link Boolean }
4325          *
4326          */
4327         public void setShowGroupConservation(Boolean value) {
4328             this.showGroupConservation = value;
4329         }
4330
4331         /**
4332          * Gets the value of the showGroupConsensus property.
4333          *
4334          * @return
4335          *     possible object is
4336          *     {@link Boolean }
4337          *
4338          */
4339         public boolean isShowGroupConsensus() {
4340             if (showGroupConsensus == null) {
4341                 return false;
4342             } else {
4343                 return showGroupConsensus;
4344             }
4345         }
4346
4347         /**
4348          * Sets the value of the showGroupConsensus property.
4349          *
4350          * @param value
4351          *     allowed object is
4352          *     {@link Boolean }
4353          *
4354          */
4355         public void setShowGroupConsensus(Boolean value) {
4356             this.showGroupConsensus = value;
4357         }
4358
4359         /**
4360          * Gets the value of the showConsensusHistogram property.
4361          *
4362          * @return
4363          *     possible object is
4364          *     {@link Boolean }
4365          *
4366          */
4367         public boolean isShowConsensusHistogram() {
4368             if (showConsensusHistogram == null) {
4369                 return true;
4370             } else {
4371                 return showConsensusHistogram;
4372             }
4373         }
4374
4375         /**
4376          * Sets the value of the showConsensusHistogram property.
4377          *
4378          * @param value
4379          *     allowed object is
4380          *     {@link Boolean }
4381          *
4382          */
4383         public void setShowConsensusHistogram(Boolean value) {
4384             this.showConsensusHistogram = value;
4385         }
4386
4387         /**
4388          * Gets the value of the showSequenceLogo property.
4389          *
4390          * @return
4391          *     possible object is
4392          *     {@link Boolean }
4393          *
4394          */
4395         public boolean isShowSequenceLogo() {
4396             if (showSequenceLogo == null) {
4397                 return false;
4398             } else {
4399                 return showSequenceLogo;
4400             }
4401         }
4402
4403         /**
4404          * Sets the value of the showSequenceLogo property.
4405          *
4406          * @param value
4407          *     allowed object is
4408          *     {@link Boolean }
4409          *
4410          */
4411         public void setShowSequenceLogo(Boolean value) {
4412             this.showSequenceLogo = value;
4413         }
4414
4415         /**
4416          * Gets the value of the normaliseSequenceLogo property.
4417          *
4418          * @return
4419          *     possible object is
4420          *     {@link Boolean }
4421          *
4422          */
4423         public boolean isNormaliseSequenceLogo() {
4424             if (normaliseSequenceLogo == null) {
4425                 return false;
4426             } else {
4427                 return normaliseSequenceLogo;
4428             }
4429         }
4430
4431         /**
4432          * Sets the value of the normaliseSequenceLogo property.
4433          *
4434          * @param value
4435          *     allowed object is
4436          *     {@link Boolean }
4437          *
4438          */
4439         public void setNormaliseSequenceLogo(Boolean value) {
4440             this.normaliseSequenceLogo = value;
4441         }
4442
4443         /**
4444          * Gets the value of the ignoreGapsinConsensus property.
4445          *
4446          * @return
4447          *     possible object is
4448          *     {@link Boolean }
4449          *
4450          */
4451         public boolean isIgnoreGapsinConsensus() {
4452             if (ignoreGapsinConsensus == null) {
4453                 return true;
4454             } else {
4455                 return ignoreGapsinConsensus;
4456             }
4457         }
4458
4459         /**
4460          * Sets the value of the ignoreGapsinConsensus property.
4461          *
4462          * @param value
4463          *     allowed object is
4464          *     {@link Boolean }
4465          *
4466          */
4467         public void setIgnoreGapsinConsensus(Boolean value) {
4468             this.ignoreGapsinConsensus = value;
4469         }
4470
4471         /**
4472          * Gets the value of the startRes property.
4473          *
4474          * @return
4475          *     possible object is
4476          *     {@link Integer }
4477          *
4478          */
4479         public Integer getStartRes() {
4480             return startRes;
4481         }
4482
4483         /**
4484          * Sets the value of the startRes property.
4485          *
4486          * @param value
4487          *     allowed object is
4488          *     {@link Integer }
4489          *
4490          */
4491         public void setStartRes(Integer value) {
4492             this.startRes = value;
4493         }
4494
4495         /**
4496          * Gets the value of the startSeq property.
4497          *
4498          * @return
4499          *     possible object is
4500          *     {@link Integer }
4501          *
4502          */
4503         public Integer getStartSeq() {
4504             return startSeq;
4505         }
4506
4507         /**
4508          * Sets the value of the startSeq property.
4509          *
4510          * @param value
4511          *     allowed object is
4512          *     {@link Integer }
4513          *
4514          */
4515         public void setStartSeq(Integer value) {
4516             this.startSeq = value;
4517         }
4518
4519         /**
4520          * Gets the value of the fontName property.
4521          *
4522          * @return
4523          *     possible object is
4524          *     {@link String }
4525          *
4526          */
4527         public String getFontName() {
4528             return fontName;
4529         }
4530
4531         /**
4532          * Sets the value of the fontName property.
4533          *
4534          * @param value
4535          *     allowed object is
4536          *     {@link String }
4537          *
4538          */
4539         public void setFontName(String value) {
4540             this.fontName = value;
4541         }
4542
4543         /**
4544          * Gets the value of the fontSize property.
4545          *
4546          * @return
4547          *     possible object is
4548          *     {@link Integer }
4549          *
4550          */
4551         public Integer getFontSize() {
4552             return fontSize;
4553         }
4554
4555         /**
4556          * Sets the value of the fontSize property.
4557          *
4558          * @param value
4559          *     allowed object is
4560          *     {@link Integer }
4561          *
4562          */
4563         public void setFontSize(Integer value) {
4564             this.fontSize = value;
4565         }
4566
4567         /**
4568          * Gets the value of the fontStyle property.
4569          *
4570          * @return
4571          *     possible object is
4572          *     {@link Integer }
4573          *
4574          */
4575         public Integer getFontStyle() {
4576             return fontStyle;
4577         }
4578
4579         /**
4580          * Sets the value of the fontStyle property.
4581          *
4582          * @param value
4583          *     allowed object is
4584          *     {@link Integer }
4585          *
4586          */
4587         public void setFontStyle(Integer value) {
4588             this.fontStyle = value;
4589         }
4590
4591         /**
4592          * Gets the value of the scaleProteinAsCdna property.
4593          *
4594          * @return
4595          *     possible object is
4596          *     {@link Boolean }
4597          *
4598          */
4599         public boolean isScaleProteinAsCdna() {
4600             if (scaleProteinAsCdna == null) {
4601                 return true;
4602             } else {
4603                 return scaleProteinAsCdna;
4604             }
4605         }
4606
4607         /**
4608          * Sets the value of the scaleProteinAsCdna property.
4609          *
4610          * @param value
4611          *     allowed object is
4612          *     {@link Boolean }
4613          *
4614          */
4615         public void setScaleProteinAsCdna(Boolean value) {
4616             this.scaleProteinAsCdna = value;
4617         }
4618
4619         /**
4620          * Gets the value of the viewName property.
4621          *
4622          * @return
4623          *     possible object is
4624          *     {@link String }
4625          *
4626          */
4627         public String getViewName() {
4628             return viewName;
4629         }
4630
4631         /**
4632          * Sets the value of the viewName property.
4633          *
4634          * @param value
4635          *     allowed object is
4636          *     {@link String }
4637          *
4638          */
4639         public void setViewName(String value) {
4640             this.viewName = value;
4641         }
4642
4643         /**
4644          * Gets the value of the sequenceSetId property.
4645          *
4646          * @return
4647          *     possible object is
4648          *     {@link String }
4649          *
4650          */
4651         public String getSequenceSetId() {
4652             return sequenceSetId;
4653         }
4654
4655         /**
4656          * Sets the value of the sequenceSetId property.
4657          *
4658          * @param value
4659          *     allowed object is
4660          *     {@link String }
4661          *
4662          */
4663         public void setSequenceSetId(String value) {
4664             this.sequenceSetId = value;
4665         }
4666
4667         /**
4668          * Gets the value of the gatheredViews property.
4669          *
4670          * @return
4671          *     possible object is
4672          *     {@link Boolean }
4673          *
4674          */
4675         public Boolean isGatheredViews() {
4676             return gatheredViews;
4677         }
4678
4679         /**
4680          * Sets the value of the gatheredViews property.
4681          *
4682          * @param value
4683          *     allowed object is
4684          *     {@link Boolean }
4685          *
4686          */
4687         public void setGatheredViews(Boolean value) {
4688             this.gatheredViews = value;
4689         }
4690
4691         /**
4692          * Gets the value of the textCol1 property.
4693          *
4694          * @return
4695          *     possible object is
4696          *     {@link Integer }
4697          *
4698          */
4699         public Integer getTextCol1() {
4700             return textCol1;
4701         }
4702
4703         /**
4704          * Sets the value of the textCol1 property.
4705          *
4706          * @param value
4707          *     allowed object is
4708          *     {@link Integer }
4709          *
4710          */
4711         public void setTextCol1(Integer value) {
4712             this.textCol1 = value;
4713         }
4714
4715         /**
4716          * Gets the value of the textCol2 property.
4717          *
4718          * @return
4719          *     possible object is
4720          *     {@link Integer }
4721          *
4722          */
4723         public Integer getTextCol2() {
4724             return textCol2;
4725         }
4726
4727         /**
4728          * Sets the value of the textCol2 property.
4729          *
4730          * @param value
4731          *     allowed object is
4732          *     {@link Integer }
4733          *
4734          */
4735         public void setTextCol2(Integer value) {
4736             this.textCol2 = value;
4737         }
4738
4739         /**
4740          * Gets the value of the textColThreshold property.
4741          *
4742          * @return
4743          *     possible object is
4744          *     {@link Integer }
4745          *
4746          */
4747         public Integer getTextColThreshold() {
4748             return textColThreshold;
4749         }
4750
4751         /**
4752          * Sets the value of the textColThreshold property.
4753          *
4754          * @param value
4755          *     allowed object is
4756          *     {@link Integer }
4757          *
4758          */
4759         public void setTextColThreshold(Integer value) {
4760             this.textColThreshold = value;
4761         }
4762
4763         /**
4764          * Gets the value of the id property.
4765          *
4766          * @return
4767          *     possible object is
4768          *     {@link String }
4769          *
4770          */
4771         public String getId() {
4772             return id;
4773         }
4774
4775         /**
4776          * Sets the value of the id property.
4777          *
4778          * @param value
4779          *     allowed object is
4780          *     {@link String }
4781          *
4782          */
4783         public void setId(String value) {
4784             this.id = value;
4785         }
4786
4787         /**
4788          * Gets the value of the complementId property.
4789          *
4790          * @return
4791          *     possible object is
4792          *     {@link String }
4793          *
4794          */
4795         public String getComplementId() {
4796             return complementId;
4797         }
4798
4799         /**
4800          * Sets the value of the complementId property.
4801          *
4802          * @param value
4803          *     allowed object is
4804          *     {@link String }
4805          *
4806          */
4807         public void setComplementId(String value) {
4808             this.complementId = value;
4809         }
4810
4811         /**
4812          * Gets the value of the width property.
4813          *
4814          * @return
4815          *     possible object is
4816          *     {@link Integer }
4817          *
4818          */
4819         public Integer getWidth() {
4820             return width;
4821         }
4822
4823         /**
4824          * Sets the value of the width property.
4825          *
4826          * @param value
4827          *     allowed object is
4828          *     {@link Integer }
4829          *
4830          */
4831         public void setWidth(Integer value) {
4832             this.width = value;
4833         }
4834
4835         /**
4836          * Gets the value of the height property.
4837          *
4838          * @return
4839          *     possible object is
4840          *     {@link Integer }
4841          *
4842          */
4843         public Integer getHeight() {
4844             return height;
4845         }
4846
4847         /**
4848          * Sets the value of the height property.
4849          *
4850          * @param value
4851          *     allowed object is
4852          *     {@link Integer }
4853          *
4854          */
4855         public void setHeight(Integer value) {
4856             this.height = value;
4857         }
4858
4859         /**
4860          * Gets the value of the xpos property.
4861          *
4862          * @return
4863          *     possible object is
4864          *     {@link Integer }
4865          *
4866          */
4867         public Integer getXpos() {
4868             return xpos;
4869         }
4870
4871         /**
4872          * Sets the value of the xpos property.
4873          *
4874          * @param value
4875          *     allowed object is
4876          *     {@link Integer }
4877          *
4878          */
4879         public void setXpos(Integer value) {
4880             this.xpos = value;
4881         }
4882
4883         /**
4884          * Gets the value of the ypos property.
4885          *
4886          * @return
4887          *     possible object is
4888          *     {@link Integer }
4889          *
4890          */
4891         public Integer getYpos() {
4892             return ypos;
4893         }
4894
4895         /**
4896          * Sets the value of the ypos property.
4897          *
4898          * @param value
4899          *     allowed object is
4900          *     {@link Integer }
4901          *
4902          */
4903         public void setYpos(Integer value) {
4904             this.ypos = value;
4905         }
4906
4907
4908         /**
4909          * <p>Java class for anonymous complex type.
4910          *
4911          * <p>The following schema fragment specifies the expected content contained within this class.
4912          *
4913          * <pre>
4914          * &lt;complexType>
4915          *   &lt;complexContent>
4916          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4917          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4918          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4919          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4920          *     &lt;/extension>
4921          *   &lt;/complexContent>
4922          * &lt;/complexType>
4923          * </pre>
4924          *
4925          *
4926          */
4927         @XmlAccessorType(XmlAccessType.FIELD)
4928         @XmlType(name = "")
4929         public static class CalcIdParam
4930             extends WebServiceParameterSet
4931         {
4932
4933             @XmlAttribute(name = "calcId", required = true)
4934             protected String calcId;
4935             @XmlAttribute(name = "needsUpdate")
4936             protected Boolean needsUpdate;
4937             @XmlAttribute(name = "autoUpdate", required = true)
4938             protected boolean autoUpdate;
4939
4940             /**
4941              * Gets the value of the calcId property.
4942              *
4943              * @return
4944              *     possible object is
4945              *     {@link String }
4946              *
4947              */
4948             public String getCalcId() {
4949                 return calcId;
4950             }
4951
4952             /**
4953              * Sets the value of the calcId property.
4954              *
4955              * @param value
4956              *     allowed object is
4957              *     {@link String }
4958              *
4959              */
4960             public void setCalcId(String value) {
4961                 this.calcId = value;
4962             }
4963
4964             /**
4965              * Gets the value of the needsUpdate property.
4966              *
4967              * @return
4968              *     possible object is
4969              *     {@link Boolean }
4970              *
4971              */
4972             public boolean isNeedsUpdate() {
4973                 if (needsUpdate == null) {
4974                     return false;
4975                 } else {
4976                     return needsUpdate;
4977                 }
4978             }
4979
4980             /**
4981              * Sets the value of the needsUpdate property.
4982              *
4983              * @param value
4984              *     allowed object is
4985              *     {@link Boolean }
4986              *
4987              */
4988             public void setNeedsUpdate(Boolean value) {
4989                 this.needsUpdate = value;
4990             }
4991
4992             /**
4993              * Gets the value of the autoUpdate property.
4994              *
4995              */
4996             public boolean isAutoUpdate() {
4997                 return autoUpdate;
4998             }
4999
5000             /**
5001              * Sets the value of the autoUpdate property.
5002              *
5003              */
5004             public void setAutoUpdate(boolean value) {
5005                 this.autoUpdate = value;
5006             }
5007
5008         }
5009
5010
5011         /**
5012          * <p>Java class for anonymous complex type.
5013          *
5014          * <p>The following schema fragment specifies the expected content contained within this class.
5015          *
5016          * <pre>
5017          * &lt;complexType>
5018          *   &lt;complexContent>
5019          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
5020          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
5021          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
5022          *     &lt;/restriction>
5023          *   &lt;/complexContent>
5024          * &lt;/complexType>
5025          * </pre>
5026          *
5027          *
5028          */
5029         @XmlAccessorType(XmlAccessType.FIELD)
5030         @XmlType(name = "")
5031         public static class HiddenColumns {
5032
5033             @XmlAttribute(name = "start")
5034             protected Integer start;
5035             @XmlAttribute(name = "end")
5036             protected Integer end;
5037
5038             /**
5039              * Gets the value of the start property.
5040              *
5041              * @return
5042              *     possible object is
5043              *     {@link Integer }
5044              *
5045              */
5046             public Integer getStart() {
5047                 return start;
5048             }
5049
5050             /**
5051              * Sets the value of the start property.
5052              *
5053              * @param value
5054              *     allowed object is
5055              *     {@link Integer }
5056              *
5057              */
5058             public void setStart(Integer value) {
5059                 this.start = value;
5060             }
5061
5062             /**
5063              * Gets the value of the end property.
5064              *
5065              * @return
5066              *     possible object is
5067              *     {@link Integer }
5068              *
5069              */
5070             public Integer getEnd() {
5071                 return end;
5072             }
5073
5074             /**
5075              * Sets the value of the end property.
5076              *
5077              * @param value
5078              *     allowed object is
5079              *     {@link Integer }
5080              *
5081              */
5082             public void setEnd(Integer value) {
5083                 this.end = value;
5084             }
5085
5086         }
5087
5088     }
5089
5090 }