xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview
Note this also generates code for included schemas
-->
-<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.ac.uk/jalview/version2" targetNamespace="www.vamsas.ac.uk/jalview/version2" elementFormDefault="qualified" attributeFormDefault="unqualified">
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
+ xmlns:vamsas="www.vamsas.ac.uk/jalview/version2"
+ targetNamespace="www.vamsas.ac.uk/jalview/version2"
+ elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:complexType name="VAMSAS">
<xs:sequence>
- <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="Tree" type="xs:string" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element ref="vamsas:SequenceSet" minOccurs="0"
+ maxOccurs="unbounded" />
</xs:sequence>
</xs:complexType>
<xs:complexType name="mapListType">
<xs:annotation>
- <xs:documentation>
- developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+ <xs:documentation>
+ developed after mapRangeType from
+ http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
</xs:documentation>
<xs:documentation>
- This effectively represents a java.util.MapList object
+ This effectively represents a java.util.MapList
+ object
</xs:documentation>
</xs:annotation>
<xs:sequence>
- <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="mapListFrom" minOccurs="0"
+ maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation> a region from start to end inclusive</xs:documentation>
+ <xs:documentation> a region from start to end inclusive
+ </xs:documentation>
</xs:annotation>
<xs:complexType>
- <xs:attribute name="start" type="xs:int" use="required"/>
- <xs:attribute name="end" type="xs:int" use="required"/>
+ <xs:attribute name="start" type="xs:int"
+ use="required" />
+ <xs:attribute name="end" type="xs:int" use="required" />
</xs:complexType>
- </xs:element>
- <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
+ </xs:element>
+ <xs:element name="mapListTo" minOccurs="0"
+ maxOccurs="unbounded">
<xs:annotation>
- <xs:documentation> a region from start to end inclusive</xs:documentation>
+ <xs:documentation> a region from start to end inclusive
+ </xs:documentation>
</xs:annotation>
<xs:complexType>
- <xs:attribute name="start" type="xs:int" use="required"/>
- <xs:attribute name="end" type="xs:int" use="required"/>
+ <xs:attribute name="start" type="xs:int"
+ use="required" />
+ <xs:attribute name="end" type="xs:int" use="required" />
</xs:complexType>
- </xs:element>
+ </xs:element>
</xs:sequence>
- <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
+ <xs:attribute name="mapFromUnit"
+ type="xs:positiveInteger" use="required">
<xs:annotation>
- <xs:documentation>number of dictionary symbol widths involved in each
- mapped position on this sequence (for example, 3 for a dna sequence exon
- region that is being mapped to a protein sequence). This is optional,
- since the unit can be usually be inferred from the dictionary type of
- each sequence involved in the mapping. </xs:documentation>
+ <xs:documentation>number of dictionary symbol widths involved in
+ each
+ mapped position on this sequence (for example, 3 for a dna
+ sequence exon
+ region that is being mapped to a protein sequence).
+ This is optional,
+ since the unit can be usually be inferred from the
+ dictionary type of
+ each sequence involved in the mapping.
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
+ <xs:attribute name="mapToUnit" type="xs:positiveInteger"
+ use="required">
<xs:annotation>
- <xs:documentation>number of dictionary symbol widths involved in each
- mapped position on this sequence (for example, 3 for a dna sequence exon
- region that is being mapped to a protein sequence). This is optional,
- since the unit can be usually be inferred from the dictionary type of
- each sequence involved in the mapping. </xs:documentation>
+ <xs:documentation>number of dictionary symbol widths involved in
+ each
+ mapped position on this sequence (for example, 3 for a dna
+ sequence exon
+ region that is being mapped to a protein sequence).
+ This is optional,
+ since the unit can be usually be inferred from the
+ dictionary type of
+ each sequence involved in the mapping.
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
<xs:complexType>
<xs:annotation>
<xs:documentation>
- Represent the jalview.datamodel.Mapping object - it also provides
- a way of storing sequences that are mapped 'to' without adding them
- to the sequence set (which will mean they are then added to the alignment too).
+ Represent the jalview.datamodel.Mapping object -
+ it also provides
+ a way of storing sequences that are mapped 'to'
+ without adding them
+ to the sequence set (which will mean they are
+ then added to the alignment too).
</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="vamsas:mapListType">
<xs:sequence>
<xs:choice minOccurs="0" maxOccurs="1">
- <xs:element ref="vamsas:Sequence"/>
+ <xs:element ref="vamsas:Sequence" />
<xs:element name="dseqFor">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:annotation>
- <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
+ <xs:documentation>The sequence whose dataset sequence is to
+ be referenced here
+ </xs:documentation>
</xs:annotation>
</xs:restriction>
</xs:simpleType>
</xs:element>
</xs:choice>
</xs:sequence>
- <xs:attribute name="mappingType" type="xs:string" use="optional">
+ <xs:attribute name="mappingType" type="xs:string"
+ use="optional">
<xs:annotation>
- <xs:documentation>Biotype of the mapping e.g. CdsToPeptide</xs:documentation>
+ <xs:documentation>Biotype of the mapping e.g. CdsToPeptide
+ </xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
- </xs:complexContent>
+ </xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="AlcodonFrame">
<xs:complexType>
<xs:sequence>
- <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodon" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:annotation>
<xs:documentation>
- specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
- Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+ specifies a series of aligned codons from an
+ associated DNA sequence alignment that when translated
+ correspond to columns of a peptide alignment.
+ Element may have
+ either all pos1,2,3 attributes specified, or none at all
+ (indicating a gapped column with no translated peptide).
</xs:documentation>
</xs:annotation>
- <xs:attribute name="pos1" type="xs:integer" use="optional"/>
- <xs:attribute name="pos2" type="xs:integer" use="optional"/>
- <xs:attribute name="pos3" type="xs:integer" use="optional"/>
+ <xs:attribute name="pos1" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="pos2" type="xs:integer"
+ use="optional" />
+ <xs:attribute name="pos3" type="xs:integer"
+ use="optional" />
</xs:complexType>
</xs:element>
- <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodMap" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
+ <xs:element ref="vamsas:Mapping" maxOccurs="1"
+ minOccurs="1">
<xs:annotation>
<xs:documentation>
- a Mapping entry and an associated protein sequence
+ a Mapping entry and an associated protein
+ sequence
</xs:documentation>
</xs:annotation>
</xs:element>
</xs:sequence>
- <xs:attribute name="dnasq" type="xs:string" use="required">
+ <xs:attribute name="dnasq" type="xs:string"
+ use="required">
<xs:annotation>
<xs:documentation>
- internal jalview id for the dnasq for this mapping.
+ internal jalview id for the dnasq for this
+ mapping.
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
-
+
</xs:element>
-
+
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:complexContent>
<xs:extension base="vamsas:SequenceType">
<xs:sequence>
- <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="DBRef" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
- </xs:sequence>
- <xs:attribute name="source" type="xs:string"/>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="accessionId" type="xs:string"/>
- <xs:attribute name="locus" type="xs:boolean" default="false">
+ <xs:element ref="vamsas:Mapping" minOccurs="0"
+ maxOccurs="1" />
+ </xs:sequence>
+ <xs:attribute name="source" type="xs:string" />
+ <xs:attribute name="version" type="xs:string" />
+ <xs:attribute name="accessionId" type="xs:string" />
+ <xs:attribute name="locus" type="xs:boolean"
+ default="false">
<xs:annotation>
<xs:documentation>
- true for gene locus mapping, source=species, version=assembly, accession=chromosome
+ true for gene locus mapping, source=species,
+ version=assembly, accession=chromosome
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="canonical" type="xs:boolean" default="false">
+ <xs:attribute name="canonical" type="xs:boolean"
+ default="false">
<xs:annotation>
<xs:documentation>
- true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+ true for the representative accession for
+ databases where multiple accessions map to the same entry
+ (eg. Uniprot)
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
</xs:element>
</xs:sequence>
- <xs:attribute name="dsseqid" type="xs:string" use="optional">
+ <xs:attribute name="dsseqid" type="xs:string"
+ use="optional">
<xs:annotation>
<xs:documentation>
- dataset sequence id for this sequence. Will be created as union of sequences.
+ dataset sequence id for this sequence. Will be
+ created as union of sequences.
</xs:documentation>
</xs:annotation>
</xs:attribute>
- <xs:attribute name="biotype" type="xs:string" use="optional">
+ <xs:attribute name="biotype" type="xs:string"
+ use="optional">
<xs:annotation>
<xs:documentation>
Biotype of the sequence (if known)
<xs:attribute name="colour" type="xs:int" />
</xs:complexType>
</xs:element>
- <xs:element name="contactmatrix" type="vamsas:MatrixType"
- maxOccurs="unbounded" minOccurs="0">
+ <xs:element name="contactmatrix"
+ type="vamsas:MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0">
</xs:element>
- <xs:element name="property" type="vamsas:property" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="property" type="vamsas:property"
+ minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
- <xs:attribute name="graph" type="xs:boolean" use="required" />
- <xs:attribute name="graphType" type="xs:int" use="optional" />
+ <xs:attribute name="graph" type="xs:boolean"
+ use="required" />
+ <xs:attribute name="graphType" type="xs:int"
+ use="optional" />
<xs:attribute name="sequenceRef" type="xs:string"
use="optional" />
<xs:attribute name="groupRef" type="xs:string"
use="optional" />
<xs:attribute name="graphGroup" type="xs:int"
use="optional" />
- <xs:attribute name="graphHeight" type="xs:int" use="optional">
- <xs:annotation><xs:documentation>height in pixels for the graph if this is a graph-type annotation.</xs:documentation></xs:annotation></xs:attribute>
+ <xs:attribute name="graphHeight" type="xs:int"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>height in pixels for the graph if this is a
+ graph-type annotation.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
<xs:attribute name="id" type="xs:string" use="optional" />
<xs:attribute name="scoreOnly" type="xs:boolean"
use="optional" default="false" />
- <xs:attribute name="score" type="xs:double" use="optional" />
+ <xs:attribute name="score" type="xs:double"
+ use="optional" />
<xs:attribute name="visible" type="xs:boolean"
use="optional" />
<xs:attribute name="centreColLabels" type="xs:boolean"
use="optional" />
- <xs:attribute name="autoCalculated" type="xs:boolean" use="optional" default="false">
- <xs:annotation><xs:documentation>is an autocalculated annotation row</xs:documentation>
- </xs:annotation></xs:attribute>
- <xs:attribute name="belowAlignment" type="xs:boolean" use="optional" default="true">
- <xs:annotation><xs:documentation>is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores</xs:documentation></xs:annotation></xs:attribute>
- <xs:attribute name="calcId" type="xs:string" use="optional">
- <xs:annotation><xs:documentation>Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system.</xs:documentation></xs:annotation>
+ <xs:attribute name="autoCalculated" type="xs:boolean"
+ use="optional" default="false">
+ <xs:annotation>
+ <xs:documentation>is an autocalculated annotation row
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="belowAlignment" type="xs:boolean"
+ use="optional" default="true">
+ <xs:annotation>
+ <xs:documentation>is to be shown below the alignment - introduced
+ in Jalview 2.8 for visualizing T-COFFEE alignment scores
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="calcId" type="xs:string"
+ use="optional">
+ <xs:annotation>
+ <xs:documentation>Optional string identifier used to group sets of
+ annotation produced by a particular calculation. Values are opaque
+ strings but have semantic meaning to Jalview's renderer, data
+ importer and calculation system.
+ </xs:documentation>
+ </xs:annotation>
</xs:attribute>
</xs:complexType>
- </xs:element>
+ </xs:element>
<xs:element name="SequenceSet">
<xs:complexType>
<xs:sequence>
- <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
+ <xs:element ref="vamsas:Sequence" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element ref="vamsas:Annotation" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element name="sequenceSetProperties" minOccurs="0"
+ maxOccurs="unbounded">
<xs:complexType>
- <xs:attribute name="key" type="xs:string"/>
- <xs:attribute name="value" type="xs:string"/>
+ <xs:attribute name="key" type="xs:string" />
+ <xs:attribute name="value" type="xs:string" />
</xs:complexType>
</xs:element>
- <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:AlcodonFrame" minOccurs="0"
+ maxOccurs="unbounded" />
+ <xs:element name="Matrix" type="vamsas:MatrixType"
+ minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation>Matrices referred to by this set of sequences.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
</xs:sequence>
- <xs:attribute name="gapChar" type="xs:string" use="required"/>
- <xs:attribute name="datasetId" type="xs:string" use="optional">
+ <xs:attribute name="gapChar" type="xs:string"
+ use="required" />
+ <xs:attribute name="datasetId" type="xs:string"
+ use="optional">
<xs:annotation>
<xs:documentation>
- reference to set where jalview will gather the dataset sequences for all sequences in the set.
+ reference to set where jalview will gather the
+ dataset sequences for all sequences in the set.
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:element name="annotationElement">
<xs:complexType>
<xs:sequence>
- <xs:element name="displayCharacter" type="xs:string" minOccurs="0"/>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="displayCharacter" type="xs:string"
+ minOccurs="0" />
+ <xs:element name="description" type="xs:string"
+ minOccurs="0" />
<xs:element name="secondaryStructure" minOccurs="0">
<xs:simpleType>
<xs:restriction base="xs:string">
- <xs:length value="1"/>
+ <xs:length value="1" />
</xs:restriction>
</xs:simpleType>
</xs:element>
- <xs:element name="value" type="xs:float" minOccurs="0"/>
+ <xs:element name="value" type="xs:float" minOccurs="0" />
</xs:sequence>
- <xs:attribute name="position" type="xs:int" use="required"/>
- <xs:attribute name="colour" type="xs:int" use="optional"/>
+ <xs:attribute name="position" type="xs:int"
+ use="required" />
+ <xs:attribute name="colour" type="xs:int" use="optional" />
</xs:complexType>
</xs:element>
<xs:complexType name="SequenceType">
<xs:sequence>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="sequence" type="xs:string" minOccurs="0" />
+ <xs:element name="name" type="xs:string" minOccurs="0" />
</xs:sequence>
- <xs:attribute name="id" type="xs:string"/>
- <xs:attribute name="description" type="xs:string"/>
+ <xs:attribute name="id" type="xs:string" />
+ <xs:attribute name="description" type="xs:string" />
</xs:complexType>
<xs:complexType name="MatrixType">
+ <xs:annotation>
+ <xs:documentation>Represents matrix data imported to Jalview, and the
+ results of any derived calculations (independent of a particular
+ view
+ on the matrix).
+ </xs:documentation>
+ </xs:annotation>
<xs:sequence>
<xs:element name="elements" type="xs:string" minOccurs="1"
maxOccurs="1">
<xs:annotation>
<xs:documentation>serialised representation of matrix as one or
- more sets of comma separated values</xs:documentation>
+ more sets of comma separated values
+ </xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="groups" type="xs:string" minOccurs="0"
</xs:element>
<xs:element name="property" type="vamsas:property"
minOccurs="0" maxOccurs="unbounded" />
- <xs:element name="mapping" type="vamsas:mapListType"
- minOccurs="0" maxOccurs="1">
- <xs:annotation>
- <xs:documentation>mapping from the matrix row and column positions to
- associated reference frame</xs:documentation>
- </xs:annotation>
- </xs:element>
</xs:sequence>
<xs:attribute name="type" type="xs:string" use="required" />
use="optional" />
<xs:attribute name="cutHeight" type="xs:double"
use="optional" />
- <xs:attribute name="id" type="xs:string" use="optional" />
+ <xs:attribute name="id" type="xs:string" use="required" />
</xs:complexType>
+ <xs:complexType name="MapOnAMatrixType">
+ <xs:annotation>
+ <xs:documentation>Defines a mapping from the local frame to a matrix
+ and its associated data specified by MatrixType
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="property" type="vamsas:property"
+ minOccurs="0" maxOccurs="unbounded" />
+ <xs:element name="mapping" type="vamsas:mapListType"
+ minOccurs="0" maxOccurs="1">
+ <xs:annotation>
+ <xs:documentation>mapping from the matrix row and column positions
+ to
+ associated reference frame
+ </xs:documentation>
+ </xs:annotation>
+ </xs:element>
+ </xs:sequence>
+
+ <xs:attribute name="matrix" type="xs:string"
+ use="required">
+
+ <xs:annotation>
+ <xs:documentation>reference to the matrix type this Map refers to
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="id" type="xs:string" use="optional" />
+ </xs:complexType>
<xs:complexType name="property">
<xs:attribute name="name" type="xs:string" />
<xs:attribute name="value" type="xs:string" />
</xs:complexType>
-
-
+
+
</xs:schema>
import java.util.Locale;
import java.util.Map;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AlignmentUtils;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Jalview.ExitCode;
}
}
+
// Show secondary structure annotations?
boolean showSSAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
- af.setAnnotationsVisibility(showSSAnnotations, true, false);
-
+
// Show sequence annotations?
boolean showAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWANNOTATIONS, av.getSubVals(), null,
"SHOW_ANNOTATIONS", true);
- af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
+ final AlignFrame _af = af;
+ // many of jalview's format/layout methods are only thread safe on the swingworker thread.
+ // all these methods should be on the alignViewController so it can coordinate such details
+ try
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ _af.setAnnotationsVisibility(showSSAnnotations, true,
+ false);
- // show temperature factor annotations?
- if (avm.getBoolean(Arg.NOTEMPFAC))
+ _af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ // show temperature factor annotations?
+ if (hideTFrows)
+ {
+ // do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ _af.getCurrentView().getAlignment(), hideThese,
+ null, false, false);
+ }
+ }
+ });
+ } catch (Exception x)
{
- // do this better (annotation types?)
- List<String> hideThese = new ArrayList<>();
- hideThese.add("Temperature Factor");
- hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(), hideThese, null,
- false, false);
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
}
// wrap alignment? do this last for formatting reasons
if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
- if (cm == null)
+ if (cm == null && _aa.sequenceRef.getDatasetSequence()!=null)
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Map;
import jalview.ws.datamodel.MappableContactMatrixI;
{
if (contactmaps != null && contactmaps.size() > 0)
{
- return contactmaps.values();
+ // defensive copy, and return non redundant set of ContactMatrixI instances
+ return new HashSet<ContactMatrixI>(contactmaps.values());
}
return Collections.EMPTY_LIST;
}
package jalview.datamodel;
-import java.awt.Color;
-import java.math.BigInteger;
import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.HashMap;
import java.util.List;
-import java.util.Spliterator;
import java.util.StringTokenizer;
import jalview.bin.Console;
-public abstract class ContactMatrix implements ContactMatrixI
+public abstract class ContactMatrix extends GroupSetHolder implements ContactMatrixI
{
/**
* are contacts reflexive ?
@Override
public double getContactAt(int column)
{
- List<Float> clist;
- Float cl = null;
- if (symmetric)
- {
- if (p < column)
- {
- clist = contacts.get(p);
- cl = clist.get(column);
- }
- else
- {
- clist = contacts.get(column);
- cl = clist.get(p);
- }
- }
- else
- {
- clist = contacts.get(p);
- cl = clist.get(column);
- }
+ Float cl = getFloatElementAt(column, p);
if (cl == null)
{
// return 0 not NaN ?
}
});
}
-
+ private Float getFloatElementAt(int column, int p)
+ {
+
+ List<Float> clist;
+ Float cl = null;
+ if (symmetric)
+ {
+ if (p < column)
+ {
+ clist = contacts.get(p);
+ cl = clist.get(column);
+ }
+ else
+ {
+ clist = contacts.get(column);
+ cl = clist.get(p);
+ }
+ }
+ else
+ {
+ clist = contacts.get(p);
+ cl = clist.get(column);
+ }
+ return cl;
+ }
+ @Override
+ public double getElementAt(int column, int row)
+ {
+ Float cl = getFloatElementAt(column, row);
+ if (cl!=null)
+ {
+ return cl;
+ }
+ throw(new RuntimeException("Out of Bounds "+column+","+row));
+ }
@Override
public float getMin()
{
{
return "Contact Matrix";
}
- GroupSet grps = new GroupSet();
- @Override
- public GroupSetI getGroupSet()
- {
- return grps;
- }
- @Override
- public void setGroupSet(GroupSet makeGroups)
- {
- grps = makeGroups;
- }
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
for (int c = 0; c < cm.getWidth(); c++)
{
ContactListI cl = cm.getContactList(c);
+ long lastsb=-1;
if (cl != null)
{
for (int h = 0; h <= cl.getContactHeight(); h++)
{
if (sb.length() > 0)
{
- sb.append('\t');
+ if (sb.length()-lastsb>320)
+ {
+ // newline
+ sb.append('\n');
+ lastsb=sb.length();
+ } else {
+ sb.append('\t');
+ }
}
sb.append(cl.getContactAt(h));
}
int rows)
{
float[][] vals = new float[cols][rows];
- StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+ StringTokenizer tabsep = new StringTokenizer(values, "" + '\t'+'\n');
int c = 0, r = 0;
while (tabsep.hasMoreTokens())
{
}
return Color.white;
}
+
+ /**
+ * direct access to column and row position of matrix
+
+ * Implementations are allowed to throw
+ * RunTimeExceptions if _column/i are out of bounds
+ *
+ * @param column
+ * @param row
+ * @return
+ */
+ double getElementAt(int column, int row);
}
--- /dev/null
+package jalview.datamodel;
+
+public class FloatContactMatrix extends GroupSetHolder implements ContactMatrixI
+{
+
+ int maxrow = 0, maxcol = 0;
+
+
+ float[][] elements;
+
+ float maxscore;
+
+
+ public FloatContactMatrix(float[][] matrix)
+ {
+ maxcol = 0;
+ for (float[] row : matrix)
+ {
+ if (row.length > maxcol)
+ {
+ maxcol = row.length;
+ }
+ maxscore = row[0];
+ for (float f : row)
+ {
+ if (maxscore < f)
+ {
+ maxscore = f;
+ }
+ }
+ }
+ maxrow = matrix.length;
+ elements = matrix;
+ }
+
+ public FloatContactMatrix(float[][] elements2, GroupSet grps2)
+ {
+ this(elements2);
+ setGroupSet(grps2);
+ }
+
+ /**
+ * getContactList(column) @returns the vector of predicted alignment errors
+ * for reference position given by column
+ */
+ @Override
+ public ContactListI getContactList(final int column)
+ {
+ if (column < 0 || column >= elements.length)
+ {
+ return null;
+ }
+
+ return new ContactListImpl(new ContactListProviderI()
+ {
+ @Override
+ public int getPosition()
+ {
+ return column;
+ }
+
+ @Override
+ public int getContactHeight()
+ {
+ return maxcol - 1;
+ }
+
+ @Override
+ public double getContactAt(int mcolumn)
+ {
+ if (mcolumn < 0 || mcolumn >= elements[column].length)
+ {
+ return -1;
+ }
+ return elements[column][mcolumn];
+ }
+ });
+ }
+
+ /**
+ * getElementAt(column, i) @returns the predicted superposition error for the
+ * ith position when column is used as reference
+ */
+ @Override
+ public double getElementAt(int _column, int i)
+ {
+ return elements[_column][i];
+ }
+
+ @Override
+ public float getMin()
+ {
+ return 0;
+ }
+
+ @Override
+ public float getMax()
+ {
+ return maxscore;
+ }
+
+ @Override
+ public String getAnnotDescr()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getType()
+ {
+ return null;
+ }
+
+ @Override
+ public int getWidth()
+ {
+ return maxcol;
+ }
+
+ @Override
+ public int getHeight()
+ {
+ return maxrow;
+ }
+}
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * holds a group set and provides getters and setters for ContactMatrixI
+ * implementations
+ *
+ * @author jprocter
+ */
+public class GroupSetHolder
+{
+
+ GroupSet grps = new GroupSet();
+
+ public GroupSetI getGroupSet()
+ {
+ return grps;
+ }
+
+ public void setGroupSet(GroupSet makeGroups)
+ {
+ grps = makeGroups;
+ }
+
+}
return width;
}
@Override
- protected double getElementAt(int _column, int i)
+ public double getElementAt(int _column, int i)
{
return Math.abs(_column - i);
}
{
return (String) getField(Model_id);
}
+
+ public String getConfidenceScoreType()
+ {
+ return (String) getField(Confidence_Score_Type);
+ }
+ public String getConfidenceScoreVersion()
+ {
+ return (String) getField(Confidence_Score_Version);
+ }
}
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ if (url!=null && !url.trim().equals("")) {
+ jalview.bin.Console.info("Opening URL: "+url);
+ showUrl(url, Desktop.instance);
+ } else {
+ jalview.bin.Console.warn("Ignoring attempt to show an empty URL.");
+ }
+
}
/**
.getFTSDataFor(getResultTable(), selectedRow,
discoveredStructuresSet);
String pageUrl = row.getModelViewUrl();
+
JPopupMenu popup = new JPopupMenu("3D Beacons");
JMenuItem viewUrl = new JMenuItem("View model web page");
+ if (pageUrl == null || "".equals(pageUrl.trim())) {
+ viewUrl.setEnabled(false);
+ viewUrl.setText("No model page available.");
+ }
viewUrl.addActionListener(new ActionListener()
{
@Override
if (!o1_qualtype.equals(o2_qualtype))
{
// prefer LDDT measure over others
- return "pLDDT".equals(o1_prov) ? -1
- : "pLDDT".equals(o2_prov) ? 1 : 0;
+ return "pLDDT".equals(o1_qualtype) ? -1
+ : "pLDDT".equals(o2_qualtype) ? 1 : 0;
}
// OR NO VALUE FOR THE QUALITY
if (eitherNull(idx_mqual, o1data, o2data))
// models, so rank on qmean - b
double o1_mq = (Double) o1data[idx_mqual];
double o2_mq = (Double) o2data[idx_mqual];
- return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
+ int res = (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
+ return ("pLDDT".equals(o1_qualtype)) ? -res : res;
}
}
else
&& tdBeaconsFilters.contains(fieldToFilterBy);
}
- private String remove_prefix(String fieldToFilterBy)
+ protected String remove_prefix(String fieldToFilterBy)
{
if (tdBeaconsFilters != null
&& tdBeaconsFilters.contains(fieldToFilterBy)
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactMatrix;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.FloatContactMatrix;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.xml.binding.jalview.MapListType;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
import jalview.xml.binding.jalview.MapListType.MapListTo;
+import jalview.xml.binding.jalview.MapOnAMatrixType;
import jalview.xml.binding.jalview.Mapping;
import jalview.xml.binding.jalview.MatrixType;
import jalview.xml.binding.jalview.NoValueColour;
Map<String, SequenceI> incompleteSeqs = null;
- List<SeqFref> frefedSequence = null;
+ List<forwardRef> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
* entry names
*/
private Map<RnaModel, String> rnaSessions = new HashMap<>();
+
+ /**
+ * map from contact matrices to their XML ids
+ */
+ private Map<ContactMatrixI,String> contactMatrices = new HashMap<>();
+ private Map<String, ContactMatrixI> contactMatrixRefs = new HashMap<>();
+ private List<jalview.xml.binding.jalview.MatrixType> xmlMatrices= new ArrayList<>();
/**
* A helper method for safely using the value of an optional attribute that
}
/**
- * base class for resolving forward references to sequences by their ID
+ * base class for resolving forward references to an as-yet unmarshalled object referenced by already unmarshalled objects
*
* @author jprocter
*
*/
- abstract class SeqFref
- {
+ abstract class forwardRef {
String sref;
String type;
- public SeqFref(String _sref, String type)
+ public forwardRef(String _sref, String type)
{
sref = _sref;
this.type = type;
return sref;
}
+ public abstract boolean isResolvable();
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+
+ @Override
+ public String toString()
+ {
+ return type + " reference to " + sref;
+ }
+ }
+ /**
+ * resolve forward references to sequences by their ID
+ * @author jprocter
+ */
+ abstract class SeqFref extends forwardRef
+ {
+ public SeqFref(String _sref, String type)
+ {
+ super(_sref, type);
+ }
public SequenceI getSrefSeq()
{
return seqRefIds.get(sref);
}
return sq;
}
-
- /**
- * @return true if the forward reference was fully resolved
- */
- abstract boolean resolve();
-
- @Override
- public String toString()
- {
- return type + " reference to " + sref;
- }
}
/**
};
return fref;
}
+
+ public forwardRef newMatrixFref(final String matRef,
+ final jalview.util.MapList mapping, final AlignmentAnnotation jaa)
+ {
+ forwardRef fref = new forwardRef(matRef,
+ "Matrix Reference for sequence and annotation")
+ {
+
+ @Override
+ boolean resolve()
+ {
+ ContactMatrixI cm = contactMatrixRefs.get(matRef);
+ PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef,
+ mapping, cm);
+
+ jaa.sequenceRef.addContactListFor(jaa, newpae);
+ return true;
+ }
+
+ @Override
+ public boolean isResolvable()
+ {
+ return (contactMatrixRefs.get(matRef) != null);
+ }
+ };
+ return fref;
+ }
public void resolveFrefedSequences()
{
- Iterator<SeqFref> nextFref = frefedSequence.iterator();
+ Iterator<forwardRef> nextFref = frefedSequence.iterator();
int toresolve = frefedSequence.size();
int unresolved = 0, failedtoresolve = 0;
while (nextFref.hasNext())
{
- SeqFref ref = nextFref.next();
+ forwardRef ref = nextFref.next();
if (ref.isResolvable())
{
try
// jms.addViewport(view);
object.getViewport().add(view);
}
+
+
+ if (storeDS)
+ {
+ // store matrices referenced by any views or annotation in this dataset
+ if (xmlMatrices!=null && xmlMatrices.size()>0)
+ {
+ Console.debug("Adding "+xmlMatrices.size()+" matrices to dataset.");
+ vamsasSet.getMatrix().addAll(xmlMatrices);
+ xmlMatrices.clear();
+ }
+ }
+
+
// object.setJalviewModelSequence(jms);
// object.getVamsasModel().addSequenceSet(vamsasSet);
object.getVamsasModel().getSequenceSet().add(vamsasSet);
.getContactMatrixFor(annotation);
if (cm != null)
{
- MatrixType xmlmat = new MatrixType();
- xmlmat.setType(cm.getType());
- xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
- xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
- // consider using an opaque to/from -> allow instance to control
- // its representation ?
- xmlmat.setElements(ContactMatrix.contactToFloatString(cm));
- if (cm.hasGroups())
- {
- for (BitSet gp : cm.getGroups())
- {
- xmlmat.getGroups().add(stringifyBitset(gp));
- }
- }
- if (cm.hasTree())
- {
- // provenance object for tree ?
- xmlmat.getNewick().add(cm.getNewick());
- xmlmat.setTreeMethod(cm.getTreeMethod());
- }
- if (cm.hasCutHeight())
- {
- xmlmat.setCutHeight(cm.getCutHeight());
- }
- // set/get properties
- if (cm instanceof MappableContactMatrixI)
- {
- jalview.util.MapList mlst = ((MappableContactMatrixI) cm)
- .getMapFor(annotation.sequenceRef);
- if (mlst != null)
- {
- MapListType mp = new MapListType();
- List<int[]> r = mlst.getFromRanges();
- for (int[] range : r)
- {
- MapListFrom mfrom = new MapListFrom();
- mfrom.setStart(range[0]);
- mfrom.setEnd(range[1]);
- // mp.addMapListFrom(mfrom);
- mp.getMapListFrom().add(mfrom);
- }
- r = mlst.getToRanges();
- for (int[] range : r)
- {
- MapListTo mto = new MapListTo();
- mto.setStart(range[0]);
- mto.setEnd(range[1]);
- // mp.addMapListTo(mto);
- mp.getMapListTo().add(mto);
- }
- mp.setMapFromUnit(
- BigInteger.valueOf(mlst.getFromRatio()));
- mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
- xmlmat.setMapping(mp);
- }
- }
- // and add to model
- an.getContactmatrix().add(xmlmat);
+ storeMatrixFor(vamsasSet, an,annotation, cm);
}
}
}
}
+ private void storeMatrixFor(SequenceSet root, Annotation an, AlignmentAnnotation annotation, ContactMatrixI cm)
+ {
+ String cmId = contactMatrices.get(cm);
+ MatrixType xmlmat=null;
+
+ // first create an xml ref for the matrix data, if none exist
+ if (cmId == null)
+ {
+ xmlmat = new MatrixType();
+ xmlmat.setType(cm.getType());
+ xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
+ xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
+ // consider using an opaque to/from -> allow instance to control
+ // its representation ?
+ xmlmat.setElements(ContactMatrix.contactToFloatString(cm));
+ if (cm.hasGroups())
+ {
+ for (BitSet gp : cm.getGroups())
+ {
+ xmlmat.getGroups().add(stringifyBitset(gp));
+ }
+ }
+ if (cm.hasTree())
+ {
+ // provenance object for tree ?
+ xmlmat.getNewick().add(cm.getNewick());
+ xmlmat.setTreeMethod(cm.getTreeMethod());
+ }
+ if (cm.hasCutHeight())
+ {
+ xmlmat.setCutHeight(cm.getCutHeight());
+ }
+ xmlmat.setId(cmId = "m"+contactMatrices.size()+System.currentTimeMillis());
+ Console.trace("Matrix data stored :"+cmId);
+ contactMatrices.put(cm, cmId);
+ contactMatrixRefs.put(cmId, cm);
+ xmlMatrices.add(xmlmat);
+ } else {
+ Console.trace("Existing Matrix stored :"+cmId);
+ }
+
+ // now store mapping
+
+ MapOnAMatrixType xmlmatmapping = new MapOnAMatrixType();
+ xmlmatmapping.setMatrix(cmId);
+
+ // Pretty much all matrices currently managed in this way are
+ // mappableContactMatrixI implementations - but check anyway
+ if (cm instanceof MappableContactMatrixI)
+ {
+ jalview.util.MapList mlst = ((MappableContactMatrixI) cm)
+ .getMapFor(annotation.sequenceRef);
+ if (mlst != null)
+ {
+ MapListType mp = new MapListType();
+ List<int[]> r = mlst.getFromRanges();
+ for (int[] range : r)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
+ // mp.addMapListFrom(mfrom);
+ mp.getMapListFrom().add(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int[] range : r)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
+ // mp.addMapListTo(mto);
+ mp.getMapListTo().add(mto);
+ }
+ mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+ xmlmatmapping.setMapping(mp);
+ }
+ }
+ // and add to model
+ an.getContactmatrix().add(xmlmatmapping);
+ }
+
private String stringifyBitset(BitSet gp)
{
StringBuilder sb = new StringBuilder();
initSeqRefs();
}
AlignFrame af = null, _af = null;
+ List<AlignFrame> toRepaint=new ArrayList<AlignFrame>();
IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
final String file = jprovider.getFilename();
if (_af != null && object.getViewport().size() > 0)
// getJalviewModelSequence().getViewportCount() > 0)
{
+ toRepaint.add(_af);
if (af == null)
{
// store a reference to the first view
} while (jarentry != null);
jin.close();
resolveFrefedSequences();
+ for (AlignFrame alignFrame:toRepaint)
+ {
+ alignFrame.repaint();
+ }
} catch (IOException ex)
{
ex.printStackTrace();
}
// ////////////////////////////////
+ // LOAD MATRICES (IF ANY)
+
+ if (vamsasSet.getMatrix()!=null && vamsasSet.getMatrix().size()>0)
+ {
+ importMatrixData(vamsasSet.getMatrix());
+ }
+
+ // ////////////////////////////////
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
if (annotation.getContactmatrix() != null
&& annotation.getContactmatrix().size() > 0)
{
- for (MatrixType xmlmat : annotation.getContactmatrix())
+ for (MapOnAMatrixType xmlmat : annotation.getContactmatrix())
{
- if (PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType()))
- {
- if (!xmlmat.getRows().equals(xmlmat.getCols()))
- {
- Console.error("Can't handle non square PAE Matrices");
- }
- else
- {
- float[][] elements = ContactMatrix
- .fromFloatStringToContacts(xmlmat.getElements(),
- xmlmat.getCols().intValue(),
- xmlmat.getRows().intValue());
- jalview.util.MapList mapping = null;
- if (xmlmat.getMapping() != null)
- {
- MapListType m = xmlmat.getMapping();
- // Mapping m = dr.getMapping();
- int fr[] = new int[m.getMapListFrom().size() * 2];
- Iterator<MapListFrom> from = m.getMapListFrom()
- .iterator();// enumerateMapListFrom();
- for (int _i = 0; from.hasNext(); _i += 2)
- {
- MapListFrom mf = from.next();
- fr[_i] = mf.getStart();
- fr[_i + 1] = mf.getEnd();
- }
- int fto[] = new int[m.getMapListTo().size() * 2];
- Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
- for (int _i = 0; to.hasNext(); _i += 2)
- {
- MapListTo mf = to.next();
- fto[_i] = mf.getStart();
- fto[_i + 1] = mf.getEnd();
- }
-
- mapping = new jalview.util.MapList(fr, fto,
- m.getMapFromUnit().intValue(),
- m.getMapToUnit().intValue());
- }
- List<BitSet> newgroups = new ArrayList<BitSet>();
- if (xmlmat.getGroups().size() > 0)
- {
- for (String sgroup : xmlmat.getGroups())
- {
- newgroups.add(deStringifyBitset(sgroup));
- }
- }
- String nwk = xmlmat.getNewick().size() > 0
- ? xmlmat.getNewick().get(0)
- : null;
- if (xmlmat.getNewick().size() > 1)
- {
- Console.log.info(
- "Ignoring additional clusterings for contact matrix");
- }
- String treeMethod = xmlmat.getTreeMethod();
- double thresh = xmlmat.getCutHeight() != null
- ? xmlmat.getCutHeight()
- : 0;
- GroupSet grpset = new GroupSet();
- grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
- PAEContactMatrix newpae = new PAEContactMatrix(
- jaa.sequenceRef, mapping, elements, grpset);
- jaa.sequenceRef.addContactListFor(jaa, newpae);
- }
- }
- else
- {
- Console.error("Ignoring CONTACT_MAP annotation with type "
- + xmlmat.getType());
- }
- }
+ restoreMatrixFor(jaa.sequenceRef, jaa, xmlmat);
+ }
}
}
return af;
}
+ private void importMatrixData(List<MatrixType> xmlmatrices)
+ {
+ for (MatrixType xmlmat:xmlmatrices)
+ {
+ if (!PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType()))
+ {
+ Console.error("Ignoring matrix '"+xmlmat.getId()+"' of type '"+xmlmat.getType());
+ continue;
+ }
+
+ if (!xmlmat.getRows().equals(xmlmat.getCols()))
+ {
+ Console.error("Can't handle non square matrices");
+ continue;
+ }
+
+ float[][] elements = ContactMatrix
+ .fromFloatStringToContacts(xmlmat.getElements(),
+ xmlmat.getCols().intValue(),
+ xmlmat.getRows().intValue());
+
+ List<BitSet> newgroups = new ArrayList<BitSet>();
+ if (xmlmat.getGroups().size() > 0)
+ {
+ for (String sgroup : xmlmat.getGroups())
+ {
+ newgroups.add(deStringifyBitset(sgroup));
+ }
+ }
+ String nwk = xmlmat.getNewick().size() > 0
+ ? xmlmat.getNewick().get(0)
+ : null;
+ if (xmlmat.getNewick().size() > 1)
+ {
+ Console.log.info(
+ "Ignoring additional clusterings for contact matrix");
+ }
+ String treeMethod = xmlmat.getTreeMethod();
+ double thresh = xmlmat.getCutHeight() != null
+ ? xmlmat.getCutHeight()
+ : 0;
+ GroupSet grpset = new GroupSet();
+ grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
+
+ FloatContactMatrix newcm = new FloatContactMatrix(elements, grpset);
+ contactMatrixRefs.put(xmlmat.getId(), newcm);
+ Console.trace("Restored base contact matrix "+xmlmat.getId());
+ }
+ }
+
+ private void restoreMatrixFor(SequenceI sequenceRef,
+ AlignmentAnnotation jaa, MapOnAMatrixType xmlmatmapping)
+ {
+ // restore mapping data to matrix data
+ jalview.util.MapList mapping = null;
+ if (xmlmatmapping.getMapping() != null)
+ {
+ MapListType m = xmlmatmapping.getMapping();
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFrom().size() * 2];
+ Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
+ for (int _i = 0; from.hasNext(); _i += 2)
+ {
+ MapListFrom mf = from.next();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListTo().size() * 2];
+ Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
+ for (int _i = 0; to.hasNext(); _i += 2)
+ {
+ MapListTo mf = to.next();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
+
+ mapping = new jalview.util.MapList(fr, fto,
+ m.getMapFromUnit().intValue(), m.getMapToUnit().intValue());
+ }
+
+ // locate matrix data in project XML and import
+ ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix());
+ if (cm == null)
+ {
+ frefedSequence
+ .add(newMatrixFref(xmlmatmapping.getMatrix(), mapping, jaa));
+ }
+ else
+ {
+ // create the PAEMatrix now
+ PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef,
+ mapping, cm);
+
+ jaa.sequenceRef.addContactListFor(jaa, newpae);
+ }
+
+ return;
+ }
+
/**
* Load Overview window, restoring colours, 'show hidden regions' flag, title
* and geometry as saved
int column;
int aaMax = aa_annotations.length - 1;
ContactMatrixI cm = viewport.getContactMatrix(_aa);
+ if (cm==null)
+ {
+ return;
+ }
while (x < eRes - sRes)
{
column = sRes + x;
Class<? extends AlignCalcWorkerI> workerClass)
{
List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+ AlignCalcWorkerI[] workers;
synchronized (canUpdate)
{
- for (AlignCalcWorkerI worker : canUpdate)
+ workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+ }
+ for (AlignCalcWorkerI worker : workers)
+ {
+ if (workerClass.equals(worker.getClass()))
{
- if (workerClass.equals(worker.getClass()))
- {
- workingClass.add(worker);
- }
+ workingClass.add(worker);
}
}
return (workingClass.size() == 0) ? null : workingClass;
* @return sequence position(s) corresponding to column in contact matrix
*/
int[] getMappedPositionsFor(SequenceI localFrame, int from, int to);
+
+ ContactMatrixI getMappedMatrix();
}
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.GroupSet;
import jalview.datamodel.GroupSetI;
import jalview.datamodel.Mapping;
public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
implements MappableContactMatrixI
{
- SequenceI refSeq = null;
-
- MapList toSeq = null;
-
/**
- * the length that refSeq is expected to be (excluding gaps, of course)
+ * the matrix that is being mapped to
*/
- int length;
+ protected ContactMatrixI mappedMatrix=null;
+
+ public ContactListI getContactList(int column)
+ {
+ return mappedMatrix.getContactList(column);
+ }
+
+ public float getMin()
+ {
+ return mappedMatrix.getMin();
+ }
+
+ public float getMax()
+ {
+ return mappedMatrix.getMax();
+ }
+
+ public int getWidth()
+ {
+ return mappedMatrix.getWidth();
+ }
+
+ public int getHeight()
+ {
+ return mappedMatrix.getHeight();
+ }
@Override
- public boolean hasReferenceSeq()
+ public ContactMatrixI getMappedMatrix()
{
- return (refSeq != null);
+ return mappedMatrix;
}
+
+ @Override
+ public GroupSetI getGroupSet()
+ {
+ return mappedMatrix.getGroupSet();
+ };
@Override
- public SequenceI getReferenceSeq()
+ public void setGroupSet(GroupSet makeGroups)
{
- return refSeq;
+ mappedMatrix.setGroupSet(makeGroups);
}
+
+ /**
+ * the sequence and how it is mapped to the matrix
+ */
+
+ SequenceI refSeq = null;
+
+ MapList toSeq = null;
/**
- * container for groups - defined on matrix columns
+ * the length that refSeq is expected to be (excluding gaps, of course)
*/
- GroupSet grps = new GroupSet();
+ int length;
@Override
- public GroupSetI getGroupSet()
+ public boolean hasReferenceSeq()
{
- return grps;
- };
+ return (refSeq != null);
+ }
@Override
- public void setGroupSet(GroupSet makeGroups)
+ public SequenceI getReferenceSeq()
{
- grps = makeGroups;
+ return refSeq;
}
@Override
}
/**
- * get a specific element of the contact matrix in its data-local coordinates
+ * get a specific element of the underlying contact matrix in its data-local coordinates
* rather than the mapped frame. Implementations are allowed to throw
* RunTimeExceptions if _column/i are out of bounds
*
* @param i
* @return
*/
- protected abstract double getElementAt(int _column, int i);
+ public double getElementAt(int _column, int i) {
+ return mappedMatrix.getElementAt(_column, i);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return 7 * (refSeq != null ? refSeq.hashCode() : 0)
+ + 11 * (toSeq != null ? toSeq.hashCode() : 0)
+ + 13 * (mappedMatrix != null ? mappedMatrix.hashCode() : 0)
+ + length * 3;
+ }
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == null || !(obj.getClass().equals(getClass())))
+ {
+ return false;
+ }
+ T them = (T) obj;
+ return mappedMatrix == them.mappedMatrix && length == them.length
+ && refSeq == them.refSeq && toSeq.equals(them.toSeq);
+
+ }
}
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.FloatContactMatrix;
import jalview.datamodel.GroupSet;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
{
- int maxrow = 0, maxcol = 0;
-
-
- float[][] elements;
-
- float maxscore;
-
-
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
throws FileFormatException
*/
public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
{
+ mappedMatrix=new FloatContactMatrix(matrix);
setRefSeq(_refSeq);
- maxcol = 0;
- for (float[] row : matrix)
- {
- if (row.length > maxcol)
- {
- maxcol = row.length;
- }
- maxscore = row[0];
- for (float f : row)
- {
- if (maxscore < f)
- {
- maxscore = f;
- }
- }
- }
- maxrow = matrix.length;
- elements = matrix;
-
}
/**
public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
float[][] elements2, GroupSet grps2)
{
- this(newRefSeq, elements2);
+ this(newRefSeq, new FloatContactMatrix(elements2,grps2));
+ toSeq = newFromMapList;
+ }
+
+ public PAEContactMatrix(SequenceI _refSeq,
+ ContactMatrixI floatContactMatrix)
+ {
+ mappedMatrix = floatContactMatrix;
+ setRefSeq(_refSeq);
+ }
+ public PAEContactMatrix(SequenceI _refSeq, MapList newFromMapList,
+ ContactMatrixI floatContactMatrix)
+ {
+ mappedMatrix = floatContactMatrix;
+ setRefSeq(_refSeq);
toSeq = newFromMapList;
- grps = grps2;
+ }
+
+ @Override
+ protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+ MapList newFromMapList)
+ {
+ return new PAEContactMatrix(newRefSeq, newFromMapList, mappedMatrix);
}
/**
- * parse a sane JSON representation of the pAE
+ * parse a sane JSON representation of the pAE and update the mappedMatrix
*
* @param pae_obj
*/
@SuppressWarnings("unchecked")
private void parse_version_2_pAE(Map<String, Object> pae_obj)
{
- maxscore = -1;
+ float maxscore = -1;
// look for a maxscore element - if there is one...
try
{
}
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
.getFirst(pae_obj, "predicted_aligned_error", "pae"));
- elements = new float[scoreRows.size()][scoreRows.size()];
+ float[][] elements = new float[scoreRows.size()][scoreRows.size()];
int row = 0, col = 0;
for (List<Long> scoreRow : scoreRows)
{
row++;
col = 0;
}
- maxcol = length;
- maxrow = length;
+ mappedMatrix=new FloatContactMatrix(elements);
}
/**
Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
// two pass - to allocate the elements array
+
+ int maxrow=-1,maxcol=-1;
while (rows.hasNext())
{
int row = rows.next().intValue();
cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
- elements = new float[maxcol][maxrow];
+ float[][] elements = new float[maxcol][maxrow];
while (scores.hasNext())
{
float escore = scores.next().floatValue();
elements[col - 1][row-1] = escore;
}
- maxscore = ((Double) MapUtils.getFirst(pae_obj,
- "max_predicted_aligned_error", "max_pae")).floatValue();
- }
-
- /**
- * getContactList(column) @returns the vector of predicted alignment errors
- * for reference position given by column
- */
- @Override
- public ContactListI getContactList(final int column)
- {
- if (column < 0 || column >= elements.length)
- {
- return null;
- }
-
- return new ContactListImpl(new ContactListProviderI()
- {
- @Override
- public int getPosition()
- {
- return column;
- }
-
- @Override
- public int getContactHeight()
- {
- return maxcol - 1;
- }
-
- @Override
- public double getContactAt(int mcolumn)
- {
- if (mcolumn < 0 || mcolumn >= elements[column].length)
- {
- return -1;
- }
- return elements[column][mcolumn];
- }
- });
- }
-
- /**
- * getElementAt(column, i) @returns the predicted superposition error for the
- * ith position when column is used as reference
- */
- @Override
- protected double getElementAt(int _column, int i)
- {
- return elements[_column][i];
- }
-
- @Override
- public float getMin()
- {
- return 0;
- }
-
- @Override
- public float getMax()
- {
- return maxscore;
+ mappedMatrix=new FloatContactMatrix(elements);
}
@Override
return PAEMATRIX;
}
- @Override
- public int getWidth()
- {
- return maxcol;
- }
- @Override
- public int getHeight()
- {
- return maxrow;
- }
public static void validateContactMatrixFile(String fileName)
throws FileFormatException, IOException
{
}
}
@Override
- protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
- MapList newFromMapList)
+ public boolean equals(Object obj)
+ {
+ return super.equals(obj);
+ }
+ @Override
+ public int hashCode()
{
- PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
- elements, new GroupSet(grps));
- return pae;
+ return super.hashCode();
}
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- * </sequence>
- * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+ "alcodon",
+ "alcodMap"
+})
@XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame
-{
-
- protected List<AlcodonFrame.Alcodon> alcodon;
-
- protected List<AlcodonFrame.AlcodMap> alcodMap;
+public class AlcodonFrame {
- /**
- * Gets the value of the alcodon property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the alcodon property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAlcodon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.Alcodon }
- *
- *
- */
- public List<AlcodonFrame.Alcodon> getAlcodon()
- {
- if (alcodon == null)
- {
- alcodon = new ArrayList<AlcodonFrame.Alcodon>();
- }
- return this.alcodon;
- }
-
- /**
- * Gets the value of the alcodMap property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the alcodMap property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAlcodMap().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.AlcodMap }
- *
- *
- */
- public List<AlcodonFrame.AlcodMap> getAlcodMap()
- {
- if (alcodMap == null)
- {
- alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
- }
- return this.alcodMap;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- * </sequence>
- * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "mapping" })
- public static class AlcodMap
- {
-
- @XmlElement(name = "Mapping", required = true)
- protected Mapping mapping;
-
- @XmlAttribute(name = "dnasq", required = true)
- protected String dnasq;
+ protected List<AlcodonFrame.Alcodon> alcodon;
+ protected List<AlcodonFrame.AlcodMap> alcodMap;
/**
+ * Gets the value of the alcodon property.
*
- * a Mapping entry and an associated protein sequence
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodon property.
*
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodon().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Mapping }
*
- */
- public Mapping getMapping()
- {
- return mapping;
- }
-
- /**
- * Sets the value of the mapping property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.Alcodon }
*
- * @param value
- * allowed object is {@link Mapping }
*
*/
- public void setMapping(Mapping value)
- {
- this.mapping = value;
+ public List<AlcodonFrame.Alcodon> getAlcodon() {
+ if (alcodon == null) {
+ alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+ }
+ return this.alcodon;
}
/**
- * Gets the value of the dnasq property.
+ * Gets the value of the alcodMap property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodMap().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.AlcodMap }
*
- * @return possible object is {@link String }
*
*/
- public String getDnasq()
- {
- return dnasq;
+ public List<AlcodonFrame.AlcodMap> getAlcodMap() {
+ if (alcodMap == null) {
+ alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+ }
+ return this.alcodMap;
}
+
/**
- * Sets the value of the dnasq property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setDnasq(String value)
- {
- this.dnasq = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "mapping"
+ })
+ public static class AlcodMap {
- }
+ @XmlElement(name = "Mapping", required = true)
+ protected Mapping mapping;
+ @XmlAttribute(name = "dnasq", required = true)
+ protected String dnasq;
- /**
- *
- * specifies a series of aligned codons from an associated DNA sequence
- * alignment that when translated correspond to columns of a peptide
- * alignment. Element may have either all pos1,2,3 attributes specified, or
- * none at all (indicating a gapped column with no translated peptide).
- *
- *
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Alcodon
- {
+ /**
+ *
+ * a Mapping entry and an associated protein
+ * sequence
+ *
+ *
+ * @return
+ * possible object is
+ * {@link Mapping }
+ *
+ */
+ public Mapping getMapping() {
+ return mapping;
+ }
- @XmlAttribute(name = "pos1")
- protected BigInteger pos1;
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value) {
+ this.mapping = value;
+ }
- @XmlAttribute(name = "pos2")
- protected BigInteger pos2;
+ /**
+ * Gets the value of the dnasq property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDnasq() {
+ return dnasq;
+ }
- @XmlAttribute(name = "pos3")
- protected BigInteger pos3;
+ /**
+ * Sets the value of the dnasq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDnasq(String value) {
+ this.dnasq = value;
+ }
- /**
- * Gets the value of the pos1 property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getPos1()
- {
- return pos1;
}
- /**
- * Sets the value of the pos1 property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPos1(BigInteger value)
- {
- this.pos1 = value;
- }
/**
- * Gets the value of the pos2 property.
*
- * @return possible object is {@link BigInteger }
+ * specifies a series of aligned codons from an
+ * associated DNA sequence alignment that when translated
+ * correspond to columns of a peptide alignment.
+ * Element may have
+ * either all pos1,2,3 attributes specified, or none at all
+ * (indicating a gapped column with no translated peptide).
+ *
*
- */
- public BigInteger getPos2()
- {
- return pos2;
- }
-
- /**
- * Sets the value of the pos2 property.
+ * <p>Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link BigInteger }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public void setPos2(BigInteger value)
- {
- this.pos2 = value;
- }
-
- /**
- * Gets the value of the pos3 property.
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @return possible object is {@link BigInteger }
*
*/
- public BigInteger getPos3()
- {
- return pos3;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Alcodon {
- /**
- * Sets the value of the pos3 property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setPos3(BigInteger value)
- {
- this.pos3 = value;
- }
+ @XmlAttribute(name = "pos1")
+ protected BigInteger pos1;
+ @XmlAttribute(name = "pos2")
+ protected BigInteger pos2;
+ @XmlAttribute(name = "pos3")
+ protected BigInteger pos3;
+
+ /**
+ * Gets the value of the pos1 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos1() {
+ return pos1;
+ }
- }
+ /**
+ * Sets the value of the pos1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos1(BigInteger value) {
+ this.pos1 = value;
+ }
+
+ /**
+ * Gets the value of the pos2 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos2() {
+ return pos2;
+ }
+
+ /**
+ * Sets the value of the pos2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos2(BigInteger value) {
+ this.pos2 = value;
+ }
+
+ /**
+ * Gets the value of the pos3 property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getPos3() {
+ return pos3;
+ }
+
+ /**
+ * Sets the value of the pos3 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setPos3(BigInteger value) {
+ this.pos3 = value;
+ }
+
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="thresholdLine" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="thresholdLine" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "annotationElement", "label", "description", "thresholdLine",
- "contactmatrix", "property" })
+@XmlType(name = "", propOrder = {
+ "annotationElement",
+ "label",
+ "description",
+ "thresholdLine",
+ "contactmatrix",
+ "property"
+})
@XmlRootElement(name = "Annotation")
-public class Annotation
-{
+public class Annotation {
- protected List<AnnotationElement> annotationElement;
+ protected List<AnnotationElement> annotationElement;
+ @XmlElement(required = true)
+ protected String label;
+ protected String description;
+ protected Annotation.ThresholdLine thresholdLine;
+ protected List<MapOnAMatrixType> contactmatrix;
+ protected List<Property> property;
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+ @XmlAttribute(name = "score")
+ protected Double score;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
- @XmlElement(required = true)
- protected String label;
-
- protected String description;
+ /**
+ * Gets the value of the annotationElement property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAnnotationElement().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AnnotationElement }
+ *
+ *
+ */
+ public List<AnnotationElement> getAnnotationElement() {
+ if (annotationElement == null) {
+ annotationElement = new ArrayList<AnnotationElement>();
+ }
+ return this.annotationElement;
+ }
- protected Annotation.ThresholdLine thresholdLine;
-
- protected List<MatrixType> contactmatrix;
-
- protected List<Property> property;
-
- @XmlAttribute(name = "graph", required = true)
- protected boolean graph;
-
- @XmlAttribute(name = "graphType")
- protected Integer graphType;
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
-
- @XmlAttribute(name = "groupRef")
- protected String groupRef;
-
- @XmlAttribute(name = "graphColour")
- protected Integer graphColour;
-
- @XmlAttribute(name = "graphGroup")
- protected Integer graphGroup;
-
- @XmlAttribute(name = "graphHeight")
- protected Integer graphHeight;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- @XmlAttribute(name = "scoreOnly")
- protected Boolean scoreOnly;
-
- @XmlAttribute(name = "score")
- protected Double score;
-
- @XmlAttribute(name = "visible")
- protected Boolean visible;
-
- @XmlAttribute(name = "centreColLabels")
- protected Boolean centreColLabels;
-
- @XmlAttribute(name = "scaleColLabels")
- protected Boolean scaleColLabels;
-
- @XmlAttribute(name = "showAllColLabels")
- protected Boolean showAllColLabels;
-
- @XmlAttribute(name = "autoCalculated")
- protected Boolean autoCalculated;
-
- @XmlAttribute(name = "belowAlignment")
- protected Boolean belowAlignment;
-
- @XmlAttribute(name = "calcId")
- protected String calcId;
-
- /**
- * Gets the value of the annotationElement property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the annotationElement property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAnnotationElement().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AnnotationElement }
- *
- *
- */
- public List<AnnotationElement> getAnnotationElement()
- {
- if (annotationElement == null)
- {
- annotationElement = new ArrayList<AnnotationElement>();
- }
- return this.annotationElement;
- }
-
- /**
- * Gets the value of the label property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getLabel()
- {
- return label;
- }
-
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setLabel(String value)
- {
- this.label = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the thresholdLine property.
- *
- * @return possible object is {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine getThresholdLine()
- {
- return thresholdLine;
- }
-
- /**
- * Sets the value of the thresholdLine property.
- *
- * @param value
- * allowed object is {@link Annotation.ThresholdLine }
- *
- */
- public void setThresholdLine(Annotation.ThresholdLine value)
- {
- this.thresholdLine = value;
- }
-
- /**
- * Gets the value of the contactmatrix property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the contactmatrix property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getContactmatrix().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link MatrixType
- * }
- *
- *
- */
- public List<MatrixType> getContactmatrix()
- {
- if (contactmatrix == null)
- {
- contactmatrix = new ArrayList<MatrixType>();
- }
- return this.contactmatrix;
- }
-
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Property }
- *
- *
- */
- public List<Property> getProperty()
- {
- if (property == null)
- {
- property = new ArrayList<Property>();
- }
- return this.property;
- }
-
- /**
- * Gets the value of the graph property.
- *
- */
- public boolean isGraph()
- {
- return graph;
- }
-
- /**
- * Sets the value of the graph property.
- *
- */
- public void setGraph(boolean value)
- {
- this.graph = value;
- }
-
- /**
- * Gets the value of the graphType property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphType()
- {
- return graphType;
- }
-
- /**
- * Sets the value of the graphType property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphType(Integer value)
- {
- this.graphType = value;
- }
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceRef()
- {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceRef(String value)
- {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the groupRef property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getGroupRef()
- {
- return groupRef;
- }
-
- /**
- * Sets the value of the groupRef property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setGroupRef(String value)
- {
- this.groupRef = value;
- }
-
- /**
- * Gets the value of the graphColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphColour()
- {
- return graphColour;
- }
-
- /**
- * Sets the value of the graphColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphColour(Integer value)
- {
- this.graphColour = value;
- }
-
- /**
- * Gets the value of the graphGroup property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphGroup()
- {
- return graphGroup;
- }
-
- /**
- * Sets the value of the graphGroup property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphGroup(Integer value)
- {
- this.graphGroup = value;
- }
-
- /**
- * Gets the value of the graphHeight property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGraphHeight()
- {
- return graphHeight;
- }
-
- /**
- * Sets the value of the graphHeight property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGraphHeight(Integer value)
- {
- this.graphHeight = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the scoreOnly property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isScoreOnly()
- {
- if (scoreOnly == null)
- {
- return false;
- }
- else
- {
- return scoreOnly;
- }
- }
-
- /**
- * Sets the value of the scoreOnly property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScoreOnly(Boolean value)
- {
- this.scoreOnly = value;
- }
-
- /**
- * Gets the value of the score property.
- *
- * @return possible object is {@link Double }
- *
- */
- public Double getScore()
- {
- return score;
- }
-
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is {@link Double }
- *
- */
- public void setScore(Double value)
- {
- this.score = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isVisible()
- {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setVisible(Boolean value)
- {
- this.visible = value;
- }
-
- /**
- * Gets the value of the centreColLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isCentreColLabels()
- {
- return centreColLabels;
- }
-
- /**
- * Sets the value of the centreColLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCentreColLabels(Boolean value)
- {
- this.centreColLabels = value;
- }
-
- /**
- * Gets the value of the scaleColLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isScaleColLabels()
- {
- return scaleColLabels;
- }
-
- /**
- * Sets the value of the scaleColLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScaleColLabels(Boolean value)
- {
- this.scaleColLabels = value;
- }
-
- /**
- * Gets the value of the showAllColLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowAllColLabels()
- {
- return showAllColLabels;
- }
-
- /**
- * Sets the value of the showAllColLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowAllColLabels(Boolean value)
- {
- this.showAllColLabels = value;
- }
-
- /**
- * Gets the value of the autoCalculated property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isAutoCalculated()
- {
- if (autoCalculated == null)
- {
- return false;
- }
- else
- {
- return autoCalculated;
- }
- }
-
- /**
- * Sets the value of the autoCalculated property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoCalculated(Boolean value)
- {
- this.autoCalculated = value;
- }
-
- /**
- * Gets the value of the belowAlignment property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isBelowAlignment()
- {
- if (belowAlignment == null)
- {
- return true;
- }
- else
- {
- return belowAlignment;
- }
- }
-
- /**
- * Sets the value of the belowAlignment property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setBelowAlignment(Boolean value)
- {
- this.belowAlignment = value;
- }
-
- /**
- * Gets the value of the calcId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCalcId()
- {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCalcId(String value)
- {
- this.calcId = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class ThresholdLine
- {
-
- @XmlAttribute(name = "label")
- protected String label;
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
- @XmlAttribute(name = "value")
- protected Float value;
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
- @XmlAttribute(name = "colour")
- protected Integer colour;
+ /**
+ * Gets the value of the thresholdLine property.
+ *
+ * @return
+ * possible object is
+ * {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine getThresholdLine() {
+ return thresholdLine;
+ }
/**
- * Gets the value of the label property.
+ * Sets the value of the thresholdLine property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Annotation.ThresholdLine }
+ *
+ */
+ public void setThresholdLine(Annotation.ThresholdLine value) {
+ this.thresholdLine = value;
+ }
+
+ /**
+ * Gets the value of the contactmatrix property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the contactmatrix property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getContactmatrix().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapOnAMatrixType }
*
- * @return possible object is {@link String }
*
*/
- public String getLabel()
- {
- return label;
+ public List<MapOnAMatrixType> getContactmatrix() {
+ if (contactmatrix == null) {
+ contactmatrix = new ArrayList<MapOnAMatrixType>();
+ }
+ return this.contactmatrix;
}
/**
- * Sets the value of the label property.
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Property }
+ *
+ *
+ */
+ public List<Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the graph property.
+ *
+ */
+ public boolean isGraph() {
+ return graph;
+ }
+
+ /**
+ * Sets the value of the graph property.
+ *
+ */
+ public void setGraph(boolean value) {
+ this.graph = value;
+ }
+
+ /**
+ * Gets the value of the graphType property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGraphType() {
+ return graphType;
+ }
+
+ /**
+ * Sets the value of the graphType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphType(Integer value) {
+ this.graphType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the groupRef property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setLabel(String value)
- {
- this.label = value;
+ public String getGroupRef() {
+ return groupRef;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the groupRef property.
*
- * @return possible object is {@link Float }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setGroupRef(String value) {
+ this.groupRef = value;
+ }
+
+ /**
+ * Gets the value of the graphColour property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Float getValue()
- {
- return value;
+ public Integer getGraphColour() {
+ return graphColour;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the graphColour property.
*
* @param value
- * allowed object is {@link Float }
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphColour(Integer value) {
+ this.graphColour = value;
+ }
+
+ /**
+ * Gets the value of the graphGroup property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public void setValue(Float value)
- {
- this.value = value;
+ public Integer getGraphGroup() {
+ return graphGroup;
}
/**
- * Gets the value of the colour property.
+ * Sets the value of the graphGroup property.
*
- * @return possible object is {@link Integer }
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphGroup(Integer value) {
+ this.graphGroup = value;
+ }
+
+ /**
+ * Gets the value of the graphHeight property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Integer getColour()
- {
- return colour;
+ public Integer getGraphHeight() {
+ return graphHeight;
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the graphHeight property.
*
* @param value
- * allowed object is {@link Integer }
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGraphHeight(Integer value) {
+ this.graphHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setColour(Integer value)
- {
- this.colour = value;
+ public String getId() {
+ return id;
}
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the scoreOnly property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isScoreOnly() {
+ if (scoreOnly == null) {
+ return false;
+ } else {
+ return scoreOnly;
+ }
+ }
+
+ /**
+ * Sets the value of the scoreOnly property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScoreOnly(Boolean value) {
+ this.scoreOnly = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return
+ * possible object is
+ * {@link Double }
+ *
+ */
+ public Double getScore() {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Double }
+ *
+ */
+ public void setScore(Double value) {
+ this.score = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the centreColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCentreColLabels() {
+ return centreColLabels;
+ }
+
+ /**
+ * Sets the value of the centreColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColLabels(Boolean value) {
+ this.centreColLabels = value;
+ }
+
+ /**
+ * Gets the value of the scaleColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isScaleColLabels() {
+ return scaleColLabels;
+ }
+
+ /**
+ * Sets the value of the scaleColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleColLabels(Boolean value) {
+ this.scaleColLabels = value;
+ }
+
+ /**
+ * Gets the value of the showAllColLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAllColLabels() {
+ return showAllColLabels;
+ }
+
+ /**
+ * Sets the value of the showAllColLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAllColLabels(Boolean value) {
+ this.showAllColLabels = value;
+ }
+
+ /**
+ * Gets the value of the autoCalculated property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAutoCalculated() {
+ if (autoCalculated == null) {
+ return false;
+ } else {
+ return autoCalculated;
+ }
+ }
+
+ /**
+ * Sets the value of the autoCalculated property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoCalculated(Boolean value) {
+ this.autoCalculated = value;
+ }
+
+ /**
+ * Gets the value of the belowAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isBelowAlignment() {
+ if (belowAlignment == null) {
+ return true;
+ } else {
+ return belowAlignment;
+ }
+ }
+
+ /**
+ * Sets the value of the belowAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setBelowAlignment(Boolean value) {
+ this.belowAlignment = value;
+ }
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine {
+
+ @XmlAttribute(name = "label")
+ protected String label;
+ @XmlAttribute(name = "value")
+ protected Float value;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getLabel() {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setLabel(String value) {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setValue(Float value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
+
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for AnnotationColourScheme complex type.
+ * <p>Java class for AnnotationColourScheme complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="AnnotationColourScheme">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="AnnotationColourScheme"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme
-{
-
- @XmlAttribute(name = "aboveThreshold")
- protected Integer aboveThreshold;
-
- @XmlAttribute(name = "annotation")
- protected String annotation;
-
- @XmlAttribute(name = "minColour")
- protected Integer minColour;
-
- @XmlAttribute(name = "maxColour")
- protected Integer maxColour;
-
- @XmlAttribute(name = "colourScheme")
- protected String colourScheme;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "perSequence")
- protected Boolean perSequence;
-
- @XmlAttribute(name = "predefinedColours")
- protected Boolean predefinedColours;
-
- /**
- * Gets the value of the aboveThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getAboveThreshold()
- {
- return aboveThreshold;
- }
-
- /**
- * Sets the value of the aboveThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setAboveThreshold(Integer value)
- {
- this.aboveThreshold = value;
- }
-
- /**
- * Gets the value of the annotation property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getAnnotation()
- {
- return annotation;
- }
-
- /**
- * Sets the value of the annotation property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setAnnotation(String value)
- {
- this.annotation = value;
- }
-
- /**
- * Gets the value of the minColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMinColour()
- {
- return minColour;
- }
-
- /**
- * Sets the value of the minColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMinColour(Integer value)
- {
- this.minColour = value;
- }
-
- /**
- * Gets the value of the maxColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMaxColour()
- {
- return maxColour;
- }
-
- /**
- * Sets the value of the maxColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMaxColour(Integer value)
- {
- this.maxColour = value;
- }
-
- /**
- * Gets the value of the colourScheme property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getColourScheme()
- {
- return colourScheme;
- }
-
- /**
- * Sets the value of the colourScheme property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setColourScheme(String value)
- {
- this.colourScheme = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the perSequence property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPerSequence()
- {
- return perSequence;
- }
-
- /**
- * Sets the value of the perSequence property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPerSequence(Boolean value)
- {
- this.perSequence = value;
- }
-
- /**
- * Gets the value of the predefinedColours property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isPredefinedColours()
- {
- return predefinedColours;
- }
-
- /**
- * Sets the value of the predefinedColours property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPredefinedColours(Boolean value)
- {
- this.predefinedColours = value;
- }
+public class AnnotationColourScheme {
+
+ @XmlAttribute(name = "aboveThreshold")
+ protected Integer aboveThreshold;
+ @XmlAttribute(name = "annotation")
+ protected String annotation;
+ @XmlAttribute(name = "minColour")
+ protected Integer minColour;
+ @XmlAttribute(name = "maxColour")
+ protected Integer maxColour;
+ @XmlAttribute(name = "colourScheme")
+ protected String colourScheme;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "perSequence")
+ protected Boolean perSequence;
+ @XmlAttribute(name = "predefinedColours")
+ protected Boolean predefinedColours;
+
+ /**
+ * Gets the value of the aboveThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getAboveThreshold() {
+ return aboveThreshold;
+ }
+
+ /**
+ * Sets the value of the aboveThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setAboveThreshold(Integer value) {
+ this.aboveThreshold = value;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotation() {
+ return annotation;
+ }
+
+ /**
+ * Sets the value of the annotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotation(String value) {
+ this.annotation = value;
+ }
+
+ /**
+ * Gets the value of the minColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMinColour() {
+ return minColour;
+ }
+
+ /**
+ * Sets the value of the minColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMinColour(Integer value) {
+ this.minColour = value;
+ }
+
+ /**
+ * Gets the value of the maxColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMaxColour() {
+ return maxColour;
+ }
+
+ /**
+ * Sets the value of the maxColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMaxColour(Integer value) {
+ this.maxColour = value;
+ }
+
+ /**
+ * Gets the value of the colourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColourScheme() {
+ return colourScheme;
+ }
+
+ /**
+ * Sets the value of the colourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColourScheme(String value) {
+ this.colourScheme = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the perSequence property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPerSequence() {
+ return perSequence;
+ }
+
+ /**
+ * Sets the value of the perSequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPerSequence(Boolean value) {
+ this.perSequence = value;
+ }
+
+ /**
+ * Gets the value of the predefinedColours property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPredefinedColours() {
+ return predefinedColours;
+ }
+
+ /**
+ * Sets the value of the predefinedColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPredefinedColours(Boolean value) {
+ this.predefinedColours = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="secondaryStructure" minOccurs="0">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <length value="1"/>
- * </restriction>
- * </simpleType>
- * </element>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
- * </sequence>
- * <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="secondaryStructure" minOccurs="0"&gt;
+ * &lt;simpleType&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;length value="1"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "displayCharacter", "description", "secondaryStructure", "value" })
+@XmlType(name = "", propOrder = {
+ "displayCharacter",
+ "description",
+ "secondaryStructure",
+ "value"
+})
@XmlRootElement(name = "annotationElement")
-public class AnnotationElement
-{
-
- protected String displayCharacter;
-
- protected String description;
-
- protected String secondaryStructure;
-
- protected Float value;
-
- @XmlAttribute(name = "position", required = true)
- protected int position;
-
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the displayCharacter property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDisplayCharacter()
- {
- return displayCharacter;
- }
-
- /**
- * Sets the value of the displayCharacter property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDisplayCharacter(String value)
- {
- this.displayCharacter = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSecondaryStructure()
- {
- return secondaryStructure;
- }
-
- /**
- * Sets the value of the secondaryStructure property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSecondaryStructure(String value)
- {
- this.secondaryStructure = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getValue()
- {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setValue(Float value)
- {
- this.value = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- */
- public int getPosition()
- {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- */
- public void setPosition(int value)
- {
- this.position = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColour(Integer value)
- {
- this.colour = value;
- }
+public class AnnotationElement {
+
+ protected String displayCharacter;
+ protected String description;
+ protected String secondaryStructure;
+ protected Float value;
+ @XmlAttribute(name = "position", required = true)
+ protected int position;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the displayCharacter property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDisplayCharacter() {
+ return displayCharacter;
+ }
+
+ /**
+ * Sets the value of the displayCharacter property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDisplayCharacter(String value) {
+ this.displayCharacter = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSecondaryStructure() {
+ return secondaryStructure;
+ }
+
+ /**
+ * Sets the value of the secondaryStructure property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSecondaryStructure(String value) {
+ this.secondaryStructure = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setValue(Float value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ */
+ public int getPosition() {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ */
+ public void setPosition(int value) {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for DoubleMatrix complex type.
+ * <p>Java class for DoubleMatrix complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="DoubleMatrix">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- * <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- * </sequence>
- * <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="DoubleMatrix"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "DoubleMatrix",
- namespace = "www.jalview.org",
- propOrder =
- { "row", "d", "e" })
-public class DoubleMatrix
-{
-
- protected List<DoubleVector> row;
-
- @XmlElement(name = "D")
- protected DoubleVector d;
-
- @XmlElement(name = "E")
- protected DoubleVector e;
-
- @XmlAttribute(name = "rows")
- protected Integer rows;
-
- @XmlAttribute(name = "columns")
- protected Integer columns;
-
- /**
- * Gets the value of the row property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the row property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getRow().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DoubleVector }
- *
- *
- */
- public List<DoubleVector> getRow()
- {
- if (row == null)
- {
- row = new ArrayList<DoubleVector>();
+@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
+ "row",
+ "d",
+ "e"
+})
+public class DoubleMatrix {
+
+ protected List<DoubleVector> row;
+ @XmlElement(name = "D")
+ protected DoubleVector d;
+ @XmlElement(name = "E")
+ protected DoubleVector e;
+ @XmlAttribute(name = "rows")
+ protected Integer rows;
+ @XmlAttribute(name = "columns")
+ protected Integer columns;
+
+ /**
+ * Gets the value of the row property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the row property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRow().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DoubleVector }
+ *
+ *
+ */
+ public List<DoubleVector> getRow() {
+ if (row == null) {
+ row = new ArrayList<DoubleVector>();
+ }
+ return this.row;
+ }
+
+ /**
+ * Gets the value of the d property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleVector }
+ *
+ */
+ public DoubleVector getD() {
+ return d;
+ }
+
+ /**
+ * Sets the value of the d property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleVector }
+ *
+ */
+ public void setD(DoubleVector value) {
+ this.d = value;
+ }
+
+ /**
+ * Gets the value of the e property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleVector }
+ *
+ */
+ public DoubleVector getE() {
+ return e;
+ }
+
+ /**
+ * Sets the value of the e property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleVector }
+ *
+ */
+ public void setE(DoubleVector value) {
+ this.e = value;
+ }
+
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getRows() {
+ return rows;
+ }
+
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setRows(Integer value) {
+ this.rows = value;
+ }
+
+ /**
+ * Gets the value of the columns property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColumns() {
+ return columns;
+ }
+
+ /**
+ * Sets the value of the columns property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColumns(Integer value) {
+ this.columns = value;
}
- return this.row;
- }
-
- /**
- * Gets the value of the d property.
- *
- * @return possible object is {@link DoubleVector }
- *
- */
- public DoubleVector getD()
- {
- return d;
- }
-
- /**
- * Sets the value of the d property.
- *
- * @param value
- * allowed object is {@link DoubleVector }
- *
- */
- public void setD(DoubleVector value)
- {
- this.d = value;
- }
-
- /**
- * Gets the value of the e property.
- *
- * @return possible object is {@link DoubleVector }
- *
- */
- public DoubleVector getE()
- {
- return e;
- }
-
- /**
- * Sets the value of the e property.
- *
- * @param value
- * allowed object is {@link DoubleVector }
- *
- */
- public void setE(DoubleVector value)
- {
- this.e = value;
- }
-
- /**
- * Gets the value of the rows property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getRows()
- {
- return rows;
- }
-
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setRows(Integer value)
- {
- this.rows = value;
- }
-
- /**
- * Gets the value of the columns property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColumns()
- {
- return columns;
- }
-
- /**
- * Sets the value of the columns property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColumns(Integer value)
- {
- this.columns = value;
- }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for DoubleVector complex type.
+ * <p>Java class for DoubleVector complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="DoubleVector">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="DoubleVector"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "DoubleVector",
- namespace = "www.jalview.org",
- propOrder =
- { "v" })
-public class DoubleVector
-{
+@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
+ "v"
+})
+public class DoubleVector {
- @XmlElement(type = Double.class)
- protected List<Double> v;
+ @XmlElement(type = Double.class)
+ protected List<Double> v;
- /**
- * Gets the value of the v property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the v property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getV().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Double }
- *
- *
- */
- public List<Double> getV()
- {
- if (v == null)
- {
- v = new ArrayList<Double>();
+ /**
+ * Gets the value of the v property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the v property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getV().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Double }
+ *
+ *
+ */
+ public List<Double> getV() {
+ if (v == null) {
+ v = new ArrayList<Double>();
+ }
+ return this.v;
}
- return this.v;
- }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for feature complex type.
+ * <p>Java class for feature complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="feature">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="otherData" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="feature"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "feature",
- namespace = "www.jalview.org",
- propOrder =
- { "otherData" })
-public class Feature
-{
-
- protected List<Feature.OtherData> otherData;
-
- @XmlAttribute(name = "begin", required = true)
- protected int begin;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "description")
- protected String description;
-
- @XmlAttribute(name = "status")
- protected String status;
-
- @XmlAttribute(name = "featureGroup")
- protected String featureGroup;
-
- @XmlAttribute(name = "score")
- protected Float score;
-
- /**
- * Gets the value of the otherData property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the otherData property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getOtherData().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature.OtherData }
- *
- *
- */
- public List<Feature.OtherData> getOtherData()
- {
- if (otherData == null)
- {
- otherData = new ArrayList<Feature.OtherData>();
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+ "otherData"
+})
+public class Feature {
+
+ protected List<Feature.OtherData> otherData;
+ @XmlAttribute(name = "begin", required = true)
+ protected int begin;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "description")
+ protected String description;
+ @XmlAttribute(name = "status")
+ protected String status;
+ @XmlAttribute(name = "featureGroup")
+ protected String featureGroup;
+ @XmlAttribute(name = "score")
+ protected Float score;
+
+ /**
+ * Gets the value of the otherData property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the otherData property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getOtherData().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature.OtherData }
+ *
+ *
+ */
+ public List<Feature.OtherData> getOtherData() {
+ if (otherData == null) {
+ otherData = new ArrayList<Feature.OtherData>();
+ }
+ return this.otherData;
}
- return this.otherData;
- }
-
- /**
- * Gets the value of the begin property.
- *
- */
- public int getBegin()
- {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- */
- public void setBegin(int value)
- {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the status property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getStatus()
- {
- return status;
- }
-
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setStatus(String value)
- {
- this.status = value;
- }
-
- /**
- * Gets the value of the featureGroup property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFeatureGroup()
- {
- return featureGroup;
- }
-
- /**
- * Sets the value of the featureGroup property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFeatureGroup(String value)
- {
- this.featureGroup = value;
- }
-
- /**
- * Gets the value of the score property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getScore()
- {
- return score;
- }
-
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setScore(Float value)
- {
- this.score = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class OtherData
- {
-
- @XmlAttribute(name = "key", required = true)
- protected String key;
-
- @XmlAttribute(name = "key2")
- protected String key2;
-
- @XmlAttribute(name = "value", required = true)
- protected String value;
/**
- * Gets the value of the key property.
+ * Gets the value of the begin property.
*
- * @return possible object is {@link String }
+ */
+ public int getBegin() {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
*
*/
- public String getKey()
- {
- return key;
+ public void setBegin(int value) {
+ this.begin = value;
}
/**
- * Sets the value of the key property.
+ * Gets the value of the end property.
*
- * @param value
- * allowed object is {@link String }
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the type property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setKey(String value)
- {
- this.key = value;
+ public String getType() {
+ return type;
}
/**
- * Gets the value of the key2 property.
+ * Sets the value of the type property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the description property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getKey2()
- {
- return key2;
+ public String getDescription() {
+ return description;
}
/**
- * Sets the value of the key2 property.
+ * Sets the value of the description property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the status property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setKey2(String value)
- {
- this.key2 = value;
+ public String getStatus() {
+ return status;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the status property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setStatus(String value) {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the featureGroup property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getValue()
- {
- return value;
+ public String getFeatureGroup() {
+ return featureGroup;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the featureGroup property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFeatureGroup(String value) {
+ this.featureGroup = value;
+ }
+
+ /**
+ * Gets the value of the score property.
*
+ * @return
+ * possible object is
+ * {@link Float }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public Float getScore() {
+ return score;
}
- }
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setScore(Float value) {
+ this.score = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class OtherData {
+
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+ @XmlAttribute(name = "key2")
+ protected String key2;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+ /**
+ * Gets the value of the key2 property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey2() {
+ return key2;
+ }
+
+ /**
+ * Sets the value of the key2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey2(String value) {
+ this.key2 = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for FeatureMatcher complex type.
+ * <p>Java class for FeatureMatcher complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="FeatureMatcher">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="FeatureMatcher"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "FeatureMatcher",
- namespace = "www.jalview.org/colours",
- propOrder =
- { "attributeName", "condition", "value" })
-public class FeatureMatcher
-{
-
- @XmlElement(namespace = "")
- protected List<String> attributeName;
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+ "attributeName",
+ "condition",
+ "value"
+})
+public class FeatureMatcher {
- @XmlElement(namespace = "", required = true)
- protected String condition;
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "", required = true)
+ protected String condition;
+ @XmlElement(namespace = "", required = true)
+ protected String value;
+ @XmlAttribute(name = "by")
+ protected FilterBy by;
- @XmlElement(namespace = "", required = true)
- protected String value;
-
- @XmlAttribute(name = "by")
- protected FilterBy by;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
}
- return this.attributeName;
- }
- /**
- * Gets the value of the condition property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCondition()
- {
- return condition;
- }
+ /**
+ * Gets the value of the condition property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCondition() {
+ return condition;
+ }
- /**
- * Sets the value of the condition property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCondition(String value)
- {
- this.condition = value;
- }
+ /**
+ * Sets the value of the condition property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCondition(String value) {
+ this.condition = value;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
- /**
- * Gets the value of the by property.
- *
- * @return possible object is {@link FilterBy }
- *
- */
- public FilterBy getBy()
- {
- return by;
- }
+ /**
+ * Gets the value of the by property.
+ *
+ * @return
+ * possible object is
+ * {@link FilterBy }
+ *
+ */
+ public FilterBy getBy() {
+ return by;
+ }
- /**
- * Sets the value of the by property.
- *
- * @param value
- * allowed object is {@link FilterBy }
- *
- */
- public void setBy(FilterBy value)
- {
- this.by = value;
- }
+ /**
+ * Sets the value of the by property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FilterBy }
+ *
+ */
+ public void setBy(FilterBy value) {
+ this.by = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
* A feature match condition, which may be simple or compound
*
- * <p>
- * Java class for FeatureMatcherSet complex type.
+ * <p>Java class for FeatureMatcherSet complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="FeatureMatcherSet">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <choice>
- * <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
- * <element name="compoundMatcher">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- * </sequence>
- * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </choice>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="FeatureMatcherSet"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;choice&gt;
+ * &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/&gt;
+ * &lt;element name="compoundMatcher"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/choice&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "FeatureMatcherSet",
- namespace = "www.jalview.org/colours",
- propOrder =
- { "matchCondition", "compoundMatcher" })
-public class FeatureMatcherSet
-{
-
- @XmlElement(namespace = "")
- protected FeatureMatcher matchCondition;
-
- @XmlElement(namespace = "")
- protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
-
- /**
- * Gets the value of the matchCondition property.
- *
- * @return possible object is {@link FeatureMatcher }
- *
- */
- public FeatureMatcher getMatchCondition()
- {
- return matchCondition;
- }
-
- /**
- * Sets the value of the matchCondition property.
- *
- * @param value
- * allowed object is {@link FeatureMatcher }
- *
- */
- public void setMatchCondition(FeatureMatcher value)
- {
- this.matchCondition = value;
- }
-
- /**
- * Gets the value of the compoundMatcher property.
- *
- * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
- {
- return compoundMatcher;
- }
-
- /**
- * Sets the value of the compoundMatcher property.
- *
- * @param value
- * allowed object is {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
- {
- this.compoundMatcher = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- * </sequence>
- * <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "matcherSet" })
- public static class CompoundMatcher
- {
-
- @XmlElement(namespace = "", required = true)
- protected List<FeatureMatcherSet> matcherSet;
-
- @XmlAttribute(name = "and", required = true)
- protected boolean and;
+@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
+ "matchCondition",
+ "compoundMatcher"
+})
+public class FeatureMatcherSet {
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcher matchCondition;
+ @XmlElement(namespace = "")
+ protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
/**
- * Gets the value of the matcherSet property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the matcherSet property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getMatcherSet().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link FeatureMatcherSet }
+ * Gets the value of the matchCondition property.
*
+ * @return
+ * possible object is
+ * {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher getMatchCondition() {
+ return matchCondition;
+ }
+
+ /**
+ * Sets the value of the matchCondition property.
*
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcher }
+ *
*/
- public List<FeatureMatcherSet> getMatcherSet()
- {
- if (matcherSet == null)
- {
- matcherSet = new ArrayList<FeatureMatcherSet>();
- }
- return this.matcherSet;
+ public void setMatchCondition(FeatureMatcher value) {
+ this.matchCondition = value;
}
/**
- * Gets the value of the and property.
+ * Gets the value of the compoundMatcher property.
*
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet.CompoundMatcher }
+ *
*/
- public boolean isAnd()
- {
- return and;
+ public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
+ return compoundMatcher;
}
/**
- * Sets the value of the and property.
+ * Sets the value of the compoundMatcher property.
*
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet.CompoundMatcher }
+ *
*/
- public void setAnd(boolean value)
- {
- this.and = value;
+ public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
+ this.compoundMatcher = value;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "matcherSet"
+ })
+ public static class CompoundMatcher {
+
+ @XmlElement(namespace = "", required = true)
+ protected List<FeatureMatcherSet> matcherSet;
+ @XmlAttribute(name = "and", required = true)
+ protected boolean and;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMatcherSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link FeatureMatcherSet }
+ *
+ *
+ */
+ public List<FeatureMatcherSet> getMatcherSet() {
+ if (matcherSet == null) {
+ matcherSet = new ArrayList<FeatureMatcherSet>();
+ }
+ return this.matcherSet;
+ }
+
+ /**
+ * Gets the value of the and property.
+ *
+ */
+ public boolean isAnd() {
+ return and;
+ }
+
+ /**
+ * Sets the value of the and property.
+ *
+ */
+ public void setAnd(boolean value) {
+ this.and = value;
+ }
+
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for FilterBy.
+ * <p>Java class for FilterBy.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
- * <p>
- *
- * <pre>
- * <simpleType name="FilterBy">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="byLabel"/>
- * <enumeration value="byScore"/>
- * <enumeration value="byAttribute"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="FilterBy"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="byLabel"/&gt;
+ * &lt;enumeration value="byScore"/&gt;
+ * &lt;enumeration value="byAttribute"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum FilterBy
-{
-
- @XmlEnumValue("byLabel")
- BY_LABEL("byLabel"), @XmlEnumValue("byScore")
- BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
- BY_ATTRIBUTE("byAttribute");
-
- private final String value;
-
- FilterBy(String v)
- {
- value = v;
- }
+public enum FilterBy {
+
+ @XmlEnumValue("byLabel")
+ BY_LABEL("byLabel"),
+ @XmlEnumValue("byScore")
+ BY_SCORE("byScore"),
+ @XmlEnumValue("byAttribute")
+ BY_ATTRIBUTE("byAttribute");
+ private final String value;
+
+ FilterBy(String v) {
+ value = v;
+ }
- public String value()
- {
- return value;
- }
+ public String value() {
+ return value;
+ }
- public static FilterBy fromValue(String v)
- {
- for (FilterBy c : FilterBy.values())
- {
- if (c.value.equals(v))
- {
- return c;
- }
+ public static FilterBy fromValue(String v) {
+ for (FilterBy c: FilterBy.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
}
- throw new IllegalArgumentException(v);
- }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import javax.xml.datatype.XMLGregorianCalendar;
+
/**
- * <p>
- * Java class for JalviewModel complex type.
+ * <p>Java class for JalviewModel complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="JalviewModel">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- * <sequence>
- * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="overview" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="tree" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequencePoint" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="axis" maxOccurs="3" minOccurs="3">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMin">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMax">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}SimilarityParams"/>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="FeatureSettings" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="JalviewModel"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
+ * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
+ * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="overview" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt;
+ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="FeatureSettings" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "JalviewModel",
- namespace = "www.jalview.org",
- propOrder =
- { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
- "userColours", "tree", "pcaViewer", "featureSettings" })
-public class JalviewModel
-{
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
-
- @XmlElement(required = true)
- protected String version;
-
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
-
- @XmlElement(name = "JSeq")
- protected List<JalviewModel.JSeq> jSeq;
-
- @XmlElement(name = "JGroup")
- protected List<JalviewModel.JGroup> jGroup;
-
- @XmlElement(name = "Viewport")
- protected List<JalviewModel.Viewport> viewport;
-
- @XmlElement(name = "UserColours")
- protected List<JalviewModel.UserColours> userColours;
-
- protected List<JalviewModel.Tree> tree;
-
- @XmlElement(name = "PcaViewer")
- protected List<JalviewModel.PcaViewer> pcaViewer;
-
- @XmlElement(name = "FeatureSettings")
- protected JalviewModel.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return possible object is {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate()
- {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
- *
- * @param value
- * allowed object is {@link XMLGregorianCalendar }
- *
- */
- public void setCreationDate(XMLGregorianCalendar value)
- {
- this.creationDate = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return possible object is {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel()
- {
- return vamsasModel;
- }
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value)
- {
- this.vamsasModel = value;
- }
-
- /**
- * Gets the value of the jSeq property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the jSeq property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getJSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
- *
- *
- */
- public List<JalviewModel.JSeq> getJSeq()
- {
- if (jSeq == null)
- {
- jSeq = new ArrayList<JalviewModel.JSeq>();
- }
- return this.jSeq;
- }
-
- /**
- * Gets the value of the jGroup property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the jGroup property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getJGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
- *
- *
- */
- public List<JalviewModel.JGroup> getJGroup()
- {
- if (jGroup == null)
- {
- jGroup = new ArrayList<JalviewModel.JGroup>();
- }
- return this.jGroup;
- }
-
- /**
- * Gets the value of the viewport property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the viewport property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getViewport().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
- *
- *
- */
- public List<JalviewModel.Viewport> getViewport()
- {
- if (viewport == null)
- {
- viewport = new ArrayList<JalviewModel.Viewport>();
- }
- return this.viewport;
- }
-
- /**
- * Gets the value of the userColours property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the userColours property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getUserColours().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
- *
- *
- */
- public List<JalviewModel.UserColours> getUserColours()
- {
- if (userColours == null)
- {
- userColours = new ArrayList<JalviewModel.UserColours>();
- }
- return this.userColours;
- }
-
- /**
- * Gets the value of the tree property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the tree property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getTree().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
- *
- *
- */
- public List<JalviewModel.Tree> getTree()
- {
- if (tree == null)
- {
- tree = new ArrayList<JalviewModel.Tree>();
- }
- return this.tree;
- }
-
- /**
- * Gets the value of the pcaViewer property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the pcaViewer property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getPcaViewer().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
- *
- *
- */
- public List<JalviewModel.PcaViewer> getPcaViewer()
- {
- if (pcaViewer == null)
- {
- pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
- }
- return this.pcaViewer;
- }
-
- /**
- * Gets the value of the featureSettings property.
- *
- * @return possible object is {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings getFeatureSettings()
- {
- return featureSettings;
- }
-
- /**
- * Sets the value of the featureSettings property.
- *
- * @param value
- * allowed object is {@link JalviewModel.FeatureSettings }
- *
- */
- public void setFeatureSettings(JalviewModel.FeatureSettings value)
- {
- this.featureSettings = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "setting", "group" })
- public static class FeatureSettings
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Setting> setting;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Group> group;
-
- /**
- * Gets the value of the setting property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the setting property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSetting().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Setting }
- *
- *
- */
- public List<JalviewModel.FeatureSettings.Setting> getSetting()
- {
- if (setting == null)
- {
- setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
- }
- return this.setting;
- }
-
- /**
- * Gets the value of the group property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the group property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Group }
- *
- *
- */
- public List<JalviewModel.FeatureSettings.Group> getGroup()
- {
- if (group == null)
- {
- group = new ArrayList<JalviewModel.FeatureSettings.Group>();
- }
- return this.group;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group
- {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay()
- {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value)
- {
- this.display = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
- public static class Setting
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
-
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
-
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- @XmlAttribute(name = "order")
- protected Float order;
-
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
-
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
-
- @XmlAttribute(name = "max")
- protected Float max;
-
- @XmlAttribute(name = "min")
- protected Float min;
-
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
-
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String
- * }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return possible object is {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet()
- {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value)
- {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay()
- {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value)
- {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getOrder()
- {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setOrder(Float value)
- {
- this.order = value;
- }
-
- /**
- * Gets the value of the mincolour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getMincolour()
- {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setMincolour(Integer value)
- {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return possible object is {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour()
- {
- if (noValueColour == null)
- {
- return NoValueColour.MIN;
- }
- else
- {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value)
- {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the threshstate property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getThreshstate()
- {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setThreshstate(Integer value)
- {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMax()
- {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMax(Float value)
- {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getMin()
- {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setMin(Float value)
- {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isColourByLabel()
- {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value)
- {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isAutoScale()
- {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value)
- {
- this.autoScale = value;
- }
-
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "seq", "annotationColours" })
- public static class JGroup
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<String> seq;
-
- @XmlElement(namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
-
- @XmlAttribute(name = "start")
- protected Integer start;
-
- @XmlAttribute(name = "end")
- protected Integer end;
-
- @XmlAttribute(name = "name")
- protected String name;
-
- @XmlAttribute(name = "colour")
- protected String colour;
-
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
-
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
-
- @XmlAttribute(name = "outlineColour")
- protected Integer outlineColour;
-
- @XmlAttribute(name = "displayBoxes")
- protected Boolean displayBoxes;
-
- @XmlAttribute(name = "displayText")
- protected Boolean displayText;
-
- @XmlAttribute(name = "colourText")
- protected Boolean colourText;
-
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
-
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
-
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
-
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
-
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
-
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
-
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
-
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the seq property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the seq property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+ "creationDate",
+ "version",
+ "vamsasModel",
+ "jSeq",
+ "jGroup",
+ "viewport",
+ "userColours",
+ "tree",
+ "pcaViewer",
+ "featureSettings"
+})
+public class JalviewModel {
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+ @XmlElement(required = true)
+ protected String version;
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+ protected List<JalviewModel.Tree> tree;
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return
+ * possible object is
+ * {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate() {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
*
+ * @param value
+ * allowed object is
+ * {@link XMLGregorianCalendar }
+ *
*/
- public List<String> getSeq()
- {
- if (seq == null)
- {
- seq = new ArrayList<String>();
- }
- return this.seq;
+ public void setCreationDate(XMLGregorianCalendar value) {
+ this.creationDate = value;
}
/**
- * Gets the value of the annotationColours property.
- *
- * @return possible object is {@link AnnotationColourScheme }
+ * Gets the value of the version property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public AnnotationColourScheme getAnnotationColours()
- {
- return annotationColours;
+ public String getVersion() {
+ return version;
}
/**
- * Sets the value of the annotationColours property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is {@link AnnotationColourScheme }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setAnnotationColours(AnnotationColourScheme value)
- {
- this.annotationColours = value;
+ public void setVersion(String value) {
+ this.version = value;
}
/**
- * Gets the value of the start property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the vamsasModel property.
*
+ * @return
+ * possible object is
+ * {@link VAMSAS }
+ *
*/
- public Integer getStart()
- {
- return start;
+ public VAMSAS getVamsasModel() {
+ return vamsasModel;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the vamsasModel property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link VAMSAS }
+ *
*/
- public void setStart(Integer value)
- {
- this.start = value;
+ public void setVamsasModel(VAMSAS value) {
+ this.vamsasModel = value;
}
/**
- * Gets the value of the end property.
+ * Gets the value of the jSeq property.
*
- * @return possible object is {@link Integer }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
*
- */
- public Integer getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link Integer }
*
- */
- public void setEnd(Integer value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the name property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
*
- * @return possible object is {@link String }
*
*/
- public String getName()
- {
- return name;
+ public List<JalviewModel.JSeq> getJSeq() {
+ if (jSeq == null) {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
+ }
+ return this.jSeq;
}
/**
- * Sets the value of the name property.
+ * Gets the value of the jGroup property.
*
- * @param value
- * allowed object is {@link String }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
*
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the colour property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
*
- * @return possible object is {@link String }
*
- */
- public String getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setColour(String value)
- {
- this.colour = value;
+ public List<JalviewModel.JGroup> getJGroup() {
+ if (jGroup == null) {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
+ }
+ return this.jGroup;
}
/**
- * Gets the value of the consThreshold property.
+ * Gets the value of the viewport property.
*
- * @return possible object is {@link Integer }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
*
- */
- public Integer getConsThreshold()
- {
- return consThreshold;
- }
-
- /**
- * Sets the value of the consThreshold property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link Integer }
*
- */
- public void setConsThreshold(Integer value)
- {
- this.consThreshold = value;
- }
-
- /**
- * Gets the value of the pidThreshold property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
*
- * @return possible object is {@link Integer }
*
*/
- public Integer getPidThreshold()
- {
- return pidThreshold;
+ public List<JalviewModel.Viewport> getViewport() {
+ if (viewport == null) {
+ viewport = new ArrayList<JalviewModel.Viewport>();
+ }
+ return this.viewport;
}
/**
- * Sets the value of the pidThreshold property.
+ * Gets the value of the userColours property.
*
- * @param value
- * allowed object is {@link Integer }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
*
- */
- public void setPidThreshold(Integer value)
- {
- this.pidThreshold = value;
- }
-
- /**
- * Gets the value of the outlineColour property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Integer }
*
- */
- public Integer getOutlineColour()
- {
- return outlineColour;
- }
-
- /**
- * Sets the value of the outlineColour property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
*
- * @param value
- * allowed object is {@link Integer }
*
*/
- public void setOutlineColour(Integer value)
- {
- this.outlineColour = value;
+ public List<JalviewModel.UserColours> getUserColours() {
+ if (userColours == null) {
+ userColours = new ArrayList<JalviewModel.UserColours>();
+ }
+ return this.userColours;
}
/**
- * Gets the value of the displayBoxes property.
+ * Gets the value of the tree property.
*
- * @return possible object is {@link Boolean }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- */
- public Boolean isDisplayBoxes()
- {
- return displayBoxes;
- }
-
- /**
- * Sets the value of the displayBoxes property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link Boolean }
*
- */
- public void setDisplayBoxes(Boolean value)
- {
- this.displayBoxes = value;
- }
-
- /**
- * Gets the value of the displayText property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
*
- * @return possible object is {@link Boolean }
*
*/
- public Boolean isDisplayText()
- {
- return displayText;
+ public List<JalviewModel.Tree> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
}
/**
- * Sets the value of the displayText property.
+ * Gets the value of the pcaViewer property.
*
- * @param value
- * allowed object is {@link Boolean }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
*
- */
- public void setDisplayText(Boolean value)
- {
- this.displayText = value;
- }
-
- /**
- * Gets the value of the colourText property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPcaViewer().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
- */
- public Boolean isColourText()
- {
- return colourText;
- }
-
- /**
- * Sets the value of the colourText property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
*
- * @param value
- * allowed object is {@link Boolean }
*
*/
- public void setColourText(Boolean value)
- {
- this.colourText = value;
+ public List<JalviewModel.PcaViewer> getPcaViewer() {
+ if (pcaViewer == null) {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
}
/**
- * Gets the value of the textCol1 property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the featureSettings property.
*
+ * @return
+ * possible object is
+ * {@link JalviewModel.FeatureSettings }
+ *
*/
- public Integer getTextCol1()
- {
- return textCol1;
+ public JalviewModel.FeatureSettings getFeatureSettings() {
+ return featureSettings;
}
/**
- * Sets the value of the textCol1 property.
+ * Sets the value of the featureSettings property.
*
* @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
- }
-
- /**
- * Gets the value of the textCol2 property.
+ * allowed object is
+ * {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value) {
+ this.featureSettings = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @return possible object is {@link Integer }
*
*/
- public Integer getTextCol2()
- {
- return textCol2;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "setting",
+ "group"
+ })
+ public static class FeatureSettings {
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
+ /**
+ * Gets the value of the setting property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSetting().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Setting> getSetting() {
+ if (setting == null) {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
+ /**
+ * Gets the value of the group property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Group> getGroup() {
+ if (group == null) {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowUnconserved()
- {
- return showUnconserved;
- }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName",
+ "matcherSet"
+ })
+ public static class Setting {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+ @XmlAttribute(name = "order")
+ protected Float order;
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour() {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value) {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay() {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value) {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getOrder() {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setOrder(Float value) {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getMincolour() {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value) {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getThreshstate() {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value) {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
}
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
/**
- * Gets the value of the normaliseSequenceLogo property.
+ * <p>Java class for anonymous complex type.
*
- * @return possible object is {@link Boolean }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
- }
-
- /**
- * Sets the value of the normaliseSequenceLogo property.
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
+ * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @param value
- * allowed object is {@link Boolean }
*
*/
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "features", "pdbids", "hiddenSequences", "rnaViewer" })
- public static class JSeq
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids> pdbids;
-
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
-
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
-
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
-
- /**
- * Gets the value of the features property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the features property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getFeatures().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Feature }
- *
- *
- */
- public List<Feature> getFeatures()
- {
- if (features == null)
- {
- features = new ArrayList<Feature>();
- }
- return this.features;
- }
-
- /**
- * Gets the value of the pdbids property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the pdbids property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getPdbids().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids> getPdbids()
- {
- if (pdbids == null)
- {
- pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
- }
- return this.pdbids;
- }
-
- /**
- * Gets the value of the hiddenSequences property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the hiddenSequences property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getHiddenSequences().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Integer }
- *
- *
- */
- public List<Integer> getHiddenSequences()
- {
- if (hiddenSequences == null)
- {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
- }
-
- /**
- * Gets the value of the rnaViewer property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the rnaViewer property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getRnaViewer().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
- {
- if (rnaViewer == null)
- {
- rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getColour()
- {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setColour(Integer value)
- {
- this.colour = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value)
- {
- this.end = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the hidden property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isHidden()
- {
- return hidden;
- }
-
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setHidden(Boolean value)
- {
- this.hidden = value;
- }
-
- /**
- * Gets the value of the viewreference property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isViewreference()
- {
- return viewreference;
- }
-
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setViewreference(Boolean value)
- {
- this.viewreference = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "structureState" })
- public static class Pdbids extends Pdbentry
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the structureState property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
- {
- if (structureState == null)
- {
- structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "value" })
- public static class StructureState
- {
-
- @XmlValue
- protected String value;
-
- @XmlAttribute(name = "visible")
- protected Boolean visible;
-
- @XmlAttribute(name = "viewId")
- protected String viewId;
-
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
-
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
-
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
-
- @XmlAttribute(name = "type")
- protected String type;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "seq",
+ "annotationColours"
+ })
+ public static class JGroup {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "colour")
+ protected String colour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "id")
+ protected String id;
/**
- * Gets the value of the value property.
+ * Gets the value of the seq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
*
- * @return possible object is {@link String }
*
*/
- public String getValue()
- {
- return value;
+ public List<String> getSeq() {
+ if (seq == null) {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
}
/**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
+ * Gets the value of the annotationColours property.
*
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
}
/**
- * Gets the value of the visible property.
+ * Sets the value of the annotationColours property.
*
- * @return possible object is {@link Boolean }
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the start property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Boolean isVisible()
- {
- return visible;
+ public Integer getStart() {
+ return start;
}
/**
- * Sets the value of the visible property.
+ * Sets the value of the start property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setVisible(Boolean value)
- {
- this.visible = value;
+ public void setStart(Integer value) {
+ this.start = value;
}
/**
- * Gets the value of the viewId property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the end property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getViewId()
- {
- return viewId;
+ public Integer getEnd() {
+ return end;
}
/**
- * Sets the value of the viewId property.
+ * Sets the value of the end property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setViewId(String value)
- {
- this.viewId = value;
+ public void setEnd(Integer value) {
+ this.end = value;
}
/**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the name property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public boolean isAlignwithAlignPanel()
- {
- if (alignwithAlignPanel == null)
- {
- return true;
- }
- else
- {
- return alignwithAlignPanel;
- }
+ public String getName() {
+ return name;
}
/**
- * Sets the value of the alignwithAlignPanel property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setAlignwithAlignPanel(Boolean value)
- {
- this.alignwithAlignPanel = value;
+ public void setName(String value) {
+ this.name = value;
}
/**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the colour property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public boolean isColourwithAlignPanel()
- {
- if (colourwithAlignPanel == null)
- {
- return false;
- }
- else
- {
- return colourwithAlignPanel;
- }
+ public String getColour() {
+ return colour;
}
/**
- * Sets the value of the colourwithAlignPanel property.
+ * Sets the value of the colour property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setColourwithAlignPanel(Boolean value)
- {
- this.colourwithAlignPanel = value;
+ public void setColour(String value) {
+ this.colour = value;
}
/**
- * Gets the value of the colourByJmol property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the consThreshold property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public boolean isColourByJmol()
- {
- if (colourByJmol == null)
- {
- return true;
- }
- else
- {
- return colourByJmol;
- }
+ public Integer getConsThreshold() {
+ return consThreshold;
}
/**
- * Sets the value of the colourByJmol property.
+ * Sets the value of the consThreshold property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setColourByJmol(Boolean value)
- {
- this.colourByJmol = value;
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
}
/**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the pidThreshold property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getType()
- {
- return type;
+ public Integer getPidThreshold() {
+ return pidThreshold;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the pidThreshold property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setType(String value)
- {
- this.type = value;
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
}
/**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the outlineColour property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Integer getWidth()
- {
- return width;
+ public Integer getOutlineColour() {
+ return outlineColour;
}
/**
- * Sets the value of the width property.
+ * Sets the value of the outlineColour property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setWidth(Integer value)
- {
- this.width = value;
+ public void setOutlineColour(Integer value) {
+ this.outlineColour = value;
}
/**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the displayBoxes property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Integer getHeight()
- {
- return height;
+ public Boolean isDisplayBoxes() {
+ return displayBoxes;
}
/**
- * Sets the value of the height property.
+ * Sets the value of the displayBoxes property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setHeight(Integer value)
- {
- this.height = value;
+ public void setDisplayBoxes(Boolean value) {
+ this.displayBoxes = value;
}
/**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the displayText property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Integer getXpos()
- {
- return xpos;
+ public Boolean isDisplayText() {
+ return displayText;
}
/**
- * Sets the value of the xpos property.
+ * Sets the value of the displayText property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setXpos(Integer value)
- {
- this.xpos = value;
+ public void setDisplayText(Boolean value) {
+ this.displayText = value;
}
/**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
+ * Gets the value of the colourText property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public Integer getYpos()
- {
- return ypos;
+ public Boolean isColourText() {
+ return colourText;
}
/**
- * Sets the value of the ypos property.
+ * Sets the value of the colourText property.
*
* @param value
- * allowed object is {@link Integer }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setYpos(Integer value)
- {
- this.ypos = value;
+ public void setColourText(Boolean value) {
+ this.colourText = value;
}
- }
-
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "secondaryStructure" })
- public static class RnaViewer
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "viewId")
- protected String viewId;
-
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
-
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the secondaryStructure property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSecondaryStructure().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
- {
- if (secondaryStructure == null)
- {
- secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewId()
- {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewId(String value)
- {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getDividerLocation()
- {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setDividerLocation(Integer value)
- {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getSelectedRna()
- {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setSelectedRna(Integer value)
- {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure
- {
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
-
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
-
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
/**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the textCol1 property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getTitle()
- {
- return title;
+ public Integer getTextCol1() {
+ return textCol1;
}
/**
- * Sets the value of the title property.
+ * Sets the value of the textCol1 property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setTitle(String value)
- {
- this.title = value;
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
}
/**
- * Gets the value of the annotationId property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the textCol2 property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public String getAnnotationId()
- {
- return annotationId;
+ public Integer getTextCol2() {
+ return textCol2;
}
/**
- * Sets the value of the annotationId property.
+ * Sets the value of the textCol2 property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setAnnotationId(String value)
- {
- this.annotationId = value;
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
}
/**
- * Gets the value of the gapped property.
- *
- * @return possible object is {@link Boolean }
+ * Gets the value of the textColThreshold property.
*
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
*/
- public Boolean isGapped()
- {
- return gapped;
+ public Integer getTextColThreshold() {
+ return textColThreshold;
}
/**
- * Sets the value of the gapped property.
+ * Sets the value of the textColThreshold property.
*
* @param value
- * allowed object is {@link Boolean }
- *
+ * allowed object is
+ * {@link Integer }
+ *
*/
- public void setGapped(Boolean value)
- {
- this.gapped = value;
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
}
/**
- * Gets the value of the viewerState property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the showUnconserved property.
*
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
*/
- public String getViewerState()
- {
- return viewerState;
+ public Boolean isShowUnconserved() {
+ return showUnconserved;
}
/**
- * Sets the value of the viewerState property.
+ * Sets the value of the showUnconserved property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link Boolean }
+ *
*/
- public void setViewerState(String value)
- {
- this.viewerState = value;
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
}
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequencePoint" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="axis" maxOccurs="3" minOccurs="3">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMin">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="seqPointMax">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}SimilarityParams"/>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
- public static class PcaViewer
- {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.Axis> axis;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected PcaDataType pcaData;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "scoreModelName")
- protected String scoreModelName;
-
- @XmlAttribute(name = "xDim")
- protected Integer xDim;
-
- @XmlAttribute(name = "yDim")
- protected Integer yDim;
-
- @XmlAttribute(name = "zDim")
- protected Integer zDim;
-
- @XmlAttribute(name = "bgColour")
- protected Integer bgColour;
-
- @XmlAttribute(name = "scaleFactor")
- protected Float scaleFactor;
-
- @XmlAttribute(name = "showLabels")
- protected Boolean showLabels;
-
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
-
- @XmlAttribute(name = "includeGaps")
- protected Boolean includeGaps;
-
- @XmlAttribute(name = "matchGaps")
- protected Boolean matchGaps;
-
- @XmlAttribute(name = "includeGappedColumns")
- protected Boolean includeGappedColumns;
-
- @XmlAttribute(name = "denominateByShortestLength")
- protected Boolean denominateByShortestLength;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the sequencePoint property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the sequencePoint property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSequencePoint().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.SequencePoint }
- *
- *
- */
- public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
- {
- if (sequencePoint == null)
- {
- sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
- }
- return this.sequencePoint;
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Gets the value of the axis property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the axis property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAxis().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.Axis }
- *
- *
- */
- public List<JalviewModel.PcaViewer.Axis> getAxis()
- {
- if (axis == null)
- {
- axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
- }
- return this.axis;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the seqPointMin property.
- *
- * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
- {
- return seqPointMin;
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the seqPointMin property.
- *
- * @param value
- * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
- {
- this.seqPointMin = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the seqPointMax property.
- *
- * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
- {
- return seqPointMax;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Sets the value of the seqPointMax property.
- *
- * @param value
- * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
- {
- this.seqPointMax = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Gets the value of the pcaData property.
- *
- * @return possible object is {@link PcaDataType }
- *
- */
- public PcaDataType getPcaData()
- {
- return pcaData;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Sets the value of the pcaData property.
- *
- * @param value
- * allowed object is {@link PcaDataType }
- *
- */
- public void setPcaData(PcaDataType value)
- {
- this.pcaData = value;
}
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
/**
- * Sets the value of the title property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setTitle(String value)
- {
- this.title = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "features",
+ "pdbids",
+ "hiddenSequences",
+ "rnaViewer"
+ })
+ public static class JSeq {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids> pdbids;
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
- /**
- * Gets the value of the scoreModelName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getScoreModelName()
- {
- return scoreModelName;
- }
+ /**
+ * Gets the value of the features property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Feature }
+ *
+ *
+ */
+ public List<Feature> getFeatures() {
+ if (features == null) {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
+ }
- /**
- * Sets the value of the scoreModelName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setScoreModelName(String value)
- {
- this.scoreModelName = value;
- }
+ /**
+ * Gets the value of the pdbids property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPdbids().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids> getPdbids() {
+ if (pdbids == null) {
+ pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
- /**
- * Gets the value of the xDim property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXDim()
- {
- return xDim;
- }
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getHiddenSequences() {
+ if (hiddenSequences == null) {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
- /**
- * Sets the value of the xDim property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXDim(Integer value)
- {
- this.xDim = value;
- }
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
+ if (rnaViewer == null) {
+ rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
- /**
- * Gets the value of the yDim property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYDim()
- {
- return yDim;
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getColour() {
+ return colour;
+ }
- /**
- * Sets the value of the yDim property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYDim(Integer value)
- {
- this.yDim = value;
- }
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setColour(Integer value) {
+ this.colour = value;
+ }
- /**
- * Gets the value of the zDim property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getZDim()
- {
- return zDim;
- }
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
- /**
- * Sets the value of the zDim property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setZDim(Integer value)
- {
- this.zDim = value;
- }
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getBgColour()
- {
- return bgColour;
- }
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setBgColour(Integer value)
- {
- this.bgColour = value;
- }
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
- /**
- * Gets the value of the scaleFactor property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getScaleFactor()
- {
- return scaleFactor;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the scaleFactor property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setScaleFactor(Float value)
- {
- this.scaleFactor = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Gets the value of the showLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowLabels()
- {
- return showLabels;
- }
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isHidden() {
+ return hidden;
+ }
- /**
- * Sets the value of the showLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value)
- {
- this.showLabels = value;
- }
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value) {
+ this.hidden = value;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isLinkToAllViews()
- {
- return linkToAllViews;
- }
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isViewreference() {
+ return viewreference;
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value)
- {
- this.linkToAllViews = value;
- }
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value) {
+ this.viewreference = value;
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isIncludeGaps()
- {
- return includeGaps;
- }
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value)
- {
- this.includeGaps = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "structureState"
+ })
+ public static class Pdbids
+ extends Pdbentry
+ {
- /**
- * Gets the value of the matchGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isMatchGaps()
- {
- return matchGaps;
- }
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
+ if (structureState == null) {
+ structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "value"
+ })
+ public static class StructureState {
+
+ @XmlValue
+ protected String value;
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value) {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isAlignwithAlignPanel() {
+ if (alignwithAlignPanel == null) {
+ return true;
+ } else {
+ return alignwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the alignwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAlignwithAlignPanel(Boolean value) {
+ this.alignwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourwithAlignPanel() {
+ if (colourwithAlignPanel == null) {
+ return false;
+ } else {
+ return colourwithAlignPanel;
+ }
+ }
+
+ /**
+ * Sets the value of the colourwithAlignPanel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourwithAlignPanel(Boolean value) {
+ this.colourwithAlignPanel = value;
+ }
+
+ /**
+ * Gets the value of the colourByJmol property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColourByJmol() {
+ if (colourByJmol == null) {
+ return true;
+ } else {
+ return colourByJmol;
+ }
+ }
+
+ /**
+ * Sets the value of the colourByJmol property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByJmol(Boolean value) {
+ this.colourByJmol = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value)
- {
- this.matchGaps = value;
- }
+ }
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns()
- {
- return includeGappedColumns;
- }
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value)
- {
- this.includeGappedColumns = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "secondaryStructure"
+ })
+ public static class RnaViewer {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+ if (secondaryStructure == null) {
+ secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewId() {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewId(String value) {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getDividerLocation() {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value) {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getSelectedRna() {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value) {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the annotationId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAnnotationId() {
+ return annotationId;
+ }
+
+ /**
+ * Sets the value of the annotationId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAnnotationId(String value) {
+ this.annotationId = value;
+ }
+
+ /**
+ * Gets the value of the gapped property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGapped() {
+ return gapped;
+ }
+
+ /**
+ * Sets the value of the gapped property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGapped(Boolean value) {
+ this.gapped = value;
+ }
+
+ /**
+ * Gets the value of the viewerState property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewerState() {
+ return viewerState;
+ }
+
+ /**
+ * Sets the value of the viewerState property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewerState(String value) {
+ this.viewerState = value;
+ }
+
+ }
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength()
- {
- return denominateByShortestLength;
- }
+ }
- /**
- * Sets the value of the denominateByShortestLength property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value)
- {
- this.denominateByShortestLength = value;
}
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
/**
- * Sets the value of the width property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @param value
- * allowed object is {@link Integer }
*
*/
- public void setWidth(Integer value)
- {
- this.width = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "sequencePoint",
+ "axis",
+ "seqPointMin",
+ "seqPointMax",
+ "pcaData"
+ })
+ public static class PcaViewer {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.Axis> axis;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
+ /**
+ * Gets the value of the sequencePoint property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequencePoint().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
+ if (sequencePoint == null) {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
+ /**
+ * Gets the value of the axis property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAxis().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.Axis> getAxis() {
+ if (axis == null) {
+ axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+ }
+ return this.axis;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
+ /**
+ * Gets the value of the seqPointMin property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+ return seqPointMin;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
+ /**
+ * Sets the value of the seqPointMin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+ this.seqPointMin = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
+ /**
+ * Gets the value of the seqPointMax property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+ return seqPointMax;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+ this.seqPointMax = value;
+ }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis
- {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return
+ * possible object is
+ * {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData() {
+ return pcaData;
+ }
- }
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value) {
+ this.pcaData = value;
+ }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax
- {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin
- {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the scoreModelName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getScoreModelName() {
+ return scoreModelName;
+ }
- }
+ /**
+ * Sets the value of the scoreModelName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setScoreModelName(String value) {
+ this.scoreModelName = value;
+ }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint
- {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
-
- @XmlAttribute(name = "yPos")
- protected Float yPos;
-
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceRef()
- {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceRef(String value)
- {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the xPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getXPos()
- {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setXPos(Float value)
- {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getYPos()
- {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setYPos(Float value)
- {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getZPos()
- {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setZPos(Float value)
- {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the xDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXDim() {
+ return xDim;
+ }
- }
+ /**
+ * Sets the value of the xDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXDim(Integer value) {
+ this.xDim = value;
+ }
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "title", "newick" })
- public static class Tree
- {
-
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
-
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
-
- @XmlAttribute(name = "fontName")
- protected String fontName;
-
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
-
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
-
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
-
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
-
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
-
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
-
- @XmlAttribute(name = "columnWise")
- protected Boolean columnWise;
-
- @XmlAttribute(name = "columnReference")
- protected String columnReference;
-
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
-
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYDim() {
+ return yDim;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
+ /**
+ * Sets the value of the yDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYDim(Integer value) {
+ this.yDim = value;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
+ /**
+ * Gets the value of the zDim property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getZDim() {
+ return zDim;
+ }
- /**
- * Gets the value of the newick property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getNewick()
- {
- return newick;
- }
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setZDim(Integer value) {
+ this.zDim = value;
+ }
- /**
- * Sets the value of the newick property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setNewick(String value)
- {
- this.newick = value;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getBgColour() {
+ return bgColour;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFontName()
- {
- return fontName;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value) {
+ this.bgColour = value;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFontName(String value)
- {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the scaleFactor property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getScaleFactor() {
+ return scaleFactor;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontSize()
- {
- return fontSize;
- }
+ /**
+ * Sets the value of the scaleFactor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setScaleFactor(Float value) {
+ this.scaleFactor = value;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontSize(Integer value)
- {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels() {
+ return showLabels;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontStyle()
- {
- return fontStyle;
- }
+ /**
+ * Sets the value of the showLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowLabels(Boolean value) {
+ this.showLabels = value;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontStyle(Integer value)
- {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews() {
+ return linkToAllViews;
+ }
- /**
- * Gets the value of the threshold property.
- *
- * @return possible object is {@link Float }
- *
- */
- public Float getThreshold()
- {
- return threshold;
- }
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is {@link Float }
- *
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps() {
+ return includeGaps;
+ }
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowBootstrap()
- {
- return showBootstrap;
- }
+ /**
+ * Sets the value of the includeGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
+ }
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value)
- {
- this.showBootstrap = value;
- }
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps() {
+ return matchGaps;
+ }
- /**
- * Gets the value of the showDistances property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowDistances()
- {
- return showDistances;
- }
+ /**
+ * Sets the value of the matchGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
+ }
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value)
- {
- this.showDistances = value;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
+ }
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked()
- {
- return markUnlinked;
- }
+ /**
+ * Sets the value of the includeGappedColumns property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
+ }
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value)
- {
- this.markUnlinked = value;
- }
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
+ }
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isFitToWindow()
- {
- return fitToWindow;
- }
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
+ }
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value)
- {
- this.fitToWindow = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
- /**
- * Gets the value of the currentTree property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isCurrentTree()
- {
- return currentTree;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value)
- {
- this.currentTree = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
- /**
- * Gets the value of the columnWise property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isColumnWise()
- {
- if (columnWise == null)
- {
- return false;
- }
- else
- {
- return columnWise;
- }
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
- /**
- * Sets the value of the columnWise property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColumnWise(Boolean value)
- {
- this.columnWise = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
- /**
- * Gets the value of the columnReference property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getColumnReference()
- {
- return columnReference;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
- /**
- * Sets the value of the columnReference property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setColumnReference(String value)
- {
- this.columnReference = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isLinkToAllViews()
- {
- if (linkToAllViews == null)
- {
- return false;
- }
- else
- {
- return linkToAllViews;
- }
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Axis {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value)
- {
- this.linkToAllViews = value;
- }
+ }
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "userColourScheme" })
- public static class UserColours
- {
-
- @XmlElement(
- name = "UserColourScheme",
- namespace = "www.jalview.org",
- required = true)
- protected JalviewUserColours userColourScheme;
-
- @XmlAttribute(name = "id")
- protected String id;
+ }
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return possible object is {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme()
- {
- return userColourScheme;
}
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value)
- {
- this.userColourScheme = value;
- }
/**
- * Gets the value of the id property.
+ * <p>Java class for anonymous complex type.
*
- * @return possible object is {@link String }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt;
+ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setId(String value)
- {
- this.id = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "newick"
+ })
+ public static class Tree {
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="overview" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(
- name = "",
- propOrder =
- { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
- public static class Viewport
- {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
-
- @XmlElement(namespace = "www.jalview.org")
- protected JalviewModel.Viewport.Overview overview;
-
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
-
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
-
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
-
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
-
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
-
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
-
- @XmlAttribute(name = "showText")
- protected Boolean showText;
-
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
-
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
-
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
-
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+ @XmlAttribute(name = "columnWise")
+ protected Boolean columnWise;
+ @XmlAttribute(name = "columnReference")
+ protected String columnReference;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNewick() {
+ return newick;
+ }
+
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNewick(String value) {
+ this.newick = value;
+ }
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap() {
+ return showBootstrap;
+ }
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value) {
+ this.showBootstrap = value;
+ }
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances() {
+ return showDistances;
+ }
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value) {
+ this.showDistances = value;
+ }
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked() {
+ return markUnlinked;
+ }
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value) {
+ this.markUnlinked = value;
+ }
- @XmlAttribute(name = "charWidth")
- protected Integer charWidth;
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow() {
+ return fitToWindow;
+ }
- @XmlAttribute(name = "charHeight")
- protected Integer charHeight;
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value) {
+ this.fitToWindow = value;
+ }
- @XmlAttribute(name = "fontName")
- protected String fontName;
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree() {
+ return currentTree;
+ }
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value) {
+ this.currentTree = value;
+ }
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
+ /**
+ * Gets the value of the columnWise property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColumnWise() {
+ if (columnWise == null) {
+ return false;
+ } else {
+ return columnWise;
+ }
+ }
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
+ /**
+ * Sets the value of the columnWise property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColumnWise(Boolean value) {
+ this.columnWise = value;
+ }
- @XmlAttribute(name = "viewName")
- protected String viewName;
+ /**
+ * Gets the value of the columnReference property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColumnReference() {
+ return columnReference;
+ }
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
+ /**
+ * Sets the value of the columnReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColumnReference(String value) {
+ this.columnReference = value;
+ }
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews() {
+ if (linkToAllViews == null) {
+ return false;
+ } else {
+ return linkToAllViews;
+ }
+ }
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
- @XmlAttribute(name = "complementId")
- protected String complementId;
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
- @XmlAttribute(name = "showComplementFeatures")
- protected Boolean showComplementFeatures;
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
- @XmlAttribute(name = "showComplementFeaturesOnTop")
- protected Boolean showComplementFeaturesOnTop;
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
- @XmlAttribute(name = "width")
- protected Integer width;
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
- @XmlAttribute(name = "height")
- protected Integer height;
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return possible object is {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours()
- {
- return annotationColours;
}
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value)
- {
- this.annotationColours = value;
- }
/**
- * Gets the value of the hiddenColumns property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the hiddenColumns property.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getHiddenColumns().add(newItem);
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.HiddenColumns }
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
- public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
- {
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
- }
- return this.hiddenColumns;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "userColourScheme"
+ })
+ public static class UserColours {
- /**
- * Gets the value of the calcIdParam property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the calcIdParam property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getCalcIdParam().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.CalcIdParam }
- *
- *
- */
- public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
- {
- if (calcIdParam == null)
- {
- calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
- }
- return this.calcIdParam;
- }
+ @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+ protected JalviewUserColours userColourScheme;
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Gets the value of the overview property.
- *
- * @return possible object is {@link JalviewModel.Viewport.Overview }
- *
- */
- public JalviewModel.Viewport.Overview getOverview()
- {
- return overview;
- }
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme() {
+ return userColourScheme;
+ }
- /**
- * Sets the value of the overview property.
- *
- * @param value
- * allowed object is {@link JalviewModel.Viewport.Overview }
- *
- */
- public void setOverview(JalviewModel.Viewport.Overview value)
- {
- this.overview = value;
- }
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value) {
+ this.userColourScheme = value;
+ }
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isConservationSelected()
- {
- return conservationSelected;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value)
- {
- this.conservationSelected = value;
}
+
/**
- * Gets the value of the pidSelected property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="overview" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
*/
- public Boolean isPidSelected()
- {
- return pidSelected;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "annotationColours",
+ "hiddenColumns",
+ "calcIdParam",
+ "overview"
+ })
+ public static class Viewport {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+ @XmlElement(namespace = "www.jalview.org")
+ protected JalviewModel.Viewport.Overview overview;
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
+ @XmlAttribute(name = "charWidth")
+ protected Integer charWidth;
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return
+ * possible object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours() {
+ return annotationColours;
+ }
+
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is
+ * {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value) {
+ this.annotationColours = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
+ if (hiddenColumns == null) {
+ hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
+
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
+ if (calcIdParam == null) {
+ calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
+
+ /**
+ * Gets the value of the overview property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview getOverview() {
+ return overview;
+ }
+
+ /**
+ * Sets the value of the overview property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public void setOverview(JalviewModel.Viewport.Overview value) {
+ this.overview = value;
+ }
+
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected() {
+ return conservationSelected;
+ }
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value)
- {
- this.pidSelected = value;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value) {
+ this.conservationSelected = value;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getBgColour()
- {
- return bgColour;
- }
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected() {
+ return pidSelected;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setBgColour(String value)
- {
- this.bgColour = value;
- }
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value) {
+ this.pidSelected = value;
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getConsThreshold()
- {
- return consThreshold;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getBgColour() {
+ return bgColour;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setConsThreshold(Integer value)
- {
- this.consThreshold = value;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setBgColour(String value) {
+ this.bgColour = value;
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getPidThreshold()
- {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getConsThreshold() {
+ return consThreshold;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setPidThreshold(Integer value)
- {
- this.pidThreshold = value;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value) {
+ this.consThreshold = value;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getPidThreshold() {
+ return pidThreshold;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value) {
+ this.pidThreshold = value;
+ }
- /**
- * Gets the value of the showFullId property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowFullId()
- {
- return showFullId;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value)
- {
- this.showFullId = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isRightAlignIds()
- {
- return rightAlignIds;
- }
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId() {
+ return showFullId;
+ }
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value)
- {
- this.rightAlignIds = value;
- }
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value) {
+ this.showFullId = value;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowText()
- {
- return showText;
- }
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds() {
+ return rightAlignIds;
+ }
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowText(Boolean value)
- {
- this.showText = value;
- }
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value) {
+ this.rightAlignIds = value;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowColourText()
- {
- return showColourText;
- }
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowText() {
+ return showText;
+ }
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value)
- {
- this.showColourText = value;
- }
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value) {
+ this.showText = value;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowUnconserved()
- {
- if (showUnconserved == null)
- {
- return false;
- }
- else
- {
- return showUnconserved;
- }
- }
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText() {
+ return showColourText;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value)
- {
- this.showUnconserved = value;
- }
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value) {
+ this.showColourText = value;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowBoxes()
- {
- return showBoxes;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved() {
+ if (showUnconserved == null) {
+ return false;
+ } else {
+ return showUnconserved;
+ }
+ }
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value)
- {
- this.showBoxes = value;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value) {
+ this.showUnconserved = value;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isWrapAlignment()
- {
- return wrapAlignment;
- }
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes() {
+ return showBoxes;
+ }
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value)
- {
- this.wrapAlignment = value;
- }
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value) {
+ this.showBoxes = value;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isRenderGaps()
- {
- return renderGaps;
- }
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment() {
+ return wrapAlignment;
+ }
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value)
- {
- this.renderGaps = value;
- }
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value) {
+ this.wrapAlignment = value;
+ }
+
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps() {
+ return renderGaps;
+ }
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value) {
+ this.renderGaps = value;
+ }
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value)
- {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures() {
+ return showSequenceFeatures;
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip()
- {
- return showNPfeatureTooltip;
- }
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value) {
+ this.showSequenceFeatures = value;
+ }
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value)
- {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip() {
+ return showNPfeatureTooltip;
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip()
- {
- return showDbRefTooltip;
- }
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value) {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value)
- {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip() {
+ return showDbRefTooltip;
+ }
- /**
- * Gets the value of the followHighlight property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isFollowHighlight()
- {
- if (followHighlight == null)
- {
- return true;
- }
- else
- {
- return followHighlight;
- }
- }
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value) {
+ this.showDbRefTooltip = value;
+ }
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value)
- {
- this.followHighlight = value;
- }
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight() {
+ if (followHighlight == null) {
+ return true;
+ } else {
+ return followHighlight;
+ }
+ }
- /**
- * Gets the value of the followSelection property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isFollowSelection()
- {
- if (followSelection == null)
- {
- return true;
- }
- else
- {
- return followSelection;
- }
- }
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value) {
+ this.followHighlight = value;
+ }
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value)
- {
- this.followSelection = value;
- }
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection() {
+ if (followSelection == null) {
+ return true;
+ } else {
+ return followSelection;
+ }
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowAnnotation()
- {
- return showAnnotation;
- }
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value) {
+ this.followSelection = value;
+ }
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value)
- {
- this.showAnnotation = value;
- }
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation() {
+ return showAnnotation;
+ }
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels()
- {
- if (centreColumnLabels == null)
- {
- return false;
- }
- else
- {
- return centreColumnLabels;
- }
- }
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value) {
+ this.showAnnotation = value;
+ }
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value)
- {
- this.centreColumnLabels = value;
- }
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels() {
+ if (centreColumnLabels == null) {
+ return false;
+ } else {
+ return centreColumnLabels;
+ }
+ }
- /**
- * Gets the value of the showGroupConservation property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowGroupConservation()
- {
- if (showGroupConservation == null)
- {
- return false;
- }
- else
- {
- return showGroupConservation;
- }
- }
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value) {
+ this.centreColumnLabels = value;
+ }
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowGroupConservation(Boolean value)
- {
- this.showGroupConservation = value;
- }
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation() {
+ if (showGroupConservation == null) {
+ return false;
+ } else {
+ return showGroupConservation;
+ }
+ }
- /**
- * Gets the value of the showGroupConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus()
- {
- if (showGroupConsensus == null)
- {
- return false;
- }
- else
- {
- return showGroupConsensus;
- }
- }
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value) {
+ this.showGroupConservation = value;
+ }
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowGroupConsensus(Boolean value)
- {
- this.showGroupConsensus = value;
- }
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus() {
+ if (showGroupConsensus == null) {
+ return false;
+ } else {
+ return showGroupConsensus;
+ }
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram()
- {
- if (showConsensusHistogram == null)
- {
- return true;
- }
- else
- {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value) {
+ this.showGroupConsensus = value;
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value)
- {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram() {
+ if (showConsensusHistogram == null) {
+ return true;
+ } else {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo()
- {
- if (showSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return showSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value) {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value)
- {
- this.showSequenceLogo = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo() {
+ if (showSequenceLogo == null) {
+ return false;
+ } else {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo()
- {
- if (normaliseSequenceLogo == null)
- {
- return false;
- }
- else
- {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value) {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value)
- {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo() {
+ if (normaliseSequenceLogo == null) {
+ return false;
+ } else {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus()
- {
- if (ignoreGapsinConsensus == null)
- {
- return true;
- }
- else
- {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value) {
+ this.normaliseSequenceLogo = value;
+ }
+
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus() {
+ if (ignoreGapsinConsensus == null) {
+ return true;
+ } else {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value)
- {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value) {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStartRes()
- {
- return startRes;
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartRes() {
+ return startRes;
+ }
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStartRes(Integer value)
- {
- this.startRes = value;
- }
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value) {
+ this.startRes = value;
+ }
- /**
- * Gets the value of the startSeq property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStartSeq()
- {
- return startSeq;
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStartSeq() {
+ return startSeq;
+ }
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStartSeq(Integer value)
- {
- this.startSeq = value;
- }
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value) {
+ this.startSeq = value;
+ }
- /**
- * Gets the value of the charWidth property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getCharWidth()
- {
- return charWidth;
- }
+ /**
+ * Gets the value of the charWidth property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getCharWidth() {
+ return charWidth;
+ }
- /**
- * Sets the value of the charWidth property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setCharWidth(Integer value)
- {
- this.charWidth = value;
- }
+ /**
+ * Sets the value of the charWidth property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setCharWidth(Integer value) {
+ this.charWidth = value;
+ }
- /**
- * Gets the value of the charHeight property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getCharHeight()
- {
- return charHeight;
- }
+ /**
+ * Gets the value of the charHeight property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getCharHeight() {
+ return charHeight;
+ }
- /**
- * Sets the value of the charHeight property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setCharHeight(Integer value)
- {
- this.charHeight = value;
- }
+ /**
+ * Sets the value of the charHeight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setCharHeight(Integer value) {
+ this.charHeight = value;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFontName()
- {
- return fontName;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFontName(String value)
- {
- this.fontName = value;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontSize()
- {
- return fontSize;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontSize(Integer value)
- {
- this.fontSize = value;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getFontStyle()
- {
- return fontStyle;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setFontStyle(Integer value)
- {
- this.fontStyle = value;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna()
- {
- if (scaleProteinAsCdna == null)
- {
- return true;
- }
- else
- {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna() {
+ if (scaleProteinAsCdna == null) {
+ return true;
+ } else {
+ return scaleProteinAsCdna;
+ }
+ }
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value)
- {
- this.scaleProteinAsCdna = value;
- }
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value) {
+ this.scaleProteinAsCdna = value;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getViewName()
- {
- return viewName;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getViewName() {
+ return viewName;
+ }
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setViewName(String value)
- {
- this.viewName = value;
- }
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setViewName(String value) {
+ this.viewName = value;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequenceSetId()
- {
- return sequenceSetId;
- }
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceSetId() {
+ return sequenceSetId;
+ }
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequenceSetId(String value)
- {
- this.sequenceSetId = value;
- }
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceSetId(String value) {
+ this.sequenceSetId = value;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isGatheredViews()
- {
- return gatheredViews;
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews() {
+ return gatheredViews;
+ }
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value)
- {
- this.gatheredViews = value;
- }
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value) {
+ this.gatheredViews = value;
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol1()
- {
- return textCol1;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol1() {
+ return textCol1;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol1(Integer value)
- {
- this.textCol1 = value;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value) {
+ this.textCol1 = value;
+ }
+
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextCol2() {
+ return textCol2;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextCol2()
- {
- return textCol2;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value) {
+ this.textCol2 = value;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextCol2(Integer value)
- {
- this.textCol2 = value;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold() {
+ return textColThreshold;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getTextColThreshold()
- {
- return textColThreshold;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value) {
+ this.textColThreshold = value;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value)
- {
- this.textColThreshold = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getComplementId() {
+ return complementId;
+ }
- /**
- * Gets the value of the complementId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getComplementId()
- {
- return complementId;
- }
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setComplementId(String value) {
+ this.complementId = value;
+ }
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setComplementId(String value)
- {
- this.complementId = value;
- }
+ /**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures() {
+ if (showComplementFeatures == null) {
+ return false;
+ } else {
+ return showComplementFeatures;
+ }
+ }
- /**
- * Gets the value of the showComplementFeatures property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowComplementFeatures()
- {
- if (showComplementFeatures == null)
- {
- return false;
- }
- else
- {
- return showComplementFeatures;
- }
- }
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value) {
+ this.showComplementFeatures = value;
+ }
- /**
- * Sets the value of the showComplementFeatures property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowComplementFeatures(Boolean value)
- {
- this.showComplementFeatures = value;
- }
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop() {
+ if (showComplementFeaturesOnTop == null) {
+ return false;
+ } else {
+ return showComplementFeaturesOnTop;
+ }
+ }
- /**
- * Gets the value of the showComplementFeaturesOnTop property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isShowComplementFeaturesOnTop()
- {
- if (showComplementFeaturesOnTop == null)
- {
- return false;
- }
- else
- {
- return showComplementFeaturesOnTop;
- }
- }
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value) {
+ this.showComplementFeaturesOnTop = value;
+ }
- /**
- * Sets the value of the showComplementFeaturesOnTop property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowComplementFeaturesOnTop(Boolean value)
- {
- this.showComplementFeaturesOnTop = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam extends WebServiceParameterSet
- {
-
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
-
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
-
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * Gets the value of the calcId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getCalcId()
- {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setCalcId(String value)
- {
- this.calcId = value;
- }
-
- /**
- * Gets the value of the needsUpdate property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isNeedsUpdate()
- {
- if (needsUpdate == null)
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam
+ extends WebServiceParameterSet
{
- return false;
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getCalcId() {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setCalcId(String value) {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate() {
+ if (needsUpdate == null) {
+ return false;
+ } else {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value) {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate() {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value) {
+ this.autoUpdate = value;
+ }
+
}
- else
- {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setNeedsUpdate(Boolean value)
- {
- this.needsUpdate = value;
- }
-
- /**
- * Gets the value of the autoUpdate property.
- *
- */
- public boolean isAutoUpdate()
- {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value)
- {
- this.autoUpdate = value;
- }
- }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns
- {
-
- @XmlAttribute(name = "start")
- protected Integer start;
-
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getStart()
- {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setStart(Integer value)
- {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getEnd()
- {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setEnd(Integer value)
- {
- this.end = value;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setStart(Integer value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setEnd(Integer value) {
+ this.end = value;
+ }
- }
+ }
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Overview
- {
-
- @XmlAttribute(name = "showHidden")
- protected Boolean showHidden;
-
- @XmlAttribute(name = "residueColour")
- protected Integer residueColour;
-
- @XmlAttribute(name = "gapColour")
- protected Integer gapColour;
-
- @XmlAttribute(name = "hiddenColour")
- protected Integer hiddenColour;
-
- @XmlAttribute(name = "title")
- protected String title;
-
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the showHidden property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public Boolean isShowHidden()
- {
- return showHidden;
- }
-
- /**
- * Sets the value of the showHidden property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setShowHidden(Boolean value)
- {
- this.showHidden = value;
- }
-
- /**
- * Gets the value of the residueColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getResidueColour()
- {
- return residueColour;
- }
-
- /**
- * Sets the value of the residueColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setResidueColour(Integer value)
- {
- this.residueColour = value;
- }
-
- /**
- * Gets the value of the gapColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getGapColour()
- {
- return gapColour;
- }
-
- /**
- * Sets the value of the gapColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setGapColour(Integer value)
- {
- this.gapColour = value;
- }
-
- /**
- * Gets the value of the hiddenColour property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHiddenColour()
- {
- return hiddenColour;
- }
-
- /**
- * Sets the value of the hiddenColour property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHiddenColour(Integer value)
- {
- this.hiddenColour = value;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTitle()
- {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTitle(String value)
- {
- this.title = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getWidth()
- {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setWidth(Integer value)
- {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getHeight()
- {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setHeight(Integer value)
- {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getXpos()
- {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setXpos(Integer value)
- {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return possible object is {@link Integer }
- *
- */
- public Integer getYpos()
- {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is {@link Integer }
- *
- */
- public void setYpos(Integer value)
- {
- this.ypos = value;
- }
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden() {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value) {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getResidueColour() {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value) {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGapColour() {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value) {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHiddenColour() {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value) {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
- }
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for JalviewUserColours complex type.
+ * <p>Java class for JalviewUserColours complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="JalviewUserColours">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="colour" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * </sequence>
- * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="filter" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
- * </sequence>
- * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="JalviewUserColours"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "JalviewUserColours",
- namespace = "www.jalview.org/colours",
- propOrder =
- { "version", "colour", "filter" })
-public class JalviewUserColours
-{
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
-
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Colour> colour;
-
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Filter> filter;
-
- @XmlAttribute(name = "schemeName")
- protected String schemeName;
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the colour property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getColour().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Colour }
- *
- *
- */
- public List<JalviewUserColours.Colour> getColour()
- {
- if (colour == null)
- {
- colour = new ArrayList<JalviewUserColours.Colour>();
- }
- return this.colour;
- }
-
- /**
- * Gets the value of the filter property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the filter property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getFilter().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Filter }
- *
- *
- */
- public List<JalviewUserColours.Filter> getFilter()
- {
- if (filter == null)
- {
- filter = new ArrayList<JalviewUserColours.Filter>();
- }
- return this.filter;
- }
-
- /**
- * Gets the value of the schemeName property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSchemeName()
- {
- return schemeName;
- }
-
- /**
- * Sets the value of the schemeName property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSchemeName(String value)
- {
- this.schemeName = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * </sequence>
- * <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "attributeName" })
- public static class Colour
- {
-
+@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
+ "version",
+ "colour",
+ "filter"
+})
+public class JalviewUserColours {
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
@XmlElement(namespace = "")
- protected List<String> attributeName;
-
- @XmlAttribute(name = "Name")
- protected String name;
-
- @XmlAttribute(name = "RGB", required = true)
- protected String rgb;
-
- @XmlAttribute(name = "minRGB")
- protected String minRGB;
-
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
-
- @XmlAttribute(name = "threshType")
- protected ThresholdType threshType;
-
- @XmlAttribute(name = "threshold")
- protected Float threshold;
-
- @XmlAttribute(name = "max")
- protected Float max;
-
- @XmlAttribute(name = "min")
- protected Float min;
-
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
-
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will
- * be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getAttributeName()
- {
- if (attributeName == null)
- {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the rgb property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getRGB()
- {
- return rgb;
- }
-
- /**
- * Sets the value of the rgb property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setRGB(String value)
- {
- this.rgb = value;
- }
-
- /**
- * Gets the value of the minRGB property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getMinRGB()
- {
- return minRGB;
- }
-
- /**
- * Sets the value of the minRGB property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setMinRGB(String value)
- {
- this.minRGB = value;
- }
+ protected List<JalviewUserColours.Colour> colour;
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Filter> filter;
+ @XmlAttribute(name = "schemeName")
+ protected String schemeName;
/**
- * Gets the value of the noValueColour property.
- *
- * @return possible object is {@link NoValueColour }
+ * Gets the value of the version property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public NoValueColour getNoValueColour()
- {
- if (noValueColour == null)
- {
- return NoValueColour.MIN;
- }
- else
- {
- return noValueColour;
- }
+ public String getVersion() {
+ return version;
}
/**
- * Sets the value of the noValueColour property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is {@link NoValueColour }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setNoValueColour(NoValueColour value)
- {
- this.noValueColour = value;
+ public void setVersion(String value) {
+ this.version = value;
}
/**
- * Gets the value of the threshType property.
+ * Gets the value of the colour property.
*
- * @return possible object is {@link ThresholdType }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the colour property.
*
- */
- public ThresholdType getThreshType()
- {
- return threshType;
- }
-
- /**
- * Sets the value of the threshType property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getColour().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is {@link ThresholdType }
*
- */
- public void setThreshType(ThresholdType value)
- {
- this.threshType = value;
- }
-
- /**
- * Gets the value of the threshold property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Colour }
*
- * @return possible object is {@link Float }
*
*/
- public Float getThreshold()
- {
- return threshold;
+ public List<JalviewUserColours.Colour> getColour() {
+ if (colour == null) {
+ colour = new ArrayList<JalviewUserColours.Colour>();
+ }
+ return this.colour;
}
/**
- * Sets the value of the threshold property.
+ * Gets the value of the filter property.
*
- * @param value
- * allowed object is {@link Float }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the filter property.
*
- */
- public void setThreshold(Float value)
- {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the max property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getFilter().add(newItem);
+ * </pre>
*
- * @return possible object is {@link Float }
*
- */
- public Float getMax()
- {
- return max;
- }
-
- /**
- * Sets the value of the max property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Filter }
*
- * @param value
- * allowed object is {@link Float }
*
*/
- public void setMax(Float value)
- {
- this.max = value;
+ public List<JalviewUserColours.Filter> getFilter() {
+ if (filter == null) {
+ filter = new ArrayList<JalviewUserColours.Filter>();
+ }
+ return this.filter;
}
/**
- * Gets the value of the min property.
- *
- * @return possible object is {@link Float }
+ * Gets the value of the schemeName property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public Float getMin()
- {
- return min;
+ public String getSchemeName() {
+ return schemeName;
}
/**
- * Sets the value of the min property.
+ * Sets the value of the schemeName property.
*
* @param value
- * allowed object is {@link Float }
- *
- */
- public void setMin(Float value)
- {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return possible object is {@link Boolean }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public Boolean isColourByLabel()
- {
- return colourByLabel;
+ public void setSchemeName(String value) {
+ this.schemeName = value;
}
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value)
- {
- this.colourByLabel = value;
- }
/**
- * Gets the value of the autoScale property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
*/
- public Boolean isAutoScale()
- {
- return autoScale;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "attributeName"
+ })
+ public static class Colour {
+
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
+ @XmlAttribute(name = "Name")
+ protected String name;
+ @XmlAttribute(name = "RGB", required = true)
+ protected String rgb;
+ @XmlAttribute(name = "minRGB")
+ protected String minRGB;
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+ @XmlAttribute(name = "threshType")
+ protected ThresholdType threshType;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "max")
+ protected Float max;
+ @XmlAttribute(name = "min")
+ protected Float min;
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName() {
+ if (attributeName == null) {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the rgb property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getRGB() {
+ return rgb;
+ }
+
+ /**
+ * Sets the value of the rgb property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setRGB(String value) {
+ this.rgb = value;
+ }
+
+ /**
+ * Gets the value of the minRGB property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMinRGB() {
+ return minRGB;
+ }
+
+ /**
+ * Sets the value of the minRGB property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMinRGB(String value) {
+ this.minRGB = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour() {
+ if (noValueColour == null) {
+ return NoValueColour.MIN;
+ } else {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value) {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshType property.
+ *
+ * @return
+ * possible object is
+ * {@link ThresholdType }
+ *
+ */
+ public ThresholdType getThreshType() {
+ return threshType;
+ }
+
+ /**
+ * Sets the value of the threshType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link ThresholdType }
+ *
+ */
+ public void setThreshType(ThresholdType value) {
+ this.threshType = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMax() {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMax(Float value) {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getMin() {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setMin(Float value) {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel() {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value) {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale() {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value) {
+ this.autoScale = value;
+ }
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value)
- {
- this.autoScale = value;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
- * </sequence>
- * <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "matcherSet" })
- public static class Filter
- {
-
- @XmlElement(namespace = "", required = true)
- protected FeatureMatcherSet matcherSet;
-
- @XmlAttribute(name = "featureType", required = true)
- protected String featureType;
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return possible object is {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet()
- {
- return matcherSet;
- }
/**
- * Sets the value of the matcherSet property.
+ * <p>Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link FeatureMatcherSet }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public void setMatcherSet(FeatureMatcherSet value)
- {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the featureType property.
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @return possible object is {@link String }
*
*/
- public String getFeatureType()
- {
- return featureType;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "matcherSet"
+ })
+ public static class Filter {
+
+ @XmlElement(namespace = "", required = true)
+ protected FeatureMatcherSet matcherSet;
+ @XmlAttribute(name = "featureType", required = true)
+ protected String featureType;
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return
+ * possible object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet() {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is
+ * {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value) {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the featureType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFeatureType() {
+ return featureType;
+ }
+
+ /**
+ * Sets the value of the featureType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFeatureType(String value) {
+ this.featureType = value;
+ }
- /**
- * Sets the value of the featureType property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFeatureType(String value)
- {
- this.featureType = value;
}
- }
-
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
*
- * This effectively represents a java.util.MapList object
+ * This effectively represents a java.util.MapList
+ * object
+ *
*
+ * <p>Java class for mapListType complex type.
*
- * <p>
- * Java class for mapListType complex type.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
- *
- * <pre>
- * <complexType name="mapListType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- * <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="mapListType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
-@XmlSeeAlso({ Mapping.class })
-public class MapListType
-{
-
- protected List<MapListType.MapListFrom> mapListFrom;
-
- protected List<MapListType.MapListTo> mapListTo;
-
- @XmlAttribute(name = "mapFromUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapFromUnit;
-
- @XmlAttribute(name = "mapToUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapToUnit;
-
- /**
- * Gets the value of the mapListFrom property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the mapListFrom property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getMapListFrom().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListFrom }
- *
- *
- */
- public List<MapListType.MapListFrom> getMapListFrom()
- {
- if (mapListFrom == null)
- {
- mapListFrom = new ArrayList<MapListType.MapListFrom>();
- }
- return this.mapListFrom;
- }
-
- /**
- * Gets the value of the mapListTo property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the mapListTo property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getMapListTo().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListTo }
- *
- *
- */
- public List<MapListType.MapListTo> getMapListTo()
- {
- if (mapListTo == null)
- {
- mapListTo = new ArrayList<MapListType.MapListTo>();
- }
- return this.mapListTo;
- }
-
- /**
- * Gets the value of the mapFromUnit property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getMapFromUnit()
- {
- return mapFromUnit;
- }
-
- /**
- * Sets the value of the mapFromUnit property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setMapFromUnit(BigInteger value)
- {
- this.mapFromUnit = value;
- }
+@XmlType(name = "mapListType", propOrder = {
+ "mapListFrom",
+ "mapListTo"
+})
+@XmlSeeAlso({
+ Mapping.class
+})
+public class MapListType {
- /**
- * Gets the value of the mapToUnit property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getMapToUnit()
- {
- return mapToUnit;
- }
-
- /**
- * Sets the value of the mapToUnit property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setMapToUnit(BigInteger value)
- {
- this.mapToUnit = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListFrom
- {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
+ protected List<MapListType.MapListFrom> mapListFrom;
+ protected List<MapListType.MapListTo> mapListTo;
+ @XmlAttribute(name = "mapFromUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapFromUnit;
+ @XmlAttribute(name = "mapToUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapToUnit;
/**
- * Gets the value of the start property.
+ * Gets the value of the mapListFrom property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMapListFrom().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListFrom }
+ *
*
*/
- public int getStart()
- {
- return start;
+ public List<MapListType.MapListFrom> getMapListFrom() {
+ if (mapListFrom == null) {
+ mapListFrom = new ArrayList<MapListType.MapListFrom>();
+ }
+ return this.mapListFrom;
}
/**
- * Sets the value of the start property.
+ * Gets the value of the mapListTo property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMapListTo().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListTo }
+ *
*
*/
- public void setStart(int value)
- {
- this.start = value;
+ public List<MapListType.MapListTo> getMapListTo() {
+ if (mapListTo == null) {
+ mapListTo = new ArrayList<MapListType.MapListTo>();
+ }
+ return this.mapListTo;
}
/**
- * Gets the value of the end property.
+ * Gets the value of the mapFromUnit property.
*
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
*/
- public int getEnd()
- {
- return end;
+ public BigInteger getMapFromUnit() {
+ return mapFromUnit;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the mapFromUnit property.
*
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
*/
- public void setEnd(int value)
- {
- this.end = value;
+ public void setMapFromUnit(BigInteger value) {
+ this.mapFromUnit = value;
}
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListTo
- {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
-
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
/**
- * Gets the value of the start property.
+ * Gets the value of the mapToUnit property.
*
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
*/
- public int getStart()
- {
- return start;
+ public BigInteger getMapToUnit() {
+ return mapToUnit;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the mapToUnit property.
*
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
*/
- public void setStart(int value)
- {
- this.start = value;
+ public void setMapToUnit(BigInteger value) {
+ this.mapToUnit = value;
}
+
/**
- * Gets the value of the end property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
*
*/
- public int getEnd()
- {
- return end;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListFrom {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
}
+
/**
- * Sets the value of the end property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
*
*/
- public void setEnd(int value)
- {
- this.end = value;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListTo {
- }
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value) {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd() {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value) {
+ this.end = value;
+ }
+
+ }
}
--- /dev/null
+//
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
+// Any modifications to this file will be lost upon recompilation of the source schema.
+// Generated on: 2023.09.01 at 02:16:11 PM BST
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * Defines a mapping from the local frame to a matrix
+ * and its associated data specified by MatrixType
+ *
+ *
+ * <p>Java class for MapOnAMatrixType complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType name="MapOnAMatrixType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="matrix" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "MapOnAMatrixType", propOrder = {
+ "property",
+ "mapping"
+})
+public class MapOnAMatrixType {
+
+ protected List<Property> property;
+ protected MapListType mapping;
+ @XmlAttribute(name = "matrix", required = true)
+ protected String matrix;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Property }
+ *
+ *
+ */
+ public List<Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the mapping property.
+ *
+ * @return
+ * possible object is
+ * {@link MapListType }
+ *
+ */
+ public MapListType getMapping() {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link MapListType }
+ *
+ */
+ public void setMapping(MapListType value) {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the matrix property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMatrix() {
+ return matrix;
+ }
+
+ /**
+ * Sets the value of the matrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMatrix(String value) {
+ this.matrix = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
*
- * Represent the jalview.datamodel.Mapping object - it also provides a way of
- * storing sequences that are mapped 'to' without adding them to the sequence
- * set (which will mean they are then added to the alignment too).
- *
+ * Represent the jalview.datamodel.Mapping object -
+ * it also provides
+ * a way of storing sequences that are mapped 'to'
+ * without adding them
+ * to the sequence set (which will mean they are
+ * then added to the alignment too).
+ *
*
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
- * <sequence>
- * <choice minOccurs="0">
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
- * <element name="dseqFor">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * </restriction>
- * </simpleType>
- * </element>
- * </choice>
- * </sequence>
- * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
+ * &lt;sequence&gt;
+ * &lt;choice minOccurs="0"&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt;
+ * &lt;element name="dseqFor"&gt;
+ * &lt;simpleType&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * &lt;/element&gt;
+ * &lt;/choice&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
+@XmlType(name = "", propOrder = {
+ "sequence",
+ "dseqFor"
+})
@XmlRootElement(name = "Mapping")
-public class Mapping extends MapListType
+public class Mapping
+ extends MapListType
{
- @XmlElement(name = "Sequence")
- protected Sequence sequence;
-
- protected String dseqFor;
-
- @XmlAttribute(name = "mappingType")
- protected String mappingType;
+ @XmlElement(name = "Sequence")
+ protected Sequence sequence;
+ protected String dseqFor;
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link Sequence }
- *
- */
- public Sequence getSequence()
- {
- return sequence;
- }
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link Sequence }
+ *
+ */
+ public Sequence getSequence() {
+ return sequence;
+ }
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link Sequence }
- *
- */
- public void setSequence(Sequence value)
- {
- this.sequence = value;
- }
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Sequence }
+ *
+ */
+ public void setSequence(Sequence value) {
+ this.sequence = value;
+ }
- /**
- * Gets the value of the dseqFor property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDseqFor()
- {
- return dseqFor;
- }
+ /**
+ * Gets the value of the dseqFor property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDseqFor() {
+ return dseqFor;
+ }
- /**
- * Sets the value of the dseqFor property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDseqFor(String value)
- {
- this.dseqFor = value;
- }
+ /**
+ * Sets the value of the dseqFor property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDseqFor(String value) {
+ this.dseqFor = value;
+ }
- /**
- * Gets the value of the mappingType property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getMappingType()
- {
- return mappingType;
- }
+ /**
+ * Gets the value of the mappingType property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getMappingType() {
+ return mappingType;
+ }
- /**
- * Sets the value of the mappingType property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setMappingType(String value)
- {
- this.mappingType = value;
- }
+ /**
+ * Sets the value of the mappingType property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setMappingType(String value) {
+ this.mappingType = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
/**
- * <p>
- * Java class for MatrixType complex type.
+ * Represents matrix data imported to Jalview, and the
+ * results of any derived calculations (independent of a particular
+ * view
+ * on the matrix).
+ *
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>Java class for MatrixType complex type.
*
- * <pre>
- * <complexType name="MatrixType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="elements" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType name="MatrixType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="elements" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "MatrixType",
- propOrder =
- { "elements", "groups", "newick", "property", "mapping" })
-public class MatrixType
-{
-
- @XmlElement(required = true)
- protected String elements;
-
- protected List<String> groups;
-
- protected List<String> newick;
-
- protected List<Property> property;
-
- protected MapListType mapping;
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
-
- @XmlAttribute(name = "rows", required = true)
- protected BigInteger rows;
-
- @XmlAttribute(name = "cols", required = true)
- protected BigInteger cols;
-
- @XmlAttribute(name = "treeMethod")
- protected String treeMethod;
-
- @XmlAttribute(name = "cutHeight")
- protected Double cutHeight;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the elements property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getElements()
- {
- return elements;
- }
-
- /**
- * Sets the value of the elements property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setElements(String value)
- {
- this.elements = value;
- }
-
- /**
- * Gets the value of the groups property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the groups property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getGroups().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getGroups()
- {
- if (groups == null)
- {
- groups = new ArrayList<String>();
+@XmlType(name = "MatrixType", propOrder = {
+ "elements",
+ "groups",
+ "newick",
+ "property"
+})
+public class MatrixType {
+
+ @XmlElement(required = true)
+ protected String elements;
+ protected List<String> groups;
+ protected List<String> newick;
+ protected List<Property> property;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+ @XmlAttribute(name = "rows", required = true)
+ protected BigInteger rows;
+ @XmlAttribute(name = "cols", required = true)
+ protected BigInteger cols;
+ @XmlAttribute(name = "treeMethod")
+ protected String treeMethod;
+ @XmlAttribute(name = "cutHeight")
+ protected Double cutHeight;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ /**
+ * Gets the value of the elements property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getElements() {
+ return elements;
}
- return this.groups;
- }
- /**
- * Gets the value of the newick property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the newick property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getNewick().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getNewick()
- {
- if (newick == null)
- {
- newick = new ArrayList<String>();
+ /**
+ * Sets the value of the elements property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setElements(String value) {
+ this.elements = value;
}
- return this.newick;
- }
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Property }
- *
- *
- */
- public List<Property> getProperty()
- {
- if (property == null)
- {
- property = new ArrayList<Property>();
+ /**
+ * Gets the value of the groups property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the groups property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getGroups().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getGroups() {
+ if (groups == null) {
+ groups = new ArrayList<String>();
+ }
+ return this.groups;
}
- return this.property;
- }
- /**
- * Gets the value of the mapping property.
- *
- * @return possible object is {@link MapListType }
- *
- */
- public MapListType getMapping()
- {
- return mapping;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the newick property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getNewick().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getNewick() {
+ if (newick == null) {
+ newick = new ArrayList<String>();
+ }
+ return this.newick;
+ }
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is {@link MapListType }
- *
- */
- public void setMapping(MapListType value)
- {
- this.mapping = value;
- }
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Property }
+ *
+ *
+ */
+ public List<Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Property>();
+ }
+ return this.property;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getType() {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
- /**
- * Gets the value of the rows property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getRows()
- {
- return rows;
- }
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getRows() {
+ return rows;
+ }
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setRows(BigInteger value)
- {
- this.rows = value;
- }
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setRows(BigInteger value) {
+ this.rows = value;
+ }
- /**
- * Gets the value of the cols property.
- *
- * @return possible object is {@link BigInteger }
- *
- */
- public BigInteger getCols()
- {
- return cols;
- }
+ /**
+ * Gets the value of the cols property.
+ *
+ * @return
+ * possible object is
+ * {@link BigInteger }
+ *
+ */
+ public BigInteger getCols() {
+ return cols;
+ }
- /**
- * Sets the value of the cols property.
- *
- * @param value
- * allowed object is {@link BigInteger }
- *
- */
- public void setCols(BigInteger value)
- {
- this.cols = value;
- }
+ /**
+ * Sets the value of the cols property.
+ *
+ * @param value
+ * allowed object is
+ * {@link BigInteger }
+ *
+ */
+ public void setCols(BigInteger value) {
+ this.cols = value;
+ }
- /**
- * Gets the value of the treeMethod property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getTreeMethod()
- {
- return treeMethod;
- }
+ /**
+ * Gets the value of the treeMethod property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTreeMethod() {
+ return treeMethod;
+ }
- /**
- * Sets the value of the treeMethod property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setTreeMethod(String value)
- {
- this.treeMethod = value;
- }
+ /**
+ * Sets the value of the treeMethod property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTreeMethod(String value) {
+ this.treeMethod = value;
+ }
- /**
- * Gets the value of the cutHeight property.
- *
- * @return possible object is {@link Double }
- *
- */
- public Double getCutHeight()
- {
- return cutHeight;
- }
+ /**
+ * Gets the value of the cutHeight property.
+ *
+ * @return
+ * possible object is
+ * {@link Double }
+ *
+ */
+ public Double getCutHeight() {
+ return cutHeight;
+ }
- /**
- * Sets the value of the cutHeight property.
- *
- * @param value
- * allowed object is {@link Double }
- *
- */
- public void setCutHeight(Double value)
- {
- this.cutHeight = value;
- }
+ /**
+ * Sets the value of the cutHeight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Double }
+ *
+ */
+ public void setCutHeight(Double value) {
+ this.cutHeight = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for NoValueColour.
+ * <p>Java class for NoValueColour.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
- * <p>
- *
- * <pre>
- * <simpleType name="NoValueColour">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="None"/>
- * <enumeration value="Min"/>
- * <enumeration value="Max"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="NoValueColour"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="None"/&gt;
+ * &lt;enumeration value="Min"/&gt;
+ * &lt;enumeration value="Max"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum NoValueColour
-{
-
- @XmlEnumValue("None")
- NONE("None"), @XmlEnumValue("Min")
- MIN("Min"), @XmlEnumValue("Max")
- MAX("Max");
-
- private final String value;
-
- NoValueColour(String v)
- {
- value = v;
- }
+public enum NoValueColour {
+
+ @XmlEnumValue("None")
+ NONE("None"),
+ @XmlEnumValue("Min")
+ MIN("Min"),
+ @XmlEnumValue("Max")
+ MAX("Max");
+ private final String value;
+
+ NoValueColour(String v) {
+ value = v;
+ }
- public String value()
- {
- return value;
- }
+ public String value() {
+ return value;
+ }
- public static NoValueColour fromValue(String v)
- {
- for (NoValueColour c : NoValueColour.values())
- {
- if (c.value.equals(v))
- {
- return c;
- }
+ public static NoValueColour fromValue(String v) {
+ for (NoValueColour c: NoValueColour.values()) {
+ if (c.value.equals(v)) {
+ return c;
+ }
+ }
+ throw new IllegalArgumentException(v);
}
- throw new IllegalArgumentException(v);
- }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlRegistry;
import javax.xml.namespace.QName;
+
/**
- * This object contains factory methods for each Java content interface and Java
- * element interface generated in the jalview.xml.binding.jalview package.
- * <p>
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each
+ * Java content interface and Java element interface
+ * generated in the jalview.xml.binding.jalview package.
+ * <p>An ObjectFactory allows you to programatically
+ * construct new instances of the Java representation
+ * for XML content. The Java representation of XML
+ * content can consist of schema derived interfaces
+ * and classes representing the binding of schema
+ * type definitions, element declarations and model
+ * groups. Factory methods for each of these are
+ * provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory
-{
-
- private final static QName _WebServiceParameterSet_QNAME = new QName(
- "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
- private final static QName _JalviewModel_QNAME = new QName(
- "www.jalview.org", "JalviewModel");
-
- private final static QName _JalviewUserColours_QNAME = new QName(
- "www.jalview.org/colours", "JalviewUserColours");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of
- * schema derived classes for package: jalview.xml.binding.jalview
- *
- */
- public ObjectFactory()
- {
- }
-
- /**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame()
- {
- return new AlcodonFrame();
- }
-
- /**
- * Create an instance of {@link MapListType }
- *
- */
- public MapListType createMapListType()
- {
- return new MapListType();
- }
-
- /**
- * Create an instance of {@link Sequence }
- *
- */
- public Sequence createSequence()
- {
- return new Sequence();
- }
-
- /**
- * Create an instance of {@link Annotation }
- *
- */
- public Annotation createAnnotation()
- {
- return new Annotation();
- }
-
- /**
- * Create an instance of {@link SequenceSet }
- *
- */
- public SequenceSet createSequenceSet()
- {
- return new SequenceSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet createFeatureMatcherSet()
- {
- return new FeatureMatcherSet();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours }
- *
- */
- public JalviewUserColours createJalviewUserColours()
- {
- return new JalviewUserColours();
- }
-
- /**
- * Create an instance of {@link Pdbentry }
- *
- */
- public Pdbentry createPdbentry()
- {
- return new Pdbentry();
- }
-
- /**
- * Create an instance of {@link Feature }
- *
- */
- public Feature createFeature()
- {
- return new Feature();
- }
-
- /**
- * Create an instance of {@link JalviewModel }
- *
- */
- public JalviewModel createJalviewModel()
- {
- return new JalviewModel();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
- {
- return new JalviewModel.FeatureSettings();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer }
- *
- */
- public JalviewModel.PcaViewer createJalviewModelPcaViewer()
- {
- return new JalviewModel.PcaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport }
- *
- */
- public JalviewModel.Viewport createJalviewModelViewport()
- {
- return new JalviewModel.Viewport();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq }
- *
- */
- public JalviewModel.JSeq createJalviewModelJSeq()
- {
- return new JalviewModel.JSeq();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
- *
- */
- public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
- {
- return new JalviewModel.JSeq.RnaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids }
- *
- */
- public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
- {
- return new JalviewModel.JSeq.Pdbids();
- }
-
- /**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix()
- {
- return new DoubleMatrix();
- }
-
- /**
- * Create an instance of {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme createAnnotationColourScheme()
- {
- return new AnnotationColourScheme();
- }
-
- /**
- * Create an instance of {@link PcaDataType }
- *
- */
- public PcaDataType createPcaDataType()
- {
- return new PcaDataType();
- }
-
- /**
- * Create an instance of {@link DoubleVector }
- *
- */
- public DoubleVector createDoubleVector()
- {
- return new DoubleVector();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.Alcodon }
- *
- */
- public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
- {
- return new AlcodonFrame.Alcodon();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.AlcodMap }
- *
- */
- public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
- {
- return new AlcodonFrame.AlcodMap();
- }
-
- /**
- * Create an instance of {@link AnnotationElement }
- *
- */
- public AnnotationElement createAnnotationElement()
- {
- return new AnnotationElement();
- }
-
- /**
- * Create an instance of {@link Mapping }
- *
- */
- public Mapping createMapping()
- {
- return new Mapping();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListFrom }
- *
- */
- public MapListType.MapListFrom createMapListTypeMapListFrom()
- {
- return new MapListType.MapListFrom();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListTo }
- *
- */
- public MapListType.MapListTo createMapListTypeMapListTo()
- {
- return new MapListType.MapListTo();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType()
- {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Sequence.DBRef }
- *
- */
- public Sequence.DBRef createSequenceDBRef()
- {
- return new Sequence.DBRef();
- }
-
- /**
- * Create an instance of {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine createAnnotationThresholdLine()
- {
- return new Annotation.ThresholdLine();
- }
-
- /**
- * Create an instance of {@link MatrixType }
- *
- */
- public MatrixType createMatrixType()
- {
- return new MatrixType();
- }
-
- /**
- * Create an instance of {@link jalview.xml.binding.jalview.Property }
- *
- */
- public jalview.xml.binding.jalview.Property createProperty()
- {
- return new jalview.xml.binding.jalview.Property();
- }
-
- /**
- * Create an instance of {@link SequenceSet.SequenceSetProperties }
- *
- */
- public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
- {
- return new SequenceSet.SequenceSetProperties();
- }
-
- /**
- * Create an instance of {@link VAMSAS }
- *
- */
- public VAMSAS createVAMSAS()
- {
- return new VAMSAS();
- }
-
- /**
- * Create an instance of {@link FeatureMatcher }
- *
- */
- public FeatureMatcher createFeatureMatcher()
- {
- return new FeatureMatcher();
- }
-
- /**
- * Create an instance of {@link WebServiceParameterSet }
- *
- */
- public WebServiceParameterSet createWebServiceParameterSet()
- {
- return new WebServiceParameterSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
- {
- return new FeatureMatcherSet.CompoundMatcher();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Colour }
- *
- */
- public JalviewUserColours.Colour createJalviewUserColoursColour()
- {
- return new JalviewUserColours.Colour();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Filter }
- *
- */
- public JalviewUserColours.Filter createJalviewUserColoursFilter()
- {
- return new JalviewUserColours.Filter();
- }
-
- /**
- * Create an instance of {@link Pdbentry.Property }
- *
- */
- public Pdbentry.Property createPdbentryProperty()
- {
- return new Pdbentry.Property();
- }
-
- /**
- * Create an instance of {@link Feature.OtherData }
- *
- */
- public Feature.OtherData createFeatureOtherData()
- {
- return new Feature.OtherData();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JGroup }
- *
- */
- public JalviewModel.JGroup createJalviewModelJGroup()
- {
- return new JalviewModel.JGroup();
- }
-
- /**
- * Create an instance of {@link JalviewModel.UserColours }
- *
- */
- public JalviewModel.UserColours createJalviewModelUserColours()
- {
- return new JalviewModel.UserColours();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Tree }
- *
- */
- public JalviewModel.Tree createJalviewModelTree()
- {
- return new JalviewModel.Tree();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
- *
- */
- public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
- {
- return new JalviewModel.FeatureSettings.Setting();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Group }
- *
- */
- public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
- {
- return new JalviewModel.FeatureSettings.Group();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
- *
- */
- public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
- {
- return new JalviewModel.PcaViewer.SequencePoint();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.Axis }
- *
- */
- public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
- {
- return new JalviewModel.PcaViewer.Axis();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
- {
- return new JalviewModel.PcaViewer.SeqPointMin();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
- {
- return new JalviewModel.PcaViewer.SeqPointMax();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
- *
- */
- public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
- {
- return new JalviewModel.Viewport.HiddenColumns();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
- *
- */
- public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
- {
- return new JalviewModel.Viewport.CalcIdParam();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.Overview }
- *
- */
- public JalviewModel.Viewport.Overview createJalviewModelViewportOverview()
- {
- return new JalviewModel.Viewport.Overview();
- }
-
- /**
- * Create an instance of
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- */
- public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
- {
- return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- */
- public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
- {
- return new JalviewModel.JSeq.Pdbids.StructureState();
- }
-
- /**
- * Create an instance of {@link JAXBElement
- * }{@code <}{@link WebServiceParameterSet }{@code >}}
- *
- */
- @XmlElementDecl(
- namespace = "www.jalview.org/xml/wsparamset",
- name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
- WebServiceParameterSet value)
- {
- return new JAXBElement<WebServiceParameterSet>(
- _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
- null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
- * }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
- public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
- {
- return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
- JalviewModel.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement
- * }{@code <}{@link JalviewUserColours }{@code >}}
- *
- */
- @XmlElementDecl(
- namespace = "www.jalview.org/colours",
- name = "JalviewUserColours")
- public JAXBElement<JalviewUserColours> createJalviewUserColours(
- JalviewUserColours value)
- {
- return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
- JalviewUserColours.class, null, value);
- }
+public class ObjectFactory {
+
+ private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
+ private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+ private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
+ *
+ */
+ public ObjectFactory() {
+ }
+
+ /**
+ * Create an instance of {@link MapListType }
+ *
+ */
+ public MapListType createMapListType() {
+ return new MapListType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence }
+ *
+ */
+ public Sequence createSequence() {
+ return new Sequence();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame() {
+ return new AlcodonFrame();
+ }
+
+ /**
+ * Create an instance of {@link Annotation }
+ *
+ */
+ public Annotation createAnnotation() {
+ return new Annotation();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet }
+ *
+ */
+ public SequenceSet createSequenceSet() {
+ return new SequenceSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet createFeatureMatcherSet() {
+ return new FeatureMatcherSet();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours createJalviewUserColours() {
+ return new JalviewUserColours();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry }
+ *
+ */
+ public Pdbentry createPdbentry() {
+ return new Pdbentry();
+ }
+
+ /**
+ * Create an instance of {@link Feature }
+ *
+ */
+ public Feature createFeature() {
+ return new Feature();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel }
+ *
+ */
+ public JalviewModel createJalviewModel() {
+ return new JalviewModel();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
+ return new JalviewModel.FeatureSettings();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer }
+ *
+ */
+ public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+ return new JalviewModel.PcaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport }
+ *
+ */
+ public JalviewModel.Viewport createJalviewModelViewport() {
+ return new JalviewModel.Viewport();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq }
+ *
+ */
+ public JalviewModel.JSeq createJalviewModelJSeq() {
+ return new JalviewModel.JSeq();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
+ return new JalviewModel.JSeq.RnaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
+ return new JalviewModel.JSeq.Pdbids();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme createAnnotationColourScheme() {
+ return new AnnotationColourScheme();
+ }
+
+ /**
+ * Create an instance of {@link PcaDataType }
+ *
+ */
+ public PcaDataType createPcaDataType() {
+ return new PcaDataType();
+ }
+
+ /**
+ * Create an instance of {@link DoubleVector }
+ *
+ */
+ public DoubleVector createDoubleVector() {
+ return new DoubleVector();
+ }
+
+ /**
+ * Create an instance of {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix createDoubleMatrix() {
+ return new DoubleMatrix();
+ }
+
+ /**
+ * Create an instance of {@link Mapping }
+ *
+ */
+ public Mapping createMapping() {
+ return new Mapping();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListFrom }
+ *
+ */
+ public MapListType.MapListFrom createMapListTypeMapListFrom() {
+ return new MapListType.MapListFrom();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListTo }
+ *
+ */
+ public MapListType.MapListTo createMapListTypeMapListTo() {
+ return new MapListType.MapListTo();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType() {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence.DBRef }
+ *
+ */
+ public Sequence.DBRef createSequenceDBRef() {
+ return new Sequence.DBRef();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement() {
+ return new AnnotationElement();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine createAnnotationThresholdLine() {
+ return new Annotation.ThresholdLine();
+ }
+
+ /**
+ * Create an instance of {@link MapOnAMatrixType }
+ *
+ */
+ public MapOnAMatrixType createMapOnAMatrixType() {
+ return new MapOnAMatrixType();
+ }
+
+ /**
+ * Create an instance of {@link jalview.xml.binding.jalview.Property }
+ *
+ */
+ public jalview.xml.binding.jalview.Property createProperty() {
+ return new jalview.xml.binding.jalview.Property();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet.SequenceSetProperties }
+ *
+ */
+ public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
+ return new SequenceSet.SequenceSetProperties();
+ }
+
+ /**
+ * Create an instance of {@link MatrixType }
+ *
+ */
+ public MatrixType createMatrixType() {
+ return new MatrixType();
+ }
+
+ /**
+ * Create an instance of {@link VAMSAS }
+ *
+ */
+ public VAMSAS createVAMSAS() {
+ return new VAMSAS();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher createFeatureMatcher() {
+ return new FeatureMatcher();
+ }
+
+ /**
+ * Create an instance of {@link WebServiceParameterSet }
+ *
+ */
+ public WebServiceParameterSet createWebServiceParameterSet() {
+ return new WebServiceParameterSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
+ return new FeatureMatcherSet.CompoundMatcher();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Colour }
+ *
+ */
+ public JalviewUserColours.Colour createJalviewUserColoursColour() {
+ return new JalviewUserColours.Colour();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Filter }
+ *
+ */
+ public JalviewUserColours.Filter createJalviewUserColoursFilter() {
+ return new JalviewUserColours.Filter();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry.Property }
+ *
+ */
+ public Pdbentry.Property createPdbentryProperty() {
+ return new Pdbentry.Property();
+ }
+
+ /**
+ * Create an instance of {@link Feature.OtherData }
+ *
+ */
+ public Feature.OtherData createFeatureOtherData() {
+ return new Feature.OtherData();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JGroup }
+ *
+ */
+ public JalviewModel.JGroup createJalviewModelJGroup() {
+ return new JalviewModel.JGroup();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.UserColours }
+ *
+ */
+ public JalviewModel.UserColours createJalviewModelUserColours() {
+ return new JalviewModel.UserColours();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Tree }
+ *
+ */
+ public JalviewModel.Tree createJalviewModelTree() {
+ return new JalviewModel.Tree();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+ *
+ */
+ public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
+ return new JalviewModel.FeatureSettings.Setting();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+ *
+ */
+ public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
+ return new JalviewModel.FeatureSettings.Group();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ */
+ public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
+ return new JalviewModel.PcaViewer.SequencePoint();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+ *
+ */
+ public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
+ return new JalviewModel.PcaViewer.Axis();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
+ return new JalviewModel.PcaViewer.SeqPointMin();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
+ return new JalviewModel.PcaViewer.SeqPointMax();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ */
+ public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
+ return new JalviewModel.Viewport.HiddenColumns();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ */
+ public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
+ return new JalviewModel.Viewport.CalcIdParam();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
+ return new JalviewModel.Viewport.Overview();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
+ return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
+ return new JalviewModel.JSeq.Pdbids.StructureState();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+ public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
+ return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
+ public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
+ return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+ return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
*
- * The results of a PCA calculation
- *
+ * The results of a PCA calculation
+ *
*
- * <p>
- * Java class for PcaDataType complex type.
+ * <p>Java class for PcaDataType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="PcaDataType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="PcaDataType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "PcaDataType",
- namespace = "www.jalview.org",
- propOrder =
- { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
-public class PcaDataType
-{
-
- @XmlElement(required = true)
- protected DoubleMatrix pairwiseMatrix;
-
- @XmlElement(required = true)
- protected DoubleMatrix tridiagonalMatrix;
+@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
+ "pairwiseMatrix",
+ "tridiagonalMatrix",
+ "eigenMatrix"
+})
+public class PcaDataType {
- @XmlElement(required = true)
- protected DoubleMatrix eigenMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix pairwiseMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix tridiagonalMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix eigenMatrix;
- /**
- * Gets the value of the pairwiseMatrix property.
- *
- * @return possible object is {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getPairwiseMatrix()
- {
- return pairwiseMatrix;
- }
+ /**
+ * Gets the value of the pairwiseMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getPairwiseMatrix() {
+ return pairwiseMatrix;
+ }
- /**
- * Sets the value of the pairwiseMatrix property.
- *
- * @param value
- * allowed object is {@link DoubleMatrix }
- *
- */
- public void setPairwiseMatrix(DoubleMatrix value)
- {
- this.pairwiseMatrix = value;
- }
+ /**
+ * Sets the value of the pairwiseMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setPairwiseMatrix(DoubleMatrix value) {
+ this.pairwiseMatrix = value;
+ }
- /**
- * Gets the value of the tridiagonalMatrix property.
- *
- * @return possible object is {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getTridiagonalMatrix()
- {
- return tridiagonalMatrix;
- }
+ /**
+ * Gets the value of the tridiagonalMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getTridiagonalMatrix() {
+ return tridiagonalMatrix;
+ }
- /**
- * Sets the value of the tridiagonalMatrix property.
- *
- * @param value
- * allowed object is {@link DoubleMatrix }
- *
- */
- public void setTridiagonalMatrix(DoubleMatrix value)
- {
- this.tridiagonalMatrix = value;
- }
+ /**
+ * Sets the value of the tridiagonalMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setTridiagonalMatrix(DoubleMatrix value) {
+ this.tridiagonalMatrix = value;
+ }
- /**
- * Gets the value of the eigenMatrix property.
- *
- * @return possible object is {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getEigenMatrix()
- {
- return eigenMatrix;
- }
+ /**
+ * Gets the value of the eigenMatrix property.
+ *
+ * @return
+ * possible object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getEigenMatrix() {
+ return eigenMatrix;
+ }
- /**
- * Sets the value of the eigenMatrix property.
- *
- * @param value
- * allowed object is {@link DoubleMatrix }
- *
- */
- public void setEigenMatrix(DoubleMatrix value)
- {
- this.eigenMatrix = value;
- }
+ /**
+ * Sets the value of the eigenMatrix property.
+ *
+ * @param value
+ * allowed object is
+ * {@link DoubleMatrix }
+ *
+ */
+ public void setEigenMatrix(DoubleMatrix value) {
+ this.eigenMatrix = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for pdbentry complex type.
+ * <p>Java class for pdbentry complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="pdbentry">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence maxOccurs="unbounded" minOccurs="0">
- * <element name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="pdbentry"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "pdbentry",
- namespace = "www.jalview.org",
- propOrder =
- { "property" })
-@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
-public class Pdbentry
-{
-
- protected List<Pdbentry.Property> property;
-
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- @XmlAttribute(name = "type")
- protected String type;
-
- @XmlAttribute(name = "file")
- protected String file;
-
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Pdbentry.Property }
- *
- *
- */
- public List<Pdbentry.Property> getProperty()
- {
- if (property == null)
- {
- property = new ArrayList<Pdbentry.Property>();
- }
- return this.property;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getType()
- {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setType(String value)
- {
- this.type = value;
- }
-
- /**
- * Gets the value of the file property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getFile()
- {
- return file;
- }
-
- /**
- * Sets the value of the file property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setFile(String value)
- {
- this.file = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property
- {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- @XmlAttribute(name = "value", required = true)
- protected String value;
+@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
+ "property"
+})
+@XmlSeeAlso({
+ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
+})
+public class Pdbentry {
+
+ protected List<Pdbentry.Property> property;
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+ @XmlAttribute(name = "type")
+ protected String type;
+ @XmlAttribute(name = "file")
+ protected String file;
/**
- * Gets the value of the name property.
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Pdbentry.Property }
+ *
*
- * @return possible object is {@link String }
+ */
+ public List<Pdbentry.Property> getProperty() {
+ if (property == null) {
+ property = new ArrayList<Pdbentry.Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the id property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getName()
- {
- return name;
+ public String getId() {
+ return id;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the id property.
*
* @param value
- * allowed object is {@link String }
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the type property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setName(String value)
- {
- this.name = value;
+ public String getType() {
+ return type;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the type property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setType(String value) {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the file property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getValue()
- {
- return value;
+ public String getFile() {
+ return file;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the file property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public void setFile(String value) {
+ this.file = value;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for property complex type.
+ * <p>Java class for property complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="property">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="property"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "property")
-public class Property
-{
-
- @XmlAttribute(name = "name")
- protected String name;
+public class Property {
- @XmlAttribute(name = "value")
- protected String value;
+ @XmlAttribute(name = "name")
+ protected String name;
+ @XmlAttribute(name = "value")
+ protected String value;
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getValue()
- {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setValue(String value)
- {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
- * <sequence>
- * <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- * </sequence>
- * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "dbRef" })
+@XmlType(name = "", propOrder = {
+ "dbRef"
+})
@XmlRootElement(name = "Sequence")
-public class Sequence extends SequenceType
+public class Sequence
+ extends SequenceType
{
- @XmlElement(name = "DBRef")
- protected List<Sequence.DBRef> dbRef;
-
- @XmlAttribute(name = "dsseqid")
- protected String dsseqid;
-
- @XmlAttribute(name = "biotype")
- protected String biotype;
-
- /**
- * Gets the value of the dbRef property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the dbRef property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getDBRef().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Sequence.DBRef }
- *
- *
- */
- public List<Sequence.DBRef> getDBRef()
- {
- if (dbRef == null)
- {
- dbRef = new ArrayList<Sequence.DBRef>();
- }
- return this.dbRef;
- }
-
- /**
- * Gets the value of the dsseqid property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDsseqid()
- {
- return dsseqid;
- }
-
- /**
- * Sets the value of the dsseqid property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDsseqid(String value)
- {
- this.dsseqid = value;
- }
-
- /**
- * Gets the value of the biotype property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getBiotype()
- {
- return biotype;
- }
-
- /**
- * Sets the value of the biotype property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setBiotype(String value)
- {
- this.biotype = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- * </sequence>
- * <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = { "mapping" })
- public static class DBRef
- {
-
- @XmlElement(name = "Mapping")
- protected Mapping mapping;
-
- @XmlAttribute(name = "source")
- protected String source;
-
- @XmlAttribute(name = "version")
- protected String version;
-
- @XmlAttribute(name = "accessionId")
- protected String accessionId;
-
- @XmlAttribute(name = "locus")
- protected Boolean locus;
-
- @XmlAttribute(name = "canonical")
- protected Boolean canonical;
+ @XmlElement(name = "DBRef")
+ protected List<Sequence.DBRef> dbRef;
+ @XmlAttribute(name = "dsseqid")
+ protected String dsseqid;
+ @XmlAttribute(name = "biotype")
+ protected String biotype;
/**
- * Gets the value of the mapping property.
+ * Gets the value of the dbRef property.
*
- * @return possible object is {@link Mapping }
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the dbRef property.
*
- */
- public Mapping getMapping()
- {
- return mapping;
- }
-
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is {@link Mapping }
- *
- */
- public void setMapping(Mapping value)
- {
- this.mapping = value;
- }
-
- /**
- * Gets the value of the source property.
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getDBRef().add(newItem);
+ * </pre>
*
- * @return possible object is {@link String }
*
- */
- public String getSource()
- {
- return source;
- }
-
- /**
- * Sets the value of the source property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence.DBRef }
*
- * @param value
- * allowed object is {@link String }
*
*/
- public void setSource(String value)
- {
- this.source = value;
+ public List<Sequence.DBRef> getDBRef() {
+ if (dbRef == null) {
+ dbRef = new ArrayList<Sequence.DBRef>();
+ }
+ return this.dbRef;
}
/**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the dsseqid property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getVersion()
- {
- return version;
+ public String getDsseqid() {
+ return dsseqid;
}
/**
- * Sets the value of the version property.
+ * Sets the value of the dsseqid property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setVersion(String value)
- {
- this.version = value;
+ public void setDsseqid(String value) {
+ this.dsseqid = value;
}
/**
- * Gets the value of the accessionId property.
- *
- * @return possible object is {@link String }
+ * Gets the value of the biotype property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getAccessionId()
- {
- return accessionId;
+ public String getBiotype() {
+ return biotype;
}
/**
- * Sets the value of the accessionId property.
+ * Sets the value of the biotype property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setAccessionId(String value)
- {
- this.accessionId = value;
+ public void setBiotype(String value) {
+ this.biotype = value;
}
- /**
- * Gets the value of the locus property.
- *
- * @return possible object is {@link Boolean }
- *
- */
- public boolean isLocus()
- {
- if (locus == null)
- {
- return false;
- }
- else
- {
- return locus;
- }
- }
/**
- * Sets the value of the locus property.
+ * <p>Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link Boolean }
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- */
- public void setLocus(Boolean value)
- {
- this.locus = value;
- }
-
- /**
- * Gets the value of the canonical property.
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
- * @return possible object is {@link Boolean }
*
*/
- public boolean isCanonical()
- {
- if (canonical == null)
- {
- return false;
- }
- else
- {
- return canonical;
- }
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "mapping"
+ })
+ public static class DBRef {
+
+ @XmlElement(name = "Mapping")
+ protected Mapping mapping;
+ @XmlAttribute(name = "source")
+ protected String source;
+ @XmlAttribute(name = "version")
+ protected String version;
+ @XmlAttribute(name = "accessionId")
+ protected String accessionId;
+ @XmlAttribute(name = "locus")
+ protected Boolean locus;
+ @XmlAttribute(name = "canonical")
+ protected Boolean canonical;
+
+ /**
+ * Gets the value of the mapping property.
+ *
+ * @return
+ * possible object is
+ * {@link Mapping }
+ *
+ */
+ public Mapping getMapping() {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value) {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSource() {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSource(String value) {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the accessionId property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getAccessionId() {
+ return accessionId;
+ }
+
+ /**
+ * Sets the value of the accessionId property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setAccessionId(String value) {
+ this.accessionId = value;
+ }
+
+ /**
+ * Gets the value of the locus property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLocus() {
+ if (locus == null) {
+ return false;
+ } else {
+ return locus;
+ }
+ }
+
+ /**
+ * Sets the value of the locus property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLocus(Boolean value) {
+ this.locus = value;
+ }
+
+ /**
+ * Gets the value of the canonical property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isCanonical() {
+ if (canonical == null) {
+ return false;
+ } else {
+ return canonical;
+ }
+ }
+
+ /**
+ * Sets the value of the canonical property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCanonical(Boolean value) {
+ this.canonical = value;
+ }
- /**
- * Sets the value of the canonical property.
- *
- * @param value
- * allowed object is {@link Boolean }
- *
- */
- public void setCanonical(Boolean value)
- {
- this.canonical = value;
}
- }
-
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "",
- propOrder =
- { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+@XmlType(name = "", propOrder = {
+ "sequence",
+ "annotation",
+ "sequenceSetProperties",
+ "alcodonFrame",
+ "matrix"
+})
@XmlRootElement(name = "SequenceSet")
-public class SequenceSet
-{
-
- @XmlElement(name = "Sequence")
- protected List<Sequence> sequence;
-
- @XmlElement(name = "Annotation")
- protected List<Annotation> annotation;
-
- protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+public class SequenceSet {
- @XmlElement(name = "AlcodonFrame")
- protected List<AlcodonFrame> alcodonFrame;
+ @XmlElement(name = "Sequence")
+ protected List<Sequence> sequence;
+ @XmlElement(name = "Annotation")
+ protected List<Annotation> annotation;
+ protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+ @XmlElement(name = "AlcodonFrame")
+ protected List<AlcodonFrame> alcodonFrame;
+ @XmlElement(name = "Matrix")
+ protected List<MatrixType> matrix;
+ @XmlAttribute(name = "gapChar", required = true)
+ protected String gapChar;
+ @XmlAttribute(name = "datasetId")
+ protected String datasetId;
- @XmlAttribute(name = "gapChar", required = true)
- protected String gapChar;
-
- @XmlAttribute(name = "datasetId")
- protected String datasetId;
-
- /**
- * Gets the value of the sequence property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the sequence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSequence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Sequence }
- *
- *
- */
- public List<Sequence> getSequence()
- {
- if (sequence == null)
- {
- sequence = new ArrayList<Sequence>();
+ /**
+ * Gets the value of the sequence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Sequence }
+ *
+ *
+ */
+ public List<Sequence> getSequence() {
+ if (sequence == null) {
+ sequence = new ArrayList<Sequence>();
+ }
+ return this.sequence;
}
- return this.sequence;
- }
- /**
- * Gets the value of the annotation property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the annotation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAnnotation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link Annotation
- * }
- *
- *
- */
- public List<Annotation> getAnnotation()
- {
- if (annotation == null)
- {
- annotation = new ArrayList<Annotation>();
+ /**
+ * Gets the value of the annotation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the annotation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAnnotation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Annotation }
+ *
+ *
+ */
+ public List<Annotation> getAnnotation() {
+ if (annotation == null) {
+ annotation = new ArrayList<Annotation>();
+ }
+ return this.annotation;
}
- return this.annotation;
- }
- /**
- * Gets the value of the sequenceSetProperties property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the sequenceSetProperties property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSequenceSetProperties().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SequenceSet.SequenceSetProperties }
- *
- *
- */
- public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
- {
- if (sequenceSetProperties == null)
- {
- sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+ /**
+ * Gets the value of the sequenceSetProperties property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequenceSetProperties().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet.SequenceSetProperties }
+ *
+ *
+ */
+ public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
+ if (sequenceSetProperties == null) {
+ sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+ }
+ return this.sequenceSetProperties;
}
- return this.sequenceSetProperties;
- }
- /**
- * Gets the value of the alcodonFrame property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the alcodonFrame property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getAlcodonFrame().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame }
- *
- *
- */
- public List<AlcodonFrame> getAlcodonFrame()
- {
- if (alcodonFrame == null)
- {
- alcodonFrame = new ArrayList<AlcodonFrame>();
+ /**
+ * Gets the value of the alcodonFrame property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAlcodonFrame().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame }
+ *
+ *
+ */
+ public List<AlcodonFrame> getAlcodonFrame() {
+ if (alcodonFrame == null) {
+ alcodonFrame = new ArrayList<AlcodonFrame>();
+ }
+ return this.alcodonFrame;
}
- return this.alcodonFrame;
- }
-
- /**
- * Gets the value of the gapChar property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getGapChar()
- {
- return gapChar;
- }
-
- /**
- * Sets the value of the gapChar property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setGapChar(String value)
- {
- this.gapChar = value;
- }
-
- /**
- * Gets the value of the datasetId property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDatasetId()
- {
- return datasetId;
- }
-
- /**
- * Sets the value of the datasetId property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDatasetId(String value)
- {
- this.datasetId = value;
- }
-
- /**
- * <p>
- * Java class for anonymous complex type.
- *
- * <p>
- * The following schema fragment specifies the expected content contained
- * within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequenceSetProperties
- {
-
- @XmlAttribute(name = "key")
- protected String key;
-
- @XmlAttribute(name = "value")
- protected String value;
/**
- * Gets the value of the key property.
+ * Gets the value of the matrix property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the matrix property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getMatrix().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link MatrixType }
*
- * @return possible object is {@link String }
*
*/
- public String getKey()
- {
- return key;
+ public List<MatrixType> getMatrix() {
+ if (matrix == null) {
+ matrix = new ArrayList<MatrixType>();
+ }
+ return this.matrix;
}
/**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is {@link String }
+ * Gets the value of the gapChar property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public void setKey(String value)
- {
- this.key = value;
+ public String getGapChar() {
+ return gapChar;
}
/**
- * Gets the value of the value property.
+ * Sets the value of the gapChar property.
*
- * @return possible object is {@link String }
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setGapChar(String value) {
+ this.gapChar = value;
+ }
+
+ /**
+ * Gets the value of the datasetId property.
*
+ * @return
+ * possible object is
+ * {@link String }
+ *
*/
- public String getValue()
- {
- return value;
+ public String getDatasetId() {
+ return datasetId;
}
/**
- * Sets the value of the value property.
+ * Sets the value of the datasetId property.
*
* @param value
- * allowed object is {@link String }
- *
+ * allowed object is
+ * {@link String }
+ *
*/
- public void setValue(String value)
- {
- this.value = value;
+ public void setDatasetId(String value) {
+ this.datasetId = value;
}
- }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequenceSetProperties {
+
+ @XmlAttribute(name = "key")
+ protected String key;
+ @XmlAttribute(name = "value")
+ protected String value;
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getKey() {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setKey(String value) {
+ this.key = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for SequenceType complex type.
+ * <p>Java class for SequenceType complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="SequenceType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="SequenceType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
-@XmlSeeAlso({ Sequence.class })
-public class SequenceType
-{
-
- protected String sequence;
-
- protected String name;
-
- @XmlAttribute(name = "id")
- protected String id;
-
- @XmlAttribute(name = "description")
- protected String description;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getSequence()
- {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setSequence(String value)
- {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getId()
- {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setId(String value)
- {
- this.id = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
+@XmlType(name = "SequenceType", propOrder = {
+ "sequence",
+ "name"
+})
+@XmlSeeAlso({
+ Sequence.class
+})
+public class SequenceType {
+
+ protected String sequence;
+ protected String name;
+ @XmlAttribute(name = "id")
+ protected String id;
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequence() {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequence(String value) {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for ThresholdType.
- *
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
- * <p>
+ * <p>Java class for ThresholdType.
*
- * <pre>
- * <simpleType name="ThresholdType">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="NONE"/>
- * <enumeration value="ABOVE"/>
- * <enumeration value="BELOW"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="ThresholdType"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="NONE"/&gt;
+ * &lt;enumeration value="ABOVE"/&gt;
+ * &lt;enumeration value="BELOW"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum ThresholdType
-{
+public enum ThresholdType {
- NONE, ABOVE, BELOW;
+ NONE,
+ ABOVE,
+ BELOW;
- public String value()
- {
- return name();
- }
+ public String value() {
+ return name();
+ }
- public static ThresholdType fromValue(String v)
- {
- return valueOf(v);
- }
+ public static ThresholdType fromValue(String v) {
+ return valueOf(v);
+ }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for VAMSAS complex type.
+ * <p>Java class for VAMSAS complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="VAMSAS">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="VAMSAS"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
-public class VAMSAS
-{
-
- @XmlElement(name = "Tree")
- protected List<String> tree;
+@XmlType(name = "VAMSAS", propOrder = {
+ "tree",
+ "sequenceSet"
+})
+public class VAMSAS {
- @XmlElement(name = "SequenceSet")
- protected List<SequenceSet> sequenceSet;
+ @XmlElement(name = "Tree")
+ protected List<String> tree;
+ @XmlElement(name = "SequenceSet")
+ protected List<SequenceSet> sequenceSet;
- /**
- * Gets the value of the tree property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the tree property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getTree().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getTree()
- {
- if (tree == null)
- {
- tree = new ArrayList<String>();
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getTree() {
+ if (tree == null) {
+ tree = new ArrayList<String>();
+ }
+ return this.tree;
}
- return this.tree;
- }
- /**
- * Gets the value of the sequenceSet property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the sequenceSet property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getSequenceSet().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link SequenceSet
- * }
- *
- *
- */
- public List<SequenceSet> getSequenceSet()
- {
- if (sequenceSet == null)
- {
- sequenceSet = new ArrayList<SequenceSet>();
+ /**
+ * Gets the value of the sequenceSet property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequenceSet().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet }
+ *
+ *
+ */
+ public List<SequenceSet> getSequenceSet() {
+ if (sequenceSet == null) {
+ sequenceSet = new ArrayList<SequenceSet>();
+ }
+ return this.sequenceSet;
}
- return this.sequenceSet;
- }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
+
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>
- * Java class for WebServiceParameterSet complex type.
+ * <p>Java class for WebServiceParameterSet complex type.
*
- * <p>
- * The following schema fragment specifies the expected content contained within
- * this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="WebServiceParameterSet">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
- * <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="WebServiceParameterSet"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/&gt;
+ * &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
- name = "WebServiceParameterSet",
- namespace = "www.jalview.org/xml/wsparamset",
- propOrder =
- { "version", "description", "serviceURL", "parameters" })
+@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
+ "version",
+ "description",
+ "serviceURL",
+ "parameters"
+})
@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
-public class WebServiceParameterSet
-{
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
-
- @XmlElement(namespace = "")
- protected String description;
-
- @XmlElement(namespace = "", required = true)
- @XmlSchemaType(name = "anyURI")
- protected List<String> serviceURL;
-
- @XmlElement(namespace = "", required = true)
- protected String parameters;
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * Gets the value of the version property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setVersion(String value)
- {
- this.version = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getDescription()
- {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setDescription(String value)
- {
- this.description = value;
- }
-
- /**
- * Gets the value of the serviceURL property.
- *
- * <p>
- * This accessor method returns a reference to the live list, not a snapshot.
- * Therefore any modification you make to the returned list will be present
- * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
- * for the serviceURL property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- *
- * <pre>
- * getServiceURL().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list {@link String }
- *
- *
- */
- public List<String> getServiceURL()
- {
- if (serviceURL == null)
- {
- serviceURL = new ArrayList<String>();
+ jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
+})
+public class WebServiceParameterSet {
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+ @XmlElement(namespace = "")
+ protected String description;
+ @XmlElement(namespace = "", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected List<String> serviceURL;
+ @XmlElement(namespace = "", required = true)
+ protected String parameters;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setVersion(String value) {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setDescription(String value) {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the serviceURL property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getServiceURL().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getServiceURL() {
+ if (serviceURL == null) {
+ serviceURL = new ArrayList<String>();
+ }
+ return this.serviceURL;
+ }
+
+ /**
+ * Gets the value of the parameters property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getParameters() {
+ return parameters;
+ }
+
+ /**
+ * Sets the value of the parameters property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setParameters(String value) {
+ this.parameters = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setName(String value) {
+ this.name = value;
}
- return this.serviceURL;
- }
-
- /**
- * Gets the value of the parameters property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getParameters()
- {
- return parameters;
- }
-
- /**
- * Sets the value of the parameters property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setParameters(String value)
- {
- this.parameters = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return possible object is {@link String }
- *
- */
- public String getName()
- {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is {@link String }
- *
- */
- public void setName(String value)
- {
- this.name = value;
- }
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2023.05.13 at 06:58:41 PM BST
+// Generated on: 2023.09.01 at 02:16:11 PM BST
//
-@javax.xml.bind.annotation.XmlSchema(
- namespace = "www.vamsas.ac.uk/jalview/version2",
- elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.jalview;
+ " \"resolution\":2.2,\n"
+ " \"title\":\"Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal\"}]\n"
+ " }}" });
+ mocks.add(new String[] {
+ "https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4gs9+OR+6bvb+OR+8ck8+OR+8ck3+OR+6x3d+OR+8ck4+OR+6x28+OR+6i7r+OR+3h82+OR+6i7q+OR+6x21+OR+4xt2+OR+5kiz+OR+7q5v+OR+6x2h+OR+7q5x+OR+3f1n+OR+3f1o+OR+2a24+OR+3f1p+OR+1p97+OR+4ghi+OR+3h7w+OR+6d09+OR+6czw+OR+7ujv+OR+5tbm+OR+5ufp+OR+4pky+OR+6d0b+OR+6d0c+OR+6x37)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort="
+ ,
+ readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/q99814_tdb_pdbfts_query_resp.txt")});
} catch (Throwable e)
{
Assert.fail("Couldn't read mock data.", e);
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import jalview.datamodel.Sequence;
+import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClientTest;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.gui.JvOptionPane;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.TDBResultAnalyser;
+import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
public class TDBeaconsFTSRestClientTest
{
private static String[][] mocks = { { "P38398.json", null },
{ "P01308.json", null },
{ "P0DTD1.json", null },
- { "P27787.json", null }
+ { "P27787.json", null },
+ { "Q99814.json", null }
// , { "P0DTD3.json", "{}" } actually results in 404, but {} is in body
};
mocks[3][1] = PDBFTSRestClientTest.readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p27787_tdb_fts_query_resp.txt");
+ mocks[4][1] = PDBFTSRestClientTest.readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/q99814_tdb_fts_query_resp.txt");
} catch (IOException e)
{
System.out.println("Search summary : \n" + response.getSearchSummary());
// System.out.println(response.getSearchSummary().size());
}
+
}
--- /dev/null
+https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/Q99814.json
--- /dev/null
+{"uniprot_entry":{"ac":"Q99814","id":"EPAS1_HUMAN","uniprot_checksum":"4838989598234FC1","sequence_length":870,"segment_start":8,"segment_end":359},"structures":[{"summary":{"model_identifier":"3f1p","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/3f1p_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3f1p","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2008-10-28","sequence_identity":97.0,"uniprot_start":239,"uniprot_end":350,"coverage":0.129,"experimental_method":"X-RAY DIFFRACTION","resolution":1.17,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"P27540","identifier_category":"UNIPROT","description":"Aryl hydrocarbon receptor nuclear translocator","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["A"]}]}},{"summary":{"model_identifier":"7q5v","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/7q5v_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/7q5v","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2021-11-04","sequence_identity":100.0,"uniprot_start":523,"uniprot_end":542,"coverage":0.023,"experimental_method":"X-RAY DIFFRACTION","resolution":1.17,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q9GZT9","identifier_category":"UNIPROT","description":"Egl nine homolog 1","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"GOL","identifier_category":"CCD","description":"GLYCEROL","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"FMT","identifier_category":"CCD","description":"FORMIC ACID","chain_ids":["A","B"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"CL","identifier_category":"CCD","description":"CHLORIDE ION","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"MG","identifier_category":"CCD","description":"MAGNESIUM ION","chain_ids":["A","B"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"OGA","identifier_category":"CCD","description":"N-OXALYLGLYCINE","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"MN","identifier_category":"CCD","description":"MANGANESE (II) ION","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"PEG","identifier_category":"CCD","description":"DI(HYDROXYETHYL)ETHER","chain_ids":["A"]}]}},{"summary":{"model_identifier":"7q5x","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/7q5x_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/7q5x","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2021-11-04","sequence_identity":100.0,"uniprot_start":523,"uniprot_end":542,"coverage":0.023,"experimental_method":"X-RAY DIFFRACTION","resolution":1.21,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q9GZT9","identifier_category":"UNIPROT","description":"Egl nine homolog 1","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"GOL","identifier_category":"CCD","description":"GLYCEROL","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"FMT","identifier_category":"CCD","description":"FORMIC ACID","chain_ids":["A","B"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"CL","identifier_category":"CCD","description":"CHLORIDE ION","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"MG","identifier_category":"CCD","description":"MAGNESIUM ION","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"AKG","identifier_category":"CCD","description":"2-OXOGLUTARIC ACID","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"MN","identifier_category":"CCD","description":"MANGANESE (II) ION","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"PEG","identifier_category":"CCD","description":"DI(HYDROXYETHYL)ETHER","chain_ids":["A"]}]}},{"summary":{"model_identifier":"3f1n","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/3f1n_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3f1n","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2008-10-28","sequence_identity":97.0,"uniprot_start":239,"uniprot_end":350,"coverage":0.129,"experimental_method":"X-RAY DIFFRACTION","resolution":1.479,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"P27540","identifier_category":"UNIPROT","description":"Aryl hydrocarbon receptor nuclear translocator","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"EDO","identifier_category":"CCD","description":"1,2-ETHANEDIOL","chain_ids":["A"]}]}},{"summary":{"model_identifier":"4ghi","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/4ghi_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/4ghi","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2012-08-07","sequence_identity":97.0,"uniprot_start":239,"uniprot_end":350,"coverage":0.129,"experimental_method":"X-RAY DIFFRACTION","resolution":1.5,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"P27540","identifier_category":"UNIPROT","description":"Aryl hydrocarbon receptor nuclear translocator","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"0X3","identifier_category":"CCD","description":"N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine","chain_ids":["A"]}]}},{"summary":{"model_identifier":"6d0c","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/6d0c_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6d0c","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2018-04-10","sequence_identity":97.0,"uniprot_start":239,"uniprot_end":350,"coverage":0.129,"experimental_method":"X-RAY DIFFRACTION","resolution":1.5,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"P27540","identifier_category":"UNIPROT","description":"Aryl hydrocarbon receptor nuclear translocator","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["A"]}]}},{"summary":{"model_identifier":"3h82","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/3h82_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/3h82","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2009-04-28","sequence_identity":97.0,"uniprot_start":239,"uniprot_end":350,"coverage":0.129,"experimental_method":"X-RAY DIFFRACTION","resolution":1.5,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"P27540","identifier_category":"UNIPROT","description":"Aryl hydrocarbon receptor nuclear translocator","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"020","identifier_category":"CCD","description":"N-(furan-2-ylmethyl)-2-nitro-4-(trifluoromethyl)aniline","chain_ids":["A"]}]}},{"summary":{"model_identifier":"6x21","model_category":"EXPERIMENTALLY DETERMINED","model_url":"https://www.ebi.ac.uk/pdbe/static/entry/6x21_updated.cif","model_format":"MMCIF","model_type":null,"model_page_url":"https://www.ebi.ac.uk/pdbe/entry/pdb/6x21","provider":"PDBe","number_of_conformers":null,"ensemble_sample_url":null,"ensemble_sample_format":null,"created":"2020-05-19","sequence_identity":97.0,"uniprot_start":239,"uniprot_end":348,"coverage":0.126,"experimental_method":"X-RAY DIFFRACTION","resolution":1.54,"confidence_type":null,"confidence_version":null,"confidence_avg_local_score":null,"oligomeric_state":null,"preferred_assembly_id":null,"entities":[{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"P27540","identifier_category":"UNIPROT","description":"Aryl hydrocarbon receptor nuclear translocator","chain_ids":["B"]},{"entity_type":"POLYMER","entity_poly_type":"POLYPEPTIDE(L)","identifier":"Q99814","identifier_category":"UNIPROT","description":"Endothelial PAS domain-containing protein 1","chain_ids":["A"]},{"entity_type":"NON-POLYMER","entity_poly_type":null,"identifier":"UKJ","identifier_category":"CCD","description":"1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene","chain_ids":["A"]}]}},{"summary":{"model_identifier":"3f1o","model_category":"EXPERIMENTALLY 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+ "pdb_id":"8ck3",
+ "resolution":1.707,
+ "title":"STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (S)-1-(3,5-Difluoro-phenyl)-5,5-difluoro-3-methanesulfonyl-5,6-dihydro-4H-cyclopenta[c]thiophen-4-ol"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"8ck3",
+ "resolution":1.707,
+ "title":"STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (S)-1-(3,5-Difluoro-phenyl)-5,5-difluoro-3-methanesulfonyl-5,6-dihydro-4H-cyclopenta[c]thiophen-4-ol"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4gs9",
+ "resolution":1.72,
+ "title":"Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with an inactive benzoxadiazole antagonist"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5tbm",
+ "resolution":1.85,
+ "title":"Crystal structure of PT2385 bound to HIF2a-B*:ARNT-B* complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5ufp",
+ "resolution":1.9,
+ "title":"Crystal structure of PT2399 bound to HIF2a-B*:ARNT-B* complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"5ufp",
+ "resolution":1.9,
+ "title":"Crystal structure of PT2399 bound to HIF2a-B*:ARNT-B* complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4pky",
+ "resolution":3.2,
+ "title":"ARNT/HIF transcription factor/coactivator complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6bvb",
+ "resolution":2.002,
+ "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4pky",
+ "resolution":3.2,
+ "title":"ARNT/HIF transcription factor/coactivator complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"4pky",
+ "resolution":3.2,
+ "title":"ARNT/HIF transcription factor/coactivator complex"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7q",
+ "resolution":1.798,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7r",
+ "resolution":1.949,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7ujv",
+ "resolution":1.8,
+ "title":"Structure of PHD2 in complex with HIF2a-CODD"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7q5v",
+ "resolution":1.17,
+ "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7q5x",
+ "resolution":1.21,
+ "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7q5v",
+ "resolution":1.17,
+ "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6bvb",
+ "resolution":2.002,
+ "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"7q5x",
+ "resolution":1.21,
+ "title":"HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542)"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7r",
+ "resolution":1.949,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7q",
+ "resolution":1.798,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6bvb",
+ "resolution":2.002,
+ "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7r",
+ "resolution":1.949,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7q",
+ "resolution":1.798,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6bvb",
+ "resolution":2.002,
+ "title":"Crystal structure of HIF-2alpha-pVHL-elongin B-elongin C"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7q",
+ "resolution":1.798,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form"},
+ {
+ "experimental_method":["X-ray diffraction"],
+ "pdb_id":"6i7r",
+ "resolution":1.949,
+ "title":"Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form"}]
+ }}
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClientTest;
+import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
import jalview.gui.JvOptionPane;
import jalview.gui.StructureChooser;
private Sequence upSeq_fer1_maize;
+ private Sequence upSeq_epas1_human;
+
// same set up as for structurechooser test
@BeforeMethod(alwaysRun = true)
upSeq_fer1_maize
.addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
upSeq_fer1_maize.createDatasetSequence();
-
+
+ upSeq_epas1_human = new Sequence("EPAS1_HUMAN","MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS\n"
+ + "VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR\n"
+ + "ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE\n"
+ + "PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN\n"
+ + "MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE\n"
+ + "SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL\n"
+ + "PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL\n"
+ + "FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP\n"
+ + "VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG\n"
+ + "PTKWAVGDQRTEFLGAAPLGPPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYEEQAFQ\n"
+ + "DLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPSAISPG\n"
+ + "ENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQGGDLLR\n"
+ + "ALDQAT");
+ upSeq_epas1_human.setDescription("Endothelial PAS domain-containing protein 1");
+ upSeq_epas1_human
+ .addDBRef(new DBRefEntry("UNIPROT", "0", "Q99814", null, true));
+ upSeq_epas1_human.createDatasetSequence();
}
@AfterMethod(alwaysRun = true)
upSeq = null;
upSeq_r1ab = null;
upSeq_fer1_maize = null;
+ upSeq_epas1_human=null;
}
@SuppressWarnings("deprecation")
pdbResponse);
assertEquals(upResponse.getNumberOfItemsFound(),
joinedResp.getNumberOfItemsFound());
+
+ // Special data test case
+ if (testUpSeq.getDisplayId(true)
+ .equals(upSeq_epas1_human.getDisplayId(true)))
+ {
+
+ TDBResultAnalyser tDBResultAnalyz = new TDBResultAnalyser(testUpSeq,
+ joinedResp.getSearchSummary(), tdbquery.lastTdbRequest,
+ ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE,
+ tdbquery.remove_prefix(
+ ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE));
+ List<FTSData> ordered = tDBResultAnalyz.getFilteredResponse();
+ List<FTSData> selected = tDBResultAnalyz.selectStructures(ordered);
+ assertEquals(((TDB_FTSData) selected.get(0)).getProvider(),
+ "AlphaFold DB");
+ // to be sufficient, should also
+ // test that adjacent ordered structure in ordered is levyLab
+ // TDB_FTSData first = (TDB_FTSData) ordered.get(0),
+ // second = (TDB_FTSData) ordered.get(1),
+ // third = (TDB_FTSData) ordered.get(2);
+ // Assert.assertEquals("pLDDT", first.getConfidenceScoreType());
+ // Assert.assertTrue(first.getConfidenceScoreType()
+ // .equals(second.getConfidenceScoreType())); // pLDDT first and
+ // // second
+ }
} catch (
{
setUp();
return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
- { upSeq_fer1_maize } };
+ { upSeq_fer1_maize },{upSeq_epas1_human} };
}
@Test(groups = { "Functional" })
name = "abcde12[345a]fg";
AssertJUnit.assertEquals("abcde12345afg",
PDBStructureChooserQuerySource.sanitizeSeqName(name));
- }
+ }
}
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
}
@Test(groups = { "Functional" })
+ public void testMatrixToFloatsAndBack()
+ {
+ int imax=2000;
+ int i=imax;
+ SequenceI sq = new Sequence("dummy","SEQ");
+ while (sq.getLength()<i)
+ {
+ sq.setSequence(sq.getSequenceAsString()+'Q');
+ }
+ float[][] paevals = new float[i][i];
+ for (i = imax - 1; i >= 0; i--)
+ {
+ for (int j = 0; j <= i; j++)
+ {
+ paevals[i][j] = ((i - j < 2)
+ || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
+ paevals[j][i] = -paevals[i][j];
+ }
+ }
+ PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
+ String content = ContactMatrix.contactToFloatString(dummyMat);
+ Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+ // 1
+ float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+ sq.getLength(), sq.getLength());
+ assertEquals(vals[3][4], paevals[3][4]);
+ assertEquals(vals[4][3], paevals[4][3]);
+
+ // test recovery
+ for (i=0;i<imax;i++)
+ {
+ for (int j=0;j<imax;j++)
+ {
+ assertEquals(vals[i][j],paevals[i][j]);
+ }
+ }
+ }
+ @Test(groups = { "Functional" })
public void testPAEsaveRestore() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
+ // verify no duplicate PAE matrix data when new view created and saved
+
+ // add reference annotations to view first, then copy
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
+
+ AlignmentViewPanel newview = af.newView("copy of PAE", true);
+
+ // redundant asserts here check all is good with the new view firest...
+ AlignmentI newviewAl = newview.getAlignment();
+ SequenceI newviewSeq = newviewAl.getSequenceAt(0);
+ // check annotation of the expected type exists
+ Assert.assertEquals(newviewSeq.getAnnotation().length, 1);
+ Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
+ // check we have just one contact matrix mapping
+ Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
+
+ // and can be found for the annotation on the sequence
+ ContactMatrixI newviewMat = newviewSeq
+ .getContactMatrixFor(newviewSeq.getAnnotation()[0]);
+ Assert.assertNotNull(newviewMat);
+
+ Assert.assertTrue(newviewMat == restoredMat);
+
+ // save the two views and restore. Now look at visible annotation to check all views have shared refs.
+
+ tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
+ ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ newAl = af.getAlignPanels().get(0).getAlignment();
+ AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
+
+ newviewAl = af.getAlignPanels().get(1).getAlignment();
+ AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+
+ // annotations are shared across alignment views - so should still have an identical pair of annotations.
+ Assert.assertTrue(view1aa==view2aa);
+ // identical annotations means identical contact matrix mappings
+ Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+
+ // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+ // Assert.assertTrue(view1aa!=view2aa);
+ // restoredMat = newAl.getContactMatrixFor(view1aa);
+ // newviewMat = newviewAl.getContactMatrixFor(view2aa);
+ // Assert.assertTrue(restoredMat!=newviewMat);
+
}
}
git://source.jalview.org / jalview.git / commitdiff