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

   1 //
   2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
   3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
   4 // Any modifications to this file will be lost upon recompilation of the source schema.
   5 // Generated on: 2023.03.09 at 07:45:02 AM GMT
   6 //
   7
   8
   9 package jalview.xml.binding.jalview;
  10
  11 import java.util.ArrayList;
  12 import java.util.List;
  13 import javax.xml.bind.annotation.XmlAccessType;
  14 import javax.xml.bind.annotation.XmlAccessorType;
  15 import javax.xml.bind.annotation.XmlAttribute;
  16 import javax.xml.bind.annotation.XmlElement;
  17 import javax.xml.bind.annotation.XmlID;
  18 import javax.xml.bind.annotation.XmlSchemaType;
  19 import javax.xml.bind.annotation.XmlType;
  20 import javax.xml.bind.annotation.XmlValue;
  21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
  22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  23 import javax.xml.datatype.XMLGregorianCalendar;
  24
  25
  26 /**
  27  * <p>Java class for JalviewModel complex type.
  28  *
  29  * <p>The following schema fragment specifies the expected content contained within this class.
  30  *
  31  * <pre>
  32  * &lt;complexType name="JalviewModel">
  33  *   &lt;complexContent>
  34  *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  35  *       &lt;sequence>
  36  *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
  37  *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
  38  *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
  39  *         &lt;sequence>
  40  *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
  41  *             &lt;complexType>
  42  *               &lt;complexContent>
  43  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  44  *                   &lt;sequence>
  45  *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
  46  *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
  47  *                       &lt;complexType>
  48  *                         &lt;complexContent>
  49  *                           &lt;extension base="{www.jalview.org}pdbentry">
  50  *                             &lt;sequence>
  51  *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
  52  *                                 &lt;complexType>
  53  *                                   &lt;simpleContent>
  54  *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
  55  *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  56  *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  57  *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  58  *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  59  *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  60  *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
  61  *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
  62  *                                     &lt;/extension>
  63  *                                   &lt;/simpleContent>
  64  *                                 &lt;/complexType>
  65  *                               &lt;/element>
  66  *                             &lt;/sequence>
  67  *                           &lt;/extension>
  68  *                         &lt;/complexContent>
  69  *                       &lt;/complexType>
  70  *                     &lt;/element>
  71  *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
  72  *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
  73  *                       &lt;complexType>
  74  *                         &lt;complexContent>
  75  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  76  *                             &lt;sequence>
  77  *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
  78  *                                 &lt;complexType>
  79  *                                   &lt;complexContent>
  80  *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  81  *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  82  *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  83  *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  84  *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
  85  *                                     &lt;/restriction>
  86  *                                   &lt;/complexContent>
  87  *                                 &lt;/complexType>
  88  *                               &lt;/element>
  89  *                             &lt;/sequence>
  90  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
  91  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
  92  *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
  93  *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
  94  *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
  95  *                           &lt;/restriction>
  96  *                         &lt;/complexContent>
  97  *                       &lt;/complexType>
  98  *                     &lt;/element>
  99  *                   &lt;/sequence>
 100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 106  *                 &lt;/restriction>
 107  *               &lt;/complexContent>
 108  *             &lt;/complexType>
 109  *           &lt;/element>
 110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 111  *             &lt;complexType>
 112  *               &lt;complexContent>
 113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 114  *                   &lt;sequence>
 115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 117  *                   &lt;/sequence>
 118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 137  *                 &lt;/restriction>
 138  *               &lt;/complexContent>
 139  *             &lt;/complexType>
 140  *           &lt;/element>
 141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 142  *             &lt;complexType>
 143  *               &lt;complexContent>
 144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 145  *                   &lt;sequence>
 146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 148  *                       &lt;complexType>
 149  *                         &lt;complexContent>
 150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 153  *                           &lt;/restriction>
 154  *                         &lt;/complexContent>
 155  *                       &lt;/complexType>
 156  *                     &lt;/element>
 157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 158  *                       &lt;complexType>
 159  *                         &lt;complexContent>
 160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 164  *                           &lt;/extension>
 165  *                         &lt;/complexContent>
 166  *                       &lt;/complexType>
 167  *                     &lt;/element>
 168  *                     &lt;element name="overview" minOccurs="0">
 169  *                       &lt;complexType>
 170  *                         &lt;complexContent>
 171  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 172  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 173  *                             &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 174  *                             &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 175  *                             &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 176  *                             &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 177  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 178  *                           &lt;/restriction>
 179  *                         &lt;/complexContent>
 180  *                       &lt;/complexType>
 181  *                     &lt;/element>
 182  *                   &lt;/sequence>
 183  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 184  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 185  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 186  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 187  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 188  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 189  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 190  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 191  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 192  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 193  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 194  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 195  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 196  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 197  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 198  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 199  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 200  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 201  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 202  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 203  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 204  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 205  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 206  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 207  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 208  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 209  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 210  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 211  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 212  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 213  *                   &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
 214  *                   &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
 215  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 216  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 217  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 218  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 219  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 220  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 221  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 222  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 223  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 224  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 225  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 226  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 227  *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 228  *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 229  *                 &lt;/restriction>
 230  *               &lt;/complexContent>
 231  *             &lt;/complexType>
 232  *           &lt;/element>
 233  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 234  *             &lt;complexType>
 235  *               &lt;complexContent>
 236  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 237  *                   &lt;sequence>
 238  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 239  *                   &lt;/sequence>
 240  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 241  *                 &lt;/restriction>
 242  *               &lt;/complexContent>
 243  *             &lt;/complexType>
 244  *           &lt;/element>
 245  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
 246  *             &lt;complexType>
 247  *               &lt;complexContent>
 248  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 249  *                   &lt;sequence minOccurs="0">
 250  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 251  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 252  *                   &lt;/sequence>
 253  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 254  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 255  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 256  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 257  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 258  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 259  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 260  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 261  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 262  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 263  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 264  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 265  *                 &lt;/restriction>
 266  *               &lt;/complexContent>
 267  *             &lt;/complexType>
 268  *           &lt;/element>
 269  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 270  *             &lt;complexType>
 271  *               &lt;complexContent>
 272  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 273  *                   &lt;sequence>
 274  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
 275  *                       &lt;complexType>
 276  *                         &lt;complexContent>
 277  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 278  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 279  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 280  *                           &lt;/restriction>
 281  *                         &lt;/complexContent>
 282  *                       &lt;/complexType>
 283  *                     &lt;/element>
 284  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
 285  *                       &lt;complexType>
 286  *                         &lt;complexContent>
 287  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 288  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 289  *                           &lt;/restriction>
 290  *                         &lt;/complexContent>
 291  *                       &lt;/complexType>
 292  *                     &lt;/element>
 293  *                     &lt;element name="seqPointMin">
 294  *                       &lt;complexType>
 295  *                         &lt;complexContent>
 296  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 297  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 298  *                           &lt;/restriction>
 299  *                         &lt;/complexContent>
 300  *                       &lt;/complexType>
 301  *                     &lt;/element>
 302  *                     &lt;element name="seqPointMax">
 303  *                       &lt;complexType>
 304  *                         &lt;complexContent>
 305  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 306  *                             &lt;attGroup ref="{www.jalview.org}position"/>
 307  *                           &lt;/restriction>
 308  *                         &lt;/complexContent>
 309  *                       &lt;/complexType>
 310  *                     &lt;/element>
 311  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 312  *                   &lt;/sequence>
 313  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
 314  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
 315  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 316  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 317  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 318  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 319  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 320  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 321  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 322  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 323  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 324  *                 &lt;/restriction>
 325  *               &lt;/complexContent>
 326  *             &lt;/complexType>
 327  *           &lt;/element>
 328  *           &lt;element name="FeatureSettings" minOccurs="0">
 329  *             &lt;complexType>
 330  *               &lt;complexContent>
 331  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 332  *                   &lt;sequence>
 333  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 334  *                       &lt;complexType>
 335  *                         &lt;complexContent>
 336  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 337  *                             &lt;sequence>
 338  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 339  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 340  *                             &lt;/sequence>
 341  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 342  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 343  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 344  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 345  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 346  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 347  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 348  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 349  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 350  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 351  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 352  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 353  *                           &lt;/restriction>
 354  *                         &lt;/complexContent>
 355  *                       &lt;/complexType>
 356  *                     &lt;/element>
 357  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 358  *                       &lt;complexType>
 359  *                         &lt;complexContent>
 360  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 361  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 362  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 363  *                           &lt;/restriction>
 364  *                         &lt;/complexContent>
 365  *                       &lt;/complexType>
 366  *                     &lt;/element>
 367  *                   &lt;/sequence>
 368  *                 &lt;/restriction>
 369  *               &lt;/complexContent>
 370  *             &lt;/complexType>
 371  *           &lt;/element>
 372  *         &lt;/sequence>
 373  *       &lt;/sequence>
 374  *     &lt;/restriction>
 375  *   &lt;/complexContent>
 376  * &lt;/complexType>
 377  * </pre>
 378  *
 379  *
 380  */
 381 @XmlAccessorType(XmlAccessType.FIELD)
 382 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
 383     "creationDate",
 384     "version",
 385     "vamsasModel",
 386     "jSeq",
 387     "jGroup",
 388     "viewport",
 389     "userColours",
 390     "tree",
 391     "pcaViewer",
 392     "featureSettings"
 393 })
 394 public class JalviewModel {
 395
 396     @XmlElement(required = true)
 397     @XmlSchemaType(name = "dateTime")
 398     protected XMLGregorianCalendar creationDate;
 399     @XmlElement(required = true)
 400     protected String version;
 401     @XmlElement(required = true)
 402     protected VAMSAS vamsasModel;
 403     @XmlElement(name = "JSeq")
 404     protected List<JalviewModel.JSeq> jSeq;
 405     @XmlElement(name = "JGroup")
 406     protected List<JalviewModel.JGroup> jGroup;
 407     @XmlElement(name = "Viewport")
 408     protected List<JalviewModel.Viewport> viewport;
 409     @XmlElement(name = "UserColours")
 410     protected List<JalviewModel.UserColours> userColours;
 411     protected List<JalviewModel.Tree> tree;
 412     @XmlElement(name = "PcaViewer")
 413     protected List<JalviewModel.PcaViewer> pcaViewer;
 414     @XmlElement(name = "FeatureSettings")
 415     protected JalviewModel.FeatureSettings featureSettings;
 416
 417     /**
 418      * Gets the value of the creationDate property.
 419      *
 420      * @return
 421      *     possible object is
 422      *     {@link XMLGregorianCalendar }
 423      *
 424      */
 425     public XMLGregorianCalendar getCreationDate() {
 426         return creationDate;
 427     }
 428
 429     /**
 430      * Sets the value of the creationDate property.
 431      *
 432      * @param value
 433      *     allowed object is
 434      *     {@link XMLGregorianCalendar }
 435      *
 436      */
 437     public void setCreationDate(XMLGregorianCalendar value) {
 438         this.creationDate = value;
 439     }
 440
 441     /**
 442      * Gets the value of the version property.
 443      *
 444      * @return
 445      *     possible object is
 446      *     {@link String }
 447      *
 448      */
 449     public String getVersion() {
 450         return version;
 451     }
 452
 453     /**
 454      * Sets the value of the version property.
 455      *
 456      * @param value
 457      *     allowed object is
 458      *     {@link String }
 459      *
 460      */
 461     public void setVersion(String value) {
 462         this.version = value;
 463     }
 464
 465     /**
 466      * Gets the value of the vamsasModel property.
 467      *
 468      * @return
 469      *     possible object is
 470      *     {@link VAMSAS }
 471      *
 472      */
 473     public VAMSAS getVamsasModel() {
 474         return vamsasModel;
 475     }
 476
 477     /**
 478      * Sets the value of the vamsasModel property.
 479      *
 480      * @param value
 481      *     allowed object is
 482      *     {@link VAMSAS }
 483      *
 484      */
 485     public void setVamsasModel(VAMSAS value) {
 486         this.vamsasModel = value;
 487     }
 488
 489     /**
 490      * Gets the value of the jSeq property.
 491      *
 492      * <p>
 493      * This accessor method returns a reference to the live list,
 494      * not a snapshot. Therefore any modification you make to the
 495      * returned list will be present inside the JAXB object.
 496      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
 497      *
 498      * <p>
 499      * For example, to add a new item, do as follows:
 500      * <pre>
 501      *    getJSeq().add(newItem);
 502      * </pre>
 503      *
 504      *
 505      * <p>
 506      * Objects of the following type(s) are allowed in the list
 507      * {@link JalviewModel.JSeq }
 508      *
 509      *
 510      */
 511     public List<JalviewModel.JSeq> getJSeq() {
 512         if (jSeq == null) {
 513             jSeq = new ArrayList<JalviewModel.JSeq>();
 514         }
 515         return this.jSeq;
 516     }
 517
 518     /**
 519      * Gets the value of the jGroup property.
 520      *
 521      * <p>
 522      * This accessor method returns a reference to the live list,
 523      * not a snapshot. Therefore any modification you make to the
 524      * returned list will be present inside the JAXB object.
 525      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
 526      *
 527      * <p>
 528      * For example, to add a new item, do as follows:
 529      * <pre>
 530      *    getJGroup().add(newItem);
 531      * </pre>
 532      *
 533      *
 534      * <p>
 535      * Objects of the following type(s) are allowed in the list
 536      * {@link JalviewModel.JGroup }
 537      *
 538      *
 539      */
 540     public List<JalviewModel.JGroup> getJGroup() {
 541         if (jGroup == null) {
 542             jGroup = new ArrayList<JalviewModel.JGroup>();
 543         }
 544         return this.jGroup;
 545     }
 546
 547     /**
 548      * Gets the value of the viewport property.
 549      *
 550      * <p>
 551      * This accessor method returns a reference to the live list,
 552      * not a snapshot. Therefore any modification you make to the
 553      * returned list will be present inside the JAXB object.
 554      * This is why there is not a <CODE>set</CODE> method for the viewport property.
 555      *
 556      * <p>
 557      * For example, to add a new item, do as follows:
 558      * <pre>
 559      *    getViewport().add(newItem);
 560      * </pre>
 561      *
 562      *
 563      * <p>
 564      * Objects of the following type(s) are allowed in the list
 565      * {@link JalviewModel.Viewport }
 566      *
 567      *
 568      */
 569     public List<JalviewModel.Viewport> getViewport() {
 570         if (viewport == null) {
 571             viewport = new ArrayList<JalviewModel.Viewport>();
 572         }
 573         return this.viewport;
 574     }
 575
 576     /**
 577      * Gets the value of the userColours property.
 578      *
 579      * <p>
 580      * This accessor method returns a reference to the live list,
 581      * not a snapshot. Therefore any modification you make to the
 582      * returned list will be present inside the JAXB object.
 583      * This is why there is not a <CODE>set</CODE> method for the userColours property.
 584      *
 585      * <p>
 586      * For example, to add a new item, do as follows:
 587      * <pre>
 588      *    getUserColours().add(newItem);
 589      * </pre>
 590      *
 591      *
 592      * <p>
 593      * Objects of the following type(s) are allowed in the list
 594      * {@link JalviewModel.UserColours }
 595      *
 596      *
 597      */
 598     public List<JalviewModel.UserColours> getUserColours() {
 599         if (userColours == null) {
 600             userColours = new ArrayList<JalviewModel.UserColours>();
 601         }
 602         return this.userColours;
 603     }
 604
 605     /**
 606      * Gets the value of the tree property.
 607      *
 608      * <p>
 609      * This accessor method returns a reference to the live list,
 610      * not a snapshot. Therefore any modification you make to the
 611      * returned list will be present inside the JAXB object.
 612      * This is why there is not a <CODE>set</CODE> method for the tree property.
 613      *
 614      * <p>
 615      * For example, to add a new item, do as follows:
 616      * <pre>
 617      *    getTree().add(newItem);
 618      * </pre>
 619      *
 620      *
 621      * <p>
 622      * Objects of the following type(s) are allowed in the list
 623      * {@link JalviewModel.Tree }
 624      *
 625      *
 626      */
 627     public List<JalviewModel.Tree> getTree() {
 628         if (tree == null) {
 629             tree = new ArrayList<JalviewModel.Tree>();
 630         }
 631         return this.tree;
 632     }
 633
 634     /**
 635      * Gets the value of the pcaViewer property.
 636      *
 637      * <p>
 638      * This accessor method returns a reference to the live list,
 639      * not a snapshot. Therefore any modification you make to the
 640      * returned list will be present inside the JAXB object.
 641      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
 642      *
 643      * <p>
 644      * For example, to add a new item, do as follows:
 645      * <pre>
 646      *    getPcaViewer().add(newItem);
 647      * </pre>
 648      *
 649      *
 650      * <p>
 651      * Objects of the following type(s) are allowed in the list
 652      * {@link JalviewModel.PcaViewer }
 653      *
 654      *
 655      */
 656     public List<JalviewModel.PcaViewer> getPcaViewer() {
 657         if (pcaViewer == null) {
 658             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
 659         }
 660         return this.pcaViewer;
 661     }
 662
 663     /**
 664      * Gets the value of the featureSettings property.
 665      *
 666      * @return
 667      *     possible object is
 668      *     {@link JalviewModel.FeatureSettings }
 669      *
 670      */
 671     public JalviewModel.FeatureSettings getFeatureSettings() {
 672         return featureSettings;
 673     }
 674
 675     /**
 676      * Sets the value of the featureSettings property.
 677      *
 678      * @param value
 679      *     allowed object is
 680      *     {@link JalviewModel.FeatureSettings }
 681      *
 682      */
 683     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
 684         this.featureSettings = value;
 685     }
 686
 687
 688     /**
 689      * <p>Java class for anonymous complex type.
 690      *
 691      * <p>The following schema fragment specifies the expected content contained within this class.
 692      *
 693      * <pre>
 694      * &lt;complexType>
 695      *   &lt;complexContent>
 696      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 697      *       &lt;sequence>
 698      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
 699      *           &lt;complexType>
 700      *             &lt;complexContent>
 701      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 702      *                 &lt;sequence>
 703      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 704      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 705      *                 &lt;/sequence>
 706      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 707      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 708      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 709      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 710      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 711      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 712      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 713      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 714      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 715      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 716      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 717      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 718      *               &lt;/restriction>
 719      *             &lt;/complexContent>
 720      *           &lt;/complexType>
 721      *         &lt;/element>
 722      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
 723      *           &lt;complexType>
 724      *             &lt;complexContent>
 725      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 726      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 727      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 728      *               &lt;/restriction>
 729      *             &lt;/complexContent>
 730      *           &lt;/complexType>
 731      *         &lt;/element>
 732      *       &lt;/sequence>
 733      *     &lt;/restriction>
 734      *   &lt;/complexContent>
 735      * &lt;/complexType>
 736      * </pre>
 737      *
 738      *
 739      */
 740     @XmlAccessorType(XmlAccessType.FIELD)
 741     @XmlType(name = "", propOrder = {
 742         "setting",
 743         "group"
 744     })
 745     public static class FeatureSettings {
 746
 747         @XmlElement(namespace = "www.jalview.org")
 748         protected List<JalviewModel.FeatureSettings.Setting> setting;
 749         @XmlElement(namespace = "www.jalview.org")
 750         protected List<JalviewModel.FeatureSettings.Group> group;
 751
 752         /**
 753          * Gets the value of the setting property.
 754          *
 755          * <p>
 756          * This accessor method returns a reference to the live list,
 757          * not a snapshot. Therefore any modification you make to the
 758          * returned list will be present inside the JAXB object.
 759          * This is why there is not a <CODE>set</CODE> method for the setting property.
 760          *
 761          * <p>
 762          * For example, to add a new item, do as follows:
 763          * <pre>
 764          *    getSetting().add(newItem);
 765          * </pre>
 766          *
 767          *
 768          * <p>
 769          * Objects of the following type(s) are allowed in the list
 770          * {@link JalviewModel.FeatureSettings.Setting }
 771          *
 772          *
 773          */
 774         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
 775             if (setting == null) {
 776                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
 777             }
 778             return this.setting;
 779         }
 780
 781         /**
 782          * Gets the value of the group property.
 783          *
 784          * <p>
 785          * This accessor method returns a reference to the live list,
 786          * not a snapshot. Therefore any modification you make to the
 787          * returned list will be present inside the JAXB object.
 788          * This is why there is not a <CODE>set</CODE> method for the group property.
 789          *
 790          * <p>
 791          * For example, to add a new item, do as follows:
 792          * <pre>
 793          *    getGroup().add(newItem);
 794          * </pre>
 795          *
 796          *
 797          * <p>
 798          * Objects of the following type(s) are allowed in the list
 799          * {@link JalviewModel.FeatureSettings.Group }
 800          *
 801          *
 802          */
 803         public List<JalviewModel.FeatureSettings.Group> getGroup() {
 804             if (group == null) {
 805                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
 806             }
 807             return this.group;
 808         }
 809
 810
 811         /**
 812          * <p>Java class for anonymous complex type.
 813          *
 814          * <p>The following schema fragment specifies the expected content contained within this class.
 815          *
 816          * <pre>
 817          * &lt;complexType>
 818          *   &lt;complexContent>
 819          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 820          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 821          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 822          *     &lt;/restriction>
 823          *   &lt;/complexContent>
 824          * &lt;/complexType>
 825          * </pre>
 826          *
 827          *
 828          */
 829         @XmlAccessorType(XmlAccessType.FIELD)
 830         @XmlType(name = "")
 831         public static class Group {
 832
 833             @XmlAttribute(name = "name", required = true)
 834             protected String name;
 835             @XmlAttribute(name = "display", required = true)
 836             protected boolean display;
 837
 838             /**
 839              * Gets the value of the name property.
 840              *
 841              * @return
 842              *     possible object is
 843              *     {@link String }
 844              *
 845              */
 846             public String getName() {
 847                 return name;
 848             }
 849
 850             /**
 851              * Sets the value of the name property.
 852              *
 853              * @param value
 854              *     allowed object is
 855              *     {@link String }
 856              *
 857              */
 858             public void setName(String value) {
 859                 this.name = value;
 860             }
 861
 862             /**
 863              * Gets the value of the display property.
 864              *
 865              */
 866             public boolean isDisplay() {
 867                 return display;
 868             }
 869
 870             /**
 871              * Sets the value of the display property.
 872              *
 873              */
 874             public void setDisplay(boolean value) {
 875                 this.display = value;
 876             }
 877
 878         }
 879
 880
 881         /**
 882          * <p>Java class for anonymous complex type.
 883          *
 884          * <p>The following schema fragment specifies the expected content contained within this class.
 885          *
 886          * <pre>
 887          * &lt;complexType>
 888          *   &lt;complexContent>
 889          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 890          *       &lt;sequence>
 891          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 892          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 893          *       &lt;/sequence>
 894          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 895          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 896          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 897          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 898          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 899          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 900          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 901          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 902          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 903          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 904          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 905          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 906          *     &lt;/restriction>
 907          *   &lt;/complexContent>
 908          * &lt;/complexType>
 909          * </pre>
 910          *
 911          *
 912          */
 913         @XmlAccessorType(XmlAccessType.FIELD)
 914         @XmlType(name = "", propOrder = {
 915             "attributeName",
 916             "matcherSet"
 917         })
 918         public static class Setting {
 919
 920             @XmlElement(namespace = "www.jalview.org")
 921             protected List<String> attributeName;
 922             @XmlElement(namespace = "www.jalview.org")
 923             protected FeatureMatcherSet matcherSet;
 924             @XmlAttribute(name = "type", required = true)
 925             protected String type;
 926             @XmlAttribute(name = "colour", required = true)
 927             protected int colour;
 928             @XmlAttribute(name = "display", required = true)
 929             protected boolean display;
 930             @XmlAttribute(name = "order")
 931             protected Float order;
 932             @XmlAttribute(name = "mincolour")
 933             protected Integer mincolour;
 934             @XmlAttribute(name = "noValueColour")
 935             protected NoValueColour noValueColour;
 936             @XmlAttribute(name = "threshold")
 937             protected Float threshold;
 938             @XmlAttribute(name = "threshstate")
 939             protected Integer threshstate;
 940             @XmlAttribute(name = "max")
 941             protected Float max;
 942             @XmlAttribute(name = "min")
 943             protected Float min;
 944             @XmlAttribute(name = "colourByLabel")
 945             protected Boolean colourByLabel;
 946             @XmlAttribute(name = "autoScale")
 947             protected Boolean autoScale;
 948
 949             /**
 950              * Gets the value of the attributeName property.
 951              *
 952              * <p>
 953              * This accessor method returns a reference to the live list,
 954              * not a snapshot. Therefore any modification you make to the
 955              * returned list will be present inside the JAXB object.
 956              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
 957              *
 958              * <p>
 959              * For example, to add a new item, do as follows:
 960              * <pre>
 961              *    getAttributeName().add(newItem);
 962              * </pre>
 963              *
 964              *
 965              * <p>
 966              * Objects of the following type(s) are allowed in the list
 967              * {@link String }
 968              *
 969              *
 970              */
 971             public List<String> getAttributeName() {
 972                 if (attributeName == null) {
 973                     attributeName = new ArrayList<String>();
 974                 }
 975                 return this.attributeName;
 976             }
 977
 978             /**
 979              * Gets the value of the matcherSet property.
 980              *
 981              * @return
 982              *     possible object is
 983              *     {@link FeatureMatcherSet }
 984              *
 985              */
 986             public FeatureMatcherSet getMatcherSet() {
 987                 return matcherSet;
 988             }
 989
 990             /**
 991              * Sets the value of the matcherSet property.
 992              *
 993              * @param value
 994              *     allowed object is
 995              *     {@link FeatureMatcherSet }
 996              *
 997              */
 998             public void setMatcherSet(FeatureMatcherSet value) {
 999                 this.matcherSet = value;
1000             }
1001
1002             /**
1003              * Gets the value of the type property.
1004              *
1005              * @return
1006              *     possible object is
1007              *     {@link String }
1008              *
1009              */
1010             public String getType() {
1011                 return type;
1012             }
1013
1014             /**
1015              * Sets the value of the type property.
1016              *
1017              * @param value
1018              *     allowed object is
1019              *     {@link String }
1020              *
1021              */
1022             public void setType(String value) {
1023                 this.type = value;
1024             }
1025
1026             /**
1027              * Gets the value of the colour property.
1028              *
1029              */
1030             public int getColour() {
1031                 return colour;
1032             }
1033
1034             /**
1035              * Sets the value of the colour property.
1036              *
1037              */
1038             public void setColour(int value) {
1039                 this.colour = value;
1040             }
1041
1042             /**
1043              * Gets the value of the display property.
1044              *
1045              */
1046             public boolean isDisplay() {
1047                 return display;
1048             }
1049
1050             /**
1051              * Sets the value of the display property.
1052              *
1053              */
1054             public void setDisplay(boolean value) {
1055                 this.display = value;
1056             }
1057
1058             /**
1059              * Gets the value of the order property.
1060              *
1061              * @return
1062              *     possible object is
1063              *     {@link Float }
1064              *
1065              */
1066             public Float getOrder() {
1067                 return order;
1068             }
1069
1070             /**
1071              * Sets the value of the order property.
1072              *
1073              * @param value
1074              *     allowed object is
1075              *     {@link Float }
1076              *
1077              */
1078             public void setOrder(Float value) {
1079                 this.order = value;
1080             }
1081
1082             /**
1083              * Gets the value of the mincolour property.
1084              *
1085              * @return
1086              *     possible object is
1087              *     {@link Integer }
1088              *
1089              */
1090             public Integer getMincolour() {
1091                 return mincolour;
1092             }
1093
1094             /**
1095              * Sets the value of the mincolour property.
1096              *
1097              * @param value
1098              *     allowed object is
1099              *     {@link Integer }
1100              *
1101              */
1102             public void setMincolour(Integer value) {
1103                 this.mincolour = value;
1104             }
1105
1106             /**
1107              * Gets the value of the noValueColour property.
1108              *
1109              * @return
1110              *     possible object is
1111              *     {@link NoValueColour }
1112              *
1113              */
1114             public NoValueColour getNoValueColour() {
1115                 if (noValueColour == null) {
1116                     return NoValueColour.MIN;
1117                 } else {
1118                     return noValueColour;
1119                 }
1120             }
1121
1122             /**
1123              * Sets the value of the noValueColour property.
1124              *
1125              * @param value
1126              *     allowed object is
1127              *     {@link NoValueColour }
1128              *
1129              */
1130             public void setNoValueColour(NoValueColour value) {
1131                 this.noValueColour = value;
1132             }
1133
1134             /**
1135              * Gets the value of the threshold property.
1136              *
1137              * @return
1138              *     possible object is
1139              *     {@link Float }
1140              *
1141              */
1142             public Float getThreshold() {
1143                 return threshold;
1144             }
1145
1146             /**
1147              * Sets the value of the threshold property.
1148              *
1149              * @param value
1150              *     allowed object is
1151              *     {@link Float }
1152              *
1153              */
1154             public void setThreshold(Float value) {
1155                 this.threshold = value;
1156             }
1157
1158             /**
1159              * Gets the value of the threshstate property.
1160              *
1161              * @return
1162              *     possible object is
1163              *     {@link Integer }
1164              *
1165              */
1166             public Integer getThreshstate() {
1167                 return threshstate;
1168             }
1169
1170             /**
1171              * Sets the value of the threshstate property.
1172              *
1173              * @param value
1174              *     allowed object is
1175              *     {@link Integer }
1176              *
1177              */
1178             public void setThreshstate(Integer value) {
1179                 this.threshstate = value;
1180             }
1181
1182             /**
1183              * Gets the value of the max property.
1184              *
1185              * @return
1186              *     possible object is
1187              *     {@link Float }
1188              *
1189              */
1190             public Float getMax() {
1191                 return max;
1192             }
1193
1194             /**
1195              * Sets the value of the max property.
1196              *
1197              * @param value
1198              *     allowed object is
1199              *     {@link Float }
1200              *
1201              */
1202             public void setMax(Float value) {
1203                 this.max = value;
1204             }
1205
1206             /**
1207              * Gets the value of the min property.
1208              *
1209              * @return
1210              *     possible object is
1211              *     {@link Float }
1212              *
1213              */
1214             public Float getMin() {
1215                 return min;
1216             }
1217
1218             /**
1219              * Sets the value of the min property.
1220              *
1221              * @param value
1222              *     allowed object is
1223              *     {@link Float }
1224              *
1225              */
1226             public void setMin(Float value) {
1227                 this.min = value;
1228             }
1229
1230             /**
1231              * Gets the value of the colourByLabel property.
1232              *
1233              * @return
1234              *     possible object is
1235              *     {@link Boolean }
1236              *
1237              */
1238             public Boolean isColourByLabel() {
1239                 return colourByLabel;
1240             }
1241
1242             /**
1243              * Sets the value of the colourByLabel property.
1244              *
1245              * @param value
1246              *     allowed object is
1247              *     {@link Boolean }
1248              *
1249              */
1250             public void setColourByLabel(Boolean value) {
1251                 this.colourByLabel = value;
1252             }
1253
1254             /**
1255              * Gets the value of the autoScale property.
1256              *
1257              * @return
1258              *     possible object is
1259              *     {@link Boolean }
1260              *
1261              */
1262             public Boolean isAutoScale() {
1263                 return autoScale;
1264             }
1265
1266             /**
1267              * Sets the value of the autoScale property.
1268              *
1269              * @param value
1270              *     allowed object is
1271              *     {@link Boolean }
1272              *
1273              */
1274             public void setAutoScale(Boolean value) {
1275                 this.autoScale = value;
1276             }
1277
1278         }
1279
1280     }
1281
1282
1283     /**
1284      * <p>Java class for anonymous complex type.
1285      *
1286      * <p>The following schema fragment specifies the expected content contained within this class.
1287      *
1288      * <pre>
1289      * &lt;complexType>
1290      *   &lt;complexContent>
1291      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1292      *       &lt;sequence>
1293      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1294      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1295      *       &lt;/sequence>
1296      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1297      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1298      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1299      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1300      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1301      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1302      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1303      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1304      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1305      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1306      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1307      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1308      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1309      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1310      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1311      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1312      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1313      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1314      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1315      *     &lt;/restriction>
1316      *   &lt;/complexContent>
1317      * &lt;/complexType>
1318      * </pre>
1319      *
1320      *
1321      */
1322     @XmlAccessorType(XmlAccessType.FIELD)
1323     @XmlType(name = "", propOrder = {
1324         "seq",
1325         "annotationColours"
1326     })
1327     public static class JGroup {
1328
1329         @XmlElement(namespace = "www.jalview.org", required = true)
1330         protected List<String> seq;
1331         @XmlElement(namespace = "www.jalview.org")
1332         protected AnnotationColourScheme annotationColours;
1333         @XmlAttribute(name = "start")
1334         protected Integer start;
1335         @XmlAttribute(name = "end")
1336         protected Integer end;
1337         @XmlAttribute(name = "name")
1338         protected String name;
1339         @XmlAttribute(name = "colour")
1340         protected String colour;
1341         @XmlAttribute(name = "consThreshold")
1342         protected Integer consThreshold;
1343         @XmlAttribute(name = "pidThreshold")
1344         protected Integer pidThreshold;
1345         @XmlAttribute(name = "outlineColour")
1346         protected Integer outlineColour;
1347         @XmlAttribute(name = "displayBoxes")
1348         protected Boolean displayBoxes;
1349         @XmlAttribute(name = "displayText")
1350         protected Boolean displayText;
1351         @XmlAttribute(name = "colourText")
1352         protected Boolean colourText;
1353         @XmlAttribute(name = "textCol1")
1354         protected Integer textCol1;
1355         @XmlAttribute(name = "textCol2")
1356         protected Integer textCol2;
1357         @XmlAttribute(name = "textColThreshold")
1358         protected Integer textColThreshold;
1359         @XmlAttribute(name = "showUnconserved")
1360         protected Boolean showUnconserved;
1361         @XmlAttribute(name = "ignoreGapsinConsensus")
1362         protected Boolean ignoreGapsinConsensus;
1363         @XmlAttribute(name = "showConsensusHistogram")
1364         protected Boolean showConsensusHistogram;
1365         @XmlAttribute(name = "showSequenceLogo")
1366         protected Boolean showSequenceLogo;
1367         @XmlAttribute(name = "normaliseSequenceLogo")
1368         protected Boolean normaliseSequenceLogo;
1369         @XmlAttribute(name = "id")
1370         protected String id;
1371
1372         /**
1373          * Gets the value of the seq property.
1374          *
1375          * <p>
1376          * This accessor method returns a reference to the live list,
1377          * not a snapshot. Therefore any modification you make to the
1378          * returned list will be present inside the JAXB object.
1379          * This is why there is not a <CODE>set</CODE> method for the seq property.
1380          *
1381          * <p>
1382          * For example, to add a new item, do as follows:
1383          * <pre>
1384          *    getSeq().add(newItem);
1385          * </pre>
1386          *
1387          *
1388          * <p>
1389          * Objects of the following type(s) are allowed in the list
1390          * {@link String }
1391          *
1392          *
1393          */
1394         public List<String> getSeq() {
1395             if (seq == null) {
1396                 seq = new ArrayList<String>();
1397             }
1398             return this.seq;
1399         }
1400
1401         /**
1402          * Gets the value of the annotationColours property.
1403          *
1404          * @return
1405          *     possible object is
1406          *     {@link AnnotationColourScheme }
1407          *
1408          */
1409         public AnnotationColourScheme getAnnotationColours() {
1410             return annotationColours;
1411         }
1412
1413         /**
1414          * Sets the value of the annotationColours property.
1415          *
1416          * @param value
1417          *     allowed object is
1418          *     {@link AnnotationColourScheme }
1419          *
1420          */
1421         public void setAnnotationColours(AnnotationColourScheme value) {
1422             this.annotationColours = value;
1423         }
1424
1425         /**
1426          * Gets the value of the start property.
1427          *
1428          * @return
1429          *     possible object is
1430          *     {@link Integer }
1431          *
1432          */
1433         public Integer getStart() {
1434             return start;
1435         }
1436
1437         /**
1438          * Sets the value of the start property.
1439          *
1440          * @param value
1441          *     allowed object is
1442          *     {@link Integer }
1443          *
1444          */
1445         public void setStart(Integer value) {
1446             this.start = value;
1447         }
1448
1449         /**
1450          * Gets the value of the end property.
1451          *
1452          * @return
1453          *     possible object is
1454          *     {@link Integer }
1455          *
1456          */
1457         public Integer getEnd() {
1458             return end;
1459         }
1460
1461         /**
1462          * Sets the value of the end property.
1463          *
1464          * @param value
1465          *     allowed object is
1466          *     {@link Integer }
1467          *
1468          */
1469         public void setEnd(Integer value) {
1470             this.end = value;
1471         }
1472
1473         /**
1474          * Gets the value of the name property.
1475          *
1476          * @return
1477          *     possible object is
1478          *     {@link String }
1479          *
1480          */
1481         public String getName() {
1482             return name;
1483         }
1484
1485         /**
1486          * Sets the value of the name property.
1487          *
1488          * @param value
1489          *     allowed object is
1490          *     {@link String }
1491          *
1492          */
1493         public void setName(String value) {
1494             this.name = value;
1495         }
1496
1497         /**
1498          * Gets the value of the colour property.
1499          *
1500          * @return
1501          *     possible object is
1502          *     {@link String }
1503          *
1504          */
1505         public String getColour() {
1506             return colour;
1507         }
1508
1509         /**
1510          * Sets the value of the colour property.
1511          *
1512          * @param value
1513          *     allowed object is
1514          *     {@link String }
1515          *
1516          */
1517         public void setColour(String value) {
1518             this.colour = value;
1519         }
1520
1521         /**
1522          * Gets the value of the consThreshold property.
1523          *
1524          * @return
1525          *     possible object is
1526          *     {@link Integer }
1527          *
1528          */
1529         public Integer getConsThreshold() {
1530             return consThreshold;
1531         }
1532
1533         /**
1534          * Sets the value of the consThreshold property.
1535          *
1536          * @param value
1537          *     allowed object is
1538          *     {@link Integer }
1539          *
1540          */
1541         public void setConsThreshold(Integer value) {
1542             this.consThreshold = value;
1543         }
1544
1545         /**
1546          * Gets the value of the pidThreshold property.
1547          *
1548          * @return
1549          *     possible object is
1550          *     {@link Integer }
1551          *
1552          */
1553         public Integer getPidThreshold() {
1554             return pidThreshold;
1555         }
1556
1557         /**
1558          * Sets the value of the pidThreshold property.
1559          *
1560          * @param value
1561          *     allowed object is
1562          *     {@link Integer }
1563          *
1564          */
1565         public void setPidThreshold(Integer value) {
1566             this.pidThreshold = value;
1567         }
1568
1569         /**
1570          * Gets the value of the outlineColour property.
1571          *
1572          * @return
1573          *     possible object is
1574          *     {@link Integer }
1575          *
1576          */
1577         public Integer getOutlineColour() {
1578             return outlineColour;
1579         }
1580
1581         /**
1582          * Sets the value of the outlineColour property.
1583          *
1584          * @param value
1585          *     allowed object is
1586          *     {@link Integer }
1587          *
1588          */
1589         public void setOutlineColour(Integer value) {
1590             this.outlineColour = value;
1591         }
1592
1593         /**
1594          * Gets the value of the displayBoxes property.
1595          *
1596          * @return
1597          *     possible object is
1598          *     {@link Boolean }
1599          *
1600          */
1601         public Boolean isDisplayBoxes() {
1602             return displayBoxes;
1603         }
1604
1605         /**
1606          * Sets the value of the displayBoxes property.
1607          *
1608          * @param value
1609          *     allowed object is
1610          *     {@link Boolean }
1611          *
1612          */
1613         public void setDisplayBoxes(Boolean value) {
1614             this.displayBoxes = value;
1615         }
1616
1617         /**
1618          * Gets the value of the displayText property.
1619          *
1620          * @return
1621          *     possible object is
1622          *     {@link Boolean }
1623          *
1624          */
1625         public Boolean isDisplayText() {
1626             return displayText;
1627         }
1628
1629         /**
1630          * Sets the value of the displayText property.
1631          *
1632          * @param value
1633          *     allowed object is
1634          *     {@link Boolean }
1635          *
1636          */
1637         public void setDisplayText(Boolean value) {
1638             this.displayText = value;
1639         }
1640
1641         /**
1642          * Gets the value of the colourText property.
1643          *
1644          * @return
1645          *     possible object is
1646          *     {@link Boolean }
1647          *
1648          */
1649         public Boolean isColourText() {
1650             return colourText;
1651         }
1652
1653         /**
1654          * Sets the value of the colourText property.
1655          *
1656          * @param value
1657          *     allowed object is
1658          *     {@link Boolean }
1659          *
1660          */
1661         public void setColourText(Boolean value) {
1662             this.colourText = value;
1663         }
1664
1665         /**
1666          * Gets the value of the textCol1 property.
1667          *
1668          * @return
1669          *     possible object is
1670          *     {@link Integer }
1671          *
1672          */
1673         public Integer getTextCol1() {
1674             return textCol1;
1675         }
1676
1677         /**
1678          * Sets the value of the textCol1 property.
1679          *
1680          * @param value
1681          *     allowed object is
1682          *     {@link Integer }
1683          *
1684          */
1685         public void setTextCol1(Integer value) {
1686             this.textCol1 = value;
1687         }
1688
1689         /**
1690          * Gets the value of the textCol2 property.
1691          *
1692          * @return
1693          *     possible object is
1694          *     {@link Integer }
1695          *
1696          */
1697         public Integer getTextCol2() {
1698             return textCol2;
1699         }
1700
1701         /**
1702          * Sets the value of the textCol2 property.
1703          *
1704          * @param value
1705          *     allowed object is
1706          *     {@link Integer }
1707          *
1708          */
1709         public void setTextCol2(Integer value) {
1710             this.textCol2 = value;
1711         }
1712
1713         /**
1714          * Gets the value of the textColThreshold property.
1715          *
1716          * @return
1717          *     possible object is
1718          *     {@link Integer }
1719          *
1720          */
1721         public Integer getTextColThreshold() {
1722             return textColThreshold;
1723         }
1724
1725         /**
1726          * Sets the value of the textColThreshold property.
1727          *
1728          * @param value
1729          *     allowed object is
1730          *     {@link Integer }
1731          *
1732          */
1733         public void setTextColThreshold(Integer value) {
1734             this.textColThreshold = value;
1735         }
1736
1737         /**
1738          * Gets the value of the showUnconserved property.
1739          *
1740          * @return
1741          *     possible object is
1742          *     {@link Boolean }
1743          *
1744          */
1745         public Boolean isShowUnconserved() {
1746             return showUnconserved;
1747         }
1748
1749         /**
1750          * Sets the value of the showUnconserved property.
1751          *
1752          * @param value
1753          *     allowed object is
1754          *     {@link Boolean }
1755          *
1756          */
1757         public void setShowUnconserved(Boolean value) {
1758             this.showUnconserved = value;
1759         }
1760
1761         /**
1762          * Gets the value of the ignoreGapsinConsensus property.
1763          *
1764          * @return
1765          *     possible object is
1766          *     {@link Boolean }
1767          *
1768          */
1769         public boolean isIgnoreGapsinConsensus() {
1770             if (ignoreGapsinConsensus == null) {
1771                 return true;
1772             } else {
1773                 return ignoreGapsinConsensus;
1774             }
1775         }
1776
1777         /**
1778          * Sets the value of the ignoreGapsinConsensus property.
1779          *
1780          * @param value
1781          *     allowed object is
1782          *     {@link Boolean }
1783          *
1784          */
1785         public void setIgnoreGapsinConsensus(Boolean value) {
1786             this.ignoreGapsinConsensus = value;
1787         }
1788
1789         /**
1790          * Gets the value of the showConsensusHistogram property.
1791          *
1792          * @return
1793          *     possible object is
1794          *     {@link Boolean }
1795          *
1796          */
1797         public boolean isShowConsensusHistogram() {
1798             if (showConsensusHistogram == null) {
1799                 return true;
1800             } else {
1801                 return showConsensusHistogram;
1802             }
1803         }
1804
1805         /**
1806          * Sets the value of the showConsensusHistogram property.
1807          *
1808          * @param value
1809          *     allowed object is
1810          *     {@link Boolean }
1811          *
1812          */
1813         public void setShowConsensusHistogram(Boolean value) {
1814             this.showConsensusHistogram = value;
1815         }
1816
1817         /**
1818          * Gets the value of the showSequenceLogo property.
1819          *
1820          * @return
1821          *     possible object is
1822          *     {@link Boolean }
1823          *
1824          */
1825         public boolean isShowSequenceLogo() {
1826             if (showSequenceLogo == null) {
1827                 return false;
1828             } else {
1829                 return showSequenceLogo;
1830             }
1831         }
1832
1833         /**
1834          * Sets the value of the showSequenceLogo property.
1835          *
1836          * @param value
1837          *     allowed object is
1838          *     {@link Boolean }
1839          *
1840          */
1841         public void setShowSequenceLogo(Boolean value) {
1842             this.showSequenceLogo = value;
1843         }
1844
1845         /**
1846          * Gets the value of the normaliseSequenceLogo property.
1847          *
1848          * @return
1849          *     possible object is
1850          *     {@link Boolean }
1851          *
1852          */
1853         public boolean isNormaliseSequenceLogo() {
1854             if (normaliseSequenceLogo == null) {
1855                 return false;
1856             } else {
1857                 return normaliseSequenceLogo;
1858             }
1859         }
1860
1861         /**
1862          * Sets the value of the normaliseSequenceLogo property.
1863          *
1864          * @param value
1865          *     allowed object is
1866          *     {@link Boolean }
1867          *
1868          */
1869         public void setNormaliseSequenceLogo(Boolean value) {
1870             this.normaliseSequenceLogo = value;
1871         }
1872
1873         /**
1874          * Gets the value of the id property.
1875          *
1876          * @return
1877          *     possible object is
1878          *     {@link String }
1879          *
1880          */
1881         public String getId() {
1882             return id;
1883         }
1884
1885         /**
1886          * Sets the value of the id property.
1887          *
1888          * @param value
1889          *     allowed object is
1890          *     {@link String }
1891          *
1892          */
1893         public void setId(String value) {
1894             this.id = value;
1895         }
1896
1897     }
1898
1899
1900     /**
1901      * <p>Java class for anonymous complex type.
1902      *
1903      * <p>The following schema fragment specifies the expected content contained within this class.
1904      *
1905      * <pre>
1906      * &lt;complexType>
1907      *   &lt;complexContent>
1908      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1909      *       &lt;sequence>
1910      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1911      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1912      *           &lt;complexType>
1913      *             &lt;complexContent>
1914      *               &lt;extension base="{www.jalview.org}pdbentry">
1915      *                 &lt;sequence>
1916      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1917      *                     &lt;complexType>
1918      *                       &lt;simpleContent>
1919      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1920      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1921      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1922      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1923      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1924      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1925      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1926      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1927      *                         &lt;/extension>
1928      *                       &lt;/simpleContent>
1929      *                     &lt;/complexType>
1930      *                   &lt;/element>
1931      *                 &lt;/sequence>
1932      *               &lt;/extension>
1933      *             &lt;/complexContent>
1934      *           &lt;/complexType>
1935      *         &lt;/element>
1936      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1937      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1938      *           &lt;complexType>
1939      *             &lt;complexContent>
1940      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1941      *                 &lt;sequence>
1942      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1943      *                     &lt;complexType>
1944      *                       &lt;complexContent>
1945      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1946      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1947      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1948      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1949      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1950      *                         &lt;/restriction>
1951      *                       &lt;/complexContent>
1952      *                     &lt;/complexType>
1953      *                   &lt;/element>
1954      *                 &lt;/sequence>
1955      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1956      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1957      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1958      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1959      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1960      *               &lt;/restriction>
1961      *             &lt;/complexContent>
1962      *           &lt;/complexType>
1963      *         &lt;/element>
1964      *       &lt;/sequence>
1965      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1966      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1967      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1968      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1969      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1970      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1971      *     &lt;/restriction>
1972      *   &lt;/complexContent>
1973      * &lt;/complexType>
1974      * </pre>
1975      *
1976      *
1977      */
1978     @XmlAccessorType(XmlAccessType.FIELD)
1979     @XmlType(name = "", propOrder = {
1980         "features",
1981         "pdbids",
1982         "hiddenSequences",
1983         "rnaViewer"
1984     })
1985     public static class JSeq {
1986
1987         @XmlElement(namespace = "www.jalview.org")
1988         protected List<Feature> features;
1989         @XmlElement(namespace = "www.jalview.org")
1990         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1991         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1992         protected List<Integer> hiddenSequences;
1993         @XmlElement(namespace = "www.jalview.org")
1994         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1995         @XmlAttribute(name = "colour")
1996         protected Integer colour;
1997         @XmlAttribute(name = "start", required = true)
1998         protected int start;
1999         @XmlAttribute(name = "end", required = true)
2000         protected int end;
2001         @XmlAttribute(name = "id", required = true)
2002         protected String id;
2003         @XmlAttribute(name = "hidden")
2004         protected Boolean hidden;
2005         @XmlAttribute(name = "viewreference")
2006         protected Boolean viewreference;
2007
2008         /**
2009          * Gets the value of the features property.
2010          *
2011          * <p>
2012          * This accessor method returns a reference to the live list,
2013          * not a snapshot. Therefore any modification you make to the
2014          * returned list will be present inside the JAXB object.
2015          * This is why there is not a <CODE>set</CODE> method for the features property.
2016          *
2017          * <p>
2018          * For example, to add a new item, do as follows:
2019          * <pre>
2020          *    getFeatures().add(newItem);
2021          * </pre>
2022          *
2023          *
2024          * <p>
2025          * Objects of the following type(s) are allowed in the list
2026          * {@link Feature }
2027          *
2028          *
2029          */
2030         public List<Feature> getFeatures() {
2031             if (features == null) {
2032                 features = new ArrayList<Feature>();
2033             }
2034             return this.features;
2035         }
2036
2037         /**
2038          * Gets the value of the pdbids property.
2039          *
2040          * <p>
2041          * This accessor method returns a reference to the live list,
2042          * not a snapshot. Therefore any modification you make to the
2043          * returned list will be present inside the JAXB object.
2044          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2045          *
2046          * <p>
2047          * For example, to add a new item, do as follows:
2048          * <pre>
2049          *    getPdbids().add(newItem);
2050          * </pre>
2051          *
2052          *
2053          * <p>
2054          * Objects of the following type(s) are allowed in the list
2055          * {@link JalviewModel.JSeq.Pdbids }
2056          *
2057          *
2058          */
2059         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2060             if (pdbids == null) {
2061                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2062             }
2063             return this.pdbids;
2064         }
2065
2066         /**
2067          * Gets the value of the hiddenSequences property.
2068          *
2069          * <p>
2070          * This accessor method returns a reference to the live list,
2071          * not a snapshot. Therefore any modification you make to the
2072          * returned list will be present inside the JAXB object.
2073          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2074          *
2075          * <p>
2076          * For example, to add a new item, do as follows:
2077          * <pre>
2078          *    getHiddenSequences().add(newItem);
2079          * </pre>
2080          *
2081          *
2082          * <p>
2083          * Objects of the following type(s) are allowed in the list
2084          * {@link Integer }
2085          *
2086          *
2087          */
2088         public List<Integer> getHiddenSequences() {
2089             if (hiddenSequences == null) {
2090                 hiddenSequences = new ArrayList<Integer>();
2091             }
2092             return this.hiddenSequences;
2093         }
2094
2095         /**
2096          * Gets the value of the rnaViewer property.
2097          *
2098          * <p>
2099          * This accessor method returns a reference to the live list,
2100          * not a snapshot. Therefore any modification you make to the
2101          * returned list will be present inside the JAXB object.
2102          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2103          *
2104          * <p>
2105          * For example, to add a new item, do as follows:
2106          * <pre>
2107          *    getRnaViewer().add(newItem);
2108          * </pre>
2109          *
2110          *
2111          * <p>
2112          * Objects of the following type(s) are allowed in the list
2113          * {@link JalviewModel.JSeq.RnaViewer }
2114          *
2115          *
2116          */
2117         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2118             if (rnaViewer == null) {
2119                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2120             }
2121             return this.rnaViewer;
2122         }
2123
2124         /**
2125          * Gets the value of the colour property.
2126          *
2127          * @return
2128          *     possible object is
2129          *     {@link Integer }
2130          *
2131          */
2132         public Integer getColour() {
2133             return colour;
2134         }
2135
2136         /**
2137          * Sets the value of the colour property.
2138          *
2139          * @param value
2140          *     allowed object is
2141          *     {@link Integer }
2142          *
2143          */
2144         public void setColour(Integer value) {
2145             this.colour = value;
2146         }
2147
2148         /**
2149          * Gets the value of the start property.
2150          *
2151          */
2152         public int getStart() {
2153             return start;
2154         }
2155
2156         /**
2157          * Sets the value of the start property.
2158          *
2159          */
2160         public void setStart(int value) {
2161             this.start = value;
2162         }
2163
2164         /**
2165          * Gets the value of the end property.
2166          *
2167          */
2168         public int getEnd() {
2169             return end;
2170         }
2171
2172         /**
2173          * Sets the value of the end property.
2174          *
2175          */
2176         public void setEnd(int value) {
2177             this.end = value;
2178         }
2179
2180         /**
2181          * Gets the value of the id property.
2182          *
2183          * @return
2184          *     possible object is
2185          *     {@link String }
2186          *
2187          */
2188         public String getId() {
2189             return id;
2190         }
2191
2192         /**
2193          * Sets the value of the id property.
2194          *
2195          * @param value
2196          *     allowed object is
2197          *     {@link String }
2198          *
2199          */
2200         public void setId(String value) {
2201             this.id = value;
2202         }
2203
2204         /**
2205          * Gets the value of the hidden property.
2206          *
2207          * @return
2208          *     possible object is
2209          *     {@link Boolean }
2210          *
2211          */
2212         public Boolean isHidden() {
2213             return hidden;
2214         }
2215
2216         /**
2217          * Sets the value of the hidden property.
2218          *
2219          * @param value
2220          *     allowed object is
2221          *     {@link Boolean }
2222          *
2223          */
2224         public void setHidden(Boolean value) {
2225             this.hidden = value;
2226         }
2227
2228         /**
2229          * Gets the value of the viewreference property.
2230          *
2231          * @return
2232          *     possible object is
2233          *     {@link Boolean }
2234          *
2235          */
2236         public Boolean isViewreference() {
2237             return viewreference;
2238         }
2239
2240         /**
2241          * Sets the value of the viewreference property.
2242          *
2243          * @param value
2244          *     allowed object is
2245          *     {@link Boolean }
2246          *
2247          */
2248         public void setViewreference(Boolean value) {
2249             this.viewreference = value;
2250         }
2251
2252
2253         /**
2254          * <p>Java class for anonymous complex type.
2255          *
2256          * <p>The following schema fragment specifies the expected content contained within this class.
2257          *
2258          * <pre>
2259          * &lt;complexType>
2260          *   &lt;complexContent>
2261          *     &lt;extension base="{www.jalview.org}pdbentry">
2262          *       &lt;sequence>
2263          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2264          *           &lt;complexType>
2265          *             &lt;simpleContent>
2266          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2267          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2268          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2269          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2270          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2271          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2272          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2273          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2274          *               &lt;/extension>
2275          *             &lt;/simpleContent>
2276          *           &lt;/complexType>
2277          *         &lt;/element>
2278          *       &lt;/sequence>
2279          *     &lt;/extension>
2280          *   &lt;/complexContent>
2281          * &lt;/complexType>
2282          * </pre>
2283          *
2284          *
2285          */
2286         @XmlAccessorType(XmlAccessType.FIELD)
2287         @XmlType(name = "", propOrder = {
2288             "structureState"
2289         })
2290         public static class Pdbids
2291             extends Pdbentry
2292         {
2293
2294             @XmlElement(namespace = "www.jalview.org")
2295             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2296
2297             /**
2298              * Gets the value of the structureState property.
2299              *
2300              * <p>
2301              * This accessor method returns a reference to the live list,
2302              * not a snapshot. Therefore any modification you make to the
2303              * returned list will be present inside the JAXB object.
2304              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2305              *
2306              * <p>
2307              * For example, to add a new item, do as follows:
2308              * <pre>
2309              *    getStructureState().add(newItem);
2310              * </pre>
2311              *
2312              *
2313              * <p>
2314              * Objects of the following type(s) are allowed in the list
2315              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2316              *
2317              *
2318              */
2319             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2320                 if (structureState == null) {
2321                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2322                 }
2323                 return this.structureState;
2324             }
2325
2326
2327             /**
2328              * <p>Java class for anonymous complex type.
2329              *
2330              * <p>The following schema fragment specifies the expected content contained within this class.
2331              *
2332              * <pre>
2333              * &lt;complexType>
2334              *   &lt;simpleContent>
2335              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2336              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2337              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2338              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2339              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2340              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2341              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2342              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2343              *     &lt;/extension>
2344              *   &lt;/simpleContent>
2345              * &lt;/complexType>
2346              * </pre>
2347              *
2348              *
2349              */
2350             @XmlAccessorType(XmlAccessType.FIELD)
2351             @XmlType(name = "", propOrder = {
2352                 "value"
2353             })
2354             public static class StructureState {
2355
2356                 @XmlValue
2357                 protected String value;
2358                 @XmlAttribute(name = "visible")
2359                 protected Boolean visible;
2360                 @XmlAttribute(name = "viewId")
2361                 protected String viewId;
2362                 @XmlAttribute(name = "alignwithAlignPanel")
2363                 protected Boolean alignwithAlignPanel;
2364                 @XmlAttribute(name = "colourwithAlignPanel")
2365                 protected Boolean colourwithAlignPanel;
2366                 @XmlAttribute(name = "colourByJmol")
2367                 protected Boolean colourByJmol;
2368                 @XmlAttribute(name = "type")
2369                 protected String type;
2370                 @XmlAttribute(name = "width")
2371                 protected Integer width;
2372                 @XmlAttribute(name = "height")
2373                 protected Integer height;
2374                 @XmlAttribute(name = "xpos")
2375                 protected Integer xpos;
2376                 @XmlAttribute(name = "ypos")
2377                 protected Integer ypos;
2378
2379                 /**
2380                  * Gets the value of the value property.
2381                  *
2382                  * @return
2383                  *     possible object is
2384                  *     {@link String }
2385                  *
2386                  */
2387                 public String getValue() {
2388                     return value;
2389                 }
2390
2391                 /**
2392                  * Sets the value of the value property.
2393                  *
2394                  * @param value
2395                  *     allowed object is
2396                  *     {@link String }
2397                  *
2398                  */
2399                 public void setValue(String value) {
2400                     this.value = value;
2401                 }
2402
2403                 /**
2404                  * Gets the value of the visible property.
2405                  *
2406                  * @return
2407                  *     possible object is
2408                  *     {@link Boolean }
2409                  *
2410                  */
2411                 public Boolean isVisible() {
2412                     return visible;
2413                 }
2414
2415                 /**
2416                  * Sets the value of the visible property.
2417                  *
2418                  * @param value
2419                  *     allowed object is
2420                  *     {@link Boolean }
2421                  *
2422                  */
2423                 public void setVisible(Boolean value) {
2424                     this.visible = value;
2425                 }
2426
2427                 /**
2428                  * Gets the value of the viewId property.
2429                  *
2430                  * @return
2431                  *     possible object is
2432                  *     {@link String }
2433                  *
2434                  */
2435                 public String getViewId() {
2436                     return viewId;
2437                 }
2438
2439                 /**
2440                  * Sets the value of the viewId property.
2441                  *
2442                  * @param value
2443                  *     allowed object is
2444                  *     {@link String }
2445                  *
2446                  */
2447                 public void setViewId(String value) {
2448                     this.viewId = value;
2449                 }
2450
2451                 /**
2452                  * Gets the value of the alignwithAlignPanel property.
2453                  *
2454                  * @return
2455                  *     possible object is
2456                  *     {@link Boolean }
2457                  *
2458                  */
2459                 public boolean isAlignwithAlignPanel() {
2460                     if (alignwithAlignPanel == null) {
2461                         return true;
2462                     } else {
2463                         return alignwithAlignPanel;
2464                     }
2465                 }
2466
2467                 /**
2468                  * Sets the value of the alignwithAlignPanel property.
2469                  *
2470                  * @param value
2471                  *     allowed object is
2472                  *     {@link Boolean }
2473                  *
2474                  */
2475                 public void setAlignwithAlignPanel(Boolean value) {
2476                     this.alignwithAlignPanel = value;
2477                 }
2478
2479                 /**
2480                  * Gets the value of the colourwithAlignPanel property.
2481                  *
2482                  * @return
2483                  *     possible object is
2484                  *     {@link Boolean }
2485                  *
2486                  */
2487                 public boolean isColourwithAlignPanel() {
2488                     if (colourwithAlignPanel == null) {
2489                         return false;
2490                     } else {
2491                         return colourwithAlignPanel;
2492                     }
2493                 }
2494
2495                 /**
2496                  * Sets the value of the colourwithAlignPanel property.
2497                  *
2498                  * @param value
2499                  *     allowed object is
2500                  *     {@link Boolean }
2501                  *
2502                  */
2503                 public void setColourwithAlignPanel(Boolean value) {
2504                     this.colourwithAlignPanel = value;
2505                 }
2506
2507                 /**
2508                  * Gets the value of the colourByJmol property.
2509                  *
2510                  * @return
2511                  *     possible object is
2512                  *     {@link Boolean }
2513                  *
2514                  */
2515                 public boolean isColourByJmol() {
2516                     if (colourByJmol == null) {
2517                         return true;
2518                     } else {
2519                         return colourByJmol;
2520                     }
2521                 }
2522
2523                 /**
2524                  * Sets the value of the colourByJmol property.
2525                  *
2526                  * @param value
2527                  *     allowed object is
2528                  *     {@link Boolean }
2529                  *
2530                  */
2531                 public void setColourByJmol(Boolean value) {
2532                     this.colourByJmol = value;
2533                 }
2534
2535                 /**
2536                  * Gets the value of the type property.
2537                  *
2538                  * @return
2539                  *     possible object is
2540                  *     {@link String }
2541                  *
2542                  */
2543                 public String getType() {
2544                     return type;
2545                 }
2546
2547                 /**
2548                  * Sets the value of the type property.
2549                  *
2550                  * @param value
2551                  *     allowed object is
2552                  *     {@link String }
2553                  *
2554                  */
2555                 public void setType(String value) {
2556                     this.type = value;
2557                 }
2558
2559                 /**
2560                  * Gets the value of the width property.
2561                  *
2562                  * @return
2563                  *     possible object is
2564                  *     {@link Integer }
2565                  *
2566                  */
2567                 public Integer getWidth() {
2568                     return width;
2569                 }
2570
2571                 /**
2572                  * Sets the value of the width property.
2573                  *
2574                  * @param value
2575                  *     allowed object is
2576                  *     {@link Integer }
2577                  *
2578                  */
2579                 public void setWidth(Integer value) {
2580                     this.width = value;
2581                 }
2582
2583                 /**
2584                  * Gets the value of the height property.
2585                  *
2586                  * @return
2587                  *     possible object is
2588                  *     {@link Integer }
2589                  *
2590                  */
2591                 public Integer getHeight() {
2592                     return height;
2593                 }
2594
2595                 /**
2596                  * Sets the value of the height property.
2597                  *
2598                  * @param value
2599                  *     allowed object is
2600                  *     {@link Integer }
2601                  *
2602                  */
2603                 public void setHeight(Integer value) {
2604                     this.height = value;
2605                 }
2606
2607                 /**
2608                  * Gets the value of the xpos property.
2609                  *
2610                  * @return
2611                  *     possible object is
2612                  *     {@link Integer }
2613                  *
2614                  */
2615                 public Integer getXpos() {
2616                     return xpos;
2617                 }
2618
2619                 /**
2620                  * Sets the value of the xpos property.
2621                  *
2622                  * @param value
2623                  *     allowed object is
2624                  *     {@link Integer }
2625                  *
2626                  */
2627                 public void setXpos(Integer value) {
2628                     this.xpos = value;
2629                 }
2630
2631                 /**
2632                  * Gets the value of the ypos property.
2633                  *
2634                  * @return
2635                  *     possible object is
2636                  *     {@link Integer }
2637                  *
2638                  */
2639                 public Integer getYpos() {
2640                     return ypos;
2641                 }
2642
2643                 /**
2644                  * Sets the value of the ypos property.
2645                  *
2646                  * @param value
2647                  *     allowed object is
2648                  *     {@link Integer }
2649                  *
2650                  */
2651                 public void setYpos(Integer value) {
2652                     this.ypos = value;
2653                 }
2654
2655             }
2656
2657         }
2658
2659
2660         /**
2661          * <p>Java class for anonymous complex type.
2662          *
2663          * <p>The following schema fragment specifies the expected content contained within this class.
2664          *
2665          * <pre>
2666          * &lt;complexType>
2667          *   &lt;complexContent>
2668          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2669          *       &lt;sequence>
2670          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2671          *           &lt;complexType>
2672          *             &lt;complexContent>
2673          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2674          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2675          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2676          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2677          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2678          *               &lt;/restriction>
2679          *             &lt;/complexContent>
2680          *           &lt;/complexType>
2681          *         &lt;/element>
2682          *       &lt;/sequence>
2683          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2684          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2685          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2686          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2687          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2688          *     &lt;/restriction>
2689          *   &lt;/complexContent>
2690          * &lt;/complexType>
2691          * </pre>
2692          *
2693          *
2694          */
2695         @XmlAccessorType(XmlAccessType.FIELD)
2696         @XmlType(name = "", propOrder = {
2697             "secondaryStructure"
2698         })
2699         public static class RnaViewer {
2700
2701             @XmlElement(namespace = "www.jalview.org", required = true)
2702             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2703             @XmlAttribute(name = "title")
2704             protected String title;
2705             @XmlAttribute(name = "viewId")
2706             protected String viewId;
2707             @XmlAttribute(name = "dividerLocation")
2708             protected Integer dividerLocation;
2709             @XmlAttribute(name = "selectedRna")
2710             protected Integer selectedRna;
2711             @XmlAttribute(name = "width")
2712             protected Integer width;
2713             @XmlAttribute(name = "height")
2714             protected Integer height;
2715             @XmlAttribute(name = "xpos")
2716             protected Integer xpos;
2717             @XmlAttribute(name = "ypos")
2718             protected Integer ypos;
2719
2720             /**
2721              * Gets the value of the secondaryStructure property.
2722              *
2723              * <p>
2724              * This accessor method returns a reference to the live list,
2725              * not a snapshot. Therefore any modification you make to the
2726              * returned list will be present inside the JAXB object.
2727              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2728              *
2729              * <p>
2730              * For example, to add a new item, do as follows:
2731              * <pre>
2732              *    getSecondaryStructure().add(newItem);
2733              * </pre>
2734              *
2735              *
2736              * <p>
2737              * Objects of the following type(s) are allowed in the list
2738              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2739              *
2740              *
2741              */
2742             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2743                 if (secondaryStructure == null) {
2744                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2745                 }
2746                 return this.secondaryStructure;
2747             }
2748
2749             /**
2750              * Gets the value of the title property.
2751              *
2752              * @return
2753              *     possible object is
2754              *     {@link String }
2755              *
2756              */
2757             public String getTitle() {
2758                 return title;
2759             }
2760
2761             /**
2762              * Sets the value of the title property.
2763              *
2764              * @param value
2765              *     allowed object is
2766              *     {@link String }
2767              *
2768              */
2769             public void setTitle(String value) {
2770                 this.title = value;
2771             }
2772
2773             /**
2774              * Gets the value of the viewId property.
2775              *
2776              * @return
2777              *     possible object is
2778              *     {@link String }
2779              *
2780              */
2781             public String getViewId() {
2782                 return viewId;
2783             }
2784
2785             /**
2786              * Sets the value of the viewId property.
2787              *
2788              * @param value
2789              *     allowed object is
2790              *     {@link String }
2791              *
2792              */
2793             public void setViewId(String value) {
2794                 this.viewId = value;
2795             }
2796
2797             /**
2798              * Gets the value of the dividerLocation property.
2799              *
2800              * @return
2801              *     possible object is
2802              *     {@link Integer }
2803              *
2804              */
2805             public Integer getDividerLocation() {
2806                 return dividerLocation;
2807             }
2808
2809             /**
2810              * Sets the value of the dividerLocation property.
2811              *
2812              * @param value
2813              *     allowed object is
2814              *     {@link Integer }
2815              *
2816              */
2817             public void setDividerLocation(Integer value) {
2818                 this.dividerLocation = value;
2819             }
2820
2821             /**
2822              * Gets the value of the selectedRna property.
2823              *
2824              * @return
2825              *     possible object is
2826              *     {@link Integer }
2827              *
2828              */
2829             public Integer getSelectedRna() {
2830                 return selectedRna;
2831             }
2832
2833             /**
2834              * Sets the value of the selectedRna property.
2835              *
2836              * @param value
2837              *     allowed object is
2838              *     {@link Integer }
2839              *
2840              */
2841             public void setSelectedRna(Integer value) {
2842                 this.selectedRna = value;
2843             }
2844
2845             /**
2846              * Gets the value of the width property.
2847              *
2848              * @return
2849              *     possible object is
2850              *     {@link Integer }
2851              *
2852              */
2853             public Integer getWidth() {
2854                 return width;
2855             }
2856
2857             /**
2858              * Sets the value of the width property.
2859              *
2860              * @param value
2861              *     allowed object is
2862              *     {@link Integer }
2863              *
2864              */
2865             public void setWidth(Integer value) {
2866                 this.width = value;
2867             }
2868
2869             /**
2870              * Gets the value of the height property.
2871              *
2872              * @return
2873              *     possible object is
2874              *     {@link Integer }
2875              *
2876              */
2877             public Integer getHeight() {
2878                 return height;
2879             }
2880
2881             /**
2882              * Sets the value of the height property.
2883              *
2884              * @param value
2885              *     allowed object is
2886              *     {@link Integer }
2887              *
2888              */
2889             public void setHeight(Integer value) {
2890                 this.height = value;
2891             }
2892
2893             /**
2894              * Gets the value of the xpos property.
2895              *
2896              * @return
2897              *     possible object is
2898              *     {@link Integer }
2899              *
2900              */
2901             public Integer getXpos() {
2902                 return xpos;
2903             }
2904
2905             /**
2906              * Sets the value of the xpos property.
2907              *
2908              * @param value
2909              *     allowed object is
2910              *     {@link Integer }
2911              *
2912              */
2913             public void setXpos(Integer value) {
2914                 this.xpos = value;
2915             }
2916
2917             /**
2918              * Gets the value of the ypos property.
2919              *
2920              * @return
2921              *     possible object is
2922              *     {@link Integer }
2923              *
2924              */
2925             public Integer getYpos() {
2926                 return ypos;
2927             }
2928
2929             /**
2930              * Sets the value of the ypos property.
2931              *
2932              * @param value
2933              *     allowed object is
2934              *     {@link Integer }
2935              *
2936              */
2937             public void setYpos(Integer value) {
2938                 this.ypos = value;
2939             }
2940
2941
2942             /**
2943              * <p>Java class for anonymous complex type.
2944              *
2945              * <p>The following schema fragment specifies the expected content contained within this class.
2946              *
2947              * <pre>
2948              * &lt;complexType>
2949              *   &lt;complexContent>
2950              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2951              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2952              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2953              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2954              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2955              *     &lt;/restriction>
2956              *   &lt;/complexContent>
2957              * &lt;/complexType>
2958              * </pre>
2959              *
2960              *
2961              */
2962             @XmlAccessorType(XmlAccessType.FIELD)
2963             @XmlType(name = "")
2964             public static class SecondaryStructure {
2965
2966                 @XmlAttribute(name = "title")
2967                 protected String title;
2968                 @XmlAttribute(name = "annotationId", required = true)
2969                 protected String annotationId;
2970                 @XmlAttribute(name = "gapped")
2971                 protected Boolean gapped;
2972                 @XmlAttribute(name = "viewerState")
2973                 protected String viewerState;
2974
2975                 /**
2976                  * Gets the value of the title property.
2977                  *
2978                  * @return
2979                  *     possible object is
2980                  *     {@link String }
2981                  *
2982                  */
2983                 public String getTitle() {
2984                     return title;
2985                 }
2986
2987                 /**
2988                  * Sets the value of the title property.
2989                  *
2990                  * @param value
2991                  *     allowed object is
2992                  *     {@link String }
2993                  *
2994                  */
2995                 public void setTitle(String value) {
2996                     this.title = value;
2997                 }
2998
2999                 /**
3000                  * Gets the value of the annotationId property.
3001                  *
3002                  * @return
3003                  *     possible object is
3004                  *     {@link String }
3005                  *
3006                  */
3007                 public String getAnnotationId() {
3008                     return annotationId;
3009                 }
3010
3011                 /**
3012                  * Sets the value of the annotationId property.
3013                  *
3014                  * @param value
3015                  *     allowed object is
3016                  *     {@link String }
3017                  *
3018                  */
3019                 public void setAnnotationId(String value) {
3020                     this.annotationId = value;
3021                 }
3022
3023                 /**
3024                  * Gets the value of the gapped property.
3025                  *
3026                  * @return
3027                  *     possible object is
3028                  *     {@link Boolean }
3029                  *
3030                  */
3031                 public Boolean isGapped() {
3032                     return gapped;
3033                 }
3034
3035                 /**
3036                  * Sets the value of the gapped property.
3037                  *
3038                  * @param value
3039                  *     allowed object is
3040                  *     {@link Boolean }
3041                  *
3042                  */
3043                 public void setGapped(Boolean value) {
3044                     this.gapped = value;
3045                 }
3046
3047                 /**
3048                  * Gets the value of the viewerState property.
3049                  *
3050                  * @return
3051                  *     possible object is
3052                  *     {@link String }
3053                  *
3054                  */
3055                 public String getViewerState() {
3056                     return viewerState;
3057                 }
3058
3059                 /**
3060                  * Sets the value of the viewerState property.
3061                  *
3062                  * @param value
3063                  *     allowed object is
3064                  *     {@link String }
3065                  *
3066                  */
3067                 public void setViewerState(String value) {
3068                     this.viewerState = value;
3069                 }
3070
3071             }
3072
3073         }
3074
3075     }
3076
3077
3078     /**
3079      * <p>Java class for anonymous complex type.
3080      *
3081      * <p>The following schema fragment specifies the expected content contained within this class.
3082      *
3083      * <pre>
3084      * &lt;complexType>
3085      *   &lt;complexContent>
3086      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3087      *       &lt;sequence>
3088      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3089      *           &lt;complexType>
3090      *             &lt;complexContent>
3091      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3092      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3093      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3094      *               &lt;/restriction>
3095      *             &lt;/complexContent>
3096      *           &lt;/complexType>
3097      *         &lt;/element>
3098      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3099      *           &lt;complexType>
3100      *             &lt;complexContent>
3101      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3102      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3103      *               &lt;/restriction>
3104      *             &lt;/complexContent>
3105      *           &lt;/complexType>
3106      *         &lt;/element>
3107      *         &lt;element name="seqPointMin">
3108      *           &lt;complexType>
3109      *             &lt;complexContent>
3110      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3111      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3112      *               &lt;/restriction>
3113      *             &lt;/complexContent>
3114      *           &lt;/complexType>
3115      *         &lt;/element>
3116      *         &lt;element name="seqPointMax">
3117      *           &lt;complexType>
3118      *             &lt;complexContent>
3119      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3120      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3121      *               &lt;/restriction>
3122      *             &lt;/complexContent>
3123      *           &lt;/complexType>
3124      *         &lt;/element>
3125      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3126      *       &lt;/sequence>
3127      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3128      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3129      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3130      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3131      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3132      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3133      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3134      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3135      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3136      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3137      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3138      *     &lt;/restriction>
3139      *   &lt;/complexContent>
3140      * &lt;/complexType>
3141      * </pre>
3142      *
3143      *
3144      */
3145     @XmlAccessorType(XmlAccessType.FIELD)
3146     @XmlType(name = "", propOrder = {
3147         "sequencePoint",
3148         "axis",
3149         "seqPointMin",
3150         "seqPointMax",
3151         "pcaData"
3152     })
3153     public static class PcaViewer {
3154
3155         @XmlElement(namespace = "www.jalview.org", required = true)
3156         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3157         @XmlElement(namespace = "www.jalview.org", required = true)
3158         protected List<JalviewModel.PcaViewer.Axis> axis;
3159         @XmlElement(namespace = "www.jalview.org", required = true)
3160         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3161         @XmlElement(namespace = "www.jalview.org", required = true)
3162         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3163         @XmlElement(namespace = "www.jalview.org", required = true)
3164         protected PcaDataType pcaData;
3165         @XmlAttribute(name = "title")
3166         protected String title;
3167         @XmlAttribute(name = "scoreModelName")
3168         protected String scoreModelName;
3169         @XmlAttribute(name = "xDim")
3170         protected Integer xDim;
3171         @XmlAttribute(name = "yDim")
3172         protected Integer yDim;
3173         @XmlAttribute(name = "zDim")
3174         protected Integer zDim;
3175         @XmlAttribute(name = "bgColour")
3176         protected Integer bgColour;
3177         @XmlAttribute(name = "scaleFactor")
3178         protected Float scaleFactor;
3179         @XmlAttribute(name = "showLabels")
3180         protected Boolean showLabels;
3181         @XmlAttribute(name = "linkToAllViews")
3182         protected Boolean linkToAllViews;
3183         @XmlAttribute(name = "width")
3184         protected Integer width;
3185         @XmlAttribute(name = "height")
3186         protected Integer height;
3187         @XmlAttribute(name = "xpos")
3188         protected Integer xpos;
3189         @XmlAttribute(name = "ypos")
3190         protected Integer ypos;
3191         @XmlAttribute(name = "includeGaps")
3192         protected Boolean includeGaps;
3193         @XmlAttribute(name = "matchGaps")
3194         protected Boolean matchGaps;
3195         @XmlAttribute(name = "includeGappedColumns")
3196         protected Boolean includeGappedColumns;
3197         @XmlAttribute(name = "denominateByShortestLength")
3198         protected Boolean denominateByShortestLength;
3199
3200         /**
3201          * Gets the value of the sequencePoint property.
3202          *
3203          * <p>
3204          * This accessor method returns a reference to the live list,
3205          * not a snapshot. Therefore any modification you make to the
3206          * returned list will be present inside the JAXB object.
3207          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3208          *
3209          * <p>
3210          * For example, to add a new item, do as follows:
3211          * <pre>
3212          *    getSequencePoint().add(newItem);
3213          * </pre>
3214          *
3215          *
3216          * <p>
3217          * Objects of the following type(s) are allowed in the list
3218          * {@link JalviewModel.PcaViewer.SequencePoint }
3219          *
3220          *
3221          */
3222         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3223             if (sequencePoint == null) {
3224                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3225             }
3226             return this.sequencePoint;
3227         }
3228
3229         /**
3230          * Gets the value of the axis property.
3231          *
3232          * <p>
3233          * This accessor method returns a reference to the live list,
3234          * not a snapshot. Therefore any modification you make to the
3235          * returned list will be present inside the JAXB object.
3236          * This is why there is not a <CODE>set</CODE> method for the axis property.
3237          *
3238          * <p>
3239          * For example, to add a new item, do as follows:
3240          * <pre>
3241          *    getAxis().add(newItem);
3242          * </pre>
3243          *
3244          *
3245          * <p>
3246          * Objects of the following type(s) are allowed in the list
3247          * {@link JalviewModel.PcaViewer.Axis }
3248          *
3249          *
3250          */
3251         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3252             if (axis == null) {
3253                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3254             }
3255             return this.axis;
3256         }
3257
3258         /**
3259          * Gets the value of the seqPointMin property.
3260          *
3261          * @return
3262          *     possible object is
3263          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3264          *
3265          */
3266         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3267             return seqPointMin;
3268         }
3269
3270         /**
3271          * Sets the value of the seqPointMin property.
3272          *
3273          * @param value
3274          *     allowed object is
3275          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3276          *
3277          */
3278         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3279             this.seqPointMin = value;
3280         }
3281
3282         /**
3283          * Gets the value of the seqPointMax property.
3284          *
3285          * @return
3286          *     possible object is
3287          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3288          *
3289          */
3290         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3291             return seqPointMax;
3292         }
3293
3294         /**
3295          * Sets the value of the seqPointMax property.
3296          *
3297          * @param value
3298          *     allowed object is
3299          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3300          *
3301          */
3302         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3303             this.seqPointMax = value;
3304         }
3305
3306         /**
3307          * Gets the value of the pcaData property.
3308          *
3309          * @return
3310          *     possible object is
3311          *     {@link PcaDataType }
3312          *
3313          */
3314         public PcaDataType getPcaData() {
3315             return pcaData;
3316         }
3317
3318         /**
3319          * Sets the value of the pcaData property.
3320          *
3321          * @param value
3322          *     allowed object is
3323          *     {@link PcaDataType }
3324          *
3325          */
3326         public void setPcaData(PcaDataType value) {
3327             this.pcaData = value;
3328         }
3329
3330         /**
3331          * Gets the value of the title property.
3332          *
3333          * @return
3334          *     possible object is
3335          *     {@link String }
3336          *
3337          */
3338         public String getTitle() {
3339             return title;
3340         }
3341
3342         /**
3343          * Sets the value of the title property.
3344          *
3345          * @param value
3346          *     allowed object is
3347          *     {@link String }
3348          *
3349          */
3350         public void setTitle(String value) {
3351             this.title = value;
3352         }
3353
3354         /**
3355          * Gets the value of the scoreModelName property.
3356          *
3357          * @return
3358          *     possible object is
3359          *     {@link String }
3360          *
3361          */
3362         public String getScoreModelName() {
3363             return scoreModelName;
3364         }
3365
3366         /**
3367          * Sets the value of the scoreModelName property.
3368          *
3369          * @param value
3370          *     allowed object is
3371          *     {@link String }
3372          *
3373          */
3374         public void setScoreModelName(String value) {
3375             this.scoreModelName = value;
3376         }
3377
3378         /**
3379          * Gets the value of the xDim property.
3380          *
3381          * @return
3382          *     possible object is
3383          *     {@link Integer }
3384          *
3385          */
3386         public Integer getXDim() {
3387             return xDim;
3388         }
3389
3390         /**
3391          * Sets the value of the xDim property.
3392          *
3393          * @param value
3394          *     allowed object is
3395          *     {@link Integer }
3396          *
3397          */
3398         public void setXDim(Integer value) {
3399             this.xDim = value;
3400         }
3401
3402         /**
3403          * Gets the value of the yDim property.
3404          *
3405          * @return
3406          *     possible object is
3407          *     {@link Integer }
3408          *
3409          */
3410         public Integer getYDim() {
3411             return yDim;
3412         }
3413
3414         /**
3415          * Sets the value of the yDim property.
3416          *
3417          * @param value
3418          *     allowed object is
3419          *     {@link Integer }
3420          *
3421          */
3422         public void setYDim(Integer value) {
3423             this.yDim = value;
3424         }
3425
3426         /**
3427          * Gets the value of the zDim property.
3428          *
3429          * @return
3430          *     possible object is
3431          *     {@link Integer }
3432          *
3433          */
3434         public Integer getZDim() {
3435             return zDim;
3436         }
3437
3438         /**
3439          * Sets the value of the zDim property.
3440          *
3441          * @param value
3442          *     allowed object is
3443          *     {@link Integer }
3444          *
3445          */
3446         public void setZDim(Integer value) {
3447             this.zDim = value;
3448         }
3449
3450         /**
3451          * Gets the value of the bgColour property.
3452          *
3453          * @return
3454          *     possible object is
3455          *     {@link Integer }
3456          *
3457          */
3458         public Integer getBgColour() {
3459             return bgColour;
3460         }
3461
3462         /**
3463          * Sets the value of the bgColour property.
3464          *
3465          * @param value
3466          *     allowed object is
3467          *     {@link Integer }
3468          *
3469          */
3470         public void setBgColour(Integer value) {
3471             this.bgColour = value;
3472         }
3473
3474         /**
3475          * Gets the value of the scaleFactor property.
3476          *
3477          * @return
3478          *     possible object is
3479          *     {@link Float }
3480          *
3481          */
3482         public Float getScaleFactor() {
3483             return scaleFactor;
3484         }
3485
3486         /**
3487          * Sets the value of the scaleFactor property.
3488          *
3489          * @param value
3490          *     allowed object is
3491          *     {@link Float }
3492          *
3493          */
3494         public void setScaleFactor(Float value) {
3495             this.scaleFactor = value;
3496         }
3497
3498         /**
3499          * Gets the value of the showLabels property.
3500          *
3501          * @return
3502          *     possible object is
3503          *     {@link Boolean }
3504          *
3505          */
3506         public Boolean isShowLabels() {
3507             return showLabels;
3508         }
3509
3510         /**
3511          * Sets the value of the showLabels property.
3512          *
3513          * @param value
3514          *     allowed object is
3515          *     {@link Boolean }
3516          *
3517          */
3518         public void setShowLabels(Boolean value) {
3519             this.showLabels = value;
3520         }
3521
3522         /**
3523          * Gets the value of the linkToAllViews property.
3524          *
3525          * @return
3526          *     possible object is
3527          *     {@link Boolean }
3528          *
3529          */
3530         public Boolean isLinkToAllViews() {
3531             return linkToAllViews;
3532         }
3533
3534         /**
3535          * Sets the value of the linkToAllViews property.
3536          *
3537          * @param value
3538          *     allowed object is
3539          *     {@link Boolean }
3540          *
3541          */
3542         public void setLinkToAllViews(Boolean value) {
3543             this.linkToAllViews = value;
3544         }
3545
3546         /**
3547          * Gets the value of the width property.
3548          *
3549          * @return
3550          *     possible object is
3551          *     {@link Integer }
3552          *
3553          */
3554         public Integer getWidth() {
3555             return width;
3556         }
3557
3558         /**
3559          * Sets the value of the width property.
3560          *
3561          * @param value
3562          *     allowed object is
3563          *     {@link Integer }
3564          *
3565          */
3566         public void setWidth(Integer value) {
3567             this.width = value;
3568         }
3569
3570         /**
3571          * Gets the value of the height property.
3572          *
3573          * @return
3574          *     possible object is
3575          *     {@link Integer }
3576          *
3577          */
3578         public Integer getHeight() {
3579             return height;
3580         }
3581
3582         /**
3583          * Sets the value of the height property.
3584          *
3585          * @param value
3586          *     allowed object is
3587          *     {@link Integer }
3588          *
3589          */
3590         public void setHeight(Integer value) {
3591             this.height = value;
3592         }
3593
3594         /**
3595          * Gets the value of the xpos property.
3596          *
3597          * @return
3598          *     possible object is
3599          *     {@link Integer }
3600          *
3601          */
3602         public Integer getXpos() {
3603             return xpos;
3604         }
3605
3606         /**
3607          * Sets the value of the xpos property.
3608          *
3609          * @param value
3610          *     allowed object is
3611          *     {@link Integer }
3612          *
3613          */
3614         public void setXpos(Integer value) {
3615             this.xpos = value;
3616         }
3617
3618         /**
3619          * Gets the value of the ypos property.
3620          *
3621          * @return
3622          *     possible object is
3623          *     {@link Integer }
3624          *
3625          */
3626         public Integer getYpos() {
3627             return ypos;
3628         }
3629
3630         /**
3631          * Sets the value of the ypos property.
3632          *
3633          * @param value
3634          *     allowed object is
3635          *     {@link Integer }
3636          *
3637          */
3638         public void setYpos(Integer value) {
3639             this.ypos = value;
3640         }
3641
3642         /**
3643          * Gets the value of the includeGaps property.
3644          *
3645          * @return
3646          *     possible object is
3647          *     {@link Boolean }
3648          *
3649          */
3650         public Boolean isIncludeGaps() {
3651             return includeGaps;
3652         }
3653
3654         /**
3655          * Sets the value of the includeGaps property.
3656          *
3657          * @param value
3658          *     allowed object is
3659          *     {@link Boolean }
3660          *
3661          */
3662         public void setIncludeGaps(Boolean value) {
3663             this.includeGaps = value;
3664         }
3665
3666         /**
3667          * Gets the value of the matchGaps property.
3668          *
3669          * @return
3670          *     possible object is
3671          *     {@link Boolean }
3672          *
3673          */
3674         public Boolean isMatchGaps() {
3675             return matchGaps;
3676         }
3677
3678         /**
3679          * Sets the value of the matchGaps property.
3680          *
3681          * @param value
3682          *     allowed object is
3683          *     {@link Boolean }
3684          *
3685          */
3686         public void setMatchGaps(Boolean value) {
3687             this.matchGaps = value;
3688         }
3689
3690         /**
3691          * Gets the value of the includeGappedColumns property.
3692          *
3693          * @return
3694          *     possible object is
3695          *     {@link Boolean }
3696          *
3697          */
3698         public Boolean isIncludeGappedColumns() {
3699             return includeGappedColumns;
3700         }
3701
3702         /**
3703          * Sets the value of the includeGappedColumns property.
3704          *
3705          * @param value
3706          *     allowed object is
3707          *     {@link Boolean }
3708          *
3709          */
3710         public void setIncludeGappedColumns(Boolean value) {
3711             this.includeGappedColumns = value;
3712         }
3713
3714         /**
3715          * Gets the value of the denominateByShortestLength property.
3716          *
3717          * @return
3718          *     possible object is
3719          *     {@link Boolean }
3720          *
3721          */
3722         public Boolean isDenominateByShortestLength() {
3723             return denominateByShortestLength;
3724         }
3725
3726         /**
3727          * Sets the value of the denominateByShortestLength property.
3728          *
3729          * @param value
3730          *     allowed object is
3731          *     {@link Boolean }
3732          *
3733          */
3734         public void setDenominateByShortestLength(Boolean value) {
3735             this.denominateByShortestLength = value;
3736         }
3737
3738
3739         /**
3740          * <p>Java class for anonymous complex type.
3741          *
3742          * <p>The following schema fragment specifies the expected content contained within this class.
3743          *
3744          * <pre>
3745          * &lt;complexType>
3746          *   &lt;complexContent>
3747          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3748          *       &lt;attGroup ref="{www.jalview.org}position"/>
3749          *     &lt;/restriction>
3750          *   &lt;/complexContent>
3751          * &lt;/complexType>
3752          * </pre>
3753          *
3754          *
3755          */
3756         @XmlAccessorType(XmlAccessType.FIELD)
3757         @XmlType(name = "")
3758         public static class Axis {
3759
3760             @XmlAttribute(name = "xPos")
3761             protected Float xPos;
3762             @XmlAttribute(name = "yPos")
3763             protected Float yPos;
3764             @XmlAttribute(name = "zPos")
3765             protected Float zPos;
3766
3767             /**
3768              * Gets the value of the xPos property.
3769              *
3770              * @return
3771              *     possible object is
3772              *     {@link Float }
3773              *
3774              */
3775             public Float getXPos() {
3776                 return xPos;
3777             }
3778
3779             /**
3780              * Sets the value of the xPos property.
3781              *
3782              * @param value
3783              *     allowed object is
3784              *     {@link Float }
3785              *
3786              */
3787             public void setXPos(Float value) {
3788                 this.xPos = value;
3789             }
3790
3791             /**
3792              * Gets the value of the yPos property.
3793              *
3794              * @return
3795              *     possible object is
3796              *     {@link Float }
3797              *
3798              */
3799             public Float getYPos() {
3800                 return yPos;
3801             }
3802
3803             /**
3804              * Sets the value of the yPos property.
3805              *
3806              * @param value
3807              *     allowed object is
3808              *     {@link Float }
3809              *
3810              */
3811             public void setYPos(Float value) {
3812                 this.yPos = value;
3813             }
3814
3815             /**
3816              * Gets the value of the zPos property.
3817              *
3818              * @return
3819              *     possible object is
3820              *     {@link Float }
3821              *
3822              */
3823             public Float getZPos() {
3824                 return zPos;
3825             }
3826
3827             /**
3828              * Sets the value of the zPos property.
3829              *
3830              * @param value
3831              *     allowed object is
3832              *     {@link Float }
3833              *
3834              */
3835             public void setZPos(Float value) {
3836                 this.zPos = value;
3837             }
3838
3839         }
3840
3841
3842         /**
3843          * <p>Java class for anonymous complex type.
3844          *
3845          * <p>The following schema fragment specifies the expected content contained within this class.
3846          *
3847          * <pre>
3848          * &lt;complexType>
3849          *   &lt;complexContent>
3850          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3851          *       &lt;attGroup ref="{www.jalview.org}position"/>
3852          *     &lt;/restriction>
3853          *   &lt;/complexContent>
3854          * &lt;/complexType>
3855          * </pre>
3856          *
3857          *
3858          */
3859         @XmlAccessorType(XmlAccessType.FIELD)
3860         @XmlType(name = "")
3861         public static class SeqPointMax {
3862
3863             @XmlAttribute(name = "xPos")
3864             protected Float xPos;
3865             @XmlAttribute(name = "yPos")
3866             protected Float yPos;
3867             @XmlAttribute(name = "zPos")
3868             protected Float zPos;
3869
3870             /**
3871              * Gets the value of the xPos property.
3872              *
3873              * @return
3874              *     possible object is
3875              *     {@link Float }
3876              *
3877              */
3878             public Float getXPos() {
3879                 return xPos;
3880             }
3881
3882             /**
3883              * Sets the value of the xPos property.
3884              *
3885              * @param value
3886              *     allowed object is
3887              *     {@link Float }
3888              *
3889              */
3890             public void setXPos(Float value) {
3891                 this.xPos = value;
3892             }
3893
3894             /**
3895              * Gets the value of the yPos property.
3896              *
3897              * @return
3898              *     possible object is
3899              *     {@link Float }
3900              *
3901              */
3902             public Float getYPos() {
3903                 return yPos;
3904             }
3905
3906             /**
3907              * Sets the value of the yPos property.
3908              *
3909              * @param value
3910              *     allowed object is
3911              *     {@link Float }
3912              *
3913              */
3914             public void setYPos(Float value) {
3915                 this.yPos = value;
3916             }
3917
3918             /**
3919              * Gets the value of the zPos property.
3920              *
3921              * @return
3922              *     possible object is
3923              *     {@link Float }
3924              *
3925              */
3926             public Float getZPos() {
3927                 return zPos;
3928             }
3929
3930             /**
3931              * Sets the value of the zPos property.
3932              *
3933              * @param value
3934              *     allowed object is
3935              *     {@link Float }
3936              *
3937              */
3938             public void setZPos(Float value) {
3939                 this.zPos = value;
3940             }
3941
3942         }
3943
3944
3945         /**
3946          * <p>Java class for anonymous complex type.
3947          *
3948          * <p>The following schema fragment specifies the expected content contained within this class.
3949          *
3950          * <pre>
3951          * &lt;complexType>
3952          *   &lt;complexContent>
3953          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3954          *       &lt;attGroup ref="{www.jalview.org}position"/>
3955          *     &lt;/restriction>
3956          *   &lt;/complexContent>
3957          * &lt;/complexType>
3958          * </pre>
3959          *
3960          *
3961          */
3962         @XmlAccessorType(XmlAccessType.FIELD)
3963         @XmlType(name = "")
3964         public static class SeqPointMin {
3965
3966             @XmlAttribute(name = "xPos")
3967             protected Float xPos;
3968             @XmlAttribute(name = "yPos")
3969             protected Float yPos;
3970             @XmlAttribute(name = "zPos")
3971             protected Float zPos;
3972
3973             /**
3974              * Gets the value of the xPos property.
3975              *
3976              * @return
3977              *     possible object is
3978              *     {@link Float }
3979              *
3980              */
3981             public Float getXPos() {
3982                 return xPos;
3983             }
3984
3985             /**
3986              * Sets the value of the xPos property.
3987              *
3988              * @param value
3989              *     allowed object is
3990              *     {@link Float }
3991              *
3992              */
3993             public void setXPos(Float value) {
3994                 this.xPos = value;
3995             }
3996
3997             /**
3998              * Gets the value of the yPos property.
3999              *
4000              * @return
4001              *     possible object is
4002              *     {@link Float }
4003              *
4004              */
4005             public Float getYPos() {
4006                 return yPos;
4007             }
4008
4009             /**
4010              * Sets the value of the yPos property.
4011              *
4012              * @param value
4013              *     allowed object is
4014              *     {@link Float }
4015              *
4016              */
4017             public void setYPos(Float value) {
4018                 this.yPos = value;
4019             }
4020
4021             /**
4022              * Gets the value of the zPos property.
4023              *
4024              * @return
4025              *     possible object is
4026              *     {@link Float }
4027              *
4028              */
4029             public Float getZPos() {
4030                 return zPos;
4031             }
4032
4033             /**
4034              * Sets the value of the zPos property.
4035              *
4036              * @param value
4037              *     allowed object is
4038              *     {@link Float }
4039              *
4040              */
4041             public void setZPos(Float value) {
4042                 this.zPos = value;
4043             }
4044
4045         }
4046
4047
4048         /**
4049          * <p>Java class for anonymous complex type.
4050          *
4051          * <p>The following schema fragment specifies the expected content contained within this class.
4052          *
4053          * <pre>
4054          * &lt;complexType>
4055          *   &lt;complexContent>
4056          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4057          *       &lt;attGroup ref="{www.jalview.org}position"/>
4058          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4059          *     &lt;/restriction>
4060          *   &lt;/complexContent>
4061          * &lt;/complexType>
4062          * </pre>
4063          *
4064          *
4065          */
4066         @XmlAccessorType(XmlAccessType.FIELD)
4067         @XmlType(name = "")
4068         public static class SequencePoint {
4069
4070             @XmlAttribute(name = "sequenceRef")
4071             protected String sequenceRef;
4072             @XmlAttribute(name = "xPos")
4073             protected Float xPos;
4074             @XmlAttribute(name = "yPos")
4075             protected Float yPos;
4076             @XmlAttribute(name = "zPos")
4077             protected Float zPos;
4078
4079             /**
4080              * Gets the value of the sequenceRef property.
4081              *
4082              * @return
4083              *     possible object is
4084              *     {@link String }
4085              *
4086              */
4087             public String getSequenceRef() {
4088                 return sequenceRef;
4089             }
4090
4091             /**
4092              * Sets the value of the sequenceRef property.
4093              *
4094              * @param value
4095              *     allowed object is
4096              *     {@link String }
4097              *
4098              */
4099             public void setSequenceRef(String value) {
4100                 this.sequenceRef = value;
4101             }
4102
4103             /**
4104              * Gets the value of the xPos property.
4105              *
4106              * @return
4107              *     possible object is
4108              *     {@link Float }
4109              *
4110              */
4111             public Float getXPos() {
4112                 return xPos;
4113             }
4114
4115             /**
4116              * Sets the value of the xPos property.
4117              *
4118              * @param value
4119              *     allowed object is
4120              *     {@link Float }
4121              *
4122              */
4123             public void setXPos(Float value) {
4124                 this.xPos = value;
4125             }
4126
4127             /**
4128              * Gets the value of the yPos property.
4129              *
4130              * @return
4131              *     possible object is
4132              *     {@link Float }
4133              *
4134              */
4135             public Float getYPos() {
4136                 return yPos;
4137             }
4138
4139             /**
4140              * Sets the value of the yPos property.
4141              *
4142              * @param value
4143              *     allowed object is
4144              *     {@link Float }
4145              *
4146              */
4147             public void setYPos(Float value) {
4148                 this.yPos = value;
4149             }
4150
4151             /**
4152              * Gets the value of the zPos property.
4153              *
4154              * @return
4155              *     possible object is
4156              *     {@link Float }
4157              *
4158              */
4159             public Float getZPos() {
4160                 return zPos;
4161             }
4162
4163             /**
4164              * Sets the value of the zPos property.
4165              *
4166              * @param value
4167              *     allowed object is
4168              *     {@link Float }
4169              *
4170              */
4171             public void setZPos(Float value) {
4172                 this.zPos = value;
4173             }
4174
4175         }
4176
4177     }
4178
4179
4180     /**
4181      * <p>Java class for anonymous complex type.
4182      *
4183      * <p>The following schema fragment specifies the expected content contained within this class.
4184      *
4185      * <pre>
4186      * &lt;complexType>
4187      *   &lt;complexContent>
4188      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4189      *       &lt;sequence minOccurs="0">
4190      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4191      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4192      *       &lt;/sequence>
4193      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4194      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4195      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4196      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4197      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4198      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4199      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4200      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4201      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4202      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4203      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4204      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4205      *     &lt;/restriction>
4206      *   &lt;/complexContent>
4207      * &lt;/complexType>
4208      * </pre>
4209      *
4210      *
4211      */
4212     @XmlAccessorType(XmlAccessType.FIELD)
4213     @XmlType(name = "", propOrder = {
4214         "title",
4215         "newick"
4216     })
4217     public static class Tree {
4218
4219         @XmlElement(namespace = "www.jalview.org")
4220         protected String title;
4221         @XmlElement(namespace = "www.jalview.org")
4222         protected String newick;
4223         @XmlAttribute(name = "fontName")
4224         protected String fontName;
4225         @XmlAttribute(name = "fontSize")
4226         protected Integer fontSize;
4227         @XmlAttribute(name = "fontStyle")
4228         protected Integer fontStyle;
4229         @XmlAttribute(name = "threshold")
4230         protected Float threshold;
4231         @XmlAttribute(name = "showBootstrap")
4232         protected Boolean showBootstrap;
4233         @XmlAttribute(name = "showDistances")
4234         protected Boolean showDistances;
4235         @XmlAttribute(name = "markUnlinked")
4236         protected Boolean markUnlinked;
4237         @XmlAttribute(name = "fitToWindow")
4238         protected Boolean fitToWindow;
4239         @XmlAttribute(name = "currentTree")
4240         protected Boolean currentTree;
4241         @XmlAttribute(name = "id")
4242         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4243         @XmlID
4244         @XmlSchemaType(name = "ID")
4245         protected String id;
4246         @XmlAttribute(name = "linkToAllViews")
4247         protected Boolean linkToAllViews;
4248         @XmlAttribute(name = "width")
4249         protected Integer width;
4250         @XmlAttribute(name = "height")
4251         protected Integer height;
4252         @XmlAttribute(name = "xpos")
4253         protected Integer xpos;
4254         @XmlAttribute(name = "ypos")
4255         protected Integer ypos;
4256
4257         /**
4258          * Gets the value of the title property.
4259          *
4260          * @return
4261          *     possible object is
4262          *     {@link String }
4263          *
4264          */
4265         public String getTitle() {
4266             return title;
4267         }
4268
4269         /**
4270          * Sets the value of the title property.
4271          *
4272          * @param value
4273          *     allowed object is
4274          *     {@link String }
4275          *
4276          */
4277         public void setTitle(String value) {
4278             this.title = value;
4279         }
4280
4281         /**
4282          * Gets the value of the newick property.
4283          *
4284          * @return
4285          *     possible object is
4286          *     {@link String }
4287          *
4288          */
4289         public String getNewick() {
4290             return newick;
4291         }
4292
4293         /**
4294          * Sets the value of the newick property.
4295          *
4296          * @param value
4297          *     allowed object is
4298          *     {@link String }
4299          *
4300          */
4301         public void setNewick(String value) {
4302             this.newick = value;
4303         }
4304
4305         /**
4306          * Gets the value of the fontName property.
4307          *
4308          * @return
4309          *     possible object is
4310          *     {@link String }
4311          *
4312          */
4313         public String getFontName() {
4314             return fontName;
4315         }
4316
4317         /**
4318          * Sets the value of the fontName property.
4319          *
4320          * @param value
4321          *     allowed object is
4322          *     {@link String }
4323          *
4324          */
4325         public void setFontName(String value) {
4326             this.fontName = value;
4327         }
4328
4329         /**
4330          * Gets the value of the fontSize property.
4331          *
4332          * @return
4333          *     possible object is
4334          *     {@link Integer }
4335          *
4336          */
4337         public Integer getFontSize() {
4338             return fontSize;
4339         }
4340
4341         /**
4342          * Sets the value of the fontSize property.
4343          *
4344          * @param value
4345          *     allowed object is
4346          *     {@link Integer }
4347          *
4348          */
4349         public void setFontSize(Integer value) {
4350             this.fontSize = value;
4351         }
4352
4353         /**
4354          * Gets the value of the fontStyle property.
4355          *
4356          * @return
4357          *     possible object is
4358          *     {@link Integer }
4359          *
4360          */
4361         public Integer getFontStyle() {
4362             return fontStyle;
4363         }
4364
4365         /**
4366          * Sets the value of the fontStyle property.
4367          *
4368          * @param value
4369          *     allowed object is
4370          *     {@link Integer }
4371          *
4372          */
4373         public void setFontStyle(Integer value) {
4374             this.fontStyle = value;
4375         }
4376
4377         /**
4378          * Gets the value of the threshold property.
4379          *
4380          * @return
4381          *     possible object is
4382          *     {@link Float }
4383          *
4384          */
4385         public Float getThreshold() {
4386             return threshold;
4387         }
4388
4389         /**
4390          * Sets the value of the threshold property.
4391          *
4392          * @param value
4393          *     allowed object is
4394          *     {@link Float }
4395          *
4396          */
4397         public void setThreshold(Float value) {
4398             this.threshold = value;
4399         }
4400
4401         /**
4402          * Gets the value of the showBootstrap property.
4403          *
4404          * @return
4405          *     possible object is
4406          *     {@link Boolean }
4407          *
4408          */
4409         public Boolean isShowBootstrap() {
4410             return showBootstrap;
4411         }
4412
4413         /**
4414          * Sets the value of the showBootstrap property.
4415          *
4416          * @param value
4417          *     allowed object is
4418          *     {@link Boolean }
4419          *
4420          */
4421         public void setShowBootstrap(Boolean value) {
4422             this.showBootstrap = value;
4423         }
4424
4425         /**
4426          * Gets the value of the showDistances property.
4427          *
4428          * @return
4429          *     possible object is
4430          *     {@link Boolean }
4431          *
4432          */
4433         public Boolean isShowDistances() {
4434             return showDistances;
4435         }
4436
4437         /**
4438          * Sets the value of the showDistances property.
4439          *
4440          * @param value
4441          *     allowed object is
4442          *     {@link Boolean }
4443          *
4444          */
4445         public void setShowDistances(Boolean value) {
4446             this.showDistances = value;
4447         }
4448
4449         /**
4450          * Gets the value of the markUnlinked property.
4451          *
4452          * @return
4453          *     possible object is
4454          *     {@link Boolean }
4455          *
4456          */
4457         public Boolean isMarkUnlinked() {
4458             return markUnlinked;
4459         }
4460
4461         /**
4462          * Sets the value of the markUnlinked property.
4463          *
4464          * @param value
4465          *     allowed object is
4466          *     {@link Boolean }
4467          *
4468          */
4469         public void setMarkUnlinked(Boolean value) {
4470             this.markUnlinked = value;
4471         }
4472
4473         /**
4474          * Gets the value of the fitToWindow property.
4475          *
4476          * @return
4477          *     possible object is
4478          *     {@link Boolean }
4479          *
4480          */
4481         public Boolean isFitToWindow() {
4482             return fitToWindow;
4483         }
4484
4485         /**
4486          * Sets the value of the fitToWindow property.
4487          *
4488          * @param value
4489          *     allowed object is
4490          *     {@link Boolean }
4491          *
4492          */
4493         public void setFitToWindow(Boolean value) {
4494             this.fitToWindow = value;
4495         }
4496
4497         /**
4498          * Gets the value of the currentTree property.
4499          *
4500          * @return
4501          *     possible object is
4502          *     {@link Boolean }
4503          *
4504          */
4505         public Boolean isCurrentTree() {
4506             return currentTree;
4507         }
4508
4509         /**
4510          * Sets the value of the currentTree property.
4511          *
4512          * @param value
4513          *     allowed object is
4514          *     {@link Boolean }
4515          *
4516          */
4517         public void setCurrentTree(Boolean value) {
4518             this.currentTree = value;
4519         }
4520
4521         /**
4522          * Gets the value of the id property.
4523          *
4524          * @return
4525          *     possible object is
4526          *     {@link String }
4527          *
4528          */
4529         public String getId() {
4530             return id;
4531         }
4532
4533         /**
4534          * Sets the value of the id property.
4535          *
4536          * @param value
4537          *     allowed object is
4538          *     {@link String }
4539          *
4540          */
4541         public void setId(String value) {
4542             this.id = value;
4543         }
4544
4545         /**
4546          * Gets the value of the linkToAllViews property.
4547          *
4548          * @return
4549          *     possible object is
4550          *     {@link Boolean }
4551          *
4552          */
4553         public boolean isLinkToAllViews() {
4554             if (linkToAllViews == null) {
4555                 return false;
4556             } else {
4557                 return linkToAllViews;
4558             }
4559         }
4560
4561         /**
4562          * Sets the value of the linkToAllViews property.
4563          *
4564          * @param value
4565          *     allowed object is
4566          *     {@link Boolean }
4567          *
4568          */
4569         public void setLinkToAllViews(Boolean value) {
4570             this.linkToAllViews = value;
4571         }
4572
4573         /**
4574          * Gets the value of the width property.
4575          *
4576          * @return
4577          *     possible object is
4578          *     {@link Integer }
4579          *
4580          */
4581         public Integer getWidth() {
4582             return width;
4583         }
4584
4585         /**
4586          * Sets the value of the width property.
4587          *
4588          * @param value
4589          *     allowed object is
4590          *     {@link Integer }
4591          *
4592          */
4593         public void setWidth(Integer value) {
4594             this.width = value;
4595         }
4596
4597         /**
4598          * Gets the value of the height property.
4599          *
4600          * @return
4601          *     possible object is
4602          *     {@link Integer }
4603          *
4604          */
4605         public Integer getHeight() {
4606             return height;
4607         }
4608
4609         /**
4610          * Sets the value of the height property.
4611          *
4612          * @param value
4613          *     allowed object is
4614          *     {@link Integer }
4615          *
4616          */
4617         public void setHeight(Integer value) {
4618             this.height = value;
4619         }
4620
4621         /**
4622          * Gets the value of the xpos property.
4623          *
4624          * @return
4625          *     possible object is
4626          *     {@link Integer }
4627          *
4628          */
4629         public Integer getXpos() {
4630             return xpos;
4631         }
4632
4633         /**
4634          * Sets the value of the xpos property.
4635          *
4636          * @param value
4637          *     allowed object is
4638          *     {@link Integer }
4639          *
4640          */
4641         public void setXpos(Integer value) {
4642             this.xpos = value;
4643         }
4644
4645         /**
4646          * Gets the value of the ypos property.
4647          *
4648          * @return
4649          *     possible object is
4650          *     {@link Integer }
4651          *
4652          */
4653         public Integer getYpos() {
4654             return ypos;
4655         }
4656
4657         /**
4658          * Sets the value of the ypos property.
4659          *
4660          * @param value
4661          *     allowed object is
4662          *     {@link Integer }
4663          *
4664          */
4665         public void setYpos(Integer value) {
4666             this.ypos = value;
4667         }
4668
4669     }
4670
4671
4672     /**
4673      * <p>Java class for anonymous complex type.
4674      *
4675      * <p>The following schema fragment specifies the expected content contained within this class.
4676      *
4677      * <pre>
4678      * &lt;complexType>
4679      *   &lt;complexContent>
4680      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4681      *       &lt;sequence>
4682      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4683      *       &lt;/sequence>
4684      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4685      *     &lt;/restriction>
4686      *   &lt;/complexContent>
4687      * &lt;/complexType>
4688      * </pre>
4689      *
4690      *
4691      */
4692     @XmlAccessorType(XmlAccessType.FIELD)
4693     @XmlType(name = "", propOrder = {
4694         "userColourScheme"
4695     })
4696     public static class UserColours {
4697
4698         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4699         protected JalviewUserColours userColourScheme;
4700         @XmlAttribute(name = "id")
4701         protected String id;
4702
4703         /**
4704          * Gets the value of the userColourScheme property.
4705          *
4706          * @return
4707          *     possible object is
4708          *     {@link JalviewUserColours }
4709          *
4710          */
4711         public JalviewUserColours getUserColourScheme() {
4712             return userColourScheme;
4713         }
4714
4715         /**
4716          * Sets the value of the userColourScheme property.
4717          *
4718          * @param value
4719          *     allowed object is
4720          *     {@link JalviewUserColours }
4721          *
4722          */
4723         public void setUserColourScheme(JalviewUserColours value) {
4724             this.userColourScheme = value;
4725         }
4726
4727         /**
4728          * Gets the value of the id property.
4729          *
4730          * @return
4731          *     possible object is
4732          *     {@link String }
4733          *
4734          */
4735         public String getId() {
4736             return id;
4737         }
4738
4739         /**
4740          * Sets the value of the id property.
4741          *
4742          * @param value
4743          *     allowed object is
4744          *     {@link String }
4745          *
4746          */
4747         public void setId(String value) {
4748             this.id = value;
4749         }
4750
4751     }
4752
4753
4754     /**
4755      * <p>Java class for anonymous complex type.
4756      *
4757      * <p>The following schema fragment specifies the expected content contained within this class.
4758      *
4759      * <pre>
4760      * &lt;complexType>
4761      *   &lt;complexContent>
4762      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4763      *       &lt;sequence>
4764      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4765      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4766      *           &lt;complexType>
4767      *             &lt;complexContent>
4768      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4769      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4770      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4771      *               &lt;/restriction>
4772      *             &lt;/complexContent>
4773      *           &lt;/complexType>
4774      *         &lt;/element>
4775      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4776      *           &lt;complexType>
4777      *             &lt;complexContent>
4778      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4779      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4780      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4781      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4782      *               &lt;/extension>
4783      *             &lt;/complexContent>
4784      *           &lt;/complexType>
4785      *         &lt;/element>
4786      *         &lt;element name="overview" minOccurs="0">
4787      *           &lt;complexType>
4788      *             &lt;complexContent>
4789      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4790      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4791      *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4792      *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4793      *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4794      *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4795      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4796      *               &lt;/restriction>
4797      *             &lt;/complexContent>
4798      *           &lt;/complexType>
4799      *         &lt;/element>
4800      *       &lt;/sequence>
4801      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4802      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4803      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4804      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4805      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4806      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4807      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4808      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4813      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4817      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4818      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4819      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4820      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4821      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4822      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4825      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4826      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4827      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4828      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4829      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4830      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4831      *       &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
4832      *       &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
4833      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4834      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4835      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4836      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4837      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4838      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4839      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4840      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4841      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4842      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4843      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4844      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4845      *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4846      *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4847      *     &lt;/restriction>
4848      *   &lt;/complexContent>
4849      * &lt;/complexType>
4850      * </pre>
4851      *
4852      *
4853      */
4854     @XmlAccessorType(XmlAccessType.FIELD)
4855     @XmlType(name = "", propOrder = {
4856         "annotationColours",
4857         "hiddenColumns",
4858         "calcIdParam",
4859         "overview"
4860     })
4861     public static class Viewport {
4862
4863         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4864         protected AnnotationColourScheme annotationColours;
4865         @XmlElement(namespace = "www.jalview.org")
4866         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4867         @XmlElement(namespace = "www.jalview.org")
4868         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4869         @XmlElement(namespace = "www.jalview.org")
4870         protected JalviewModel.Viewport.Overview overview;
4871         @XmlAttribute(name = "conservationSelected")
4872         protected Boolean conservationSelected;
4873         @XmlAttribute(name = "pidSelected")
4874         protected Boolean pidSelected;
4875         @XmlAttribute(name = "bgColour")
4876         protected String bgColour;
4877         @XmlAttribute(name = "consThreshold")
4878         protected Integer consThreshold;
4879         @XmlAttribute(name = "pidThreshold")
4880         protected Integer pidThreshold;
4881         @XmlAttribute(name = "title")
4882         protected String title;
4883         @XmlAttribute(name = "showFullId")
4884         protected Boolean showFullId;
4885         @XmlAttribute(name = "rightAlignIds")
4886         protected Boolean rightAlignIds;
4887         @XmlAttribute(name = "showText")
4888         protected Boolean showText;
4889         @XmlAttribute(name = "showColourText")
4890         protected Boolean showColourText;
4891         @XmlAttribute(name = "showUnconserved")
4892         protected Boolean showUnconserved;
4893         @XmlAttribute(name = "showBoxes")
4894         protected Boolean showBoxes;
4895         @XmlAttribute(name = "wrapAlignment")
4896         protected Boolean wrapAlignment;
4897         @XmlAttribute(name = "renderGaps")
4898         protected Boolean renderGaps;
4899         @XmlAttribute(name = "showSequenceFeatures")
4900         protected Boolean showSequenceFeatures;
4901         @XmlAttribute(name = "showNPfeatureTooltip")
4902         protected Boolean showNPfeatureTooltip;
4903         @XmlAttribute(name = "showDbRefTooltip")
4904         protected Boolean showDbRefTooltip;
4905         @XmlAttribute(name = "followHighlight")
4906         protected Boolean followHighlight;
4907         @XmlAttribute(name = "followSelection")
4908         protected Boolean followSelection;
4909         @XmlAttribute(name = "showAnnotation")
4910         protected Boolean showAnnotation;
4911         @XmlAttribute(name = "centreColumnLabels")
4912         protected Boolean centreColumnLabels;
4913         @XmlAttribute(name = "showGroupConservation")
4914         protected Boolean showGroupConservation;
4915         @XmlAttribute(name = "showGroupConsensus")
4916         protected Boolean showGroupConsensus;
4917         @XmlAttribute(name = "showConsensusHistogram")
4918         protected Boolean showConsensusHistogram;
4919         @XmlAttribute(name = "showSequenceLogo")
4920         protected Boolean showSequenceLogo;
4921         @XmlAttribute(name = "normaliseSequenceLogo")
4922         protected Boolean normaliseSequenceLogo;
4923         @XmlAttribute(name = "ignoreGapsinConsensus")
4924         protected Boolean ignoreGapsinConsensus;
4925         @XmlAttribute(name = "startRes")
4926         protected Integer startRes;
4927         @XmlAttribute(name = "startSeq")
4928         protected Integer startSeq;
4929         @XmlAttribute(name = "charWidth")
4930         protected Integer charWidth;
4931         @XmlAttribute(name = "charHeight")
4932         protected Integer charHeight;
4933         @XmlAttribute(name = "fontName")
4934         protected String fontName;
4935         @XmlAttribute(name = "fontSize")
4936         protected Integer fontSize;
4937         @XmlAttribute(name = "fontStyle")
4938         protected Integer fontStyle;
4939         @XmlAttribute(name = "scaleProteinAsCdna")
4940         protected Boolean scaleProteinAsCdna;
4941         @XmlAttribute(name = "viewName")
4942         protected String viewName;
4943         @XmlAttribute(name = "sequenceSetId")
4944         protected String sequenceSetId;
4945         @XmlAttribute(name = "gatheredViews")
4946         protected Boolean gatheredViews;
4947         @XmlAttribute(name = "textCol1")
4948         protected Integer textCol1;
4949         @XmlAttribute(name = "textCol2")
4950         protected Integer textCol2;
4951         @XmlAttribute(name = "textColThreshold")
4952         protected Integer textColThreshold;
4953         @XmlAttribute(name = "id")
4954         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4955         @XmlID
4956         @XmlSchemaType(name = "ID")
4957         protected String id;
4958         @XmlAttribute(name = "complementId")
4959         protected String complementId;
4960         @XmlAttribute(name = "showComplementFeatures")
4961         protected Boolean showComplementFeatures;
4962         @XmlAttribute(name = "showComplementFeaturesOnTop")
4963         protected Boolean showComplementFeaturesOnTop;
4964         @XmlAttribute(name = "width")
4965         protected Integer width;
4966         @XmlAttribute(name = "height")
4967         protected Integer height;
4968         @XmlAttribute(name = "xpos")
4969         protected Integer xpos;
4970         @XmlAttribute(name = "ypos")
4971         protected Integer ypos;
4972
4973         /**
4974          * Gets the value of the annotationColours property.
4975          *
4976          * @return
4977          *     possible object is
4978          *     {@link AnnotationColourScheme }
4979          *
4980          */
4981         public AnnotationColourScheme getAnnotationColours() {
4982             return annotationColours;
4983         }
4984
4985         /**
4986          * Sets the value of the annotationColours property.
4987          *
4988          * @param value
4989          *     allowed object is
4990          *     {@link AnnotationColourScheme }
4991          *
4992          */
4993         public void setAnnotationColours(AnnotationColourScheme value) {
4994             this.annotationColours = value;
4995         }
4996
4997         /**
4998          * Gets the value of the hiddenColumns property.
4999          *
5000          * <p>
5001          * This accessor method returns a reference to the live list,
5002          * not a snapshot. Therefore any modification you make to the
5003          * returned list will be present inside the JAXB object.
5004          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
5005          *
5006          * <p>
5007          * For example, to add a new item, do as follows:
5008          * <pre>
5009          *    getHiddenColumns().add(newItem);
5010          * </pre>
5011          *
5012          *
5013          * <p>
5014          * Objects of the following type(s) are allowed in the list
5015          * {@link JalviewModel.Viewport.HiddenColumns }
5016          *
5017          *
5018          */
5019         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5020             if (hiddenColumns == null) {
5021                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5022             }
5023             return this.hiddenColumns;
5024         }
5025
5026         /**
5027          * Gets the value of the calcIdParam property.
5028          *
5029          * <p>
5030          * This accessor method returns a reference to the live list,
5031          * not a snapshot. Therefore any modification you make to the
5032          * returned list will be present inside the JAXB object.
5033          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5034          *
5035          * <p>
5036          * For example, to add a new item, do as follows:
5037          * <pre>
5038          *    getCalcIdParam().add(newItem);
5039          * </pre>
5040          *
5041          *
5042          * <p>
5043          * Objects of the following type(s) are allowed in the list
5044          * {@link JalviewModel.Viewport.CalcIdParam }
5045          *
5046          *
5047          */
5048         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5049             if (calcIdParam == null) {
5050                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5051             }
5052             return this.calcIdParam;
5053         }
5054
5055         /**
5056          * Gets the value of the overview property.
5057          *
5058          * @return
5059          *     possible object is
5060          *     {@link JalviewModel.Viewport.Overview }
5061          *
5062          */
5063         public JalviewModel.Viewport.Overview getOverview() {
5064             return overview;
5065         }
5066
5067         /**
5068          * Sets the value of the overview property.
5069          *
5070          * @param value
5071          *     allowed object is
5072          *     {@link JalviewModel.Viewport.Overview }
5073          *
5074          */
5075         public void setOverview(JalviewModel.Viewport.Overview value) {
5076             this.overview = value;
5077         }
5078
5079         /**
5080          * Gets the value of the conservationSelected property.
5081          *
5082          * @return
5083          *     possible object is
5084          *     {@link Boolean }
5085          *
5086          */
5087         public Boolean isConservationSelected() {
5088             return conservationSelected;
5089         }
5090
5091         /**
5092          * Sets the value of the conservationSelected property.
5093          *
5094          * @param value
5095          *     allowed object is
5096          *     {@link Boolean }
5097          *
5098          */
5099         public void setConservationSelected(Boolean value) {
5100             this.conservationSelected = value;
5101         }
5102
5103         /**
5104          * Gets the value of the pidSelected property.
5105          *
5106          * @return
5107          *     possible object is
5108          *     {@link Boolean }
5109          *
5110          */
5111         public Boolean isPidSelected() {
5112             return pidSelected;
5113         }
5114
5115         /**
5116          * Sets the value of the pidSelected property.
5117          *
5118          * @param value
5119          *     allowed object is
5120          *     {@link Boolean }
5121          *
5122          */
5123         public void setPidSelected(Boolean value) {
5124             this.pidSelected = value;
5125         }
5126
5127         /**
5128          * Gets the value of the bgColour property.
5129          *
5130          * @return
5131          *     possible object is
5132          *     {@link String }
5133          *
5134          */
5135         public String getBgColour() {
5136             return bgColour;
5137         }
5138
5139         /**
5140          * Sets the value of the bgColour property.
5141          *
5142          * @param value
5143          *     allowed object is
5144          *     {@link String }
5145          *
5146          */
5147         public void setBgColour(String value) {
5148             this.bgColour = value;
5149         }
5150
5151         /**
5152          * Gets the value of the consThreshold property.
5153          *
5154          * @return
5155          *     possible object is
5156          *     {@link Integer }
5157          *
5158          */
5159         public Integer getConsThreshold() {
5160             return consThreshold;
5161         }
5162
5163         /**
5164          * Sets the value of the consThreshold property.
5165          *
5166          * @param value
5167          *     allowed object is
5168          *     {@link Integer }
5169          *
5170          */
5171         public void setConsThreshold(Integer value) {
5172             this.consThreshold = value;
5173         }
5174
5175         /**
5176          * Gets the value of the pidThreshold property.
5177          *
5178          * @return
5179          *     possible object is
5180          *     {@link Integer }
5181          *
5182          */
5183         public Integer getPidThreshold() {
5184             return pidThreshold;
5185         }
5186
5187         /**
5188          * Sets the value of the pidThreshold property.
5189          *
5190          * @param value
5191          *     allowed object is
5192          *     {@link Integer }
5193          *
5194          */
5195         public void setPidThreshold(Integer value) {
5196             this.pidThreshold = value;
5197         }
5198
5199         /**
5200          * Gets the value of the title property.
5201          *
5202          * @return
5203          *     possible object is
5204          *     {@link String }
5205          *
5206          */
5207         public String getTitle() {
5208             return title;
5209         }
5210
5211         /**
5212          * Sets the value of the title property.
5213          *
5214          * @param value
5215          *     allowed object is
5216          *     {@link String }
5217          *
5218          */
5219         public void setTitle(String value) {
5220             this.title = value;
5221         }
5222
5223         /**
5224          * Gets the value of the showFullId property.
5225          *
5226          * @return
5227          *     possible object is
5228          *     {@link Boolean }
5229          *
5230          */
5231         public Boolean isShowFullId() {
5232             return showFullId;
5233         }
5234
5235         /**
5236          * Sets the value of the showFullId property.
5237          *
5238          * @param value
5239          *     allowed object is
5240          *     {@link Boolean }
5241          *
5242          */
5243         public void setShowFullId(Boolean value) {
5244             this.showFullId = value;
5245         }
5246
5247         /**
5248          * Gets the value of the rightAlignIds property.
5249          *
5250          * @return
5251          *     possible object is
5252          *     {@link Boolean }
5253          *
5254          */
5255         public Boolean isRightAlignIds() {
5256             return rightAlignIds;
5257         }
5258
5259         /**
5260          * Sets the value of the rightAlignIds property.
5261          *
5262          * @param value
5263          *     allowed object is
5264          *     {@link Boolean }
5265          *
5266          */
5267         public void setRightAlignIds(Boolean value) {
5268             this.rightAlignIds = value;
5269         }
5270
5271         /**
5272          * Gets the value of the showText property.
5273          *
5274          * @return
5275          *     possible object is
5276          *     {@link Boolean }
5277          *
5278          */
5279         public Boolean isShowText() {
5280             return showText;
5281         }
5282
5283         /**
5284          * Sets the value of the showText property.
5285          *
5286          * @param value
5287          *     allowed object is
5288          *     {@link Boolean }
5289          *
5290          */
5291         public void setShowText(Boolean value) {
5292             this.showText = value;
5293         }
5294
5295         /**
5296          * Gets the value of the showColourText property.
5297          *
5298          * @return
5299          *     possible object is
5300          *     {@link Boolean }
5301          *
5302          */
5303         public Boolean isShowColourText() {
5304             return showColourText;
5305         }
5306
5307         /**
5308          * Sets the value of the showColourText property.
5309          *
5310          * @param value
5311          *     allowed object is
5312          *     {@link Boolean }
5313          *
5314          */
5315         public void setShowColourText(Boolean value) {
5316             this.showColourText = value;
5317         }
5318
5319         /**
5320          * Gets the value of the showUnconserved property.
5321          *
5322          * @return
5323          *     possible object is
5324          *     {@link Boolean }
5325          *
5326          */
5327         public boolean isShowUnconserved() {
5328             if (showUnconserved == null) {
5329                 return false;
5330             } else {
5331                 return showUnconserved;
5332             }
5333         }
5334
5335         /**
5336          * Sets the value of the showUnconserved property.
5337          *
5338          * @param value
5339          *     allowed object is
5340          *     {@link Boolean }
5341          *
5342          */
5343         public void setShowUnconserved(Boolean value) {
5344             this.showUnconserved = value;
5345         }
5346
5347         /**
5348          * Gets the value of the showBoxes property.
5349          *
5350          * @return
5351          *     possible object is
5352          *     {@link Boolean }
5353          *
5354          */
5355         public Boolean isShowBoxes() {
5356             return showBoxes;
5357         }
5358
5359         /**
5360          * Sets the value of the showBoxes property.
5361          *
5362          * @param value
5363          *     allowed object is
5364          *     {@link Boolean }
5365          *
5366          */
5367         public void setShowBoxes(Boolean value) {
5368             this.showBoxes = value;
5369         }
5370
5371         /**
5372          * Gets the value of the wrapAlignment property.
5373          *
5374          * @return
5375          *     possible object is
5376          *     {@link Boolean }
5377          *
5378          */
5379         public Boolean isWrapAlignment() {
5380             return wrapAlignment;
5381         }
5382
5383         /**
5384          * Sets the value of the wrapAlignment property.
5385          *
5386          * @param value
5387          *     allowed object is
5388          *     {@link Boolean }
5389          *
5390          */
5391         public void setWrapAlignment(Boolean value) {
5392             this.wrapAlignment = value;
5393         }
5394
5395         /**
5396          * Gets the value of the renderGaps property.
5397          *
5398          * @return
5399          *     possible object is
5400          *     {@link Boolean }
5401          *
5402          */
5403         public Boolean isRenderGaps() {
5404             return renderGaps;
5405         }
5406
5407         /**
5408          * Sets the value of the renderGaps property.
5409          *
5410          * @param value
5411          *     allowed object is
5412          *     {@link Boolean }
5413          *
5414          */
5415         public void setRenderGaps(Boolean value) {
5416             this.renderGaps = value;
5417         }
5418
5419         /**
5420          * Gets the value of the showSequenceFeatures property.
5421          *
5422          * @return
5423          *     possible object is
5424          *     {@link Boolean }
5425          *
5426          */
5427         public Boolean isShowSequenceFeatures() {
5428             return showSequenceFeatures;
5429         }
5430
5431         /**
5432          * Sets the value of the showSequenceFeatures property.
5433          *
5434          * @param value
5435          *     allowed object is
5436          *     {@link Boolean }
5437          *
5438          */
5439         public void setShowSequenceFeatures(Boolean value) {
5440             this.showSequenceFeatures = value;
5441         }
5442
5443         /**
5444          * Gets the value of the showNPfeatureTooltip property.
5445          *
5446          * @return
5447          *     possible object is
5448          *     {@link Boolean }
5449          *
5450          */
5451         public Boolean isShowNPfeatureTooltip() {
5452             return showNPfeatureTooltip;
5453         }
5454
5455         /**
5456          * Sets the value of the showNPfeatureTooltip property.
5457          *
5458          * @param value
5459          *     allowed object is
5460          *     {@link Boolean }
5461          *
5462          */
5463         public void setShowNPfeatureTooltip(Boolean value) {
5464             this.showNPfeatureTooltip = value;
5465         }
5466
5467         /**
5468          * Gets the value of the showDbRefTooltip property.
5469          *
5470          * @return
5471          *     possible object is
5472          *     {@link Boolean }
5473          *
5474          */
5475         public Boolean isShowDbRefTooltip() {
5476             return showDbRefTooltip;
5477         }
5478
5479         /**
5480          * Sets the value of the showDbRefTooltip property.
5481          *
5482          * @param value
5483          *     allowed object is
5484          *     {@link Boolean }
5485          *
5486          */
5487         public void setShowDbRefTooltip(Boolean value) {
5488             this.showDbRefTooltip = value;
5489         }
5490
5491         /**
5492          * Gets the value of the followHighlight property.
5493          *
5494          * @return
5495          *     possible object is
5496          *     {@link Boolean }
5497          *
5498          */
5499         public boolean isFollowHighlight() {
5500             if (followHighlight == null) {
5501                 return true;
5502             } else {
5503                 return followHighlight;
5504             }
5505         }
5506
5507         /**
5508          * Sets the value of the followHighlight property.
5509          *
5510          * @param value
5511          *     allowed object is
5512          *     {@link Boolean }
5513          *
5514          */
5515         public void setFollowHighlight(Boolean value) {
5516             this.followHighlight = value;
5517         }
5518
5519         /**
5520          * Gets the value of the followSelection property.
5521          *
5522          * @return
5523          *     possible object is
5524          *     {@link Boolean }
5525          *
5526          */
5527         public boolean isFollowSelection() {
5528             if (followSelection == null) {
5529                 return true;
5530             } else {
5531                 return followSelection;
5532             }
5533         }
5534
5535         /**
5536          * Sets the value of the followSelection property.
5537          *
5538          * @param value
5539          *     allowed object is
5540          *     {@link Boolean }
5541          *
5542          */
5543         public void setFollowSelection(Boolean value) {
5544             this.followSelection = value;
5545         }
5546
5547         /**
5548          * Gets the value of the showAnnotation property.
5549          *
5550          * @return
5551          *     possible object is
5552          *     {@link Boolean }
5553          *
5554          */
5555         public Boolean isShowAnnotation() {
5556             return showAnnotation;
5557         }
5558
5559         /**
5560          * Sets the value of the showAnnotation property.
5561          *
5562          * @param value
5563          *     allowed object is
5564          *     {@link Boolean }
5565          *
5566          */
5567         public void setShowAnnotation(Boolean value) {
5568             this.showAnnotation = value;
5569         }
5570
5571         /**
5572          * Gets the value of the centreColumnLabels property.
5573          *
5574          * @return
5575          *     possible object is
5576          *     {@link Boolean }
5577          *
5578          */
5579         public boolean isCentreColumnLabels() {
5580             if (centreColumnLabels == null) {
5581                 return false;
5582             } else {
5583                 return centreColumnLabels;
5584             }
5585         }
5586
5587         /**
5588          * Sets the value of the centreColumnLabels property.
5589          *
5590          * @param value
5591          *     allowed object is
5592          *     {@link Boolean }
5593          *
5594          */
5595         public void setCentreColumnLabels(Boolean value) {
5596             this.centreColumnLabels = value;
5597         }
5598
5599         /**
5600          * Gets the value of the showGroupConservation property.
5601          *
5602          * @return
5603          *     possible object is
5604          *     {@link Boolean }
5605          *
5606          */
5607         public boolean isShowGroupConservation() {
5608             if (showGroupConservation == null) {
5609                 return false;
5610             } else {
5611                 return showGroupConservation;
5612             }
5613         }
5614
5615         /**
5616          * Sets the value of the showGroupConservation property.
5617          *
5618          * @param value
5619          *     allowed object is
5620          *     {@link Boolean }
5621          *
5622          */
5623         public void setShowGroupConservation(Boolean value) {
5624             this.showGroupConservation = value;
5625         }
5626
5627         /**
5628          * Gets the value of the showGroupConsensus property.
5629          *
5630          * @return
5631          *     possible object is
5632          *     {@link Boolean }
5633          *
5634          */
5635         public boolean isShowGroupConsensus() {
5636             if (showGroupConsensus == null) {
5637                 return false;
5638             } else {
5639                 return showGroupConsensus;
5640             }
5641         }
5642
5643         /**
5644          * Sets the value of the showGroupConsensus property.
5645          *
5646          * @param value
5647          *     allowed object is
5648          *     {@link Boolean }
5649          *
5650          */
5651         public void setShowGroupConsensus(Boolean value) {
5652             this.showGroupConsensus = value;
5653         }
5654
5655         /**
5656          * Gets the value of the showConsensusHistogram property.
5657          *
5658          * @return
5659          *     possible object is
5660          *     {@link Boolean }
5661          *
5662          */
5663         public boolean isShowConsensusHistogram() {
5664             if (showConsensusHistogram == null) {
5665                 return true;
5666             } else {
5667                 return showConsensusHistogram;
5668             }
5669         }
5670
5671         /**
5672          * Sets the value of the showConsensusHistogram property.
5673          *
5674          * @param value
5675          *     allowed object is
5676          *     {@link Boolean }
5677          *
5678          */
5679         public void setShowConsensusHistogram(Boolean value) {
5680             this.showConsensusHistogram = value;
5681         }
5682
5683         /**
5684          * Gets the value of the showSequenceLogo property.
5685          *
5686          * @return
5687          *     possible object is
5688          *     {@link Boolean }
5689          *
5690          */
5691         public boolean isShowSequenceLogo() {
5692             if (showSequenceLogo == null) {
5693                 return false;
5694             } else {
5695                 return showSequenceLogo;
5696             }
5697         }
5698
5699         /**
5700          * Sets the value of the showSequenceLogo property.
5701          *
5702          * @param value
5703          *     allowed object is
5704          *     {@link Boolean }
5705          *
5706          */
5707         public void setShowSequenceLogo(Boolean value) {
5708             this.showSequenceLogo = value;
5709         }
5710
5711         /**
5712          * Gets the value of the normaliseSequenceLogo property.
5713          *
5714          * @return
5715          *     possible object is
5716          *     {@link Boolean }
5717          *
5718          */
5719         public boolean isNormaliseSequenceLogo() {
5720             if (normaliseSequenceLogo == null) {
5721                 return false;
5722             } else {
5723                 return normaliseSequenceLogo;
5724             }
5725         }
5726
5727         /**
5728          * Sets the value of the normaliseSequenceLogo property.
5729          *
5730          * @param value
5731          *     allowed object is
5732          *     {@link Boolean }
5733          *
5734          */
5735         public void setNormaliseSequenceLogo(Boolean value) {
5736             this.normaliseSequenceLogo = value;
5737         }
5738
5739         /**
5740          * Gets the value of the ignoreGapsinConsensus property.
5741          *
5742          * @return
5743          *     possible object is
5744          *     {@link Boolean }
5745          *
5746          */
5747         public boolean isIgnoreGapsinConsensus() {
5748             if (ignoreGapsinConsensus == null) {
5749                 return true;
5750             } else {
5751                 return ignoreGapsinConsensus;
5752             }
5753         }
5754
5755         /**
5756          * Sets the value of the ignoreGapsinConsensus property.
5757          *
5758          * @param value
5759          *     allowed object is
5760          *     {@link Boolean }
5761          *
5762          */
5763         public void setIgnoreGapsinConsensus(Boolean value) {
5764             this.ignoreGapsinConsensus = value;
5765         }
5766
5767         /**
5768          * Gets the value of the startRes property.
5769          *
5770          * @return
5771          *     possible object is
5772          *     {@link Integer }
5773          *
5774          */
5775         public Integer getStartRes() {
5776             return startRes;
5777         }
5778
5779         /**
5780          * Sets the value of the startRes property.
5781          *
5782          * @param value
5783          *     allowed object is
5784          *     {@link Integer }
5785          *
5786          */
5787         public void setStartRes(Integer value) {
5788             this.startRes = value;
5789         }
5790
5791         /**
5792          * Gets the value of the startSeq property.
5793          *
5794          * @return
5795          *     possible object is
5796          *     {@link Integer }
5797          *
5798          */
5799         public Integer getStartSeq() {
5800             return startSeq;
5801         }
5802
5803         /**
5804          * Sets the value of the startSeq property.
5805          *
5806          * @param value
5807          *     allowed object is
5808          *     {@link Integer }
5809          *
5810          */
5811         public void setStartSeq(Integer value) {
5812             this.startSeq = value;
5813         }
5814
5815         /**
5816          * Gets the value of the charWidth property.
5817          *
5818          * @return
5819          *     possible object is
5820          *     {@link Integer }
5821          *
5822          */
5823         public Integer getCharWidth() {
5824             return charWidth;
5825         }
5826
5827         /**
5828          * Sets the value of the charWidth property.
5829          *
5830          * @param value
5831          *     allowed object is
5832          *     {@link Integer }
5833          *
5834          */
5835         public void setCharWidth(Integer value) {
5836             this.charWidth = value;
5837         }
5838
5839         /**
5840          * Gets the value of the charHeight property.
5841          *
5842          * @return
5843          *     possible object is
5844          *     {@link Integer }
5845          *
5846          */
5847         public Integer getCharHeight() {
5848             return charHeight;
5849         }
5850
5851         /**
5852          * Sets the value of the charHeight property.
5853          *
5854          * @param value
5855          *     allowed object is
5856          *     {@link Integer }
5857          *
5858          */
5859         public void setCharHeight(Integer value) {
5860             this.charHeight = value;
5861         }
5862
5863         /**
5864          * Gets the value of the fontName property.
5865          *
5866          * @return
5867          *     possible object is
5868          *     {@link String }
5869          *
5870          */
5871         public String getFontName() {
5872             return fontName;
5873         }
5874
5875         /**
5876          * Sets the value of the fontName property.
5877          *
5878          * @param value
5879          *     allowed object is
5880          *     {@link String }
5881          *
5882          */
5883         public void setFontName(String value) {
5884             this.fontName = value;
5885         }
5886
5887         /**
5888          * Gets the value of the fontSize property.
5889          *
5890          * @return
5891          *     possible object is
5892          *     {@link Integer }
5893          *
5894          */
5895         public Integer getFontSize() {
5896             return fontSize;
5897         }
5898
5899         /**
5900          * Sets the value of the fontSize property.
5901          *
5902          * @param value
5903          *     allowed object is
5904          *     {@link Integer }
5905          *
5906          */
5907         public void setFontSize(Integer value) {
5908             this.fontSize = value;
5909         }
5910
5911         /**
5912          * Gets the value of the fontStyle property.
5913          *
5914          * @return
5915          *     possible object is
5916          *     {@link Integer }
5917          *
5918          */
5919         public Integer getFontStyle() {
5920             return fontStyle;
5921         }
5922
5923         /**
5924          * Sets the value of the fontStyle property.
5925          *
5926          * @param value
5927          *     allowed object is
5928          *     {@link Integer }
5929          *
5930          */
5931         public void setFontStyle(Integer value) {
5932             this.fontStyle = value;
5933         }
5934
5935         /**
5936          * Gets the value of the scaleProteinAsCdna property.
5937          *
5938          * @return
5939          *     possible object is
5940          *     {@link Boolean }
5941          *
5942          */
5943         public boolean isScaleProteinAsCdna() {
5944             if (scaleProteinAsCdna == null) {
5945                 return true;
5946             } else {
5947                 return scaleProteinAsCdna;
5948             }
5949         }
5950
5951         /**
5952          * Sets the value of the scaleProteinAsCdna property.
5953          *
5954          * @param value
5955          *     allowed object is
5956          *     {@link Boolean }
5957          *
5958          */
5959         public void setScaleProteinAsCdna(Boolean value) {
5960             this.scaleProteinAsCdna = value;
5961         }
5962
5963         /**
5964          * Gets the value of the viewName property.
5965          *
5966          * @return
5967          *     possible object is
5968          *     {@link String }
5969          *
5970          */
5971         public String getViewName() {
5972             return viewName;
5973         }
5974
5975         /**
5976          * Sets the value of the viewName property.
5977          *
5978          * @param value
5979          *     allowed object is
5980          *     {@link String }
5981          *
5982          */
5983         public void setViewName(String value) {
5984             this.viewName = value;
5985         }
5986
5987         /**
5988          * Gets the value of the sequenceSetId property.
5989          *
5990          * @return
5991          *     possible object is
5992          *     {@link String }
5993          *
5994          */
5995         public String getSequenceSetId() {
5996             return sequenceSetId;
5997         }
5998
5999         /**
6000          * Sets the value of the sequenceSetId property.
6001          *
6002          * @param value
6003          *     allowed object is
6004          *     {@link String }
6005          *
6006          */
6007         public void setSequenceSetId(String value) {
6008             this.sequenceSetId = value;
6009         }
6010
6011         /**
6012          * Gets the value of the gatheredViews property.
6013          *
6014          * @return
6015          *     possible object is
6016          *     {@link Boolean }
6017          *
6018          */
6019         public Boolean isGatheredViews() {
6020             return gatheredViews;
6021         }
6022
6023         /**
6024          * Sets the value of the gatheredViews property.
6025          *
6026          * @param value
6027          *     allowed object is
6028          *     {@link Boolean }
6029          *
6030          */
6031         public void setGatheredViews(Boolean value) {
6032             this.gatheredViews = value;
6033         }
6034
6035         /**
6036          * Gets the value of the textCol1 property.
6037          *
6038          * @return
6039          *     possible object is
6040          *     {@link Integer }
6041          *
6042          */
6043         public Integer getTextCol1() {
6044             return textCol1;
6045         }
6046
6047         /**
6048          * Sets the value of the textCol1 property.
6049          *
6050          * @param value
6051          *     allowed object is
6052          *     {@link Integer }
6053          *
6054          */
6055         public void setTextCol1(Integer value) {
6056             this.textCol1 = value;
6057         }
6058
6059         /**
6060          * Gets the value of the textCol2 property.
6061          *
6062          * @return
6063          *     possible object is
6064          *     {@link Integer }
6065          *
6066          */
6067         public Integer getTextCol2() {
6068             return textCol2;
6069         }
6070
6071         /**
6072          * Sets the value of the textCol2 property.
6073          *
6074          * @param value
6075          *     allowed object is
6076          *     {@link Integer }
6077          *
6078          */
6079         public void setTextCol2(Integer value) {
6080             this.textCol2 = value;
6081         }
6082
6083         /**
6084          * Gets the value of the textColThreshold property.
6085          *
6086          * @return
6087          *     possible object is
6088          *     {@link Integer }
6089          *
6090          */
6091         public Integer getTextColThreshold() {
6092             return textColThreshold;
6093         }
6094
6095         /**
6096          * Sets the value of the textColThreshold property.
6097          *
6098          * @param value
6099          *     allowed object is
6100          *     {@link Integer }
6101          *
6102          */
6103         public void setTextColThreshold(Integer value) {
6104             this.textColThreshold = value;
6105         }
6106
6107         /**
6108          * Gets the value of the id property.
6109          *
6110          * @return
6111          *     possible object is
6112          *     {@link String }
6113          *
6114          */
6115         public String getId() {
6116             return id;
6117         }
6118
6119         /**
6120          * Sets the value of the id property.
6121          *
6122          * @param value
6123          *     allowed object is
6124          *     {@link String }
6125          *
6126          */
6127         public void setId(String value) {
6128             this.id = value;
6129         }
6130
6131         /**
6132          * Gets the value of the complementId property.
6133          *
6134          * @return
6135          *     possible object is
6136          *     {@link String }
6137          *
6138          */
6139         public String getComplementId() {
6140             return complementId;
6141         }
6142
6143         /**
6144          * Sets the value of the complementId property.
6145          *
6146          * @param value
6147          *     allowed object is
6148          *     {@link String }
6149          *
6150          */
6151         public void setComplementId(String value) {
6152             this.complementId = value;
6153         }
6154
6155         /**
6156          * Gets the value of the showComplementFeatures property.
6157          *
6158          * @return
6159          *     possible object is
6160          *     {@link Boolean }
6161          *
6162          */
6163         public boolean isShowComplementFeatures() {
6164             if (showComplementFeatures == null) {
6165                 return false;
6166             } else {
6167                 return showComplementFeatures;
6168             }
6169         }
6170
6171         /**
6172          * Sets the value of the showComplementFeatures property.
6173          *
6174          * @param value
6175          *     allowed object is
6176          *     {@link Boolean }
6177          *
6178          */
6179         public void setShowComplementFeatures(Boolean value) {
6180             this.showComplementFeatures = value;
6181         }
6182
6183         /**
6184          * Gets the value of the showComplementFeaturesOnTop property.
6185          *
6186          * @return
6187          *     possible object is
6188          *     {@link Boolean }
6189          *
6190          */
6191         public boolean isShowComplementFeaturesOnTop() {
6192             if (showComplementFeaturesOnTop == null) {
6193                 return false;
6194             } else {
6195                 return showComplementFeaturesOnTop;
6196             }
6197         }
6198
6199         /**
6200          * Sets the value of the showComplementFeaturesOnTop property.
6201          *
6202          * @param value
6203          *     allowed object is
6204          *     {@link Boolean }
6205          *
6206          */
6207         public void setShowComplementFeaturesOnTop(Boolean value) {
6208             this.showComplementFeaturesOnTop = value;
6209         }
6210
6211         /**
6212          * Gets the value of the width property.
6213          *
6214          * @return
6215          *     possible object is
6216          *     {@link Integer }
6217          *
6218          */
6219         public Integer getWidth() {
6220             return width;
6221         }
6222
6223         /**
6224          * Sets the value of the width property.
6225          *
6226          * @param value
6227          *     allowed object is
6228          *     {@link Integer }
6229          *
6230          */
6231         public void setWidth(Integer value) {
6232             this.width = value;
6233         }
6234
6235         /**
6236          * Gets the value of the height property.
6237          *
6238          * @return
6239          *     possible object is
6240          *     {@link Integer }
6241          *
6242          */
6243         public Integer getHeight() {
6244             return height;
6245         }
6246
6247         /**
6248          * Sets the value of the height property.
6249          *
6250          * @param value
6251          *     allowed object is
6252          *     {@link Integer }
6253          *
6254          */
6255         public void setHeight(Integer value) {
6256             this.height = value;
6257         }
6258
6259         /**
6260          * Gets the value of the xpos property.
6261          *
6262          * @return
6263          *     possible object is
6264          *     {@link Integer }
6265          *
6266          */
6267         public Integer getXpos() {
6268             return xpos;
6269         }
6270
6271         /**
6272          * Sets the value of the xpos property.
6273          *
6274          * @param value
6275          *     allowed object is
6276          *     {@link Integer }
6277          *
6278          */
6279         public void setXpos(Integer value) {
6280             this.xpos = value;
6281         }
6282
6283         /**
6284          * Gets the value of the ypos property.
6285          *
6286          * @return
6287          *     possible object is
6288          *     {@link Integer }
6289          *
6290          */
6291         public Integer getYpos() {
6292             return ypos;
6293         }
6294
6295         /**
6296          * Sets the value of the ypos property.
6297          *
6298          * @param value
6299          *     allowed object is
6300          *     {@link Integer }
6301          *
6302          */
6303         public void setYpos(Integer value) {
6304             this.ypos = value;
6305         }
6306
6307
6308         /**
6309          * <p>Java class for anonymous complex type.
6310          *
6311          * <p>The following schema fragment specifies the expected content contained within this class.
6312          *
6313          * <pre>
6314          * &lt;complexType>
6315          *   &lt;complexContent>
6316          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6317          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6318          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6319          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6320          *     &lt;/extension>
6321          *   &lt;/complexContent>
6322          * &lt;/complexType>
6323          * </pre>
6324          *
6325          *
6326          */
6327         @XmlAccessorType(XmlAccessType.FIELD)
6328         @XmlType(name = "")
6329         public static class CalcIdParam
6330             extends WebServiceParameterSet
6331         {
6332
6333             @XmlAttribute(name = "calcId", required = true)
6334             protected String calcId;
6335             @XmlAttribute(name = "needsUpdate")
6336             protected Boolean needsUpdate;
6337             @XmlAttribute(name = "autoUpdate", required = true)
6338             protected boolean autoUpdate;
6339
6340             /**
6341              * Gets the value of the calcId property.
6342              *
6343              * @return
6344              *     possible object is
6345              *     {@link String }
6346              *
6347              */
6348             public String getCalcId() {
6349                 return calcId;
6350             }
6351
6352             /**
6353              * Sets the value of the calcId property.
6354              *
6355              * @param value
6356              *     allowed object is
6357              *     {@link String }
6358              *
6359              */
6360             public void setCalcId(String value) {
6361                 this.calcId = value;
6362             }
6363
6364             /**
6365              * Gets the value of the needsUpdate property.
6366              *
6367              * @return
6368              *     possible object is
6369              *     {@link Boolean }
6370              *
6371              */
6372             public boolean isNeedsUpdate() {
6373                 if (needsUpdate == null) {
6374                     return false;
6375                 } else {
6376                     return needsUpdate;
6377                 }
6378             }
6379
6380             /**
6381              * Sets the value of the needsUpdate property.
6382              *
6383              * @param value
6384              *     allowed object is
6385              *     {@link Boolean }
6386              *
6387              */
6388             public void setNeedsUpdate(Boolean value) {
6389                 this.needsUpdate = value;
6390             }
6391
6392             /**
6393              * Gets the value of the autoUpdate property.
6394              *
6395              */
6396             public boolean isAutoUpdate() {
6397                 return autoUpdate;
6398             }
6399
6400             /**
6401              * Sets the value of the autoUpdate property.
6402              *
6403              */
6404             public void setAutoUpdate(boolean value) {
6405                 this.autoUpdate = value;
6406             }
6407
6408         }
6409
6410
6411         /**
6412          * <p>Java class for anonymous complex type.
6413          *
6414          * <p>The following schema fragment specifies the expected content contained within this class.
6415          *
6416          * <pre>
6417          * &lt;complexType>
6418          *   &lt;complexContent>
6419          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6420          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6421          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6422          *     &lt;/restriction>
6423          *   &lt;/complexContent>
6424          * &lt;/complexType>
6425          * </pre>
6426          *
6427          *
6428          */
6429         @XmlAccessorType(XmlAccessType.FIELD)
6430         @XmlType(name = "")
6431         public static class HiddenColumns {
6432
6433             @XmlAttribute(name = "start")
6434             protected Integer start;
6435             @XmlAttribute(name = "end")
6436             protected Integer end;
6437
6438             /**
6439              * Gets the value of the start property.
6440              *
6441              * @return
6442              *     possible object is
6443              *     {@link Integer }
6444              *
6445              */
6446             public Integer getStart() {
6447                 return start;
6448             }
6449
6450             /**
6451              * Sets the value of the start property.
6452              *
6453              * @param value
6454              *     allowed object is
6455              *     {@link Integer }
6456              *
6457              */
6458             public void setStart(Integer value) {
6459                 this.start = value;
6460             }
6461
6462             /**
6463              * Gets the value of the end property.
6464              *
6465              * @return
6466              *     possible object is
6467              *     {@link Integer }
6468              *
6469              */
6470             public Integer getEnd() {
6471                 return end;
6472             }
6473
6474             /**
6475              * Sets the value of the end property.
6476              *
6477              * @param value
6478              *     allowed object is
6479              *     {@link Integer }
6480              *
6481              */
6482             public void setEnd(Integer value) {
6483                 this.end = value;
6484             }
6485
6486         }
6487
6488
6489         /**
6490          * <p>Java class for anonymous complex type.
6491          *
6492          * <p>The following schema fragment specifies the expected content contained within this class.
6493          *
6494          * <pre>
6495          * &lt;complexType>
6496          *   &lt;complexContent>
6497          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6498          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
6499          *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6500          *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6501          *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6502          *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6503          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6504          *     &lt;/restriction>
6505          *   &lt;/complexContent>
6506          * &lt;/complexType>
6507          * </pre>
6508          *
6509          *
6510          */
6511         @XmlAccessorType(XmlAccessType.FIELD)
6512         @XmlType(name = "")
6513         public static class Overview {
6514
6515             @XmlAttribute(name = "showHidden")
6516             protected Boolean showHidden;
6517             @XmlAttribute(name = "residueColour")
6518             protected Integer residueColour;
6519             @XmlAttribute(name = "gapColour")
6520             protected Integer gapColour;
6521             @XmlAttribute(name = "hiddenColour")
6522             protected Integer hiddenColour;
6523             @XmlAttribute(name = "title")
6524             protected String title;
6525             @XmlAttribute(name = "width")
6526             protected Integer width;
6527             @XmlAttribute(name = "height")
6528             protected Integer height;
6529             @XmlAttribute(name = "xpos")
6530             protected Integer xpos;
6531             @XmlAttribute(name = "ypos")
6532             protected Integer ypos;
6533
6534             /**
6535              * Gets the value of the showHidden property.
6536              *
6537              * @return
6538              *     possible object is
6539              *     {@link Boolean }
6540              *
6541              */
6542             public Boolean isShowHidden() {
6543                 return showHidden;
6544             }
6545
6546             /**
6547              * Sets the value of the showHidden property.
6548              *
6549              * @param value
6550              *     allowed object is
6551              *     {@link Boolean }
6552              *
6553              */
6554             public void setShowHidden(Boolean value) {
6555                 this.showHidden = value;
6556             }
6557
6558             /**
6559              * Gets the value of the residueColour property.
6560              *
6561              * @return
6562              *     possible object is
6563              *     {@link Integer }
6564              *
6565              */
6566             public Integer getResidueColour() {
6567                 return residueColour;
6568             }
6569
6570             /**
6571              * Sets the value of the residueColour property.
6572              *
6573              * @param value
6574              *     allowed object is
6575              *     {@link Integer }
6576              *
6577              */
6578             public void setResidueColour(Integer value) {
6579                 this.residueColour = value;
6580             }
6581
6582             /**
6583              * Gets the value of the gapColour property.
6584              *
6585              * @return
6586              *     possible object is
6587              *     {@link Integer }
6588              *
6589              */
6590             public Integer getGapColour() {
6591                 return gapColour;
6592             }
6593
6594             /**
6595              * Sets the value of the gapColour property.
6596              *
6597              * @param value
6598              *     allowed object is
6599              *     {@link Integer }
6600              *
6601              */
6602             public void setGapColour(Integer value) {
6603                 this.gapColour = value;
6604             }
6605
6606             /**
6607              * Gets the value of the hiddenColour property.
6608              *
6609              * @return
6610              *     possible object is
6611              *     {@link Integer }
6612              *
6613              */
6614             public Integer getHiddenColour() {
6615                 return hiddenColour;
6616             }
6617
6618             /**
6619              * Sets the value of the hiddenColour property.
6620              *
6621              * @param value
6622              *     allowed object is
6623              *     {@link Integer }
6624              *
6625              */
6626             public void setHiddenColour(Integer value) {
6627                 this.hiddenColour = value;
6628             }
6629
6630             /**
6631              * Gets the value of the title property.
6632              *
6633              * @return
6634              *     possible object is
6635              *     {@link String }
6636              *
6637              */
6638             public String getTitle() {
6639                 return title;
6640             }
6641
6642             /**
6643              * Sets the value of the title property.
6644              *
6645              * @param value
6646              *     allowed object is
6647              *     {@link String }
6648              *
6649              */
6650             public void setTitle(String value) {
6651                 this.title = value;
6652             }
6653
6654             /**
6655              * Gets the value of the width property.
6656              *
6657              * @return
6658              *     possible object is
6659              *     {@link Integer }
6660              *
6661              */
6662             public Integer getWidth() {
6663                 return width;
6664             }
6665
6666             /**
6667              * Sets the value of the width property.
6668              *
6669              * @param value
6670              *     allowed object is
6671              *     {@link Integer }
6672              *
6673              */
6674             public void setWidth(Integer value) {
6675                 this.width = value;
6676             }
6677
6678             /**
6679              * Gets the value of the height property.
6680              *
6681              * @return
6682              *     possible object is
6683              *     {@link Integer }
6684              *
6685              */
6686             public Integer getHeight() {
6687                 return height;
6688             }
6689
6690             /**
6691              * Sets the value of the height property.
6692              *
6693              * @param value
6694              *     allowed object is
6695              *     {@link Integer }
6696              *
6697              */
6698             public void setHeight(Integer value) {
6699                 this.height = value;
6700             }
6701
6702             /**
6703              * Gets the value of the xpos property.
6704              *
6705              * @return
6706              *     possible object is
6707              *     {@link Integer }
6708              *
6709              */
6710             public Integer getXpos() {
6711                 return xpos;
6712             }
6713
6714             /**
6715              * Sets the value of the xpos property.
6716              *
6717              * @param value
6718              *     allowed object is
6719              *     {@link Integer }
6720              *
6721              */
6722             public void setXpos(Integer value) {
6723                 this.xpos = value;
6724             }
6725
6726             /**
6727              * Gets the value of the ypos property.
6728              *
6729              * @return
6730              *     possible object is
6731              *     {@link Integer }
6732              *
6733              */
6734             public Integer getYpos() {
6735                 return ypos;
6736             }
6737
6738             /**
6739              * Sets the value of the ypos property.
6740              *
6741              * @param value
6742              *     allowed object is
6743              *     {@link Integer }
6744              *
6745              */
6746             public void setYpos(Integer value) {
6747                 this.ypos = value;
6748             }
6749
6750         }
6751
6752     }
6753
6754 }